analysis of sequence from tem31_1 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR MGPRLSVWLLLLPAALLLHEEHSRAAAKGGCAGSGCGKCDCHGVKGQKGERGLPGLQGVIGFPGMQGPEG PQGPPGQKGDTGEPGLPGTKGTRGPPGASGYPGNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGL PGFAGNPGPPGLPGMKGDPGEILGHVPGMLLKGERGFPGIPGTPGPPGLPGLQGPVGPPGFTGPPGPPGP PGPPGEKGQMGLSFQGPKGDKGDQGVSGPPGVPGQAQVQEKGDFATKGEKGQKGEPGFQGMPGVGEKGEP GKPGPRGKPGKDGDKGEKGSPGFPGEPGYPGLIGRQGPQGEKGEAGPPGPPGIVIGTGPLGEKGERGYPG TPGPRGEPGPKGFPGLPGQPGPPGLPVPGQAGAPGFPGERGEKGDRGFPGTSLPGPSGRDGLPGPPGSPG PPGQPGYTNGIVECQPGPPGDQGPPGIPGQPGFIGEIGEKGQKGESCLICDIDGYRGPPGPQGPPGEIGF PGQPGAKGDRGLPGRDGVAGVPGPQGTPGLIGQPGAKGEPGEFYFDLRLKGDKGDPGFPGQPGMPGRAGS PGRDGHPGLPGPKGSPGSVGLKGERGPPGGVGFPGSRGDTGPPGPPGYGPAGPIGDKGQAGFPGGPGSPG LPGPKGEPGKIVPLPGPPGAEGLPGSPGFPGPQGDRGFPGTPGRPGLPGEKGAVGQPGIGFPGPPGPKGV DGLPGDMGPPGTPGRPGFNGLPGNPGVQGQKGEPGVGLPGLKGLPGLPGIPGTPGEKGSIGVPGVPGEHG AIGPPGLQGIRGEPGPPGLPGSVGSPGVPGIGPPGARGPPGGQGPPGLSGPPGIKGEKGFPGFPGLDMPG PKGDKGAQGLPGITGQSGLPGLPGQQGAPGIPGFPGSKGEMGVMGTPGQPGSPGPVGAPGLPGEKGDHGF PGSSGPRGDPGLKGDKGDVGLPGKPGSMDKVDMGSMKGQKGDQGEKGQIGPIGEKGSRGDPGTPGVPGKD GQAGQPGQPGPKGDPGISGTPGAPGLPGPKGSVGGMGLPGTPGEKGVPGIPGPQGSPGLPGDKGAKGEKG QAGPPGIGIPGLRGEKGDQGIAGFPGSPGEKGEKGSIGIPGMPGSPGLKGSPGSVGYPGSPGLPGEKGDK GLPGLDGIPGVKGEAGLPGTPGPTGPAGQKGEPGSDGIPGSAGEKGEPGLPGRGFPGFPGAKGDKGSKGE VGFPGLAGSPGIPGSKGEQGFMGPPGPQGQPGLPGSPGHATEGPKGDRGPQGQPGLPGLPGPMGPPGLPG IDGVKGDKGNPGWPGAPGVPGPKGDPGFQGMPGIGGSPGITGSKGDMGPPGVPGFQGPKGLPGLQGIKGD QGDQGVPGAKGLPGPPGPPGPYDIIKGEPGLPGPEGPPGLKGLQGLPGPKGQQGVTGLVGIPGPPGIPGF DGAPGQKGEMGPAGPTGPRGFPGPPGPDGLPGSMGPPGTPSVDHGFLVTRHSQTIDDPQCPSGTKILYHG YSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGEN IRPFISRCAVCEAPAMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRS APFIECHGRGTCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN . . . . . 1 MGPRLSVWLLLLPAALLLHEEHSRAAAKGGCAGSGCGKCDCHGVKGQKGE 50 ___HHHHHH_HHHHHHHHHHHHHHHHH_______________________ . . . . . 51 RGLPGLQGVIGFPGMQGPEGPQGPPGQKGDTGEPGLPGTKGTRGPPGASG 100 ______EEEE________________________________________ . . . . . 101 YPGNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGLPGFAGNPGPP 150 __________________________________________________ . . . . . 151 GLPGMKGDPGEILGHVPGMLLKGERGFPGIPGTPGPPGLPGLQGPVGPPG 200 __________EEE_____EEEE____________________________ . . . . . 201 FTGPPGPPGPPGPPGEKGQMGLSFQGPKGDKGDQGVSGPPGVPGQAQVQE 250 ______________________________________________EEE_ . . . . . 251 KGDFATKGEKGQKGEPGFQGMPGVGEKGEPGKPGPRGKPGKDGDKGEKGS 300 __________________________________________________ . . . . . 301 PGFPGEPGYPGLIGRQGPQGEKGEAGPPGPPGIVIGTGPLGEKGERGYPG 350 ___________EEE____________________________________ . . . . . 351 TPGPRGEPGPKGFPGLPGQPGPPGLPVPGQAGAPGFPGERGEKGDRGFPG 400 __________________________________________________ . . . . . 401 TSLPGPSGRDGLPGPPGSPGPPGQPGYTNGIVECQPGPPGDQGPPGIPGQ 450 _____________________________EEEEE________________ . . . . . 451 PGFIGEIGEKGQKGESCLICDIDGYRGPPGPQGPPGEIGFPGQPGAKGDR 500 __EEEE_________EEEEEE_____________________________ . . . . . 501 GLPGRDGVAGVPGPQGTPGLIGQPGAKGEPGEFYFDLRLKGDKGDPGFPG 550 ________________________________EEEEE_____________ . . . . . 551 QPGMPGRAGSPGRDGHPGLPGPKGSPGSVGLKGERGPPGGVGFPGSRGDT 600 _____________________________EEEE_________________ . . . . . 601 GPPGPPGYGPAGPIGDKGQAGFPGGPGSPGLPGPKGEPGKIVPLPGPPGA 650 _______________________________________EEEE_______ . . . . . 651 EGLPGSPGFPGPQGDRGFPGTPGRPGLPGEKGAVGQPGIGFPGPPGPKGV 700 __________________________________________________ . . . . . 701 DGLPGDMGPPGTPGRPGFNGLPGNPGVQGQKGEPGVGLPGLKGLPGLPGI 750 __________________________________________________ . . . . . 751 PGTPGEKGSIGVPGVPGEHGAIGPPGLQGIRGEPGPPGLPGSVGSPGVPG 800 __________________________________________________ . . . . . 801 IGPPGARGPPGGQGPPGLSGPPGIKGEKGFPGFPGLDMPGPKGDKGAQGL 850 __________________________________________________ . . . . . 851 PGITGQSGLPGLPGQQGAPGIPGFPGSKGEMGVMGTPGQPGSPGPVGAPG 900 _______________________________EEE________________ . . . . . 901 LPGEKGDHGFPGSSGPRGDPGLKGDKGDVGLPGKPGSMDKVDMGSMKGQK 950 __________________________________________________ . . . . . 951 GDQGEKGQIGPIGEKGSRGDPGTPGVPGKDGQAGQPGQPGPKGDPGISGT 1000 __________________________________________________ . . . . . 1001 PGAPGLPGPKGSVGGMGLPGTPGEKGVPGIPGPQGSPGLPGDKGAKGEKG 1050 __________________________________________________ . . . . . 1051 QAGPPGIGIPGLRGEKGDQGIAGFPGSPGEKGEKGSIGIPGMPGSPGLKG 1100 __________________________________________________ . . . . . 1101 SPGSVGYPGSPGLPGEKGDKGLPGLDGIPGVKGEAGLPGTPGPTGPAGQK 1150 __________________________________________________ . . . . . 1151 GEPGSDGIPGSAGEKGEPGLPGRGFPGFPGAKGDKGSKGEVGFPGLAGSP 1200 __________________________________________________ . . . . . 1201 GIPGSKGEQGFMGPPGPQGQPGLPGSPGHATEGPKGDRGPQGQPGLPGLP 1250 __________________________________________________ . . . . . 1251 GPMGPPGLPGIDGVKGDKGNPGWPGAPGVPGPKGDPGFQGMPGIGGSPGI 1300 __________________________________________________ . . . . . 1301 TGSKGDMGPPGVPGFQGPKGLPGLQGIKGDQGDQGVPGAKGLPGPPGPPG 1350 __________________________________________________ . . . . . 1351 PYDIIKGEPGLPGPEGPPGLKGLQGLPGPKGQQGVTGLVGIPGPPGIPGF 1400 __EEE_______________________________EEE___________ . . . . . 1401 DGAPGQKGEMGPAGPTGPRGFPGPPGPDGLPGSMGPPGTPSVDHGFLVTR 1450 _____________________________________________EEEEE . . . . . 1451 HSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTM 1500 EEE__________EEEEEE__EEEEE_________________EEEE___ . . . . . 1501 PFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAV 1550 _EEE_______________EEEE________________________EEE . . . . . 1551 CEAPAMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALAS 1600 EE__HHHHHHHHHEEEE_________EEEE__EEEE______________ . . . . . 1601 PGSCLEEFRSAPFIECHGRGTCNYYANAYSFWLATIERSEMFKKPTPSTL 1650 ____HHHHH____EEE_________HHHHHHHHHHHHHHHHH______HH . 1651 KAGELRTHVSRCQVCMRRT 1669 HHHH_________EEE___ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 0.0 % beta-contents : 0.0 % coil-contents : 100.0 % class : irregular method : 2 alpha-contents : 0.0 % beta-contents : 0.0 % coil-contents : 100.0 % class : irregular ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -1.29 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -7.20 -2.32 -12.00 -12.00 0.00 -12.00 0.00 -46.81 -0.69 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -4.76 -2.32 -12.00 -12.00 0.00 -12.00 0.00 -43.77 ID: tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN AC: xxx Len: 1610 1:I 1588 Sc: -43.77 Pv: 1.619682e-01 NO_GPI_SITE GPI: learning from protozoa -15.96 0.00 0.00 0.00 -4.00 0.00 -4.00 -1.47 0.00 -6.89 -8.58 -12.00 -12.00 0.00 -12.00 0.00 -76.90 -23.12 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -6.22 -8.58 -12.00 -12.00 0.00 -12.00 0.00 -73.92 ID: tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN AC: xxx Len: 1610 1:I 1589 Sc: -73.92 Pv: 4.054731e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? tem31.1t_gi 0.696 1485 Y 0.511 28 Y 0.973 5 Y 0.772 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? tem31.1t_gi 0.618 1600 Y 0.386 26 Y 0.986 3 Y 0.642 Y # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? tem31.1t_gi 0.792 1592 Y 0.521 1592 Y 0.987 9 Y 0.082 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR 1-8 MGPRLSVW llllpaalll 9-18 19-24 HEEHSR aaakggcagsgcgkcdc 25-41 42-60 HGVKGQKGERGLPGLQGVI gfpgmqgpegpqgppgqkgdtg 61-82 83-104 EPGLPGTKGTRGPPGASGYPGN pglpgipgqdgppgppgipgcng 105-127 128-129 TK gergplgppglpgfagnpgppglpgmkgdp 130-160 g 161-175 EILGHVPGMLLKGER gfpgipgtpgppglpglqgpvgppgftgpp 176-215 gppgppgppg 216-233 EKGQMGLSFQGPKGDKGD qgvsgppgvpgqaqvq 234-249 250-269 EKGDFATKGEKGQKGEPGFQ gmpgvgekgepgkpgprgkpgkdgdkgekg 270-302 spg 303-316 FPGEPGYPGLIGRQ gpqgekgeagppgppgivigtgplg 317-341 342-343 EK gergypgtpgprgepgpkgfpglpgqpgpp 344-385 glpvpgqagapg 386-403 FPGERGEKGDRGFPGTSL pgpsgrdglpgppgspgppgqpg 404-426 427-434 YTNGIVEC qpgppgdqgppgipgqpgfigeigekgqkg 435-465 e 466-476 SCLICDIDGYR gppgpqgppgeigfpgqpg 477-495 496-564 AKGDRGLPGRDGVAGVPGPQGTPGLIGQPG AKGEPGEFYFDLRLKGDKGDPGFPGQPGMP GRAGSPGRD ghpglpgpkgspgsvglkg 565-583 584-593 ERGPPGGVGF pgsrgdtgppgppgygpagpigdkgqagfp 594-640 ggpgspglpgpkgepgk 641-642 IV plpgppgaeglpgspg 643-658 659-684 FPGPQGDRGFPGTPGRPGLPGEKGAV gqpgigfpgppgpkgvdglpg 685-705 706-731 DMGPPGTPGRPGFNGLPGNPGVQGQK gepgvglpglkglpglpgipgtpg 732-755 756-778 EKGSIGVPGVPGEHGAIGPPGLQ girgepgppglpgsvgspgvpgigppgarg 779-823 ppggqgppglsgppg 824-854 IKGEKGFPGFPGLDMPGPKGDKGAQGLPGI T gqsglpglpgqqgapgipgfpg 855-876 877-946 SKGEMGVMGTPGQPGSPGPVGAPGLPGEKG DHGFPGSSGPRGDPGLKGDKGDVGLPGKPG SMDKVDMGSM kgqkgdqgekgqig 947-960 961-976 PIGEKGSRGDPGTPGV pgkdgqagqpgqpgpkgdpg 977-996 997-1052 ISGTPGAPGLPGPKGSVGGMGLPGTPGEKG VPGIPGPQGSPGLPGDKGAKGEKGQA gppgigipg 1053-1061 1062-1084 LRGEKGDQGIAGFPGSPGEKGEK gsigipgmpgspglkgspgsvgypgspglp 1085-1115 g 1116-1132 EKGDKGLPGLDGIPGVK geaglpgtpgptgpag 1133-1148 1149-1165 QKGEPGSDGIPGSAGEK gepglpgrgfpgfpgakg 1166-1183 1184-1206 DKGSKGEVGFPGLAGSPGIPGSK geqgfmgppgpqgqpglpgspg 1207-1228 1229-1238 HATEGPKGDR gpqgqpglpglpgpmgppglpg 1239-1260 1261-1268 IDGVKGDK gnpgwpgapgvpgpkgdpgfqgmpgiggsp 1269-1305 gitgskg 1306-1334 DMGPPGVPGFQGPKGLPGLQGIKGDQGDQ gvpgakglpgppgppgp 1335-1351 1352-1355 YDII kgepglpgpegppglkglqglpgpkgqqgv 1356-1405 tglvgipgppgipgfdgapg 1406-1410 QKGEM gpagptgprgfpgppgpdglpgsmgppg 1411-1438 1439-1669 TPSVDHGFLVTRHSQTIDDPQCPSGTKILY HGYSLLYVQGNERAHGQDLGTAGSCLRKFS TMPFLFCNINNVCNFASRNDYSYWLSTPEP MPMSMAPITGENIRPFISRCAVCEAPAMVM AVHSQTIQIPPCPSGWSSLWIGYSFVMHTS AGAEGSGQALASPGSCLEEFRSAPFIECHG RGTCNYYANAYSFWLATIERSEMFKKPTPS TLKAGELRTHVSRCQVCMRRT low complexity regions: SEG 25 3.0 3.3 >tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR 1-1 M gprlsvwllllpaalllheehsraaakggc 2-464 agsgcgkcdchgvkgqkgerglpglqgvig fpgmqgpegpqgppgqkgdtgepglpgtkg trgppgasgypgnpglpgipgqdgppgppg ipgcngtkgergplgppglpgfagnpgppg lpgmkgdpgeilghvpgmllkgergfpgip gtpgppglpglqgpvgppgftgppgppgpp gppgekgqmglsfqgpkgdkgdqgvsgppg vpgqaqvqekgdfatkgekgqkgepgfqgm pgvgekgepgkpgprgkpgkdgdkgekgsp gfpgepgypgligrqgpqgekgeagppgpp givigtgplgekgergypgtpgprgepgpk gfpglpgqpgppglpvpgqagapgfpgerg ekgdrgfpgtslpgpsgrdglpgppgspgp pgqpgytngivecqpgppgdqgppgipgqp gfigeigekgqkg 465-476 ESCLICDIDGYR gppgpqgppgeigfpgqpgakgdrglpgrd 477-1441 gvagvpgpqgtpgligqpgakgepgefyfd lrlkgdkgdpgfpgqpgmpgragspgrdgh pglpgpkgspgsvglkgergppggvgfpgs rgdtgppgppgygpagpigdkgqagfpggp gspglpgpkgepgkivplpgppgaeglpgs pgfpgpqgdrgfpgtpgrpglpgekgavgq pgigfpgppgpkgvdglpgdmgppgtpgrp gfnglpgnpgvqgqkgepgvglpglkglpg lpgipgtpgekgsigvpgvpgehgaigppg lqgirgepgppglpgsvgspgvpgigppga rgppggqgppglsgppgikgekgfpgfpgl dmpgpkgdkgaqglpgitgqsglpglpgqq gapgipgfpgskgemgvmgtpgqpgspgpv gapglpgekgdhgfpgssgprgdpglkgdk gdvglpgkpgsmdkvdmgsmkgqkgdqgek gqigpigekgsrgdpgtpgvpgkdgqagqp gqpgpkgdpgisgtpgapglpgpkgsvggm glpgtpgekgvpgipgpqgspglpgdkgak gekgqagppgigipglrgekgdqgiagfpg spgekgekgsigipgmpgspglkgspgsvg ypgspglpgekgdkglpgldgipgvkgeag lpgtpgptgpagqkgepgsdgipgsagekg epglpgrgfpgfpgakgdkgskgevgfpgl agspgipgskgeqgfmgppgpqgqpglpgs pghategpkgdrgpqgqpglpglpgpmgpp glpgidgvkgdkgnpgwpgapgvpgpkgdp gfqgmpgiggspgitgskgdmgppgvpgfq gpkglpglqgikgdqgdqgvpgakglpgpp gppgpydiikgepglpgpegppglkglqgl pgpkgqqgvtglvgipgppgipgfdgapgq kgemgpagptgprgfpgppgpdglpgsmgp pgtps 1442-1669 VDHGFLVTRHSQTIDDPQCPSGTKILYHGY SLLYVQGNERAHGQDLGTAGSCLRKFSTMP FLFCNINNVCNFASRNDYSYWLSTPEPMPM SMAPITGENIRPFISRCAVCEAPAMVMAVH SQTIQIPPCPSGWSSLWIGYSFVMHTSAGA EGSGQALASPGSCLEEFRSAPFIECHGRGT CNYYANAYSFWLATIERSEMFKKPTPSTLK AGELRTHVSRCQVCMRRT low complexity regions: SEG 45 3.4 3.75 >tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR 1-42 MGPRLSVWLLLLPAALLLHEEHSRAAAKGG CAGSGCGKCDCH gvkgqkgerglpglqgvigfpgmqgpegpq 43-1440 gppgqkgdtgepglpgtkgtrgppgasgyp gnpglpgipgqdgppgppgipgcngtkger gplgppglpgfagnpgppglpgmkgdpgei lghvpgmllkgergfpgipgtpgppglpgl qgpvgppgftgppgppgppgppgekgqmgl sfqgpkgdkgdqgvsgppgvpgqaqvqekg dfatkgekgqkgepgfqgmpgvgekgepgk pgprgkpgkdgdkgekgspgfpgepgypgl igrqgpqgekgeagppgppgivigtgplge kgergypgtpgprgepgpkgfpglpgqpgp pglpvpgqagapgfpgergekgdrgfpgts lpgpsgrdglpgppgspgppgqpgytngiv ecqpgppgdqgppgipgqpgfigeigekgq kgesclicdidgyrgppgpqgppgeigfpg qpgakgdrglpgrdgvagvpgpqgtpglig qpgakgepgefyfdlrlkgdkgdpgfpgqp gmpgragspgrdghpglpgpkgspgsvglk gergppggvgfpgsrgdtgppgppgygpag pigdkgqagfpggpgspglpgpkgepgkiv plpgppgaeglpgspgfpgpqgdrgfpgtp grpglpgekgavgqpgigfpgppgpkgvdg lpgdmgppgtpgrpgfnglpgnpgvqgqkg epgvglpglkglpglpgipgtpgekgsigv pgvpgehgaigppglqgirgepgppglpgs vgspgvpgigppgargppggqgppglsgpp gikgekgfpgfpgldmpgpkgdkgaqglpg itgqsglpglpgqqgapgipgfpgskgemg vmgtpgqpgspgpvgapglpgekgdhgfpg ssgprgdpglkgdkgdvglpgkpgsmdkvd mgsmkgqkgdqgekgqigpigekgsrgdpg tpgvpgkdgqagqpgqpgpkgdpgisgtpg apglpgpkgsvggmglpgtpgekgvpgipg pqgspglpgdkgakgekgqagppgigipgl rgekgdqgiagfpgspgekgekgsigipgm pgspglkgspgsvgypgspglpgekgdkgl pgldgipgvkgeaglpgtpgptgpagqkge pgsdgipgsagekgepglpgrgfpgfpgak gdkgskgevgfpglagspgipgskgeqgfm gppgpqgqpglpgspghategpkgdrgpqg qpglpglpgpmgppglpgidgvkgdkgnpg wpgapgvpgpkgdpgfqgmpgiggspgitg skgdmgppgvpgfqgpkglpglqgikgdqg dqgvpgakglpgppgppgpydiikgepglp gpegppglkglqglpgpkgqqgvtglvgip gppgipgfdgapgqkgemgpagptgprgfp gppgpdglpgsmgppgtp 1441-1669 SVDHGFLVTRHSQTIDDPQCPSGTKILYHG YSLLYVQGNERAHGQDLGTAGSCLRKFSTM PFLFCNINNVCNFASRNDYSYWLSTPEPMP MSMAPITGENIRPFISRCAVCEAPAMVMAV HSQTIQIPPCPSGWSSLWIGYSFVMHTSAG AEGSGQALASPGSCLEEFRSAPFIECHGRG TCNYYANAYSFWLATIERSEMFKKPTPSTL KAGELRTHVSRCQVCMRRT low complexity regions: XNU # Score cutoff = 21, Search from offsets 1 to 4 # both members of each repeat flagged # lambda = 0.347, K = 0.200, H = 0.664 >tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR MGPRLSVWllllpaalllheeHSRAAAKGGCAGSGCGKCDCHgvkgqkgerglpglqgvi gfpgmqgpegpqgppgqkgdtgepglpgtkgtrgppgasgypgnpglpgipgqdgppgpp gipgcngtkgergplgppglpgfagnpgppglpgmkgdpgeILGHVPGMLLKGERgfpgi pgtpgppglpglqgpvgppgftgppgppgppgppgekgqmgLSFqgpkgdkgdqgvsgpp gvpgQAQVQEKGDFATkgekgqkgepgfqgmpgvgekgepgkpgprgkpgkdgdkgekgs pgfpgepgypgligrqgpqgekgeagppgppgIVIGTGPLgekgergypgtpgprgepgp kgfpglpgqpgppglpvpgqagapgfpgergekgdrgfpgtslpgpsgrdglpgppgspg ppgqpgYTNGIVECqpgppgdqgppgipgqpgfigeigekgqkgeSCLICDIDGYRgppg pqgppgeigfpgqpgakgdrglpgrdgvagvpgpqgtpgligqpgakgepgeFYFDLRLk gdkgdpgfpgqpgmpgragspgrdghpglpgpkgspgsvglkgergppggvgfpgsrgdt gppgppgygpagpigdkgqagfpggpgspglpgpkgepgkivplpgppgaeglpgspgfp gpqgdrgfpgtpgrpglpgekgavgqpgigfpgppgpkgvdglpgdmgppgtpgrpgfng lpgnpgvqgqkgepgvglpglkglpglpgipgtpgekgsigvpgvpgehgaigppglqgi rgepgppglpgsvgspgvpgigppgargppggqgppglsgppgikgekgfpgfpgLDMPg