analysis of sequence from tem15 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPCQICVCDSGSVLCDDIICDDQ ELDCPNPEIPFGECCAVCPQPPTAPTRPPNGQGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPGI CESCPTGPQNYSPQYDSYDVKSGVAVGGLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQGPPGEPGQAG PSGPPGPPGAIGPSGPAGKDGESGRPGRPGERGLPGPPGIKGPAGIPGFPGMKGHRGFDGRNGEKGETGA PGLKGENGLPGENGAPGPMGPRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAK GEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGPAGIPGAPGLMGARGPPGPAG ANGAPGLRGGAGEPGKNGAKGEPGPRGERGEAGIPGVPGAKGEDGKDGSPGEPGANGLPGAAGERGAPGF RGPAGPNGIPGEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPGSPGGPGSDGKPGPPGSQGES GRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPGGPGPQGPPGKNGETGPQGPPGPTGPGGDKG DTGPPGPQGLQGLPGTGGPPGENGKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP PGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGPRGPTGPIGPP GPAGQPGDKGEGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPG VAGPPGGSGPAGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPGKDGPPGPAGN TGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIAGITGARGLAGPPGMPGPRGSPGPQGVKGES GKPGANGLSGERGPPGPQGLPGLAGTAGEPGRDGNPGSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPG PPGPVGPAGKSGDRGESGPAGPAGAPGPAGSRGAPGPQGPRGDKGETGERGAAGIKGHRGFPGNPGAPGS PGPAGQQGAIGSPGPAGPRGPVGPSGPPGKDGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPP GAPGPCCGGVGAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLISPDGSRKNPAR NCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSSAEKKHVWFGE SMDGGFQFSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEF KAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLPIVDIAPYDIGGPDQEFGVDVGPVCFL ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > gi|115306|sp|P02461|CA13_HUMAN . . . . . 1 MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPC 50 __________EEE_____HHHHHHHHHH______________________ . . . . . 51 QICVCDSGSVLCDDIICDDQELDCPNPEIPFGECCAVCPQPPTAPTRPPN 100 EEEEE____________________________EEEE_____________ . . . . . 101 GQGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPGICESCPTGPQN 150 __________________________________________________ . . . . . 151 YSPQYDSYDVKSGVAVGGLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQ 200 _____________EEE__________________________________ . . . . . 201 GPPGEPGQAGPSGPPGPPGAIGPSGPAGKDGESGRPGRPGERGLPGPPGI 250 __________________________________________________ . . . . . 251 KGPAGIPGFPGMKGHRGFDGRNGEKGETGAPGLKGENGLPGENGAPGPMG 300 __________________________________________________ . . . . . 301 PRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAK 350 __________________________________________________ . . . . . 351 GEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGP 400 __________________________________________________ . . . . . 401 AGIPGAPGLMGARGPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERG 450 __________________________________________________ . . . . . 