pkgdkgaqglpgitgqsglpglpgqqgapgipgfpgskgemgvmgtpgqpgspgpvgapg lpgekgdhgfpgssgprgdpglkgdkgdvglpgkpgsmdkvdmgsmkgqkgdqgekgqig pigekgsrgdpgtpgvpgkdgqagqpgqpgpkgdpgisgtpgapglpgpkgsvggmglpg tpgekgvpgipgpqgspglpgdkgakgekgqagppgigipglrgekgdqgiagfpgspge kgekgsigipgmpgspglkgspgsvgypgspglpgekgdkglpgldgipgvkgeaglpgt pgptgpagqkgepgsdgipgsagekgepglpgrgfpgfpgakgdkgskgevgfpglagsp gipgskgeqgfmgppgpqgqpglpgspghategpkgdrgpqgqpglpglpgpmgppglpg idgvkgdkgnpgwpgapgvpgpkgdpgfqgmpgiggspgitgskgdmgppgvpgfqgpkg lpglqgikgdqgdqgvpgakglpgppgppgpYDIIKgepglpgpegppglkglqglpgpk gqqgvtglvgipgppgipgfdgapgqkgemgpagptgprgfpgppgpdglpgsmgppgtp sVDHGFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTM PFLFCNINNVCNFASRNDYSYWLSTpepmpmsmaPITGENIRPFISRCAVCEAPAMVMAV HSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRG TCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT 1 - 8 MGPRLSVW 9 - 21 ll llpaalllhe e 22 - 42 HSRAAAKGG CAGSGCGKCD CH 43 - 161 gvkgqkge rglpglqgvi gfpgmqgpeg pqgppgqkgd tgepglpgtk gtrgppgasg yp gnpglpgi pgqdgppgpp gipgcngtkg ergplgppgl pgfagnpgpp glpgmkgdpg e 162 - 175 ILGHVPGML LKGER 176 - 221 gfpgi pgtpgppglp glqgpvgppg ftgppgppgp pgppgekgqm g 222 - 224 LSF 225 - 244 qgpkgd kgdqgvsgpp gvpg 245 - 256 QAQVQE KGDFAT 257 - 332 kgek gqkgepgfqg mpgvgekgep gkpgprgkpg kdgdkgekgs pgfpgepgyp gligrq gpqg ekgeagppgp pg 333 - 340 IVIGTGPL 341 - 426 gekgergypg tpgprgepgp kgfpglpgqp gppglpvpgq agapgfpger gekgdrgfpg tslpgpsgrd glpgppgspg ppgqpg 427 - 434 YTNG IVEC 435 - 465 qpgppg dqgppgipgq pgfigeigek gqkge 466 - 476 SCLIC DIDGYR 477 - 532 gppg pqgppgeigf pgqpgakgdr glpgrdgvag vpgpqgtpgl igqpgakgep ge 533 - 539 FYFDLRL 540 - 835 k gdkgdpgfpg qpgmpgrags pgrdghpglp gpkgspgsvg lkgergppgg vgfpgsrgd t gppgppgygp agpigdkgqa gfpggpgspg lpgpkgepgk ivplpgppga eglpgspgf p gpqgdrgfpg tpgrpglpge kgavgqpgig fpgppgpkgv dglpgdmgpp gtpgrpgfn g lpgnpgvqgq kgepgvglpg lkglpglpgi pgtpgekgsi gvpgvpgehg aigppglqg i rgepgppglp gsvgspgvpg igppgargpp ggqgppglsg ppgikgekgf pgfpg 836 - 839 LDMP 840 - 1351 g pkgdkgaqgl pgitgqsglp glpgqqgapg ipgfpgskge mgvmgtpgqp gspgpvgap g lpgekgdhgf pgssgprgdp glkgdkgdvg lpgkpgsmdk vdmgsmkgqk gdqgekgqi g pigekgsrgd pgtpgvpgkd gqagqpgqpg pkgdpgisgt pgapglpgpk gsvggmglp g tpgekgvpgi pgpqgspglp gdkgakgekg qagppgigip glrgekgdqg iagfpgspg e kgekgsigip gmpgspglkg spgsvgypgs pglpgekgdk glpgldgipg vkgeaglpg t pgptgpagqk gepgsdgipg sagekgepgl pgrgfpgfpg akgdkgskge vgfpglags p gipgskgeqg fmgppgpqgq pglpgspgha tegpkgdrgp qgqpglpglp gpmgppglp g idgvkgdkgn pgwpgapgvp gpkgdpgfqg mpgiggspgi tgskgdmgpp gvpgfqgpk g lpglqgikgd qgdqgvpgak glpgppgppg p 1352 - 1356 YDIIK 1357 - 1441 gepg lpgpegppgl kglqglpgpk gqqgvtglvg ipgppgipgf dgapgqkgem gpagpt gprg fpgppgpdgl pgsmgppgtp s 1442 - 1525 VDHGFLVTR HSQTIDDPQC PSGTKILYHG YSLLYVQGNE RAHGQDLGTA GSCLRKFSTM P FLFCNINNV CNFASRNDYS YWLST 1526 - 1534 pepmp msma 1535 - 1669 PITGEN IRPFISRCAV CEAPAMVMAV HSQTIQIPPC PSGWSSLWIG YSFVMHTSAG AEGS GQALAS PGSCLEEFRS APFIECHGRG TCNYYANAYS FWLATIERSE MFKKPTPSTL KAGE LRTHVS RCQVCMRRT low complexity regions: DUST >tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR MGPRLSVWLLLLPAALLLHEEHSRAAAKGGCAGSGCGKCDCHGVKGQKGERGLPGLQGVI GFPGMQGPEGPQGPPGQKGDTGEPGLPGTKGTRGPPGASGYPGNPGLPGIPGQDGPPGPP GIPGCNGTKGERGPLGPPGLPGFAGNPGPPGLPGMKGDPGEILGHVPGMLLKGERGFPGI PGTPGPPGLPGLQGPVGPPGFTGPPGPPGPPGPPGEKGQMGLSFQGPKGDKGDQGVSGPP GVPGQAQVQEKGDFATKGEKGQKGEPGFQGMPGVGEKGEPGKPGPRGKPGKDGDKGEKGS PGFPGEPGYPGLIGRQGPQGEKGEAGPPGPPGIVIGTGPLGEKGERGYPGTPGPRGEPGP KGFPGLPGQPGPPGLPVPGQAGAPGFPGERGEKGDRGFPGTSLPGPSGRDGLPGPPGSPG PPGQPGYTNGIVECQPGPPGDQGPPGIPGQPGFIGEIGEKGQKGESCLICDIDGYRGPPG PQGPPGEIGFPGQPGAKGDRGLPGRDGVAGVPGPQGTPGLIGQPGAKGEPGEFYFDLRLK GDKGDPGFPGQPGMPGRAGSPGRDGHPGLPGPKGSPGSVGLKGERGPPGGVGFPGSRGDT GPPGPPGYGPAGPIGDKGQAGFPGGPGSPGLPGPKGEPGKIVPLPGPPGAEGLPGSPGFP GPQGDRGFPGTPGRPGLPGEKGAVGQPGIGFPGPPGPKGVDGLPGDMGPPGTPGRPGFNG LPGNPGVQGQKGEPGVGLPGLKGLPGLPGIPGTPGEKGSIGVPGVPGEHGAIGPPGLQGI RGEPGPPGLPGSVGSPGVPGIGPPGARGPPGGQGPPGLSGPPGIKGEKGFPGFPGLDMPG PKGDKGAQGLPGITGQSGLPGLPGQQGAPGIPGFPGSKGEMGVMGTPGQPGSPGPVGAPG LPGEKGDHGFPGSSGPRGDPGLKGDKGDVGLPGKPGSMDKVDMGSMKGQKGDQGEKGQIG PIGEKGSRGDPGTPGVPGKDGQAGQPGQPGPKGDPGISGTPGAPGLPGPKGSVGGMGLPG TPGEKGVPGIPGPQGSPGLPGDKGAKGEKGQAGPPGIGIPGLRGEKGDQGIAGFPGSPGE KGEKGSIGIPGMPGSPGLKGSPGSVGYPGSPGLPGEKGDKGLPGLDGIPGVKGEAGLPGT PGPTGPAGQKGEPGSDGIPGSAGEKGEPGLPGRGFPGFPGAKGDKGSKGEVGFPGLAGSP GIPGSKGEQGFMGPPGPQGQPGLPGSPGHATEGPKGDRGPQGQPGLPGLPGPMGPPGLPG IDGVKGDKGNPGWPGAPGVPGPKGDPGFQGMPGIGGSPGITGSKGDMGPPGVPGFQGPKG LPGLQGIKGDQGDQGVPGAKGLPGPPGPPGPYDIIKGEPGLPGPEGPPGLKGLQGLPGPK GQQGVTGLVGIPGPPGIPGFDGAPGQKGEMGPAGPTGPRGFPGPPGPDGLPGSMGPPGTP SVDHGFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTM PFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAV HSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRG TCNYYANAYSFWLATIERSEMFKKPTPSTLKAGELRTHVSRCQVCMRRT ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN sequence: 1610 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MGPRLSVWLL LLPAALLLHE EHSRAAAKGG CAGSGCGKCD CHGVKGQKGE RGLPGLQGVI ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 120 GFPGMQGPEG PQGPPGQKGD TGEPGLPGTK GTRGPPGASG YPGNPGLPGI PGQDGPPGPP ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 180 GIPGCNGTKG ERGPLGPPGL PGFAGNPGPP GLPGMKGDPG EILGHVPGML LKGERGFPGI ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 240 PGTPGPPGLP GLQGPVGPPG FTGPPGPPGP PGPPGEKGQM GLSFQGPKGD KGDQGVSGPP ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 300 GVPGQAQVQE KGDFATKGEK GQKGEPGFQG MPGVGEKGEP GKPGPRGKPG KDGDKGEKGS ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 360 PGFPGEPGYP GLIGRQGPQG EKGEAGPPGP PGIVIGTGPL GEKGERGYPG TPGPRGEPGP ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 420 KGFPGLPGQP GPPGLPVPGQ AGAPGFPGER GEKGDRGFPG TSLPGPSGRD GLPGPPGSPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 480 PPGQPGYTNG IVECQPGPPG DQGPPGIPGQ PGFIGEIGEK GQKGESCLIC DIDGYRGPPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 540 PQGPPGEIGF PGQPGAKGDR GLPGRDGVAG VPGPQGTPGL IGQPGAKGEP GEFYFDLRLK ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 600 GDKGDPGFPG QPGMPGRAGS PGRDGHPGLP GPKGSPGSVG LKGERGPPGG VGFPGSRGDT ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 660 GPPGPPGYGP AGPIGDKGQA GFPGGPGSPG LPGPKGEPGK IVPLPGPPGA EGLPGSPGFP ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 720 GPQGDRGFPG TPGRPGLPGE KGAVGQPGIG FPGPPGPKGV DGLPGDMGPP GTPGRPGFNG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 780 LPGNPGVQGQ KGEPGVGLPG LKGLPGLPGI PGTPGEKGSI GVPGVPGEHG AIGPPGLQGI ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 840 RGEPGPPGLP GSVGSPGVPG IGPPGARGPP GGQGPPGLSG PPGIKGEKGF PGFPGLDMPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 900 PKGDKGAQGL PGITGQSGLP GLPGQQGAPG IPGFPGSKGE MGVMGTPGQP GSPGPVGAPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 960 LPGEKGDHGF PGSSGPRGDP GLKGDKGDVG LPGKPGSMDK VDMGSMKGQK GDQGEKGQIG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 1020 PIGEKGSRGD PGTPGVPGKD GQAGQPGQPG PKGDPGISGT PGAPGLPGPK GSVGGMGLPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 1080 TPGEKGVPGI PGPQGSPGLP GDKGAKGEKG QAGPPGIGIP GLRGEKGDQG IAGFPGSPGE ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 1140 KGEKGSIGIP GMPGSPGLKG SPGSVGYPGS PGLPGEKGDK GLPGLDGIPG VKGEAGLPGT ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 1200 PGPTGPAGQK GEPGSDGIPG SAGEKGEPGL PGRGFPGFPG AKGDKGSKGE VGFPGLAGSP ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 1260 GIPGSKGEQG FMGPPGPQGQ PGLPGSPGHA TEGPKGDRGP QGQPGLPGLP GPMGPPGLPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 1320 IDGVKGDKGN PGWPGAPGVP GPKGDPGFQG MPGIGGSPGI TGSKGDMGPP GVPGFQGPKG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 1380 LPGLQGIKGD QGDQGVPGAK GLPGPPGPPG PYDIIKGEPG LPGPEGPPGL KGLQGLPGPK ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 1440 GQQGVTGLVG IPGPPGIPGF DGAPGQKGEM GPAGPTGPRG FPGPPGPDGL PGSMGPPGTP ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 1500 SVDHGFLVTR HSQTIDDPQC PSGTKILYHG YSLLYVQGNE RAHGQDLGTA GSCLRKFSTM ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 1560 PFLFCNINNV CNFASRNDYS YWLSTPEPMP MSMAPITGEN IRPFISRCAV CEAPAMVMAV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | HSQTIQIPPC PSGWSSLWIG YSFVMHTSAG AEGSGQALAS PGSCLEEFRS ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ---------- ---------- ---------- ---------- ---------- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** tem31_1.___inter___ is a single sequence Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok Using sequence file: tem31_1.___inter___ (1 sequences) MGPRLSVWLLLLPAALLLHEEHSRAAAKGGCAGSGCGKCDCHGVKGQKGE RGLPGLQGVIGFPGMQGPEGPQGPPGQKGDTGEPGLPGTKGTRGPPGASG YPGNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGLPGFAGNPGPP GLPGMKGDPGEILGHVPGMLLKGERGFPGIPGTPGPPGLPGLQGPVGPPG FTGPPGPPGPPGPPGEKGQMGLSFQGPKGDKGDQGVSGPPGVPGQAQVQE KGDFATKGEKGQKGEPGFQGMPGVGEKGEPGKPGPRGKPGKDGDKGEKGS PGFPGEPGYPGLIGRQGPQGEKGEAGPPGPPGIVIGTGPLGEKGERGYPG TPGPRGEPGPKGFPGLPGQPGPPGLPVPGQAGAPGFPGERGEKGDRGFPG TSLPGPSGRDGLPGPPGSPGPPGQPGYTNGIVECQPGPPGDQGPPGIPGQ PGFIGEIGEKGQKGESCLICDIDGYRGPPGPQGPPGEIGFPGQPGAKGDR GLPGRDGVAGVPGPQGTPGLIGQPGAKGEPGEFYFDLRLKGDKGDPGFPG QPGMPGRAGSPGRDGHPGLPGPKGSPGSVGLKGERGPPGGVGFPGSRGDT GPPGPPGYGPAGPIGDKGQAGFPGGPGSPGLPGPKGEPGKIVPLPGPPGA EGLPGSPGFPGPQGDRGFPGTPGRPGLPGEKGAVGQPGIGFPGPPGPKGV DGLPGDMGPPGTPGRPGFNGLPGNPGVQGQKGEPGVGLPGLKGLPGLPGI PGTPGEKGSIGVPGVPGEHGAIGPPGLQGIRGEPGPPGLPGSVGSPGVPG IGPPGARGPPGGQGPPGLSGPPGIKGEKGFPGFPGLDMPGPKGDKGAQGL PGITGQSGLPGLPGQQGAPGIPGFPGSKGEMGVMGTPGQPGSPGPVGAPG LPGEKGDHGFPGSSGPRGDPGLKGDKGDVGLPGKPGSMDKVDMGSMKGQK GDQGEKGQIGPIGEKGSRGDPGTPGVPGKDGQAGQPGQPGPKGDPGISGT PGAPGLPGPKGSVGGMGLPGTPGEKGVPGIPGPQGSPGLPGDKGAKGEKG QAGPPGIGIPGLRGEKGDQGIAGFPGSPGEKGEKGSIGIPGMPGSPGLKG SPGSVGYPGSPGLPGEKGDKGLPGLDGIPGVKGEAGLPGTPGPTGPAGQK GEPGSDGIPGSAGEKGEPGLPGRGFPGFPGAKGDKGSKGEVGFPGLAGSP GIPGSKGEQGFMGPPGPQGQPGLPGSPGHATEGPKGDRGPQGQPGLPGLP GPMGPPGLPGIDGVKGDKGNPGWPGAPGVPGPKGDPGFQGMPGIGGSPGI TGSKGDMGPPGVPGFQGPKGLPGLQGIKGDQGDQGVPGAKGLPGPPGPPG PYDIIKGEPGLPGPEGPPGLKGLQGLPGPKGQQGVTGLVGIPGPPGIPGF DGAPGQKGEMGPAGPTGPRGFPGPPGPDGLPGSMGPPGTPSVDHGFLVTR HSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTM PFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAV CEAPAMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALAS PGSCLEEFRSAPFIECHGRGTCNYYANAYSFWLATIERSEMFKKPTPSTL KAGELRTHVSRCQVCMRRT (p)rokaryotic or (e)ukaryotic: e Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 1024 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 1 21 0.977 Putative 2 135 155 0.650 Putative 3 186 206 0.760 Putative 4 323 343 0.633 Putative 5 734 754 0.682 Putative 6 786 806 1.025 Certain 7 881 901 0.650 Putative 8 1242 1262 0.819 Putative 9 1285 1305 0.747 Putative 10 1383 1403 0.980 Putative 11 1519 1539 0.667 Putative 12 1569 1589 1.404 Certain Warning! Only printing 30 out of 1024 structures ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 5 6 8 9 11 12 Loop length 0 113 30 527 31 435 22 213 29 80 K+R profile 2.00 3.00 2.00 3.00 2.00 + + + + + CYT-EXT prof - - - - - 0.33 0.66 0.68 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 12.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -2.08 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 2 3 6 7 8 9 11 12 Loop length 0 113 30 579 74 340 22 213 29 80 K+R profile 2.00 3.00 + 3.00 2.00 + + + + + CYT-EXT prof - - 0.58 - - 0.33 0.67 0.66 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.49 -> Orientation: N-in ---------------------------------------------------------------------- Structure 3 Transmembrane segments included in this structure: Segment 2 3 5 6 8 9 11 12 Loop length 134 30 527 31 435 22 213 29 80 K+R profile + + + + + 3.00 2.00 3.00 2.00 CYT-EXT prof 0.29 0.66 0.68 0.77 -0.35 - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -10.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 2.04 -> Orientation: N-out ---------------------------------------------------------------------- Structure 4 Transmembrane segments included in this structure: Segment 1 2 3 4 6 8 9 11 12 Loop length 0 113 30 116 442 435 22 213 29 80 K+R profile 2.00 3.00 + 3.00 2.00 + + + + + CYT-EXT prof - - 0.67 - - 0.33 0.62 0.68 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.37 -> Orientation: N-in ---------------------------------------------------------------------- Structure 5 Transmembrane segments included in this structure: Segment 1 2 3 5 6 8 9 10 12 Loop length 0 113 30 527 31 435 22 77 165 80 K+R profile 2.00 3.00 2.00 3.00 + + + + + + CYT-EXT prof - - - - 0.86 0.33 0.66 0.68 0.60 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.06 -> Orientation: N-in ---------------------------------------------------------------------- Structure 6 Transmembrane segments included in this structure: Segment 1 2 3 5 6 8 9 12 Loop length 0 113 30 527 31 435 22 263 80 K+R profile 2.00 3.00 2.00 3.00 + + + + + CYT-EXT prof - - - - -0.35 0.33 0.66 0.68 0.87 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -2.88 -> Orientation: N-in ---------------------------------------------------------------------- Structure 7 Transmembrane segments included in this structure: Segment 1 2 3 5 6 9 10 11 12 Loop length 0 113 30 527 31 478 77 115 29 80 K+R profile 2.00 3.00 2.00 + 2.00 + + + + + CYT-EXT prof - - - 0.60 - 0.33 0.66 0.71 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.47 -> Orientation: N-in ---------------------------------------------------------------------- Structure 8 Transmembrane segments included in this structure: Segment 1 2 3 5 6 8 10 11 12 Loop length 0 113 30 527 31 435 120 115 29 80 K+R profile 2.00 3.00 2.00 + 2.00 + + + + + CYT-EXT prof - - - 0.77 - 0.33 0.66 0.68 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.28 -> Orientation: N-in ---------------------------------------------------------------------- Structure 9 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 10 11 12 Loop length 0 113 30 527 31 74 481 115 29 80 K+R profile 2.00 3.00 2.00 + 2.00 + + + + + CYT-EXT prof - - - 0.69 - 0.33 0.66 0.58 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.26 -> Orientation: N-in ---------------------------------------------------------------------- Structure 10 Transmembrane segments included in this structure: Segment 1 3 4 5 6 8 9 11 12 Loop length 0 164 116 390 31 435 22 213 29 80 K+R profile 2.00 + 2.00 3.00 2.00 + + + + + CYT-EXT prof - 0.62 - - - 0.43 0.65 0.68 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.57 -> Orientation: N-in ---------------------------------------------------------------------- Structure 11 Transmembrane segments included in this structure: Segment 1 2 4 5 6 8 9 11 12 Loop length 0 113 167 390 31 435 22 213 29 80 K+R profile 2.00 + 2.00 3.00 2.00 + + + + + CYT-EXT prof - 0.67 - - - 0.33 0.65 0.68 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.41 -> Orientation: N-in ---------------------------------------------------------------------- Structure 12 Transmembrane segments included in this structure: Segment 1 5 6 8 9 11 12 Loop length 0 712 31 435 22 213 29 80 K+R profile 2.00 2.00 3.00 2.00 + + + + CYT-EXT prof - - - - 0.62 0.68 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.72 -> Orientation: N-in ---------------------------------------------------------------------- Structure 13 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 9 11 12 Loop length 0 113 30 527 31 74 383 213 29 80 K+R profile 2.00 3.00 2.00 + 2.00 + + + + + CYT-EXT prof - - - 0.70 - 0.33 0.66 0.58 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.28 -> Orientation: N-in ---------------------------------------------------------------------- Structure 14 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 8 11 12 Loop length 0 113 30 527 31 74 340 256 29 80 K+R profile 2.00 3.00 2.00 + 2.00 + + + + + CYT-EXT prof - - - 0.66 - 0.33 0.66 0.58 0.84 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.40 -> Orientation: N-in ---------------------------------------------------------------------- Structure 15 Transmembrane segments included in this structure: Segment 1 2 3 5 6 11 12 Loop length 0 113 30 527 31 712 29 80 K+R profile 2.00 3.00 2.00 2.00 + + + + CYT-EXT prof - - - - 0.33 0.66 0.73 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.37 -> Orientation: N-in ---------------------------------------------------------------------- Structure 16 Transmembrane segments included in this structure: Segment 1 2 3 5 6 8 9 10 11 12 Loop length 0 113 30 527 31 435 22 77 115 29 80 K+R profile 2.00 3.00 2.00 3.00 + + + + + + 2.00 CYT-EXT prof - - - - 0.74 -0.35 0.33 0.66 0.68 0.60 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.88 -> Orientation: N-in ---------------------------------------------------------------------- Structure 17 Transmembrane segments included in this structure: Segment 1 2 3 4 5 6 7 8 9 11 12 Loop length 0 113 30 116 390 31 74 340 22 213 29 80 K+R profile 2.00 3.00 + + 3.00 2.00 + + 2.00 + + + CYT-EXT prof - - 0.65 0.58 - - 0.33 0.62 - 0.66 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.78 -> Orientation: N-in ---------------------------------------------------------------------- Structure 18 Transmembrane segments included in this structure: Segment 2 3 6 7 8 9 11 12 Loop length 134 30 579 74 340 22 213 29 80 K+R profile + + + + + 3.00 + 3.00 2.00 CYT-EXT prof 0.29 0.67 0.66 0.77 -0.35 - 0.58 - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -8.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 1.45 -> Orientation: N-out ---------------------------------------------------------------------- Structure 19 Transmembrane segments included in this structure: Segment 2 3 4 6 8 9 11 12 Loop length 134 30 116 442 435 22 213 29 80 K+R profile + + + + + 3.00 + 3.00 2.00 CYT-EXT prof 0.29 0.62 0.68 0.77 -0.35 - 0.67 - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -8.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 1.34 -> Orientation: N-out ---------------------------------------------------------------------- Structure 20 Transmembrane segments included in this structure: Segment 1 2 3 6 7 8 9 10 12 Loop length 0 113 30 579 74 340 22 77 165 80 K+R profile 2.00 3.00 + 3.00 + + + + + + CYT-EXT prof - - 0.58 - 0.86 0.33 0.67 0.66 0.60 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.46 -> Orientation: N-in ---------------------------------------------------------------------- Structure 21 Transmembrane segments included in this structure: Segment 2 3 5 6 8 9 10 12 Loop length 134 30 527 31 435 22 77 165 80 K+R profile + + + + + 3.00 2.00 3.00 + CYT-EXT prof 0.29 0.66 0.68 0.60 -0.35 - - - 0.86 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -8.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 1.02 -> Orientation: N-out ---------------------------------------------------------------------- Structure 22 Transmembrane segments included in this structure: Segment 1 2 3 4 6 8 9 10 12 Loop length 0 113 30 116 442 435 22 77 165 80 K+R profile 2.00 3.00 + 3.00 + + + + + + CYT-EXT prof - - 0.67 - 0.86 0.33 0.62 0.68 0.60 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.35 -> Orientation: N-in ---------------------------------------------------------------------- Structure 23 Transmembrane segments included in this structure: Segment 1 2 3 6 7 8 9 12 Loop length 0 113 30 579 74 340 22 263 80 K+R profile 2.00 3.00 + 3.00 + + + + + CYT-EXT prof - - 0.58 - -0.35 0.33 0.67 0.66 0.87 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -2.29 -> Orientation: N-in ---------------------------------------------------------------------- Structure 24 Transmembrane segments included in this structure: Segment 2 3 5 6 8 9 12 Loop length 134 30 527 31 435 22 263 80 K+R profile + + + + 3.00 2.00 3.00 + CYT-EXT prof 0.29 0.66 0.68 0.87 - - - -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -8.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 2.85 -> Orientation: N-out ---------------------------------------------------------------------- Structure 25 Transmembrane segments included in this structure: Segment 1 2 3 4 6 8 9 12 Loop length 0 113 30 116 442 435 22 263 80 K+R profile 2.00 3.00 + 3.00 + + + + + CYT-EXT prof - - 0.67 - -0.35 0.33 0.62 0.68 0.87 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -2.18 -> Orientation: N-in ---------------------------------------------------------------------- Structure 26 Transmembrane segments included in this structure: Segment 1 2 3 6 7 9 10 11 12 Loop length 0 113 30 579 74 383 77 115 29 80 K+R profile 2.00 3.00 + + 2.00 + + + + + CYT-EXT prof - - 0.58 0.60 - 0.33 0.67 0.70 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 7.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.89 -> Orientation: N-in ---------------------------------------------------------------------- Structure 27 Transmembrane segments included in this structure: Segment 2 3 5 6 9 10 11 12 Loop length 134 30 527 31 478 77 115 29 80 K+R profile + + + + + 3.00 2.00 + 2.00 CYT-EXT prof 0.29 0.66 0.71 0.74 -0.35 - - 0.60 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -7.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 1.44 -> Orientation: N-out ---------------------------------------------------------------------- Structure 28 Transmembrane segments included in this structure: Segment 1 2 3 4 6 9 10 11 12 Loop length 0 113 30 116 442 478 77 115 29 80 K+R profile 2.00 3.00 + + 2.00 + + + + + CYT-EXT prof - - 0.67 0.60 - 0.33 0.62 0.71 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 7.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.77 -> Orientation: N-in ---------------------------------------------------------------------- Structure 29 Transmembrane segments included in this structure: Segment 1 2 3 6 7 8 10 11 12 Loop length 0 113 30 579 74 340 120 115 29 80 K+R profile 2.00 3.00 + + 2.00 + + + + + CYT-EXT prof - - 0.58 0.77 - 0.33 0.67 0.66 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 7.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.68 -> Orientation: N-in ---------------------------------------------------------------------- Structure 30 Transmembrane segments included in this structure: Segment 2 3 5 6 8 10 11 12 Loop length 134 30 527 31 435 120 115 29 80 K+R profile + + + + + 3.00 2.00 + 2.00 CYT-EXT prof 0.29 0.66 0.68 0.74 -0.35 - - 0.77 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -7.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 1.24 -> Orientation: N-out ---------------------------------------------------------------------- "tem31_1" 1669 1 21 #f 0.977083 135 155 #f 0.65 186 206 #f 0.760417 323 343 #f 0.633333 734 754 #f 0.682292 786 806 #t 1.025 881 901 #f 0.65 1242 1262 #f 0.81875 1285 1305 #f 0.746875 1383 1403 #f 0.980208 1519 1539 #f 0.666667 1569 1589 #t 1.40417 ************************************ *TOPPREDM with prokaryotic function* ************************************ tem31_1.___inter___ is a single sequence Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok Using sequence file: tem31_1.___inter___ (1 sequences) MGPRLSVWLLLLPAALLLHEEHSRAAAKGGCAGSGCGKCDCHGVKGQKGE RGLPGLQGVIGFPGMQGPEGPQGPPGQKGDTGEPGLPGTKGTRGPPGASG YPGNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGLPGFAGNPGPP GLPGMKGDPGEILGHVPGMLLKGERGFPGIPGTPGPPGLPGLQGPVGPPG FTGPPGPPGPPGPPGEKGQMGLSFQGPKGDKGDQGVSGPPGVPGQAQVQE KGDFATKGEKGQKGEPGFQGMPGVGEKGEPGKPGPRGKPGKDGDKGEKGS PGFPGEPGYPGLIGRQGPQGEKGEAGPPGPPGIVIGTGPLGEKGERGYPG TPGPRGEPGPKGFPGLPGQPGPPGLPVPGQAGAPGFPGERGEKGDRGFPG TSLPGPSGRDGLPGPPGSPGPPGQPGYTNGIVECQPGPPGDQGPPGIPGQ PGFIGEIGEKGQKGESCLICDIDGYRGPPGPQGPPGEIGFPGQPGAKGDR GLPGRDGVAGVPGPQGTPGLIGQPGAKGEPGEFYFDLRLKGDKGDPGFPG QPGMPGRAGSPGRDGHPGLPGPKGSPGSVGLKGERGPPGGVGFPGSRGDT GPPGPPGYGPAGPIGDKGQAGFPGGPGSPGLPGPKGEPGKIVPLPGPPGA EGLPGSPGFPGPQGDRGFPGTPGRPGLPGEKGAVGQPGIGFPGPPGPKGV DGLPGDMGPPGTPGRPGFNGLPGNPGVQGQKGEPGVGLPGLKGLPGLPGI PGTPGEKGSIGVPGVPGEHGAIGPPGLQGIRGEPGPPGLPGSVGSPGVPG IGPPGARGPPGGQGPPGLSGPPGIKGEKGFPGFPGLDMPGPKGDKGAQGL PGITGQSGLPGLPGQQGAPGIPGFPGSKGEMGVMGTPGQPGSPGPVGAPG LPGEKGDHGFPGSSGPRGDPGLKGDKGDVGLPGKPGSMDKVDMGSMKGQK GDQGEKGQIGPIGEKGSRGDPGTPGVPGKDGQAGQPGQPGPKGDPGISGT PGAPGLPGPKGSVGGMGLPGTPGEKGVPGIPGPQGSPGLPGDKGAKGEKG QAGPPGIGIPGLRGEKGDQGIAGFPGSPGEKGEKGSIGIPGMPGSPGLKG SPGSVGYPGSPGLPGEKGDKGLPGLDGIPGVKGEAGLPGTPGPTGPAGQK GEPGSDGIPGSAGEKGEPGLPGRGFPGFPGAKGDKGSKGEVGFPGLAGSP GIPGSKGEQGFMGPPGPQGQPGLPGSPGHATEGPKGDRGPQGQPGLPGLP GPMGPPGLPGIDGVKGDKGNPGWPGAPGVPGPKGDPGFQGMPGIGGSPGI TGSKGDMGPPGVPGFQGPKGLPGLQGIKGDQGDQGVPGAKGLPGPPGPPG PYDIIKGEPGLPGPEGPPGLKGLQGLPGPKGQQGVTGLVGIPGPPGIPGF DGAPGQKGEMGPAGPTGPRGFPGPPGPDGLPGSMGPPGTPSVDHGFLVTR HSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTM PFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAV CEAPAMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALAS PGSCLEEFRSAPFIECHGRGTCNYYANAYSFWLATIERSEMFKKPTPSTL KAGELRTHVSRCQVCMRRT (p)rokaryotic or (e)ukaryotic: p Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 1024 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 1 21 0.977 Putative 2 135 155 0.650 Putative 3 186 206 0.760 Putative 4 323 343 0.633 Putative 5 734 754 0.682 Putative 6 786 806 1.025 Certain 7 881 901 0.650 Putative 8 1242 1262 0.819 Putative 9 1285 1305 0.747 Putative 10 1383 1403 0.980 Putative 11 1519 1539 0.667 Putative 12 1569 1589 1.404 Certain Warning! Only printing 30 out of 1024 structures ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 5 6 8 9 11 12 Loop length 0 113 30 527 31 435 22 213 29 80 K+R profile 2.00 3.00 2.00 3.00 2.00 + + + + + CYT-EXT prof - - - - - 0.33 0.66 0.68 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 12.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -2.08 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 2 3 6 7 8 9 11 12 Loop length 0 113 30 579 74 340 22 213 29 80 K+R profile 2.00 3.00 + 3.00 2.00 + + + + + CYT-EXT prof - - 0.58 - - 0.33 0.67 0.66 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.49 -> Orientation: N-in ---------------------------------------------------------------------- Structure 3 Transmembrane segments included in this structure: Segment 2 3 5 6 8 9 11 12 Loop length 134 30 527 31 435 22 213 29 80 K+R profile + + + + + 3.00 2.00 3.00 2.00 CYT-EXT prof 0.29 0.66 0.68 0.77 -0.35 - - - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -10.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 2.04 -> Orientation: N-out ---------------------------------------------------------------------- Structure 4 Transmembrane segments included in this structure: Segment 1 2 3 4 6 8 9 11 12 Loop length 0 113 30 116 442 435 22 213 29 80 K+R profile 2.00 3.00 + 3.00 2.00 + + + + + CYT-EXT prof - - 0.67 - - 0.33 0.62 0.68 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.37 -> Orientation: N-in ---------------------------------------------------------------------- Structure 5 Transmembrane segments included in this structure: Segment 1 2 3 5 6 8 9 10 12 Loop length 0 113 30 527 31 435 22 77 165 80 K+R profile 2.00 3.00 2.00 3.00 + + + + + + CYT-EXT prof - - - - 0.86 0.33 0.66 0.68 0.60 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.06 -> Orientation: N-in ---------------------------------------------------------------------- Structure 6 Transmembrane segments included in this structure: Segment 1 2 3 5 6 8 9 12 Loop length 0 113 30 527 31 435 22 263 80 K+R profile 2.00 3.00 2.00 3.00 + + + + + CYT-EXT prof - - - - -0.35 0.33 0.66 0.68 0.87 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 10.