451 EAGIPGVPGAKGEDGKDGSPGEPGANGLPGAAGERGAPGFRGPAGPNGIP 500 __________________________________________________ . . . . . 501 GEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPGSPGGPGSDGK 550 __________________________________________________ . . . . . 551 PGPPGSQGESGRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPG 600 __________________________________________________ . . . . . 601 GPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGLQGLPGTGGPP 650 __________________________________________________ . . . . . 651 GENGKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP 700 __________________________________________________ . . . . . 701 PGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPG 750 __________________________________________________ . . . . . 751 ADGVPGKDGPRGPTGPIGPPGPAGQPGDKGEGGAPGLPGIAGPRGSPGER 800 __________________________________________________ . . . . . 801 GETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPGVAGPPGGSGP 850 __________________________________________________ . . . . . 851 AGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPG 900 __________________________________________________ . . . . . 901 KDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIA 950 _______________________________________________EEE . . . . . 951 GITGARGLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGL 1000 EEE_______________________________________________ . . . . . 1001 PGLAGTAGEPGRDGNPGSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPG 1050 __________________________________________________ . . . . . 1051 PPGPVGPAGKSGDRGESGPAGPAGAPGPAGSRGAPGPQGPRGDKGETGER 1100 _________________________________________________H . . . . . 1101 GAAGIKGHRGFPGNPGAPGSPGPAGQQGAIGSPGPAGPRGPVGPSGPPGK 1150 HHHH______________________________________________ . . . . . 1151 DGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCCGGV 1200 __________________________________________________ . . . . . 1201 GAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLIS 1250 __EEEE___________________EEEE_____________HHHHHH__ . . . . . 1251 PDGSRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGE 1300 ____________HHHHH_________EEE________EEEEEEEE_____ . . . . . 1301 TCISANPLNVPRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPEDVL 1350 EEE____________________EEEEEEE__________________HH . . . . . 1351 DVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEF 1400 HHHHHHHHHHHHHHHHEEEEE_____________HHHHHHHH________ . . . . . 1401 KAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLPIVDIAPYDIG 1450 ______EEEEEEE____________HHHHHHH_______EEEEE______ . 1451 GPDQEFGVDVGPVCFL 1466 _____EEEEE______ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ 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 -15.12 0.00 0.00 0.00 0.00 0.00 0.00 -0.03 -0.39 -6.36 -3.35 -12.00 -12.00 0.00 -12.00 0.00 -61.24 -12.02 -1.74 -1.49 -0.40 0.00 0.00 0.00 0.00 0.00 -4.59 -3.35 -12.00 -12.00 0.00 -12.00 0.00 -59.58 ID: gi|115306|sp|P02461|CA13_HUMAN AC: xxx Len: 1400 1:I 1380 Sc: -59.58 Pv: 3.625512e-01 NO_GPI_SITE GPI: learning from protozoa -21.80 0.00 -0.05 -0.27 -4.00 0.00 0.00 -0.10 -0.05 -5.52 -11.49 -12.00 -12.00 0.00 -12.00 0.00 -79.28 -20.41 -0.19 -0.31 0.00 -4.00 0.00 0.00 0.00 0.00 -6.46 -11.49 -12.00 -12.00 0.00 -12.00 0.00 -78.86 ID: gi|115306|sp|P02461|CA13_HUMAN AC: xxx Len: 1400 1:I 1381 Sc: -78.86 Pv: 4.885877e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? gi|115306|s 0.962 24 Y 0.867 24 Y 0.986 10 Y 0.910 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? gi|115306|s 0.553 422 Y 0.586 24 Y 0.982 7 Y 0.706 Y # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? gi|115306|s 0.480 422 Y 0.489 24 Y 0.964 1361 Y 0.796 Y ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR 1-10 MMSFVQKGSW lllall 11-16 17-88 HPTIILAQQEAVEGGCSHLGQSYADRDVWK PEPCQICVCDSGSVLCDDIICDDQELDCPN PEIPFGECCAVC pqpptaptrppngqgpqgpkgdpgppgipg 89-140 rngdpgipgqpgspgspgppgi 141-166 CESCPTGPQNYSPQYDSYDVKSGVAV gglagypgpagppgppgppgtsghpgspgs 167-228 pgyqgppgepgqagpsgppgppgaigpsgp ag 229-230 KD gesgrpgrpgerglpgppgikgpagipgfp 231-261 g 262-293 MKGHRGFDGRNGEKGETGAPGLKGENGLPG EN gapgpmgprgapgergrpglpgaagargnd 294-348 gargsdgqpgppgppgtagfpgspg 349-353 AKGEV gpagspgsngapg 354-366 367-368 QR gepgpqghagaqgppgppgingspggkg 369-396 397-403 EMGPAGI pgapglmgargppgpagangapglrggage 404-435 pg 436-437 KN gakgepgprgergeagipg 438-456 457-476 VPGAKGEDGKDGSPGEPGAN glpgaagergapgfrgpagpng 477-498 499-499 I pgekgpagergapgpagprgaagepgrdgv 500-576 pggpgmrgmpgspggpgsdgkpgppgsqge sgrpgppgpsgprgqpg 577-587 VMGFPGPKGND gapgkngerggpggpgpqgppgknge 588-613 614-614 T gpqgppgptgpggdkgdtgppgpqglqglp 615-723 gtggppgengkpgepgpkgdagapgapggk gdagapgergppglagapglrggagppgpe ggkgaagppgppgaagtpg 724-734 LQGMPGERGGL gspgpkgdkgepggpgadgvpgkdgprgpt 735-861 gpigppgpagqpgdkgeggapglpgiagpr gspgergetgppgpagfpgapgqngepggk gergapgekgeggppgvagppggsgpagpp gpqgvkg 862-863 ER gspggpgaagfpgarglpgppgsngnpgpp 864-918 gpsgspgkdgppgpagntgapgspg 919-932 VSGPKGDAGQPGEK gspgaqgppgapgplgiagitgarglagpp 933-975 gmpgprgspgpqg 976-992 VKGESGKPGANGLSGER gppgpqglpglagtag 993-1008 1009-1037 EPGRDGNPGSDGLPGRDGSPGGKGDRGEN gspgapgapghpgppgpvgpag 1038-1059 1060-1066 KSGDRGE sgpagpagapgpagsrgapgpqgprg 1067-1092 1093-1109 DKGETGERGAAGIKGHR gfpgnpgapgspgpagqqgaigspgpagpr 1110-1149 gpvgpsgppg 1150-1151 KD gtsghpgpigppgprgnrgergsegspghp 1152-1218 gqpgppgppgapgpccggvgaaaiagigge kaggfap 1219-1353 YYGDEPMDFKINTDEIMTSLKSVNGQIESL ISPDGSRKNPARNCRDLKFCHPELKSGEYW VDPNQGCKLDAIKVFCNMETGETCISANPL NVPRKHWWTDSSAEKKHVWFGESMDGGFQF SYGNPELPEDVLDVQ laflrllssras 1354-1365 1366-1466 QNITYHCKNSIAYMDQASGNVKKALKLMGS NEGEFKAEGNSKFTYTVLEDGCTKHTGEWS KTVFEYRTRKAVRLPIVDIAPYDIGGPDQE FGVDVGPVCFL low complexity regions: SEG 25 3.0 3.3 >gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR 1-46 MMSFVQKGSWLLLALLHPTIILAQQEAVEG GCSHLGQSYADRDVWK pepcqicvcdsgsvlcddiicddqeldcpn 47-148 peipfgeccavcpqpptaptrppngqgpqg pkgdpgppgipgrngdpgipgqpgspgspg ppgicescptgp 149-166 QNYSPQYDSYDVKSGVAV gglagypgpagppgppgppgtsghpgspgs 167-1218 