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -2.88 -> Orientation: N-in ---------------------------------------------------------------------- Structure 7 Transmembrane segments included in this structure: Segment 1 2 3 5 6 9 10 11 12 Loop length 0 113 30 527 31 478 77 115 29 80 K+R profile 2.00 3.00 2.00 + 2.00 + + + + + CYT-EXT prof - - - 0.60 - 0.33 0.66 0.71 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.47 -> Orientation: N-in ---------------------------------------------------------------------- Structure 8 Transmembrane segments included in this structure: Segment 1 2 3 5 6 8 10 11 12 Loop length 0 113 30 527 31 435 120 115 29 80 K+R profile 2.00 3.00 2.00 + 2.00 + + + + + CYT-EXT prof - - - 0.77 - 0.33 0.66 0.68 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.28 -> Orientation: N-in ---------------------------------------------------------------------- Structure 9 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 10 11 12 Loop length 0 113 30 527 31 74 481 115 29 80 K+R profile 2.00 3.00 2.00 + 2.00 + + + + + CYT-EXT prof - - - 0.69 - 0.33 0.66 0.58 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.26 -> Orientation: N-in ---------------------------------------------------------------------- Structure 10 Transmembrane segments included in this structure: Segment 1 3 4 5 6 8 9 11 12 Loop length 0 164 116 390 31 435 22 213 29 80 K+R profile 2.00 + 2.00 3.00 2.00 + + + + + CYT-EXT prof - 0.62 - - - 0.43 0.65 0.68 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.57 -> Orientation: N-in ---------------------------------------------------------------------- Structure 11 Transmembrane segments included in this structure: Segment 1 2 4 5 6 8 9 11 12 Loop length 0 113 167 390 31 435 22 213 29 80 K+R profile 2.00 + 2.00 3.00 2.00 + + + + + CYT-EXT prof - 0.67 - - - 0.33 0.65 0.68 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.41 -> Orientation: N-in ---------------------------------------------------------------------- Structure 12 Transmembrane segments included in this structure: Segment 1 5 6 8 9 11 12 Loop length 0 712 31 435 22 213 29 80 K+R profile 2.00 2.00 3.00 2.00 + + + + CYT-EXT prof - - - - 0.62 0.68 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.72 -> Orientation: N-in ---------------------------------------------------------------------- Structure 13 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 9 11 12 Loop length 0 113 30 527 31 74 383 213 29 80 K+R profile 2.00 3.00 2.00 + 2.00 + + + + + CYT-EXT prof - - - 0.70 - 0.33 0.66 0.58 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.28 -> Orientation: N-in ---------------------------------------------------------------------- Structure 14 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 8 11 12 Loop length 0 113 30 527 31 74 340 256 29 80 K+R profile 2.00 3.00 2.00 + 2.00 + + + + + CYT-EXT prof - - - 0.66 - 0.33 0.66 0.58 0.84 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.40 -> Orientation: N-in ---------------------------------------------------------------------- Structure 15 Transmembrane segments included in this structure: Segment 1 2 3 5 6 11 12 Loop length 0 113 30 527 31 712 29 80 K+R profile 2.00 3.00 2.00 2.00 + + + + CYT-EXT prof - - - - 0.33 0.66 0.73 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.37 -> Orientation: N-in ---------------------------------------------------------------------- Structure 16 Transmembrane segments included in this structure: Segment 1 2 3 5 6 8 9 10 11 12 Loop length 0 113 30 527 31 435 22 77 115 29 80 K+R profile 2.00 3.00 2.00 3.00 + + + + + + 2.00 CYT-EXT prof - - - - 0.74 -0.35 0.33 0.66 0.68 0.60 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -1.88 -> Orientation: N-in ---------------------------------------------------------------------- Structure 17 Transmembrane segments included in this structure: Segment 1 2 3 4 5 6 7 8 9 11 12 Loop length 0 113 30 116 390 31 74 340 22 213 29 80 K+R profile 2.00 3.00 + + 3.00 2.00 + + 2.00 + + + CYT-EXT prof - - 0.65 0.58 - - 0.33 0.62 - 0.66 0.77 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.78 -> Orientation: N-in ---------------------------------------------------------------------- Structure 18 Transmembrane segments included in this structure: Segment 2 3 6 7 8 9 11 12 Loop length 134 30 579 74 340 22 213 29 80 K+R profile + + + + + 3.00 + 3.00 2.00 CYT-EXT prof 0.29 0.67 0.66 0.77 -0.35 - 0.58 - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -8.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 1.45 -> Orientation: N-out ---------------------------------------------------------------------- Structure 19 Transmembrane segments included in this structure: Segment 2 3 4 6 8 9 11 12 Loop length 134 30 116 442 435 22 213 29 80 K+R profile + + + + + 3.00 + 3.00 2.00 CYT-EXT prof 0.29 0.62 0.68 0.77 -0.35 - 0.67 - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -8.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 1.34 -> Orientation: N-out ---------------------------------------------------------------------- Structure 20 Transmembrane segments included in this structure: Segment 1 2 3 6 7 8 9 10 12 Loop length 0 113 30 579 74 340 22 77 165 80 K+R profile 2.00 3.00 + 3.00 + + + + + + CYT-EXT prof - - 0.58 - 0.86 0.33 0.67 0.66 0.60 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.46 -> Orientation: N-in ---------------------------------------------------------------------- Structure 21 Transmembrane segments included in this structure: Segment 2 3 5 6 8 9 10 12 Loop length 134 30 527 31 435 22 77 165 80 K+R profile + + + + + 3.00 2.00 3.00 + CYT-EXT prof 0.29 0.66 0.68 0.60 -0.35 - - - 0.86 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -8.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 1.02 -> Orientation: N-out ---------------------------------------------------------------------- Structure 22 Transmembrane segments included in this structure: Segment 1 2 3 4 6 8 9 10 12 Loop length 0 113 30 116 442 435 22 77 165 80 K+R profile 2.00 3.00 + 3.00 + + + + + + CYT-EXT prof - - 0.67 - 0.86 0.33 0.62 0.68 0.60 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.35 -> Orientation: N-in ---------------------------------------------------------------------- Structure 23 Transmembrane segments included in this structure: Segment 1 2 3 6 7 8 9 12 Loop length 0 113 30 579 74 340 22 263 80 K+R profile 2.00 3.00 + 3.00 + + + + + CYT-EXT prof - - 0.58 - -0.35 0.33 0.67 0.66 0.87 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -2.29 -> Orientation: N-in ---------------------------------------------------------------------- Structure 24 Transmembrane segments included in this structure: Segment 2 3 5 6 8 9 12 Loop length 134 30 527 31 435 22 263 80 K+R profile + + + + 3.00 2.00 3.00 + CYT-EXT prof 0.29 0.66 0.68 0.87 - - - -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -8.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 2.85 -> Orientation: N-out ---------------------------------------------------------------------- Structure 25 Transmembrane segments included in this structure: Segment 1 2 3 4 6 8 9 12 Loop length 0 113 30 116 442 435 22 263 80 K+R profile 2.00 3.00 + 3.00 + + + + + CYT-EXT prof - - 0.67 - -0.35 0.33 0.62 0.68 0.87 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 8.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -2.18 -> Orientation: N-in ---------------------------------------------------------------------- Structure 26 Transmembrane segments included in this structure: Segment 1 2 3 6 7 9 10 11 12 Loop length 0 113 30 579 74 383 77 115 29 80 K+R profile 2.00 3.00 + + 2.00 + + + + + CYT-EXT prof - - 0.58 0.60 - 0.33 0.67 0.70 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 7.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.89 -> Orientation: N-in ---------------------------------------------------------------------- Structure 27 Transmembrane segments included in this structure: Segment 2 3 5 6 9 10 11 12 Loop length 134 30 527 31 478 77 115 29 80 K+R profile + + + + + 3.00 2.00 + 2.00 CYT-EXT prof 0.29 0.66 0.71 0.74 -0.35 - - 0.60 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -7.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 1.44 -> Orientation: N-out ---------------------------------------------------------------------- Structure 28 Transmembrane segments included in this structure: Segment 1 2 3 4 6 9 10 11 12 Loop length 0 113 30 116 442 478 77 115 29 80 K+R profile 2.00 3.00 + + 2.00 + + + + + CYT-EXT prof - - 0.67 0.60 - 0.33 0.62 0.71 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 7.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.77 -> Orientation: N-in ---------------------------------------------------------------------- Structure 29 Transmembrane segments included in this structure: Segment 1 2 3 6 7 8 10 11 12 Loop length 0 113 30 579 74 340 120 115 29 80 K+R profile 2.00 3.00 + + 2.00 + + + + + CYT-EXT prof - - 0.58 0.77 - 0.33 0.67 0.66 0.74 -0.35 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 7.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: undecided CYT-EXT difference: -0.68 -> Orientation: N-in ---------------------------------------------------------------------- Structure 30 Transmembrane segments included in this structure: Segment 2 3 5 6 8 10 11 12 Loop length 134 30 527 31 435 120 115 29 80 K+R profile + + + + + 3.00 2.00 + 2.00 CYT-EXT prof 0.29 0.66 0.68 0.74 -0.35 - - 0.77 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -7.00 Tm probability: 0.00 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): -0.1429 NEG: 9.0000 POS: 12.0000 -> Orientation: N-in CYT-EXT difference: 1.24 -> Orientation: N-out ---------------------------------------------------------------------- "tem31_1" 1669 1 21 #f 0.977083 135 155 #f 0.65 186 206 #f 0.760417 323 343 #f 0.633333 734 754 #f 0.682292 786 806 #t 1.025 881 901 #f 0.65 1242 1262 #f 0.81875 1285 1305 #f 0.746875 1383 1403 #f 0.980208 1519 1539 #f 0.666667 1569 1589 #t 1.40417 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem31_1.___saps___ SAPS. Version of April 11, 1996. Date run: Tue Oct 31 16:17:55 2000 File: /people/maria/tem31_1.___saps___ ID tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN DE COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR number of residues: 1669; molecular weight: 160.6 kdal 1 MGPRLSVWLL LLPAALLLHE EHSRAAAKGG CAGSGCGKCD CHGVKGQKGE RGLPGLQGVI 61 GFPGMQGPEG PQGPPGQKGD TGEPGLPGTK GTRGPPGASG YPGNPGLPGI PGQDGPPGPP 121 GIPGCNGTKG ERGPLGPPGL PGFAGNPGPP GLPGMKGDPG EILGHVPGML LKGERGFPGI 181 PGTPGPPGLP GLQGPVGPPG FTGPPGPPGP PGPPGEKGQM GLSFQGPKGD KGDQGVSGPP 241 GVPGQAQVQE KGDFATKGEK GQKGEPGFQG MPGVGEKGEP GKPGPRGKPG KDGDKGEKGS 301 PGFPGEPGYP GLIGRQGPQG EKGEAGPPGP PGIVIGTGPL GEKGERGYPG TPGPRGEPGP 361 KGFPGLPGQP GPPGLPVPGQ AGAPGFPGER GEKGDRGFPG TSLPGPSGRD GLPGPPGSPG 421 PPGQPGYTNG IVECQPGPPG DQGPPGIPGQ PGFIGEIGEK GQKGESCLIC DIDGYRGPPG 481 PQGPPGEIGF PGQPGAKGDR GLPGRDGVAG VPGPQGTPGL IGQPGAKGEP GEFYFDLRLK 541 GDKGDPGFPG QPGMPGRAGS PGRDGHPGLP GPKGSPGSVG LKGERGPPGG VGFPGSRGDT 601 GPPGPPGYGP AGPIGDKGQA GFPGGPGSPG LPGPKGEPGK IVPLPGPPGA EGLPGSPGFP 661 GPQGDRGFPG TPGRPGLPGE KGAVGQPGIG FPGPPGPKGV DGLPGDMGPP GTPGRPGFNG 721 LPGNPGVQGQ KGEPGVGLPG LKGLPGLPGI PGTPGEKGSI GVPGVPGEHG AIGPPGLQGI 781 RGEPGPPGLP GSVGSPGVPG IGPPGARGPP GGQGPPGLSG PPGIKGEKGF PGFPGLDMPG 841 PKGDKGAQGL PGITGQSGLP GLPGQQGAPG IPGFPGSKGE MGVMGTPGQP GSPGPVGAPG 901 LPGEKGDHGF PGSSGPRGDP GLKGDKGDVG LPGKPGSMDK VDMGSMKGQK GDQGEKGQIG 961 PIGEKGSRGD PGTPGVPGKD GQAGQPGQPG PKGDPGISGT PGAPGLPGPK GSVGGMGLPG 1021 TPGEKGVPGI PGPQGSPGLP GDKGAKGEKG QAGPPGIGIP GLRGEKGDQG IAGFPGSPGE 1081 KGEKGSIGIP GMPGSPGLKG SPGSVGYPGS PGLPGEKGDK GLPGLDGIPG VKGEAGLPGT 1141 PGPTGPAGQK GEPGSDGIPG SAGEKGEPGL PGRGFPGFPG AKGDKGSKGE VGFPGLAGSP 1201 GIPGSKGEQG FMGPPGPQGQ PGLPGSPGHA TEGPKGDRGP QGQPGLPGLP GPMGPPGLPG 1261 IDGVKGDKGN PGWPGAPGVP GPKGDPGFQG MPGIGGSPGI TGSKGDMGPP GVPGFQGPKG 1321 LPGLQGIKGD QGDQGVPGAK GLPGPPGPPG PYDIIKGEPG LPGPEGPPGL KGLQGLPGPK 1381 GQQGVTGLVG IPGPPGIPGF DGAPGQKGEM GPAGPTGPRG FPGPPGPDGL PGSMGPPGTP 1441 SVDHGFLVTR HSQTIDDPQC PSGTKILYHG YSLLYVQGNE RAHGQDLGTA GSCLRKFSTM 1501 PFLFCNINNV CNFASRNDYS YWLSTPEPMP MSMAPITGEN IRPFISRCAV CEAPAMVMAV 1561 HSQTIQIPPC PSGWSSLWIG YSFVMHTSAG AEGSGQALAS PGSCLEEFRS APFIECHGRG 1621 TCNYYANAYS FWLATIERSE MFKKPTPSTL KAGELRTHVS RCQVCMRRT -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A- : 58( 3.5%); C : 20( 1.2%); D : 58( 3.5%); E : 70( 4.2%); F : 46( 2.8%) G++:478(28.6%); H : 16( 1.0%); I : 58( 3.5%); K : 93( 5.6%); L- : 92( 5.5%) M : 31( 1.9%); N- : 16( 1.0%); P++:325(19.5%); Q : 73( 4.4%); R : 45( 2.7%) S : 72( 4.3%); T- : 43( 2.6%); V- : 51( 3.1%); W : 6( 0.4%); Y- : 18( 1.1%) KR : 138 ( 8.3%); ED : 128 ( 7.7%); AGP ++: 861 ( 51.6%); KRED : 266 ( 15.9%); KR-ED : 10 ( 0.6%); FIKMNY- : 262 ( 15.7%); LVIFM - : 278 ( 16.7%); ST - : 115 ( 6.9%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 000+000000 000000000- -00+000+00 0000000+0- 0000+00+0- +000000000 61 00000000-0 0000000+0- 00-000000+ 00+0000000 0000000000 000-000000 121 00000000+0 -+00000000 0000000000 00000+0-00 -000000000 0+0-+00000 181 0000000000 0000000000 0000000000 00000-+000 0000000+0- +0-0000000 241 000000000- +0-000+0-+ 00+0-00000 00000-+0-0 0+000+0+00 +-0-+0-+00 301 00000-0000 0000+00000 -+0-000000 0000000000 0-+0-+0000 0000+0-000 361 +000000000 0000000000 00000000-+ 0-+0-+0000 00000000+- 0000000000 421 0000000000 00-0000000 -000000000 00000-00-+ 00+0-00000 -0-00+0000 481 000000-000 000000+0-+ 0000+-0000 0000000000 000000+0-0 0-000-0+0+ 541 0-+0-00000 000000+000 00+-000000 00+0000000 0+0-+00000 000000+0-0 601 0000000000 00000-+000 0000000000 0000+0-00+ 0000000000 -000000000 661 0000-+0000 000+00000- +000000000 0000000+00 -0000-0000 0000+00000 721 0000000000 +0-0000000 0+00000000 00000-+000 0000000-00 0000000000 781 +0-0000000 0000000000 000000+000 0000000000 0000+0-+00 000000-000 841 0+0-+00000 0000000000 0000000000 0000000+0- 0000000000 0000000000 901 000-+0-000 000000+0-0 00+0-+0-00 000+0000-+ 0-0000+00+ 0-00-+0000 961 000-+00+0- 00000000+- 0000000000 0+0-000000 000000000+ 0000000000 1021 000-+00000 0000000000 0-+00+0-+0 0000000000 00+0-+0-00 000000000- 1081 +0-+000000 00000000+0 0000000000 00000-+0-+ 00000-0000 0+0-000000 1141 000000000+ 0-000-0000 000-+0-000 00+0000000 0+0-+00+0- 0000000000 1201 00000+0-00 0000000000 0000000000 0-00+0-+00 0000000000 0000000000 1261 0-00+0-+00 0000000000 00+0-00000 0000000000 000+0-0000 00000000+0 1321 0000000+0- 00-000000+ 0000000000 00-00+0-00 0000-00000 +00000000+ 1381 0000000000 0000000000 -00000+0-0 00000000+0 0000000-00 0000000000 1441 00-000000+ 00000--000 0000+00000 000000000- +0000-0000 0000++0000 1501 0000000000 00000+0-00 000000-000 00000000-0 0+0000+000 0-00000000 1561 0000000000 0000000000 0000000000 0-00000000 00000--0+0 0000-000+0 1621 0000000000 000000-+0- 00++000000 +00-0+0000 +00000++0 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 10/30 or 12/45 or 15/60): none Negative charge clusters (cmin = 9/30 or 12/45 or 14/60): none Mixed charge clusters (cmin = 14/30 or 19/45 or 23/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS. There are no high scoring positive charge segments. There are no high scoring negative charge segments. There are no high scoring mixed charge segments. There are no high scoring uncharged segments. C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 5 | 5 | 6 | 59 | 10 | 10 | 13 | 12 | 12 | 16 | 6 | 8 | lmin1 6 | 6 | 8 | 71 | 12 | 12 | 15 | 15 | 15 | 19 | 8 | 10 | lmin2 7 | 7 | 9 | 79 | 13 | 13 | 17 | 17 | 16 | 21 | 9 | 11 | (Significance level: 0.010000; Minimal displayed length: 6) There are no charge runs or patterns exceeding the given minimal lengths. Run count statistics: + runs >= 3: 0 - runs >= 3: 0 * runs >= 4: 0 0 runs >= 39: 2, at 176; 1553; -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. There are no high scoring hydrophobic segments. There are no high scoring transmembrane segments. 2. SPACINGS OF C. H2N-30-C-4-C-2-C-1-C-83-C-308-C-32-C-2-C-989-C-32-C-11-C-5-C-36-C-2-C-18-C-33-C-11-C-5-C-39-C-2-C-4-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-18-H-2-H-8-C-4-C-2-C-1-C-H-82-C-39-H-268-C-32-C-2-C-95-H-202-H-138-H-320-H-214-H-6-H-8-C-8-H-13-H-9-C-11-C-5-C-36-C-2-C-9-H-8-C-15-H-17-C-11-C-H-4-C-35-H-3-C-2-C-4-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 5 Aligned matching blocks: [ 48- 59] KGERGLPGLQGV [ 497- 508] KGDRGLPGRDGV ______________________________ [ 54- 58]--------[ ] [ 190- 194]-( 42)-[ 237- 241] [ 775- 780]-( 38)-[ 819- 823] [1322-1327]--------[ ] [ 54- 58] PGLQG [ 190- 194] PGLQG [ 775- 780] PGLQGI [1322-1327] PGLQGI [ 237- 241] SGPPG [ 819- 823] SGPPG ______________________________ [ 63- 71] PGMQGPEGP [1359-1367] PGLPGPEGP ______________________________ [ 67- 68]-( 4)-[ 73- 77] [ 414- 415]-( 4)-[ 420- 424] [ 73- 77] GPPGQ [ 420- 424] GPPGQ ______________________________ [ 75- 79] PGQKG [1404-1408] PGQKG ______________________________ [ 76- 83] GQKGDTGE [ 948- 955] GQKGDQGE ______________________________ [ 93- 97]--------[ ] [ 476- 480]-( -5)-[ 476- 486] [ 585- 590]--------[ ] [ 807- 812]-( -6)-[ 807- 817] [ 93- 97] RGPPG [ 476- 480] RGPPG [ 585- 590] RGPPGG [ 807- 812] RGPPGG [ 476- 486] RGPPGPQGPPG [ 807- 817] RGPPGGQGPPG ______________________________ [ 94- 98] GPPGA [ 646- 650] GPPGA [ 802- 806] GPPGA ______________________________ [ 91- 92]-( 3)-[ 96- 97]-( 4)-[ 102- 106] [ 711- 712]-( 3)-[ 716- 717]-( 4)-[ 722- 726] [ 102- 106] PGNPG [ 722- 726] PGNPG ______________________________ [ 105- 112]-( -7)-[ 106- 110] [ 745- 752]-( -7)-[ 746- 750] [ ]--------[ 849- 853] [ ]--------[1257-1261] [ 105- 112] PGLPGIPG [ 745- 752] PGLPGIPG [ 106- 110] GLPGI [ 746- 750] GLPGI [ 849- 853] GLPGI [1257-1261] GLPGI ______________________________ [ 112- 121] GQDGPPGPPG [1219-1228] GQPGLPGSPG [1242-1251] GQPGLPGLPG with superset: [ 113- 118] QDGPPG [ 369- 374] QPGPPG [ 435- 440] QPGPPG [ 551- 556] QPGMPG [ 889- 894] QPGSPG [ 985- 990] QPGQPG [1051-1056] QAGPPG [1220-1225] QPGLPG [1243-1248] QPGLPG ______________________________ [ 118- 124] GPPGIPG [ 443- 449] GPPGIPG [1053-1061] GPPGIGIPG [1393-1399] GPPGI__PG with superset: [ 118- 122] GPPGI [ 329- 333] GPPGI [ 443- 447] GPPGI [ 820- 824] GPPGI [1053-1057] GPPGI [1393-1397] GPPGI ______________________________ [ ]--------[ 129- 133]--------[ ]--------[ ] [ 171- 179]-( -8)-[ 172- 176]-( -5)-[ 172- 182]-( -11)-[ 172- 179] [ ]--------[ 343- 347]-( -5)-[ 343- 353]-( -11)-[ 343- 350] [ 581- 589]-( -8)-[ 582- 586]--------[ ]--------[ 582- 589] [ 171- 179] LKGERGFPG [ 581- 589] LKGERGPPG [ 129- 133] KGERG [ 172- 176] KGERG [ 343- 347] KGERG [ 582- 586] KGERG [ 172- 182] KGERGFPGIPG [ 343- 353] KGERGYPGTPG [ 172- 179] KGERGFPG [ 343- 350] KGERGYPG [ 582- 589] KGERGPPG ______________________________ [ ]--------[ 156- 160] [ ]--------[ 543- 548] [ 986- 996]-( -5)-[ 992- 996] [1277-1287]-( -5)-[1283-1288] [ 986- 996] PGQPGPKGDPG [1277-1287] PGVPGPKGDPG [ 156- 160] KGDPG [ 543- 548] KGDPGF [ 992- 996] KGDPG [1283-1288] KGDPGF ______________________________ [ 175- 191] RGFPGIPGTPGPPGLPG [ 666- 679] RGFPGTPGRPGLPG with superset: [ 175- 179] RGFPG [ 396- 400] RGFPG [ 666- 670] RGFPG [1173-1177] RGFPG [1419-1423] RGFPG and: [ 175- 182] RGFPGIPG [ 666- 673] RGFPGTPG [1173-1180] RGFPGFPG [1419-1426] RGFPGPPG ______________________________ [ 202- 213] TGPPGPPGPPGP [ 600- 610] TGPPGPPG_YGP [1416-1427] TGPRGFPGPPGP with superset: [ 81- 88] TGEPGLPG [ 202- 209] TGPPGPPG [ 600- 607] TGPPGPPG [1416-1423] TGPRGFPG ______________________________ [ 206- 216] GPPGPPGPPGE [ 477- 487] GPPGPQGPPGE ______________________________ [ 206- 211] GPPGPP [ 209- 214] GPPGPP [ 326- 331] GPPGPP [ 477- 482] GPPGPQ [ 601- 606] GPPGPP [ 693- 697] GPPGP [1213-1218] GPPGPQ [1344-1349] GPPGPP [1347-1351] GPPGP [1423-1427] GPPGP ______________________________ [ 224- 229] FQGPKG [1315-1320] FQGPKG ______________________________ [ 221- 222]-( 3)-[ 226- 235] [ 835- 836]-( 3)-[ 840- 849] [ 226- 235] GPKGDKGDQG [ 840- 849] GPKGDKGAQG with superset: [ 226- 230] GPKGD [ 840- 844] GPKGD [ 990- 994] GPKGD [1233-1237] GPKGD [1281-1285] GPKGD ______________________________ [ 231- 235]--------[ ]--------[ 217- 236] [ 950- 954]-( 8)-[ 963- 967]--------[ ] [1066-1070]-( 11)-[1082-1086]--------[ ] [1328-1332]--------[ ]--------[1319-1336] [ 231- 235] KGDQG [ 950- 954] KGDQG [1066-1070] KGDQG [1328-1332] KGDQG [ 963- 967] GEKGS [1082-1086] GEKGS [ 217- 236] KGQMGLSFQGPKGDKGDQGV [1319-1336] KGLPGL__QGIKGDQGDQGV ______________________________ [ 238- 246] GPPG__VPGQA [ 371- 381] GPPGLPVPGQA ______________________________ [ 258- 265] GEKGQKGE [ 458- 465] GEKGQKGE with superset: [ 215- 219] GEKGQ [ 258- 262] GEKGQ [ 458- 462] GEKGQ [ 954- 958] GEKGQ [1047-1051] GEKGQ ______________________________ [ 261- 267] GQKGEPG [ 729- 735] GQKGEPG [1148-1154] GQKGEPG ______________________________ [ 263- 273] KGEPGFQGMPG [1283-1293] KGDPGFQGMPG with superset: [ 266- 270] PGFQG [1286-1290] PGFQG [1313-1317] PGFQG ______________________________ [ 272- 290] PGVGEKGEPGKPGPRGKPG [1159-1177] PGSAGEKGEPGLPGRGFPG ______________________________ [ 280- 290] PGKPGPRGKPG [ 349- 359] PGTPGPRGEPG ______________________________ [ 280- 284] PGKPG [ 932- 936] PGKPG ______________________________ [ 275- 278]-( 4)-[ 283- 284]-( 4)-[ 289- 293] [ 963- 966]-( 4)-[ 971- 972]-( 4)-[ 977- 981] [ 275- 278] GEKG [ 963- 966] GEKG [ 289- 293] PGKDG [ 977- 981] PGKDG ______________________________ [ 295- 305] KGEKGSPGFPG [ 825- 835] KGEKGFPGFPG with superset: [ 257- 261] KGEKG [ 295- 299] KGEKG [ 825- 829] KGEKG [1046-1050] KGEKG [1081-1085] KGEKG ______________________________ [ 295- 311] KGEKGSPGFPGEPGYPG [ 540- 556] KGDKGDPGFPGQPGMPG with superset: [ 301- 305] PGFPG [ 384- 388] PGFPG [ 546- 550] PGFPG [ 657- 661] PGFPG [ 831- 835] PGFPG [ 872- 876] PGFPG [1176-1180] PGFPG ______________________________ [ 304- 305]-( 4)-[ 310- 314] [ 512- 513]-( 4)-[ 518- 522] [ 310- 314] PGLIG [ 518- 522] PGLIG ______________________________ [ 319- 327] QGEKGEAGP [ 953- 961] QGEKGQIGP ______________________________ [ 320- 333] GEKGEAGPPGPPGI [1047-1059] GEKGQAGPPG_IGI ______________________________ [ 320- 324] GEKGE [ 341- 345] GEKGE [1079-1083] GEKGE [1163-1167] GEKGE ______________________________ [ 322- 332] KGEAGPPGPPG [1132-1142] KGEAGLPGTPG ______________________________ [ 358- 365] PGPKGFPG [ 570- 577] PGPKGSPG [ 632- 639] PGPKGEPG [ 989- 996] PGPKGDPG [1280-1287] PGPKGDPG with superset: [ 358- 362] PGPKG [ 570- 574] PGPKG [ 632- 636] PGPKG [ 695- 699] PGPKG [ 839- 843] PGPKG [ 989- 993] PGPKG [1007-1011] PGPKG [1280-1284] PGPKG [1377-1381] PGPKG ______________________________ [ 361- 368] KGFPGLPG [ 828- 835] KGFPGFPG ______________________________ [ 367- 379] PGQPGPPG_LPVPG [ 887- 900] PGQPGSPGPVGAPG with superset: [ 367- 371] PGQPG [ 422- 426] PGQPG [ 448- 452] PGQPG [ 491- 495] PGQPG [ 549- 553] PGQPG [ 887- 891] PGQPG [ 986- 990] PGQPG and: [ 367- 374] PGQPGPPG [ 549- 556] PGQPGMPG [ 887- 894] PGQPGSPG ______________________________ [ 371- 379] GPPGLPVPG [ 785- 791] GPPGL__PG [1254-1260] GPPGL__PG with superset: [ 371- 375] GPPGL [ 773- 777] GPPGL [ 785- 789] GPPGL [ 814- 818] GPPGL [1254-1258] GPPGL [1366-1370] GPPGL ______________________________ [ 387- 395]-( -9)-[ 387- 400]--------[ ] [ 899- 907]-( -9)-[ 899- 912]-( -4)-[ 909- 913] [1060-1068]--------[ ]--------[1073-1077] [1111-1119]--------[ ]--------[ ] [ 387- 395] PGERGEKGD [ 899- 907] PGLPGEKGD [1060-1068] PGLRGEKGD [1111-1119] PGLPGEKGD [ 387- 400] PGERGEKGDRGFPG [ 899- 912] PGLPGEKGDHGFPG [ 909- 913] GFPGS [1073-1077] GFPGS ______________________________ [ 385- 388]-( 4)-[ 393- 400] [ 489- 492]-( 4)-[ 497- 504] [ 385- 388] GFPG [ 489- 492] GFPG [ 393- 400] KGDRGFPG [ 497- 504] KGDRGLPG with superset: [ 393- 397] KGDRG [ 497- 501] KGDRG [1235-1239] KGDRG ______________________________ [ 396- 400]--------[ ]--------[ ] [ 666- 670]-( -5)-[ 666- 679]-( -14)-[ 666- 673] [1173-1177]--------[ ]--------[1173-1180] [1419-1423]-( -5)-[1419-1432]-( -14)-[1419-1426] [ 396- 400] RGFPG [ 666- 670] RGFPG [1173-1177] RGFPG [1419-1423] RGFPG [ 666- 679] RGFPGTPGRPGLPG [1419-1432] RGFPGPPGPDGLPG [ 666- 673] RGFPGTPG [1173-1180] RGFPGFPG [1419-1426] RGFPGPPG ______________________________ [ 454- 461] IGEIGEKG [ 959- 966] IGPIGEKG ______________________________ [ 485- 504] PGEIGFPGQPGAKGDRGLPG [ 687- 705] PG_IGFPGPPGPKGVDGLPG with superset: [ 60- 64] IGFPG [ 488- 492] IGFPG [ 689- 693] IGFPG ______________________________ [ 491- 495]--------[ ]--------[ 503- 507] [ 549- 553]-( -5)-[ 549- 556]-( 4)-[ 561- 565] [ 887- 891]-( -5)-[ 887- 894]--------[ ] [ 986- 990]--------[ ]--------[ ] [ 491- 495] PGQPG [ 549- 553] PGQPG [ 887- 891] PGQPG [ 986- 990] PGQPG [ 549- 556] PGQPGMPG [ 887- 894] PGQPGSPG [ 503- 507] PGRDG [ 561- 565] PGRDG ______________________________ [ 497- 505] KGDRGLPGR [1165-1173] KGEPGLPGR ______________________________ [ 510- 514] GVPGP [1278-1282] GVPGP ______________________________ [ 522- 531] GQPGAKGEPG [ 987- 996] GQPGPKGDPG [1335-1344] GVPGAKGLPG with superset: [ 492- 498] GQPGAKG [ 522- 528] GQPGAKG [ 987- 993] GQPGPKG [1177-1183] GFPGAKG [1335-1341] GVPGAKG ______________________________ [ 512- 520]-( 4)-[ 525- 529] [1031-1039]-( 4)-[1044-1048] [ 512- 520] PGPQGTPGL [1031-1039] PGPQGSPGL [ 525- 529] GAKGE [1044-1048] GAKGE ______________________________ [ 539- 545] LKGDKGD [ 922- 928] LKGDKGD ______________________________ [ 540- 556] KGDKGDPGFPGQPGMPG [1265-1281] KGDKGNPGWPGAPGVPG with superset: [ 228- 232] KGDKG [ 540- 544] KGDKG [ 842- 846] KGDKG [ 923- 927] KGDKG [1117-1121] KGDKG [1182-1186] KGDKG [1265-1269] KGDKG and: [ 540- 547] KGDKGDPG [1117-1124] KGDKGLPG [1265-1272] KGDKGNPG ______________________________ [ 552- 556] PGMPG [1090-1094] PGMPG ______________________________ [ 555- 562] PGRAGSPG [1194-1201] PGLAGSPG ______________________________ [ 567- 580] PGLPGPKGSPGSVG [1093-1106] PGSPGLKGSPGSVG with superset: [ 298- 302] KGSPG [ 573- 577] KGSPG [1099-1103] KGSPG ______________________________ [ 558- 562]-( 4)-[ 567- 577] [ 620- 624]-( 4)-[ 629- 639] [ 558- 562] AGSPG [ 620- 624] AGFPG [ 567- 577] PGLPGPKGSPG [ 629- 639] PGLPGPKGEPG ______________________________ [ 591- 595] VGFPG [1191-1195] VGFPG ______________________________ [ ]--------[ 592- 596]--------[ ] [ 839- 847]-( 25)-[ 873- 877]-( -8)-[ 870- 880] [ ]--------[ 909- 913]--------[ ] [1037-1045]-( 27)-[1073-1077]-( -8)-[1070-1080] [ 839- 847] PGPKGDKGA [1037-1045] PGLPGDKGA [ 592- 596] GFPGS [ 873- 877] GFPGS [ 909- 913] GFPGS [1073-1077] GFPGS [ 870- 880] GIPGFPGSKGE [1070-1080] GIAGFPGSPGE ______________________________ [ 595- 599] GSRGD [ 966- 970] GSRGD ______________________________ [ 609- 613] GPAGP [1411-1415] GPAGP ______________________________ [ 617- 624] KGQAGFPG [1049-1056] KGQAGPPG ______________________________ [ 615- 616]-( 3)-[ 620- 627] [1067-1068]-( 3)-[1072-1079] [ 620- 627] AGFPGGPG [1072-1079] AGFPGSPG ______________________________ [ 626- 636] PGSPGLPGPKG [1108-1118] PGSPGLPGEKG with superset: [ 416- 420] PGSPG [ 626- 630] PGSPG [ 654- 658] PGSPG [ 890- 894] PGSPG [1075-1079] PGSPG [1093-1097] PGSPG [1108-1112] PGSPG [1224-1228] PGSPG and: [ 416- 423] PGSPGPPG [ 626- 633] PGSPGLPG [ 654- 661] PGSPGFPG [1108-1115] PGSPGLPG ______________________________ [ 630- 636] GLPGPKG [1005-1011] GLPGPKG [1375-1381] GLPGPKG ______________________________ [ ]--------[ 652- 658] [ 781- 788]-( -1)-[ 788- 792] [ ]--------[1222-1228] [1419-1426]-( 2)-[1429-1433] [ 781- 788] RGEPGPPG [1419-1426] RGFPGPPG with superset: [ 355- 360] RGEPGP [ 476- 481] RGPPGP [ 781- 786] RGEPGP [1419-1424] RGFPGP [ 652- 658] GLPGSPG [ 788- 792] GLPGS [1222-1228] GLPGSPG [1429-1433] GLPGS ______________________________ [ 658- 662]--------[ ]--------[ ] [ 690- 694]-( -5)-[ 690- 697]-( 3)-[ 701- 713] [1420-1424]-( -5)-[1420-1427]-( 0)-[1428-1440] [ 658- 662] GFPGP [ 690- 694] GFPGP [1420-1424] GFPGP [ 690- 697] GFPGPPGP [1420-1427] GFPGPPGP [ 701- 713] DGLPGDMGPPGTP [1428-1440] DGLPGSMGPPGTP with superset: [ 410- 414] DGLPG [ 701- 705] DGLPG [1428-1432] DGLPG ______________________________ [ 664- 676] GDRGFPGTPGRPG [ 705- 717] GDMGPPGTPGRPG [ 966- 978] GSRGDPGTPGVPG with superset: [ 344- 353] GERGYPGTPG [ 394- 405] GDRGFPGTSLPG [ 664- 673] GDRGFPGTPG [ 705- 714] GDMGPPGTPG [ 966- 975] GSRGDPGT__PG ______________________________ [ 692- 697]-( 4)-[ 702- 706] [1028-1033]-( 4)-[1038-1042] [ 692- 697] PGPPGP [1028-1033] PGIPGP [ 702- 706] GLPGD [1038-1042] GLPGD ______________________________ [ 707- 714] MGPPGTPG [1253-1260] MGPPGLPG [1307-1314] MGPPGVPG with superset: [ 707- 711] MGPPG [1212-1216] MGPPG [1253-1257] MGPPG [1307-1311] MGPPG [1434-1438] MGPPG ______________________________ [ 731- 740] KGEPGVGLPG [1165-1172] KGEP__GLPG [1356-1363] KGEP__GLPG ______________________________ [ 736- 740] VGLPG [ 929- 933] VGLPG ______________________________ [ 739- 743]-( -5)-[ 739- 746]--------[ ] [ 920- 924]--------[ ]--------[ ] [1096-1100]-( -5)-[1096-1103]-( 38)-[1142-1146] [1368-1372]--------[ ]--------[1414-1418] [ 739- 743] PGLKG [ 920- 924] PGLKG [1096-1100] PGLKG [1368-1372] PGLKG [ 739- 746] PGLKGLPG [1096-1103] PGLKGSPG [1142-1146] GPTGP [1414-1418] GPTGP ______________________________ [ 742- 746]-( -5)-[ 742- 756]-( -15)-[ 742- 750] [1120-1124]-( -5)-[1120-1134]-( -15)-[1120-1128] [1319-1323]--------[ ]--------[1319-1327] [1340-1344]--------[ ]--------[ ] [ 742- 746] KGLPG [1120-1124] KGLPG [1319-1323] KGLPG [1340-1344] KGLPG [ 742- 756] KGLPGLPGIPGTPGE [1120-1134] KGLPGLDGIPGVKGE [ 742- 750] KGLPGLPGI [1120-1128] KGLPGLDGI [1319-1327] KGLPGLQGI ______________________________ [ 743- 749] GLPGLPG [ 858- 864] GLPGLPG [1245-1251] GLPGLPG ______________________________ [ 748- 767] PGIPGTPGEKGSIGVPGVPG [1075-1094] PGSPGEKGEKGSIGIPGMPG with superset: [ 296- 300] GEKGS [ 755- 759] GEKGS [ 963- 967] GEKGS [1082-1086] GEKGS ______________________________ [ 748- 762] PGIPGTPGEKGSIGV [ 869- 883] PGIPGFPGSKGEMGV ______________________________ [ 751- 755]-( -5)-[ 751- 758] [ 971- 975]--------[ ] [1017-1023]-( -5)-[1019-1026] [1136-1142]--------[ ] [ 751- 755] __PGTPG [ 971- 975] __PGTPG [1017-1023] GLPGTPG [1136-1142] GLPGTPG [ 751- 758] PGTPGEKG [1019-1026] PGTPGEKG ______________________________ [ 772- 776] IGPPG [ 801- 805] IGPPG ______________________________ [ 784- 785]-( 4)-[ 790- 800] [1096-1097]-( 4)-[1102-1112] [ 790- 800] PGSVGSPGVPG [1102-1112] PGSVGYPGSPG with superset: [ 576- 580] PGSVG [ 790- 794] PGSVG [1102-1106] PGSVG ______________________________ [ 796- 803] PGVPG_IGP [1310-1318] PGVPGFQGP ______________________________ [ 797- 803] GVPGI_GP [1026-1033] GVPGIPGP ______________________________ [ 810- 818] PGGQGPPGL [1250-1258] PGPMGPPGL [1362-1370] PGPEGPPGL ______________________________ [ 816- 817]-( 4)-[ 822- 835] [1153-1154]-( 4)-[1159-1172] [ 822- 835] PGIKGEKGFPGFPG [1159-1172] PGSAGEKGEPGLPG with superset: [ 524- 529] PGAKGE [ 632- 637] PGPKGE [ 822- 827] PGIKGE [ 875- 880] PGSKGE [1075-1080] PGSPGE [1129-1134] PGVKGE [1159-1164] PGSAGE [1203-1208] PGSKGE [1404-1409] PGQKGE and: [ 822- 829] PGIKGEKG [1075-1082] PGSPGEKG [1159-1166] PGSAGEKG ______________________________ [ 825- 836] KGEKGFPGFPGL [1185-1196] KGSKGEVGFPGL ______________________________ [ 839- 852] PGPKGDKGAQGLPG [ 920- 933] PGLKGDKGDVGLPG with superset: [ 842- 850] KGDKGAQGL [ 923- 931] KGDKGDVGL [1117-1125] KGDKGLPGL ______________________________ [ 845- 856]-( 18)-[ 875- 882] [1371-1382]-( 21)-[1404-1411] [ 845- 856] KGAQGLPGITGQ [1371-1382] KGLQGLPGPKGQ [ 875- 882] PGSKGEMG [1404-1411] PGQKGEMG ______________________________ [ 851- 855] PGITG [1298-1302] PGITG ______________________________ [ 872- 879] PGFPGSKG [1176-1183] PGFPGAKG ______________________________ [ 876- 880] GSKGE [1186-1190] GSKGE [1204-1208] GSKGE ______________________________ [ 917- 921] RGDPG [ 968- 972] RGDPG ______________________________ [ 950- 963] KGDQGEKGQIGP__IG [1043-1058] KGAKGEKGQAGPPGIG ______________________________ [ 974- 978] PGVPG [1277-1281] PGVPG [1310-1314] PGVPG ______________________________ [1001-1011]-( -5)-[1007-1011] [1274-1284]-( -5)-[1280-1284] [ ]--------[1377-1381] [1001-1011] PGAPGLPGPKG [1274-1284] PGAPGVPGPKG [1007-1011] PGPKG [1280-1284] PGPKG [1377-1381] PGPKG ______________________________ [ ]--------[ ]--------[ ]--------[1019-1026]-------- [1034-1035]-( 4)-[1040-1041]-( 4)-[1046-1050]-( 24)-[1075-1082]-( -8)- [1069-1070]-( 4)-[1075-1076]-( 4)-[1081-1085]-( 25)-[1111-1118]-( -8)- [ ] [1075-1085] [1111-1121] [1046-1050] KGEKG [1081-1085] KGEKG [1019-1026] PGTPGEKG [1075-1082] PGSPGEKG [1111-1118] PGLPGEKG [1075-1085] PGSPGEKGEKG [1111-1121] PGLPGEKGDKG ______________________________ [1028-1032] PGIPG [1200-1204] PGIPG [1395-1399] PGIPG ______________________________ [1029-1033] GIPGP [1390-1394] GIPGP ______________________________ [1031-1041] PGPQGSPGLPG [1215-1225] PGPQGQPGLPG ______________________________ [1057-1061] IGIPG [1087-1091] IGIPG ______________________________ [1060-1061]-( -2)-[1060-1071]-( 3)-[1075-1086] [1078-1079]-( -2)-[1078-1089]-( 3)-[1093-1104] [1060-1071] PGLRGEKGDQGI [1078-1089] PGEKGEKGSIGI [1075-1086] PGSPGEKGEKGS [1093-1104] PGSPGLKGSPGS ______________________________ [1111-1112]-( 4)-[1117-1121]-( -5)-[1117-1124] [1176-1177]-( 4)-[1182-1186]--------[ ] [1259-1260]-( 4)-[1265-1269]-( -5)-[1265-1272] [1117-1121] KGDKG [1182-1186] KGDKG [1265-1269] KGDKG [1117-1124] KGDKGLPG [1265-1272] KGDKGNPG ______________________________ [1120-1134] KGLPGLDGIPGVKGE [1150-1164] KGEPGSDGIPGSAGE ______________________________ [1150-1154]--------[ ]--------[1186-1193] [1165-1169]-( -5)-[1165-1172]-( 31)-[1204-1211] [1356-1360]-( -5)-[1356-1363]--------[ ] [1150-1154] KGEPG [1165-1169] KGEPG [1356-1360] KGEPG [1165-1172] KGEPGLPG [1356-1363] KGEPGLPG [1186-1193] GSKGEVGF [1204-1211] GSKGEQGF ______________________________ [1154-1164] GSDGIPGSAGE [1198-1208] GSPGIPGSKGE ______________________________ [1179-1183] PGAKG [1337-1341] PGAKG ______________________________ [1233-1237] GPKGD [1281-1285] GPKGD ______________________________ [1451-1455] HSQTI [1561-1565] HSQTI Highly repetitive regions: From 49 to 1364 with major motif GEPGLPGL. From 70 to 1370 with major motif GPQGPPGL. From 84 to 1364 with major motif PGLPGP. From 107 to 1382 with major motif LPGPPGP. From 115 to 1400 with major motif GPPGVPGI. From 117 to 1427 with major motif PGPPGP. From 176 to 1427 with major motif GFPGQPGP. From 299 to 1205 with major motif GSPGFPGE. B. SEPARATED AND TANDEM REPEATS: 11-letter reduced alphabet. (i= LVIF; += KR; -= ED; s= AG; o= ST; n= NQ; a= YW; p= P; h= H; m= M; c= C) Repeat core block length: 9 Aligned matching blocks: [ 94- 104] sppssosapsn [ 197- 207] sppsiosppsp [ 232- 242] s-nsiosppsi [ 414- 424] sppsopsppsn [ 437- 447] spps-nsppsi [ 477- 486] sppspnspps [ 802- 812] sppss+sppss [ 814- 824] sppsiosppsi [ 993-1003] s-psiosopss [1417-1427] sp+sipsppsp ______________________________ [ 263- 275] +s-psinsmpsis [1283-1295] +s-psinsmpsis ______________________________ [ 277- 286] +s-ps+psp+ [ 322- 331] +s-ssppspp [ 346- 355] +sapsopsp+ [ 476- 485] +sppspnspp [ 597- 606] +s-osppspp [1025-1033] +sipsipsp [1340-1349] +sipsppspp [1356-1365] +s-psipsp- [1371-1380] +sinsipsp+ [1419-1428] +sipsppsp- ______________________________ [ 679- 682]-( 4)-[ 687- 703] [1047-1050]-( 4)-[1055-1071] [ 679- 682] s-+s [1047-1050] s-+s [ 687- 703] psisipsppsp+si-si [1055-1071] psisipsi+s-+s-nsi with superset: [ 687- 696] psisipspps [ 734- 743] psisipsi+s [ 799- 808] psisppss+s [1055-1064] psisipsi+s [1171-1180] ps+sipsips and: [ 687- 699] psisipsppsp+s [1055-1067] psisipsi+s-+s [1171-1183] ps+sipsipss+s Highly repetitive regions: From 48 to 1313 with major motif sossosooio. From 49 to 1427 with major motif ossoiooiooi. From 85 to 1211 with major motif oiooioossos. From 103 to 1432 with major motif o+oooooioo. From 150 to 1331 with major motif ooioossoss. From 266 to 1300 with major motif ooi+oiooio. -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 69 (Expected range: 141--218) low 1 ........LL LL.AALLL.E E...AAA.GG .......... .......... .......... 61 .......... ...PP..... .......... ....PP.... .......... .....PP.PP 121 .......... ......PP.. ........PP .......... .........L L......... 181 .....PP... .......PP. ...PP.PP.P P.PP...... .......... ........PP 241 .......... .......... .......... .......... .......... .......... 301 .......... .......... ......PP.P P......... .......... .......... 361 .......... .PP....... .......... .......... .......... ....PP.... 421 PP........ .......PP. ...PP..... .......... .......... .......PP. 481 ...PP..... .......... .......... .......... .......... .......... 541 .......... .......... .......... .......... ......PPGG .......... 601 .PP.PP.... .......... ...GG..... .......... ......PP.. .......... 661 .......... .......... .......... ...PP..... ........PP .......... 721 .......... .......... .......... .......... .......... ...PP..... 781 .....PP... .......... ..PP....PP GG..PP.... PP........ .......... 841 .......... .......... ....QQ.... .......... .......... .......... 901 .......... ..SS...... .......... .......... .......... .......... 961 .......... .......... .......... .......... .......... ...GG..... 1021 .......... .......... .......... ...PP..... .......... .......... 1081 .......... .......... .......... .......... .......... .......... 1141 .......... .......... .......... .......... .......... .......... 1201 .......... ...PP..... .......... .......... .......... ....PP.... 1261 .......... .......... .......... ....GG.... ........PP .......... 1321 .......... .......... ....PP.PP. ...II..... ......PP.. .......... 1381 .QQ....... ...PP..... .......... .......... ...PP..... .....PP... 1441 .......... .....DD... .......... ..LL...... .......... .......... 1501 .......NN. .......... .......... .......... .......... .......... 1561 .......PP. ....SS.... .......... .......... .....EE... .......... 1621 ...YY..... .......... ..KK...... .......... ......RR. 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 23 (6-10) 2 (11-20) 22 (>=21) 23 3. Clusters of amino acid multiplets (cmin = 9/30 or 11/45 or 13/60): none 4. Significant specific amino acid altplet counts: Letters Observed (Critical number) GK 87 (71) at 28 (l= 2) 37 (l= 2) 45 (l= 2) 48 (l= 2) 78 (l= 2) 90 (l= 2) 129 (l= 2) 156 (l= 2) 172 (l= 2) 217 (l= 2) 228 (l= 2) 231 (l= 2) 251 (l= 2) 257 (l= 2) 260 (l= 2) 263 (l= 2) 277 (l= 2) 281 (l= 2) 287 (l= 2) 290 (l= 2) 295 (l= 2) 298 (l= 2) 322 (l= 2) 343 (l= 2) 361 (l= 2) 393 (l= 2) 460 (l= 2) 463 (l= 2) 497 (l= 2) 527 (l= 2) 540 (l= 2) 543 (l= 2) 573 (l= 2) 582 (l= 2) 617 (l= 2) 635 (l= 2) 639 (l= 2) 681 (l= 2) 698 (l= 2) 731 (l= 2) 742 (l= 2) 757 (l= 2) 825 (l= 2) 828 (l= 2) 842 (l= 2) 845 (l= 2) 878 (l= 2) 905 (l= 2) 923 (l= 2) 926 (l= 2) 933 (l= 2) 947 (l= 2) 950 (l= 2) 956 (l= 2) 965 (l= 2) 978 (l= 2) 992 (l= 2) 1010 (l= 2) 1025 (l= 2) 1043 (l= 2) 1046 (l= 2) 1049 (l= 2) 1066 (l= 2) 1081 (l= 2) 1084 (l= 2) 1099 (l= 2) 1117 (l= 2) 1120 (l= 2) 1132 (l= 2) 1150 (l= 2) 1165 (l= 2) 1182 (l= 2) 1185 (l= 2) 1188 (l= 2) 1206 (l= 2) 1235 (l= 2) 1265 (l= 2) 1268 (l= 2) 1283 (l= 2) 1304 (l= 2) 1319 (l= 2) 1328 (l= 2) 1340 (l= 2) 1356 (l= 2) 1371 (l= 2) 1380 (l= 2) 1407 (l= 2) GE 58 (57) at 49 (l= 2) 69 (l= 2) 82 (l= 2) 130 (l= 2) 160 (l= 2) 173 (l= 2) 215 (l= 2) 258 (l= 2) 264 (l= 2) 275 (l= 2) 278 (l= 2) 296 (l= 2) 305 (l= 2) 320 (l= 2) 323 (l= 2) 341 (l= 2) 344 (l= 2) 356 (l= 2) 388 (l= 2) 391 (l= 2) 455 (l= 2) 458 (l= 2) 464 (l= 2) 486 (l= 2) 528 (l= 2) 531 (l= 2) 583 (l= 2) 636 (l= 2) 651 (l= 2) 679 (l= 2) 732 (l= 2) 755 (l= 2) 767 (l= 2) 782 (l= 2) 826 (l= 2) 879 (l= 2) 903 (l= 2) 954 (l= 2) 963 (l= 2) 1023 (l= 2) 1047 (l= 2) 1064 (l= 2) 1079 (l= 2) 1082 (l= 2) 1115 (l= 2) 1133 (l= 2) 1151 (l= 2) 1163 (l= 2) 1166 (l= 2) 1189 (l= 2) 1207 (l= 2) 1232 (l= 2) 1357 (l= 2) 1365 (l= 2) 1408 (l= 2) 1538 (l= 2) 1592 (l= 2) 1653 (l= 2) GP 264 (187) at 2 (l= 2) 54 (l= 2) 63 (l= 2) 67 (l= 2) 70 (l= 2) 73 (l= 2) 75 (l= 2) 84 (l= 2) 87 (l= 2) 94 (l= 2) 96 (l= 2) 102 (l= 2) 105 (l= 2) 108 (l= 2) 111 (l= 2) 115 (l= 2) 117 (l= 3) 120 (l= 2) 123 (l= 2) 133 (l= 2) 136 (l= 2) 138 (l= 2) 141 (l= 2) 147 (l= 3) 150 (l= 2) 153 (l= 2) 159 (l= 2) 167 (l= 2) 178 (l= 2) 181 (l= 2) 184 (l= 3) 187 (l= 2) 190 (l= 2) 194 (l= 2) 197 (l= 2) 199 (l= 2) 203 (l= 2) 205 (l= 3) 208 (l= 3) 211 (l= 3) 214 (l= 2) 226 (l= 2) 238 (l= 2) 240 (l= 2) 243 (l= 2) 266 (l= 2) 272 (l= 2) 280 (l= 2) 283 (l= 3) 289 (l= 2) 301 (l= 2) 304 (l= 2) 307 (l= 2) 310 (l= 2) 317 (l= 2) 326 (l= 2) 328 (l= 3) 331 (l= 2) 338 (l= 2) 349 (l= 2) 352 (l= 3) 358 (l= 3) 364 (l= 2) 367 (l= 2) 370 (l= 3) 373 (l= 2) 378 (l= 2) 384 (l= 2) 387 (l= 2) 399 (l= 2) 404 (l= 3) 413 (l= 3) 416 (l= 2) 419 (l= 3) 422 (l= 2) 425 (l= 2) 436 (l= 3) 439 (l= 2) 443 (l= 2) 445 (l= 2) 448 (l= 2) 451 (l= 2) 477 (l= 2) 479 (l= 3) 483 (l= 2) 485 (l= 2) 491 (l= 2) 494 (l= 2) 503 (l= 2) 512 (l= 3) 518 (l= 2) 524 (l= 2) 530 (l= 2) 546 (l= 2) 549 (l= 2) 552 (l= 2) 555 (l= 2) 561 (l= 2) 567 (l= 2) 570 (l= 3) 576 (l= 2) 586 (l= 2) 588 (l= 2) 594 (l= 2) 601 (l= 2) 603 (l= 3) 606 (l= 2) 609 (l= 2) 612 (l= 2) 623 (l= 2) 625 (l= 3) 629 (l= 2) 632 (l= 3) 638 (l= 2) 645 (l= 3) 648 (l= 2) 654 (l= 2) 657 (l= 2) 660 (l= 3) 669 (l= 2) 672 (l= 2) 675 (l= 2) 678 (l= 2) 687 (l= 2) 692 (l= 3) 695 (l= 3) 704 (l= 2) 708 (l= 2) 710 (l= 2) 713 (l= 2) 716 (l= 2) 722 (l= 2) 725 (l= 2) 734 (l= 2) 739 (l= 2) 745 (l= 2) 748 (l= 2) 751 (l= 2) 754 (l= 2) 763 (l= 2) 766 (l= 2) 773 (l= 2) 775 (l= 2) 784 (l= 3) 787 (l= 2) 790 (l= 2) 796 (l= 2) 799 (l= 2) 802 (l= 2) 804 (l= 2) 808 (l= 2) 810 (l= 2) 814 (l= 2) 816 (l= 2) 820 (l= 2) 822 (l= 2) 831 (l= 2) 834 (l= 2) 839 (l= 3) 851 (l= 2) 860 (l= 2) 863 (l= 2) 869 (l= 2) 872 (l= 2) 875 (l= 2) 887 (l= 2) 890 (l= 2) 893 (l= 3) 899 (l= 2) 902 (l= 2) 911 (l= 2) 915 (l= 2) 920 (l= 2) 932 (l= 2) 935 (l= 2) 960 (l= 2) 971 (l= 2) 974 (l= 2) 977 (l= 2) 986 (l= 2) 989 (l= 3) 995 (l= 2) 1001 (l= 2) 1004 (l= 2) 1007 (l= 3) 1019 (l= 2) 1022 (l= 2) 1028 (l= 2) 1031 (l= 3) 1037 (l= 2) 1040 (l= 2) 1053 (l= 2) 1055 (l= 2) 1060 (l= 2) 1075 (l= 2) 1078 (l= 2) 1090 (l= 2) 1093 (l= 2) 1096 (l= 2) 1102 (l= 2) 1108 (l= 2) 1111 (l= 2) 1114 (l= 2) 1123 (l= 2) 1129 (l= 2) 1138 (l= 2) 1141 (l= 3) 1145 (l= 2) 1153 (l= 2) 1159 (l= 2) 1168 (l= 2) 1171 (l= 2) 1176 (l= 2) 1179 (l= 2) 1194 (l= 2) 1200 (l= 2) 1203 (l= 2) 1213 (l= 2) 1215 (l= 3) 1221 (l= 2) 1224 (l= 2) 1227 (l= 2) 1233 (l= 2) 1239 (l= 2) 1244 (l= 2) 1247 (l= 2) 1250 (l= 3) 1254 (l= 2) 1256 (l= 2) 1259 (l= 2) 1271 (l= 2) 1274 (l= 2) 1277 (l= 2) 1280 (l= 3) 1286 (l= 2) 1292 (l= 2) 1298 (l= 2) 1308 (l= 2) 1310 (l= 2) 1313 (l= 2) 1317 (l= 2) 1322 (l= 2) 1337 (l= 2) 1343 (l= 3) 1346 (l= 3) 1349 (l= 3) 1359 (l= 2) 1362 (l= 3) 1366 (l= 2) 1368 (l= 2) 1377 (l= 3) 1392 (l= 3) 1395 (l= 2) 1398 (l= 2) 1404 (l= 2) 1411 (l= 2) 1414 (l= 2) 1417 (l= 2) 1422 (l= 3) 1425 (l= 3) 1431 (l= 2) 1435 (l= 2) 1437 (l= 2) 1601 (l= 2) GQ 62 (59) at 46 (l= 2) 57 (l= 2) 66 (l= 2) 72 (l= 2) 76 (l= 2) 112 (l= 2) 193 (l= 2) 218 (l= 2) 225 (l= 2) 234 (l= 2) 244 (l= 2) 261 (l= 2) 269 (l= 2) 316 (l= 2) 319 (l= 2) 368 (l= 2) 379 (l= 2) 423 (l= 2) 442 (l= 2) 449 (l= 2) 461 (l= 2) 482 (l= 2) 492 (l= 2) 515 (l= 2) 522 (l= 2) 550 (l= 2) 618 (l= 2) 663 (l= 2) 685 (l= 2) 728 (l= 3) 778 (l= 2) 812 (l= 3) 848 (l= 2) 855 (l= 2) 864 (l= 2) 866 (l= 2) 888 (l= 2) 948 (l= 2) 953 (l= 2) 957 (l= 2) 981 (l= 2) 984 (l= 2) 987 (l= 2) 1034 (l= 2) 1050 (l= 2) 1069 (l= 2) 1148 (l= 2) 1209 (l= 2) 1218 (l= 3) 1241 (l= 3) 1289 (l= 2) 1316 (l= 2) 1325 (l= 2) 1331 (l= 2) 1334 (l= 2) 1374 (l= 2) 1381 (l= 2) 1383 (l= 2) 1405 (l= 2) 1477 (l= 2) 1484 (l= 2) 1595 (l= 2) KE 22 (19) at 216 (l= 2) 250 (l= 2) 259 (l= 2) 276 (l= 2) 297 (l= 2) 321 (l= 2) 342 (l= 2) 392 (l= 2) 459 (l= 2) 680 (l= 2) 756 (l= 2) 827 (l= 2) 904 (l= 2) 955 (l= 2) 964 (l= 2) 1024 (l= 2) 1048 (l= 2) 1065 (l= 2) 1080 (l= 2) 1083 (l= 2) 1116 (l= 2) 1164 (l= 2) NC 4 (3) at 125 (l= 2) 1505 (l= 2) 1511 (l= 2) 1622 (l= 2) B. CHARGE ALPHABET. 1. Total number of charge multiplets: 6 (Expected range: 6-- 33) 3 +plets (f+: 8.3%), 3 -plets (f-: 7.7%) Total number of charge altplets: 50 (Critical number: 38) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 1 (6-10) 0 (11-20) 1 (>=21) 5 3. Significant specific charge altplet counts: Letters Observed (Critical number) +- 50 (38) at 50 (l= 2) 131 (l= 2) 174 (l= 2) 216 (l= 2) 230 (l= 2) 250 (l= 2) 259 (l= 2) 276 (l= 2) 291 (l= 2) 294 (l= 2) 297 (l= 2) 321 (l= 2) 342 (l= 2) 345 (l= 2) 389 (l= 2) 392 (l= 2) 395 (l= 2) 409 (l= 2) 459 (l= 2) 499 (l= 2) 505 (l= 2) 542 (l= 2) 563 (l= 2) 584 (l= 2) 616 (l= 2) 665 (l= 2) 680 (l= 2) 756 (l= 2) 827 (l= 2) 844 (l= 2) 904 (l= 2) 925 (l= 2) 939 (l= 2) 955 (l= 2) 964 (l= 2) 979 (l= 2) 1024 (l= 2) 1042 (l= 2) 1048 (l= 2) 1065 (l= 2) 1080 (l= 2) 1083 (l= 2) 1116 (l= 2) 1119 (l= 2) 1164 (l= 2) 1184 (l= 2) 1237 (l= 2) 1267 (l= 2) 1480 (l= 2) 1637 (l= 2) -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 9- 12 1 L 4 4 0 43- 162 3 G.. 40 40 ! 0 173- 223 3 G.. 17 17 ! 0 226- 246 3 G.. 7 7 ! 0 258- 275 3 G.. 6 6 ! 0 275- 376 3 G.. 33 20 ! 1 379- 402 3 G.. 8 8 ! 0 405- 428 3 G.. 8 8 ! 0 437- 466 3 G.. 10 10 ! 0 474- 533 3 G.. 20 20 ! 0 541- 609 3 G.. 23 23 ! 0 609- 641 3 G.. 11 11 ! 0 646- 690 3 G.. 15 15 ! 0 690- 737 3 G.. 16 16 ! 0 737- 802 3 G.. 22 22 ! 0 802- 837 3 G.. 12 12 ! 0 821- 860 10 P......... 4 4 0 840- 938 3 G.. 33 33 ! 0 840-1061 6 G..G.. 36 19 ! /1/././3/././ 948-1058 3 G.. 37 37 ! 0 1058-1174 3 G.. 39 39 ! 0 1174-1230 3 G.. 19 19 ! 0 1214-1253 10 P..P...... 4 4 /0/././1/././././././ 1233-1352 3 G.. 40 40 ! 0 1343-1374 8 P....... 4 4 0 1357-1440 3 G.. 28 28 ! 0 1576-1605 6 S..... 5 5 ! 0 B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 8) Location Period Element Copies Core Errors 279- 332 9 *00000..0 6 6 /0/1/0/2/1/0/././0/ -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 8-1273 (2.) W(1265)W 1 of 7 0.0014 large maximal spacing 125- 434 (1.) C( 309)C 2 of 21 0.0187 large 2. maximal spacing 174- 216 (1.) -( 42)- 2 of 129 0.9713 small 2. maximal spacing 470-1460 (3.) C( 990)C 1 of 21 0.0000 large 1. maximal spacing 508- 511 (2.) V( 3)V 52 of 52 0.0067 large minimal spacing 762- 765 (2.) V( 3)V 50 of 52 0.0067 matching minimum 783- 827 (2.) -( 44)- 1 of 129 0.9914 small 1. maximal spacing 1491-1538 (4.) G( 47)G 1 of 479 0.0000 large 1. maximal spacing 1538-1573 (4.) G( 35)G 2 of 479 0.0000 large 2. maximal spacing 1557-1560 (4.) V( 3)V 51 of 52 0.0067 matching minimum ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Pfam (from /data/patterns/pfam) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/pfam/Pfam Sequence file: tem31_1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Collagen Collagen triple helix repeat (20 copies) 664.0 7.8e-196 21 C4 C-terminal tandem repeated domain in type 4 519.5 2.4e-152 2 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Collagen 1/21 43 102 .. 1 60 [] 49.8 5.9e-11 Collagen 2/21 103 162 .. 1 60 [] 47.0 4.1e-10 Collagen 3/21 188 246 .. 1 60 [] 31.0 2.7e-05 Collagen 4/21 278 337 .. 1 60 [] 46.8 4.7e-10 Collagen 5/21 338 396 .. 1 60 [] 33.1 6.2e-06 Collagen 6/21 408 466 .. 1 60 [] 11.5 0.00078 Collagen 7/21 472 530 .. 1 60 [] 51.4 1.9e-11 Collagen 8/21 547 606 .. 1 60 [] 42.6 9.1e-09 Collagen 9/21 609 669 .. 1 60 [] 10.4 0.00089 Collagen 10/21 673 731 .. 1 60 [] 32.3 1.1e-05 Collagen 11/21 740 799 .. 1 60 [] 49.2 9.4e-11 Collagen 12/21 814 872 .. 1 60 [] 33.6 4.4e-06 Collagen 13/21 876 935 .. 1 60 [] 55.4 1.2e-12 Collagen 14/21 936 995 .. 1 60 [] 25.8 0.00014 Collagen 15/21 996 1055 .. 1 60 [] 48.4 1.5e-10 Collagen 16/21 1058 1117 .. 1 60 [] 55.7 1e-12 Collagen 17/21 1118 1177 .. 1 60 [] 35.2 1.5e-06 Collagen 18/21 1178 1236 .. 1 60 [] 24.3 0.00017 Collagen 19/21 1239 1298 .. 1 60 [] 53.3 5.4e-12 Collagen 20/21 1305 1365 .. 1 60 [] 25.8 0.00014 Collagen 21/21 1366 1425 .. 1 60 [] 61.1 2.4e-14 C4 1/2 1445 1554 .. 1 116 [] 258.2 1.1e-73 C4 2/2 1555 1668 .. 1 116 [] 268.7 7.7e-77 Alignments of top-scoring domains: Collagen: domain 1 of 21, from 43 to 102: score 49.8, E = 5.9e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G+ G++G+pG G G+pG +G+ Gp+GppG +G G pG pG tem31.1t_g 43 GVKGQKGERGLPGLQGVIGFPGMQGPEGPQGPPGQKGDTGEPGLPGT 89 pGppGapGapGpp<-* +G +G+pGa G p tem31.1t_g 90 KGTRGPPGASGYP 102 Collagen: domain 2 of 21, from 103 to 162: score 47.0, E = 4.1e-10 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G pG+pG pG GppGppG pG +G +G++Gp G+pG PG +G pGp tem31.1t_g 103 GNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGLPGFAGNPGP 149 pGppGapGapGpp<-* pG pG +G+pG+ tem31.1t_g 150 PGLPGMKGDPGEI 162 Collagen: domain 3 of 21, from 188 to 246: score 31.0, E = 2.7e-05 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G pG++Gp GppG +GppGppGp+G+pG++G G + ++Gp+G G tem31.1t_g 188 GLPGLQGPVGPPGFTGPPGPPGPPGPPGEKGQMGLS-FQGPKGDKGD 233 pGppGapGapGpp<-* +G G+pG pG++ tem31.1t_g 234 QGVSGPPGVPGQA 246 Collagen: domain 4 of 21, from 278 to 337: score 46.8, E = 4.7e-10 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pG+pGp+G pG +G++G++G +G+pG+pG pG G++Gp+G+ G tem31.1t_g 278 GEPGKPGPRGKPGKDGDKGEKGSPGFPGEPGYPGLIGRQGPQGEKGE 324 pGppGapGapGpp<-* +GppG+pG tem31.1t_g 325 AGPPGPPGIVIGT 337 Collagen: domain 5 of 21, from 338 to 396: score 33.1, E = 6.2e-06 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp Gp G+ G++G pG pGp+G+pGp+G+pG pG pG+pG P pG++G+ tem31.1t_g 338 GPLGEKGERGYPGTPGPRGEPGPKGFPGLPGQPGPPGLP-VPGQAGA 383 pGppGapGapGpp<-* pG pG+ G++G + tem31.1t_g 384 PGFPGERGEKGDR 396 Collagen: domain 6 of 21, from 408 to 466: score 11.5, E = 0.00078 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+ G+pGppG pGppG pG + pGppG+ GpPG pG+pG+ tem31.1t_g 408 GRDGLPGPPGSPGPPGQPGYTNGI-VECQPGPPGDQGPPGIPGQPGF 453 pGppGapGapGpp<-* G+ G++G +G+ tem31.1t_g 454 IGEIGEKGQKGES 466 Collagen: domain 7 of 21, from 472 to 530: score 51.4, E = 1.9e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +GppGp+GppG+ G+pG++Ga+G++G pG +G G pGp G tem31.1t_g 472 -IDGYRGPPGPQGPPGEIGFPGQPGAKGDRGLPGRDGVAGVPGPQGT 517 pGppGapGapGpp<-* pG G+pGa+G+p tem31.1t_g 518 PGLIGQPGAKGEP 530 Collagen: domain 8 of 21, from 547 to 606: score 42.6, E = 9.1e-09 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G pG+pG pG +G pG+ G+pG +G++G+pG G +G+ GppG G+ tem31.1t_g 547 GFPGQPGMPGRAGSPGRDGHPGLPGPKGSPGSVGLKGERGPPGGVGF 593 pGppGapGapGpp<-* pG +G G+pGpp tem31.1t_g 594 PGSRGDTGPPGPP 606 Collagen: domain 9 of 21, from 609 to 669: score 10.4, E = 0.00089 *->GppGppGppGppGppGppGppGpaGapGppGppGe.pGpPGppGppG Gp+Gp G +G +G pG pG pG +G++G+pG + pGpPG+ G pG tem31.1t_g 609 GPAGPIGDKGQAGFPGGPGSPGLPGPKGEPGKIVPlPGPPGAEGLPG 655 ppGppGapGapGpp<-* +pG pG+ G+ G p tem31.1t_g 656 SPGFPGPQGDRGFP 669 Collagen: domain 10 of 21, from 673 to 731: score 32.3, E = 1.1e-05 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pG+pG++G+ G+pG G+pGp+G++G G pG+ GpPG pG+pG+ tem31.1t_g 673 GRPGLPGEKGAVGQPGI-GFPGPPGPKGVDGLPGDMGPPGTPGRPGF 718 pGppGapGapGpp<-* G pG+pG G+ tem31.1t_g 719 NGLPGNPGVQGQK 731 Collagen: domain 11 of 21, from 740 to 799: score 49.2, E = 9.4e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G+pG pG pG pG++G G +G pG+ G+ G+pG +G +G+pGp tem31.1t_g 740 GLKGLPGLPGIPGTPGEKGSIGVPGVPGEHGAIGPPGLQGIRGEPGP 786 pGppGapGapGpp<-* pG pG G+pG p tem31.1t_g 787 PGLPGSVGSPGVP 799 Collagen: domain 12 of 21, from 814 to 872: score 33.6, E = 4.4e-06 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp GppG+ GppG G++G pG+pG + pGp+G++G+ G PG G+ G tem31.1t_g 814 GPPGLSGPPGIKGEKGFPGFPGLD-MPGPKGDKGAQGLPGITGQSGL 859 pGppGapGapGpp<-* pG pG+ GapG p tem31.1t_g 860 PGLPGQQGAPGIP 872 Collagen: domain 13 of 21, from 876 to 935: score 55.4, E = 1.2e-12 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G++G G pG+pG pGp G++G pG++G+ G+pG+ Gp+G pG tem31.1t_g 876 GSKGEMGVMGTPGQPGSPGPVGAPGLPGEKGDHGFPGSSGPRGDPGL 922 pGppGapGapGpp<-* +G +G G pG+p tem31.1t_g 923 KGDKGDVGLPGKP 935 Collagen: domain 14 of 21, from 936 to 995: score 25.8, E = 0.00014 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G + G++G+ G++G+ G+ G++G +G+pG PG pG++G+ tem31.1t_g 936 GSMDKVDMGSMKGQKGDQGEKGQIGPIGEKGSRGDPGTPGVPGKDGQ 982 pGppGapGapGpp<-* +G+pG+pG++G p tem31.1t_g 983 AGQPGQPGPKGDP 995 Collagen: domain 15 of 21, from 996 to 1055: score 48.4, E = 1.5e-10 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G G pG+pG+pGp+G G G +G pG++G pG pGp+G+pG pG tem31.1t_g 996 GISGTPGAPGLPGPKGSVGGMGLPGTPGEKGVPGIPGPQGSPGLPGD 1042 pGppGapGapGpp<-* +G +G++G +Gpp tem31.1t_g 1043 KGAKGEKGQAGPP 1055 Collagen: domain 16 of 21, from 1058 to 1117: score 55.7, E = 1e-12 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G pG++G++G++G +G pG pG++G++G+ G pG pG+PG +G pG+ tem31.1t_g 1058 GIPGLRGEKGDQGIAGFPGSPGEKGEKGSIGIPGMPGSPGLKGSPGS 1104 pGppGapGapGpp<-* G pG pG pG+ tem31.1t_g 1105 VGYPGSPGLPGEK 1117 Collagen: domain 17 of 21, from 1118 to 1177: score 35.2, E = 1.5e-06 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G+pG G pG +G++G pG +G+ Gp+G +GepG++G pG +G tem31.1t_g 1118 GDKGLPGLDGIPGVKGEAGLPGTPGPTGPAGQKGEPGSDGIPGSAGE 1164 pGppGapGapGpp<-* +G+pG pG p tem31.1t_g 1165 KGEPGLPGRGFPG 1177 Collagen: domain 18 of 21, from 1178 to 1236: score 24.3, E = 0.00017 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp pG G +G G+ G pG +G +G pG++G +G+ GpPGp+G+pG tem31.1t_g 1178 -FPGAKGDKGSKGEVGFPGLAGSPGIPGSKGEQGFMGPPGPQGQPGL 1223 pGppGapGapGpp<-* pG pG + + + tem31.1t_g 1224 PGSPGHATEGPKG 1236 Collagen: domain 19 of 21, from 1239 to 1298: score 53.3, E = 5.4e-12 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp Gp G+pG pG+pGp GppG pG +G +G++G+pG pG+PG pGp G tem31.1t_g 1239 GPQGQPGLPGLPGPMGPPGLPGIDGVKGDKGNPGWPGAPGVPGPKGD 1285 pGppGapGapGpp<-* pG +G pG G p tem31.1t_g 1286 PGFQGMPGIGGSP 1298 Collagen: domain 20 of 21, from 1305 to 1365: score 25.8, E = 0.00014 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G GppG pG +Gp+G pG +G +G +G++G pG++G PGppGppGp tem31.1t_g 1305 GDMGPPGVPGFQGPKGLPGLQGIKGDQGDQGVPGAKGLPGPPGPPGP 1351 .pGppGapGapGpp<-* +G+pG pGp tem31.1t_g 1352 yDIIKGEPGLPGPE 1365 Collagen: domain 21 of 21, from 1366 to 1425: score 61.1, E = 2.4e-14 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp GppG+ G G+pGp+G G +G G pGppG pG++G+PG++G++Gp tem31.1t_g 1366 GPPGLKGLQGLPGPKGQQGVTGLVGIPGPPGIPGFDGAPGQKGEMGP 1412 pGppGapGapGpp<-* +Gp+G+ G pGpp tem31.1t_g 1413 AGPTGPRGFPGPP 1425 C4: domain 1 of 2, from 1445 to 1554: score 258.2, E = 1.1e-73 *->gfliavHSQttsiPqCPaGwssLWtGYSflmvtganeeGhGQdLgsp gfl+++HSQt++ PqCP+G++ L++GYS+l+v+g ne++hGQdLg++ tem31.1t_g 1445 GFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQG-NERAHGQDLGTA 1490 GSCLerFrtmPFieCngrgvCnYasRndySfWLstiepedqFkaPmpmtp GSCL++F+tmPF++Cn+++vCn+asRndyS+WLst+ep +Pm+m+p tem31.1t_g 1491 GSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEP-----MPMSMAP 1535 kagreirpyISRCqVCekp<-* ++g++irp+ISRC+VCe+p tem31.1t_g 1536 ITGENIRPFISRCAVCEAP 1554 C4: domain 2 of 2, from 1555 to 1668: score 268.7, E = 7.7e-77 *->gfliavHSQttsiPqCPaGwssLWtGYSflmvtganeeGhGQdLgsp ++++avHSQt++iP+CP+GwssLW+GYSf+m+t+a++eG+GQ+L+sp tem31.1t_g 1555 AMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASP 1601 GSCLerFrtmPFieCngrgvCnYasRndySfWLstiepedqFkaPmpmtp GSCLe+Fr++PFieC+grg+CnY++ n ySfWL+tie++++Fk+P p+t+ tem31.1t_g 1602 GSCLEEFRSAPFIECHGRGTCNYYA-NAYSFWLATIERSEMFKKPTPSTL 1650 kagreirpyISRCqVCekp<-* kag e+r+++SRCqVC+++ tem31.1t_g 1651 KAG-ELRTHVSRCQVCMRR 1668 // Start with PfamFrag (from /data/patterns/pfam) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/pfam/PfamFrag Sequence file: tem31_1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Collagen Collagen triple helix repeat (20 copie 756.1 1.4e-223 30 C4 C-terminal tandem repeated domain in t 515.6 3.5e-151 2 zf-CONSTANS CONSTANS family zinc finger 2.9 21 1 Nebulin_repeat Nebulin repeat 2.7 82 1 Reeler Reeler domain 0.4 79 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Collagen 1/30 43 96 .. 7 60 .] 45.0 7.1e-11 Collagen 2/30 97 156 .. 1 60 [] 54.1 2.2e-13 Collagen 3/30 172 223 .. 9 60 .] 40.0 1.6e-09 Collagen 4/30 224 246 .. 38 60 .] 11.7 0.1 Collagen 5/30 258 273 .. 1 16 [. 7.5 1.4 Collagen 6/30 278 332 .. 1 55 [. 46.5 2.7e-11 Collagen 7/30 338 376 .. 10 48 .. 31.3 4.1e-07 Collagen 8/30 379 400 .. 1 22 [. 16.3 0.0054 Collagen 9/30 404 425 .. 39 60 .] 12.3 0.067 Collagen 10/30 436 466 .. 30 60 .] 19.9 0.00057 Collagen 11/30 474 530 .. 4 60 .] 50.0 3e-12 Collagen 12/30 540 573 .. 27 60 .] 26.0 1.2e-05 Collagen 13/30 574 607 .. 1 34 [. 21.2 0.00025 Collagen 14/30 609 641 .. 22 54 .. 17.5 0.0026 Collagen 15/30 645 688 .. 15 58 .. 27.5 4.5e-06 Collagen 16/30 690 737 .. 13 60 .] 26.7 7.6e-06 Collagen 17/30 740 799 .. 1 60 [] 47.2 1.8e-11 Collagen 18/30 802 835 .. 7 40 .. 20.7 0.00033 Collagen 19/30 838 896 .. 1 60 [] 55.5 9.2e-14 Collagen 20/30 897 937 .. 7 47 .. 32.0 2.6e-07 Collagen 21/30 948 995 .. 13 60 .] 39.9 1.8e-09 Collagen 22/30 996 1055 .. 1 60 [] 46.5 2.8e-11 Collagen 23/30 1058 1086 .. 1 29 [. 24.9 2.3e-05 Collagen 24/30 1088 1131 .. 1 44 [. 39.7 2e-09 Collagen 25/30 1133 1172 .. 1 40 [. 36.8 1.3e-08 Collagen 26/30 1174 1233 .. 1 60 [] 41.8 5.2e-10 Collagen 27/30 1239 1298 .. 1 60 [] 51.3 1.3e-12 Collagen 28/30 1299 1351 .. 1 53 [. 37.9 6.4e-09 Collagen 29/30 1357 1384 .. 1 28 [. 18.7 0.0012 Collagen 30/30 1387 1440 .. 1 54 [. 42.3 3.9e-10 Reeler 1/1 1445 1464 .. 61 84 .. 0.4 79 C4 1/2 1445 1554 .. 1 116 [] 256.3 4.1e-73 zf-CONSTANS 1/1 1548 1558 .. 1 12 [. 2.9 21 Nebulin_repeat 1/1 1552 1566 .. 1 15 [. 2.7 82 C4 2/2 1555 1668 .. 1 116 [] 266.7 3e-76 Alignments of top-scoring domains: Collagen: domain 1 of 30, from 43 to 96: score 45.0, E = 7.1e-11 *->GppGppGppGppGppGpaGapGppGppGepGpPGppGppGppGppGa G +G G++G pG +G G+pG++Gp G+ GpPG++G G pG pG tem31.1t_g 43 GVKGQKGERGLPGLQGVIGFPGMQGPEGPQGPPGQKGDTGEPGLPGT 89 pGapGpp<-* +G Gpp tem31.1t_g 90 KGTRGPP 96 Collagen: domain 2 of 30, from 97 to 156: score 54.1, E = 2.2e-13 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+ G pG pG+pG pG GppGp+G pG +G +Ge+Gp GppG pG+ tem31.1t_g 97 GASGYPGNPGLPGIPGQDGPPGPPGIPGCNGTKGERGPLGPPGLPGF 143 pGppGapGapGpp<-* +G+pG+pG pG tem31.1t_g 144 AGNPGPPGLPGMK 156 Collagen: domain 3 of 30, from 172 to 223: score 40.0, E = 1.6e-09 *->pGppGppGppGppGpaGapGppGppGepGpPGppGppGppGppGapG +G++G pG pG pGp+G pG +Gp G+pG+ GppGppGppGppG++G tem31.1t_g 172 KGERGFPGIPGTPGPPGLPGLQGPVGPPGFTGPPGPPGPPGPPGEKG 218 apGpp<-* +G tem31.1t_g 219 QMGLS 223 Collagen: domain 4 of 30, from 224 to 246: score 11.7, E = 0.1 *->pPGppGppGppGppGapGapGpp<-* ++Gp+G G +G G+pG pG++ tem31.1t_g 224 FQGPKGDKGDQGVSGPPGVPGQA 246 Collagen: domain 5 of 30, from 258 to 273: score 7.5, E = 1.4 *->GppGppGppGppGppG<-* G++G+ G+pG +G+pG tem31.1t_g 258 GEKGQKGEPGFQGMPG 273 Collagen: domain 6 of 30, from 278 to 332: score 46.5, E = 2.7e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pG+pGp+G pG +G++G++G +G+pG+pG pG G++Gp+G+ G tem31.1t_g 278 GEPGKPGPRGKPGKDGDKGEKGSPGFPGEPGYPGLIGRQGPQGEKGE 324 pGppGapG<-* +GppG+pG tem31.1t_g 325 AGPPGPPG 332 Collagen: domain 7 of 30, from 338 to 376: score 31.3, E = 4.1e-07 *->GppGppGppGppGpaGapGppGppGepGpPGppGppGpp<-* Gp G++G++G pG +G++G+pGp+G+pG PG+pGppG p tem31.1t_g 338 GPLGEKGERGYPGTPGPRGEPGPKGFPGLPGQPGPPGLP 376 Collagen: domain 8 of 30, from 379 to 400: score 16.3, E = 0.0054 *->GppGppGppGppGppGppGppG<-* G +G pG pG++G++G++G+pG tem31.1t_g 379 GQAGAPGFPGERGEKGDRGFPG 400 Collagen: domain 9 of 30, from 404 to 425: score 12.3, E = 0.067 *->PGppGppGppGppGapGapGpp<-* PGp G++G pGppG pG+pG+p tem31.1t_g 404 PGPSGRDGLPGPPGSPGPPGQP 425 Collagen: domain 10 of 30, from 436 to 466: score 19.9, E = 0.00057 *->pGppGepGpPGppGppGppGppGapGapGpp<-* pGppG+ GpPG pG+pG+ G+ G++G +G+ tem31.1t_g 436 PGPPGDQGPPGIPGQPGFIGEIGEKGQKGES 466 Collagen: domain 11 of 30, from 474 to 530: score 50.0, E = 3e-12 *->GppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGppGp G +GppGp+GppG+ G+pG++Ga+G++G pG +G G pGp G pG tem31.1t_g 474 GYRGPPGPQGPPGEIGFPGQPGAKGDRGLPGRDGVAGVPGPQGTPGL 520 pGapGapGpp<-* G+pGa+G+p tem31.1t_g 521 IGQPGAKGEP 530 Collagen: domain 12 of 30, from 540 to 573: score 26.0, E = 1.2e-05 *->pGppGppGepGpPGppGppGppGppGapGapGpp<-* +G++G+pG+pG+PG pG++G+pG +G pG pGp tem31.1t_g 540 KGDKGDPGFPGQPGMPGRAGSPGRDGHPGLPGPK 573 Collagen: domain 13 of 30, from 574 to 607: score 21.2, E = 0.00025 *->GppGppGppGppGppGppGppGpaGapGppGppG<-* G pG+ G +G++GppG G+pG +G GppGppG tem31.1t_g 574 GSPGSVGLKGERGPPGGVGFPGSRGDTGPPGPPG 607 Collagen: domain 14 of 30, from 609 to 641: score 17.5, E = 0.0026 *->GpaGapGppGppGepGpPGppGppGppGppGap<-* GpaG+ G++G +G+pG PG+pG pGp+G+pG++ tem31.1t_g 609 GPAGPIGDKGQAGFPGGPGSPGLPGPKGEPGKI 641 Collagen: domain 15 of 30, from 645 to 688: score 27.5, E = 4.5e-06 *->pGppGppGpaGapGppGppGepGpPGppGppGppGppGapGapG<-* pGppG+ G +G+pG pGp+G++G+PG pG+pG pG++Ga G pG tem31.1t_g 645 PGPPGAEGLPGSPGFPGPQGDRGFPGTPGRPGLPGEKGAVGQPG 688 Collagen: domain 16 of 30, from 690 to 737: score 26.7, E = 7.6e-06 *->GppGppGppGpaGapGppGppGepGpPGppGppGppGppGapGapGp G pGppGp+G +G pG+ GppG pG+PG G pG pG +G++G+pG tem31.1t_g 690 GFPGPPGPKGVDGLPGDMGPPGTPGRPGFNGLPGNPGVQGQKGEPGV 736 p<-* tem31.1t_g 737 G 737 Collagen: domain 17 of 30, from 740 to 799: score 47.2, E = 1.8e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G+pG pG pG pG++G G +G pG+ G+ G+pG +G +G+pGp tem31.1t_g 740 GLKGLPGLPGIPGTPGEKGSIGVPGVPGEHGAIGPPGLQGIRGEPGP 786 pGppGapGapGpp<-* pG pG G+pG p tem31.1t_g 787 PGLPGSVGSPGVP 799 Collagen: domain 18 of 30, from 802 to 835: score 20.7, E = 0.00033 *->GppGppGppGppGppGpaGapGppGppGepGpPG<-* GppG++GppG GppG +G+pG +G +G+pG+PG tem31.1t_g 802 GPPGARGPPGGQGPPGLSGPPGIKGEKGFPGFPG 835 Collagen: domain 19 of 30, from 838 to 896: score 55.5, E = 9.2e-14 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp pGp G +G++G pG G+ G +G pG +G+pG pG+PG++G++G tem31.1t_g 838 -MPGPKGDKGAQGLPGITGQSGLPGLPGQQGAPGIPGFPGSKGEMGV 883 pGppGapGapGpp<-* G pG+pG+pGp+ tem31.1t_g 884 MGTPGQPGSPGPV 896 Collagen: domain 20 of 30, from 897 to 937: score 32.0, E = 2.6e-07 *->GppGppGppGppGppGpaGapGppGppGepGpPGppGppGp<-* G+pG+pG++G+ G+pG +G++G+pG +G++G G pG+pG+ tem31.1t_g 897 GAPGLPGEKGDHGFPGSSGPRGDPGLKGDKGDVGLPGKPGS 937 Collagen: domain 21 of 30, from 948 to 995: score 39.9, E = 1.8e-09 *->GppGppGppGpaGapGppGppGepGpPGppGppGppGppGapGapGp G++G+ G++G+ G+ G++G +G+pG PG pG++G++G+pG+pG++G tem31.1t_g 948 GQKGDQGEKGQIGPIGEKGSRGDPGTPGVPGKDGQAGQPGQPGPKGD 994 p<-* p tem31.1t_g 995 P 995 Collagen: domain 22 of 30, from 996 to 1055: score 46.5, E = 2.8e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G G pG+pG+pGp+G G G +G pG++G pG pGp+G+pG pG tem31.1t_g 996 GISGTPGAPGLPGPKGSVGGMGLPGTPGEKGVPGIPGPQGSPGLPGD 1042 pGppGapGapGpp<-* +G +G++G +Gpp tem31.1t_g 1043 KGAKGEKGQAGPP 1055 Collagen: domain 23 of 30, from 1058 to 1086: score 24.9, E = 2.3e-05 *->GppGppGppGppGppGppGppGpaGapGp<-* G pG++G++G++G +G pG pG++G++G+ tem31.1t_g 1058 GIPGLRGEKGDQGIAGFPGSPGEKGEKGS 1086 Collagen: domain 24 of 30, from 1088 to 1131: score 39.7, E = 2e-09 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGp<-* G pG pG+pG+ G pG G pG +G pG++G++G pG +G pG+ tem31.1t_g 1088 GIPGMPGSPGLKGSPGSVGYPGSPGLPGEKGDKGLPGLDGIPGV 1131 Collagen: domain 25 of 30, from 1133 to 1172: score 36.8, E = 1.3e-08 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPG<-* G++G+pG pGp+Gp+G +G+pG +G pG++G +GepG PG tem31.1t_g 1133 GEAGLPGTPGPTGPAGQKGEPGSDGIPGSAGEKGEPGLPG 1172 Collagen: domain 26 of 30, from 1174 to 1233: score 41.8, E = 5.2e-10 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G pG pG++G+ G +G+ G+pG aG+pG pG +Ge G+ GppGp G+ tem31.1t_g 1174 GFPGFPGAKGDKGSKGEVGFPGLAGSPGIPGSKGEQGFMGPPGPQGQ 1220 pGppGapGapGpp<-* pG pG pG + + tem31.1t_g 1221 PGLPGSPGHATEG 1233 Collagen: domain 27 of 30, from 1239 to 1298: score 51.3, E = 1.3e-12 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp Gp G+pG pG+pGp GppG pG +G +G++G+pG pG+PG pGp G tem31.1t_g 1239 GPQGQPGLPGLPGPMGPPGLPGIDGVKGDKGNPGWPGAPGVPGPKGD 1285 pGppGapGapGpp<-* pG +G pG G p tem31.1t_g 1286 PGFQGMPGIGGSP 1298 Collagen: domain 28 of 30, from 1299 to 1351: score 37.9, E = 6.4e-09 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G G+ G GppG pG Gp+G +G +G +G++G+ G PG++G pGp tem31.1t_g 1299 GITGSKGDMGPPGVPGFQGPKGLPGLQGIKGDQGDQGVPGAKGLPGP 1345 pGppGa<-* pGppG+ tem31.1t_g 1346 PGPPGP 1351 Collagen: domain 29 of 30, from 1357 to 1384: score 18.7, E = 0.0012 *->GppGppGppGppGppGppGppGpaGapG<-* G+pG+pGp GppG +G G pGp+G +G tem31.1t_g 1357 GEPGLPGPEGPPGLKGLQGLPGPKGQQG 1384 Collagen: domain 30 of 30, from 1387 to 1440: score 42.3, E = 3.9e-10 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G G pGppG pG +G+pG++G+ G++Gp Gp+G+pGpPGp+G pG+ tem31.1t_g 1387 GLVGIPGPPGIPGFDGAPGQKGEMGPAGPTGPRGFPGPPGPDGLPGS 1433 pGppGap<-* GppG p tem31.1t_g 1434 MGPPGTP 1440 Reeler: domain 1 of 1, from 1445 to 1464: score 0.4, E = 79 *->GFlLtalkegregdseedpaGsss<-* GFl+t++ + +d++++p G + tem31.1t_g 1445 GFLVTRHSQ--TIDDPQCPSG--T 1464 C4: domain 1 of 2, from 1445 to 1554: score 256.3, E = 4.1e-73 *->gfliavHSQttsiPqCPaGwssLWtGYSflmvtganeeGhGQdLgsp gfl+++HSQt++ PqCP+G++ L++GYS+l+v+g ne++hGQdLg++ tem31.1t_g 1445 GFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQG-NERAHGQDLGTA 1490 GSCLerFrtmPFieCngrgvCnYasRndySfWLstiepedqFkaPmpmtp GSCL++F+tmPF++Cn+++vCn+asRndyS+WLst+ep +Pm+m+p tem31.1t_g 1491 GSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEP-----MPMSMAP 1535 kagreirpyISRCqVCekp<-* ++g++irp+ISRC+VCe+p tem31.1t_g 1536 ITGENIRPFISRCAVCEAP 1554 zf-CONSTANS: domain 1 of 1, from 1548 to 1558: score 2.9, E = 21 *->CDaCeeapAaVf<-* C +Ce apA+V+ tem31.1t_g 1548 CAVCE-APAMVM 1558 Nebulin_repeat: domain 1 of 1, from 1552 to 1566: score 2.7, E = 82 *->DtPeivlAKknaklq<-* ++P +v A +++ +q tem31.1t_g 1552 EAPAMVMAVHSQTIQ 1566 C4: domain 2 of 2, from 1555 to 1668: score 266.7, E = 3e-76 *->gfliavHSQttsiPqCPaGwssLWtGYSflmvtganeeGhGQdLgsp ++++avHSQt++iP+CP+GwssLW+GYSf+m+t+a++eG+GQ+L+sp tem31.1t_g 1555 AMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASP 1601 GSCLerFrtmPFieCngrgvCnYasRndySfWLstiepedqFkaPmpmtp GSCLe+Fr++PFieC+grg+CnY++ n ySfWL+tie++++Fk+P p+t+ tem31.1t_g 1602 GSCLEEFRSAPFIECHGRGTCNYYA-NAYSFWLATIERSEMFKKPTPSTL 1650 kagreirpyISRCqVCekp<-* kag e+r+++SRCqVC+++ tem31.1t_g 1651 KAG-ELRTHVSRCQVCMRR 1668 // Start with Repeat Library (from /data/patterns/repeats-Miguel-Andrade/hmm) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/repeats-Miguel-Andrade/hmm/repeats.hmm-lib Sequence file: tem31_1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Prosite --------------------------------------------------------- | ppsearch (c) 1994 EMBL Data Library | | based on MacPattern (c) 1990-1994 R. Fuchs | --------------------------------------------------------- PROSITE pattern search started: Tue Oct 31 16:21:16 2000 Sequence file: tem31_1 ---------------------------------------- Sequence tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN (1669 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 126: NGTK Total matches: 1 Matching pattern PS00004 CAMP_PHOSPHO_SITE: 1495: RKFS 1643: KKPT Total matches: 2 Matching pattern PS00005 PKC_PHOSPHO_SITE: 407: SGR 945: SMK 1649: TLK Total matches: 3 Matching pattern PS00006 CK2_PHOSPHO_SITE: 128: TKGE 256: TKGE 407: SGRD 596: SRGD 753: TPGE 877: SKGE 967: SRGD 1021: TPGE 1077: SPGE 1161: SAGE 1187: SKGE 1205: SKGE 1303: SKGD 1454: TIDD 1515: SRND 1524: STPE 1603: SCLE Total matches: 17 Matching pattern PS00008 MYRISTYL: 29: GGCAGS 30: GCAGSG 33: GSGCGK 35: GCGKCD 85: GLPGTK 88: GTKGTR 121: GIPGCN 124: GCNGTK 332: GIVIGT 430: GIVECQ 492: GQPGAK 522: GQPGAK 574: GSPGSV 788: GLPGSV 944: GSMKGQ 1011: GSVGGM 1100: GSPGSV 1157: GIPGSA 1201: GIPGSK 1295: GGSPGI 1299: GITGSK 1335: GVPGAK 1429: GLPGSM 1478: GNERAH 1484: GQDLGT 1488: GTAGSC 1590: GAEGSG 1593: GSGQAL 1595: GQALAS Total matches: 29 Matching pattern PS00016 RGD: 597: RGD 917: RGD 968: RGD Total matches: 3 Total no of hits in this sequence: 55 ======================================== 1314 pattern(s) searched in 1 sequence(s), 1669 residues. Total no of hits in all sequences: 55. Search time: 00:00 min ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Profile Search ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with motif search against own library ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** argv[1]=P argv[2]=-m /data/patterns/own/motif.fa argv[4]=-seq tem31_1 ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** SeqTyp=2 : PROTEIN search; >APC D-Box is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 1669 units ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~ ~~~ Start with HMM-search search against own library hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/own/own-hmm.lib Sequence file: tem31_1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/own/own-hmm-f.lib Sequence file: tem31_1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ L. Aravind's signalling DB IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR (1669 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value RHOGEF RHO-type GTPase GDP exchange factor 28 0.15 DNASE1 DNASE-1/Sphingomyelinase like domain 23 3.9 14-3-3 14-3-3 protein alpha Helical domain 22 5.5 UBA Ubiquitin pathway associated domain 22 7.1 MATH The Meprin associated TRAF homology domain 22 7.3 ARR Arrestin domain 22 8.4 >RHOGEF RHO-type GTPase GDP exchange factor Length = 176 Score = 27.6 bits (61), Expect = 0.15 Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 15/49 (30%) Query: 1480 ERAHGQDLGTAGSCLRK-------FSTMPF--------LFCNINNVCNF 1513 ER + ++L T R F MP LF N+ + F Sbjct: 9 ERVYVRELYTVLLGYRAEMDNPEMFDLMPPLLRNKKDILFGNMAEIYEF 57 >DNASE1 DNASE-1/Sphingomyelinase like domain Length = 388 Score = 22.8 bits (48), Expect = 3.9 Identities = 5/22 (22%), Positives = 9/22 (40%) Query: 242 VPGQAQVQEKGDFATKGEKGQK 263 + QA + K +F + K Sbjct: 107 ILAQALGEGKDNFIMCPMEALK 128 >14-3-3 14-3-3 protein alpha Helical domain Length = 270 Score = 22.3 bits (47), Expect = 5.5 Identities = 4/23 (17%), Positives = 7/23 (30%) Query: 1034 QGSPGLPGDKGAKGEKGQAGPPG 1056 + +GA+ P G Sbjct: 240 SAAAAGGNTEGAQENAPSNAPEG 262 >UBA Ubiquitin pathway associated domain Length = 255 Score = 22.0 bits (46), Expect = 7.1 Identities = 10/43 (23%), Positives = 16/43 (36%) Query: 227 PKGDKGDQGVSGPPGVPGQAQVQEKGDFATKGEKGQKGEPGFQ 269 GD + G + ++ G+ A G +GE FQ Sbjct: 181 AVGDNMQDVMEGADDMVEGEDIEVTGEAAAAGLGQGEGEGSFQ 223 >MATH The Meprin associated TRAF homology domain Length = 209 Score = 21.8 bits (46), Expect = 7.3 Identities = 4/18 (22%), Positives = 6/18 (33%), Gaps = 3/18 (16%) Query: 1248 GLPGPMGPP---GLPGID 1262 +P P P P + Sbjct: 3 RVPSPPPPAEMSSGPVAE 20 >ARR Arrestin domain Length = 454 Score = 21.7 bits (46), Expect = 8.4 Identities = 8/22 (36%), Positives = 9/22 (40%), Gaps = 1/22 (4%) Query: 425 PGYTNGIVECQPGPPGDQGPPG 446 + V QP PGD G P Sbjct: 145 APKSASSVTLQPA-PGDTGKPC 165 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 6 Number of calls to ALIGN: 6 Length of query: 1669 Total length of test sequences: 20182 Effective length of test sequences: 16839.0 Effective search space size: 27568712.7 Initial X dropoff for ALIGN: 25.0 bits Y. Wolf's SCOP PSSM IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= tem31.1t_gi|1345649|sp|P02462|CA14_HUMAN COLLAGEN ALPHA 1(IV) CHAIN PRECURSOR (1669 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|2618754 [18..216] NAD(P)-binding Rossmann-fold domains 30 0.22 gi|1827450 [37..347] Protein kinases (PK), catalytic core 26 5.2 gi|545756 [40..338] beta-Lactamase/D-ala carboxypeptidase 25 8.5 >gi|2618754 [18..216] NAD(P)-binding Rossmann-fold domains Length = 199 Score = 30.4 bits (67), Expect = 0.22 Identities = 13/154 (8%), Positives = 33/154 (20%), Gaps = 6/154 (3%) Query: 1446 FLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFC 1505 LV R + + + ++ V + A G ++ T Sbjct: 28 LLVARSETLLQELKEELRGLTGTAQPAVRCVAVDLSAAGGVNEAVEVARQEAGT----DP 83 Query: 1506 NINNVCNFASRNDYSYWLSTPEPMPMSMAPITGENIRPFISRCAVCEAPAMVMAVHSQTI 1565 + + N A S+ + + ++ + Sbjct: 84 DHVLLINNAGSLGDISKFSSFSDLNEVNSYLSLNVRSAL--ALNAGMLRVFPSRPGLRWS 141 Query: 1566 QIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALA 1599 + ++ A + LA Sbjct: 142 VVNISSLFAVQALPNWALYCTAKADRKMMFSVLA 175 >gi|1827450 [37..347] Protein kinases (PK), catalytic core Length = 311 Score = 25.9 bits (55), Expect = 5.2 Identities = 9/112 (8%), Positives = 25/112 (22%), Gaps = 6/112 (5%) Query: 1443 DHGFLVTRHSQTIDDPQCPSGTKILYHGYSLLYV-----QGNERAHGQDLGTAGSCLRKF 1497 + + + H ++ + G + DL G C+ ++ Sbjct: 159 LVDYGLAYRYCPEGVHKEYKEDPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQW 218 Query: 1498 STMPFLFCNINNVCNFASRNDYSYWL-STPEPMPMSMAPITGENIRPFISRC 1548 T + + + + Y I ++ Sbjct: 219 LTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPEKNKPGEIAKYMETV 270 >gi|545756 [40..338] beta-Lactamase/D-ala carboxypeptidase Length = 299 Score = 25.3 bits (55), Expect = 8.5 Identities = 15/65 (23%), Positives = 20/65 (30%), Gaps = 5/65 (7%) Query: 1429 GLPGSMGP-PGTPSVDHGFLVTRHSQTIDDPQCPSGTKILYH--GYSLLYVQGNERAHGQ 1485 GLP P D +V + P G Y Y L + RA G+ Sbjct: 79 GLPAIREMLPTEALYDWRLMVDTLAAE--APWWTPGQGHGYEAITYGWLVGELLRRADGR 136 Query: 1486 DLGTA 1490 G + Sbjct: 137 GPGES 141 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 3 Number of calls to ALIGN: 3 Length of query: 1669 Total length of test sequences: 256703 Effective length of test sequences: 211865.0 Effective search space size: 345753101.0 Initial X dropoff for ALIGN: 25.0 bits