pgyqgppgepgqagpsgppgppgaigpsgp agkdgesgrpgrpgerglpgppgikgpagi pgfpgmkghrgfdgrngekgetgapglkge nglpgengapgpmgprgapgergrpglpga agargndgargsdgqpgppgppgtagfpgs pgakgevgpagspgsngapgqrgepgpqgh agaqgppgppgingspggkgemgpagipga pglmgargppgpagangapglrggagepgk ngakgepgprgergeagipgvpgakgedgk dgspgepganglpgaagergapgfrgpagp ngipgekgpagergapgpagprgaagepgr dgvpggpgmrgmpgspggpgsdgkpgppgs qgesgrpgppgpsgprgqpgvmgfpgpkgn dgapgkngerggpggpgpqgppgkngetgp qgppgptgpggdkgdtgppgpqglqglpgt ggppgengkpgepgpkgdagapgapggkgd agapgergppglagapglrggagppgpegg kgaagppgppgaagtpglqgmpgergglgs pgpkgdkgepggpgadgvpgkdgprgptgp igppgpagqpgdkgeggapglpgiagprgs pgergetgppgpagfpgapgqngepggkge rgapgekgeggppgvagppggsgpagppgp qgvkgergspggpgaagfpgarglpgppgs ngnpgppgpsgspgkdgppgpagntgapgs pgvsgpkgdagqpgekgspgaqgppgapgp lgiagitgarglagppgmpgprgspgpqgv kgesgkpganglsgergppgpqglpglagt agepgrdgnpgsdglpgrdgspggkgdrge ngspgapgapghpgppgpvgpagksgdrge sgpagpagapgpagsrgapgpqgprgdkge tgergaagikghrgfpgnpgapgspgpagq qgaigspgpagprgpvgpsgppgkdgtsgh pgpigppgprgnrgergsegspghpgqpgp pgppgapgpccggvgaaaiagiggekaggf ap 1219-1466 YYGDEPMDFKINTDEIMTSLKSVNGQIESL ISPDGSRKNPARNCRDLKFCHPELKSGEYW VDPNQGCKLDAIKVFCNMETGETCISANPL NVPRKHWWTDSSAEKKHVWFGESMDGGFQF SYGNPELPEDVLDVQLAFLRLLSSRASQNI TYHCKNSIAYMDQASGNVKKALKLMGSNEG EFKAEGNSKFTYTVLEDGCTKHTGEWSKTV FEYRTRKAVRLPIVDIAPYDIGGPDQEFGV DVGPVCFL low complexity regions: SEG 45 3.4 3.75 >gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR 1-88 MMSFVQKGSWLLLALLHPTIILAQQEAVEG GCSHLGQSYADRDVWKPEPCQICVCDSGSV LCDDIICDDQELDCPNPEIPFGECCAVC pqpptaptrppngqgpqgpkgdpgppgipg 89-1218 rngdpgipgqpgspgspgppgicescptgp qnyspqydsydvksgvavgglagypgpagp pgppgppgtsghpgspgspgyqgppgepgq agpsgppgppgaigpsgpagkdgesgrpgr pgerglpgppgikgpagipgfpgmkghrgf dgrngekgetgapglkgenglpgengapgp mgprgapgergrpglpgaagargndgargs dgqpgppgppgtagfpgspgakgevgpags pgsngapgqrgepgpqghagaqgppgppgi ngspggkgemgpagipgapglmgargppgp agangapglrggagepgkngakgepgprge rgeagipgvpgakgedgkdgspgepgangl pgaagergapgfrgpagpngipgekgpage rgapgpagprgaagepgrdgvpggpgmrgm pgspggpgsdgkpgppgsqgesgrpgppgp sgprgqpgvmgfpgpkgndgapgkngergg pggpgpqgppgkngetgpqgppgptgpggd kgdtgppgpqglqglpgtggppgengkpge pgpkgdagapgapggkgdagapgergppgl agapglrggagppgpeggkgaagppgppga agtpglqgmpgergglgspgpkgdkgepgg pgadgvpgkdgprgptgpigppgpagqpgd kgeggapglpgiagprgspgergetgppgp agfpgapgqngepggkgergapgekgeggp pgvagppggsgpagppgpqgvkgergspgg pgaagfpgarglpgppgsngnpgppgpsgs pgkdgppgpagntgapgspgvsgpkgdagq pgekgspgaqgppgapgplgiagitgargl agppgmpgprgspgpqgvkgesgkpgangl sgergppgpqglpglagtagepgrdgnpgs dglpgrdgspggkgdrgengspgapgapgh pgppgpvgpagksgdrgesgpagpagapgp agsrgapgpqgprgdkgetgergaagikgh rgfpgnpgapgspgpagqqgaigspgpagp rgpvgpsgppgkdgtsghpgpigppgprgn rgergsegspghpgqpgppgppgapgpccg gvgaaaiagiggekaggfap 1219-1466 YYGDEPMDFKINTDEIMTSLKSVNGQIESL ISPDGSRKNPARNCRDLKFCHPELKSGEYW VDPNQGCKLDAIKVFCNMETGETCISANPL NVPRKHWWTDSSAEKKHVWFGESMDGGFQF SYGNPELPEDVLDVQLAFLRLLSSRASQNI TYHCKNSIAYMDQASGNVKKALKLMGSNEG EFKAEGNSKFTYTVLEDGCTKHTGEWSKTV FEYRTRKAVRLPIVDIAPYDIGGPDQEFGV DVGPVCFL 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 >gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPCQICVCDSGSV LCDDIICDDQELDCPNPEIPFGECcavcpqpptaptrppngqgpqgpkgdpgppgipgrn gdpgipgqpgspgspgppgicescptgpQNYSPQYDSYDVKSGVavgglagypgpagppg ppgppgtsghpgspgspgyqgppgepgqagpsgppgppgaigpsgpagkdgesgrpgrpg erglpgppgikgpagipgfpgmkghrgfdgrngekgetgapglkgenglpgengapgpmg prgapgergrpglpgaagargndgargsdgqpgppgppgtagfpgspgakgevgpagspg sngapgqrgepgpqghagaqgppgppgingspggkgemgpagipgapglmgargppgpag angapglrggagepgkngakgepgprgergeagipgvpgakgedgkdgspgepganglpg aagergapgfrgpagpngipgekgpagergapgpagprgaagepgrdgvpggpgmrgmpg spggpgsdgkpgppgsqgesgrpgppgpsgprgqpgvmgfpgpkgndgapgkngerggpg gpgpqgppgkngetgpqgppgptgpggdkgdtgppgpqglqglpgtggppgengkpgepg pkgdagapgapggkgdagapgergppglagapglrggagppgpeggkgaagppgppgaag tpglqgmpgergglgspgpkgdkgepggpgadgvpgkdgprgptgpigppgpagqpgdkg eggapglpgiagprgspgergetgppgpagfpgapgqngepggkgergapgekgeggppg vagppggsgpagppgpqgvkgergspggpgaagfpgarglpgppgsngnpgppgpsgspg kdgppgpagntgapgspgvsgpkgdagqpgekgspgaqgppgapgplgiagitgarglag ppgmpgprgspgpqgvkgesgkpganglsgergppgpqglpglagtagepgrdgnpgsdg lpgrdgspggkgdrgengspgapgapghpgppgpvgpagksgdrgesgpagpagapgpag srgapgpqgprgdkgetgergaagikghrgfpgnpgapgspgpagqqgaigspgpagprg pvgpsgppgkdgtsghpgpigppgprgnrgergsegspghpgqpgppgppgapgpCCggv gaaaiagiggEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLISPDGSRKNPAR NCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSS AEKKHVWFGESMDGGFQFSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMD QASGNVKKALKLMGSNEGEFKAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLP IVDIAPYDIGGPDQEFGVDVGPVCFL 1 - 84 MMSFVQKGSW LLLALLHPTI ILAQQEAVEG GCSHLGQSYA DRDVWKPEPC QICVCDSGSV LCDDIICDDQ ELDCPNPEIP FGEC 85 - 148 cavcpq pptaptrppn gqgpqgpkgd pgppgipgrn gdpgipgqpg spgspgppgi cesc ptgp 149 - 164 QN YSPQYDSYDV KSGV 165 - 1195 avggla gypgpagppg ppgppgtsgh pgspgspgyq gppgepgqag psgppgppga igps gpagkd gesgrpgrpg erglpgppgi kgpagipgfp gmkghrgfdg rngekgetga pglk genglp gengapgpmg prgapgergr pglpgaagar gndgargsdg qpgppgppgt agfp gspgak gevgpagspg sngapgqrge pgpqghagaq gppgppging spggkgemgp agip gapglm gargppgpag angapglrgg agepgkngak gepgprgerg eagipgvpga kged gkdgsp gepganglpg aagergapgf rgpagpngip gekgpagerg apgpagprga agep grdgvp ggpgmrgmpg spggpgsdgk pgppgsqges grpgppgpsg prgqpgvmgf pgpk gndgap gkngerggpg gpgpqgppgk ngetgpqgpp gptgpggdkg dtgppgpqgl qglp gtggpp gengkpgepg pkgdagapga pggkgdagap gergppglag apglrggagp pgpe ggkgaa gppgppgaag tpglqgmpge rgglgspgpk gdkgepggpg adgvpgkdgp rgpt gpigpp gpagqpgdkg eggapglpgi agprgspger getgppgpag fpgapgqnge pggk gergap gekgeggppg vagppggsgp agppgpqgvk gergspggpg aagfpgargl pgpp gsngnp gppgpsgspg kdgppgpagn tgapgspgvs gpkgdagqpg ekgspgaqgp pgap gplgia gitgarglag ppgmpgprgs pgpqgvkges gkpganglsg ergppgpqgl pgla gtagep grdgnpgsdg lpgrdgspgg kgdrgengsp gapgapghpg ppgpvgpagk sgdr gesgpa gpagapgpag srgapgpqgp rgdkgetger gaagikghrg fpgnpgapgs pgpa gqqgai gspgpagprg pvgpsgppgk dgtsghpgpi gppgprgnrg ergsegspgh pgqp gppgpp gapgp 1196 - 1197 CC 1198 - 1210 ggv gaaaiagigg 1211 - 1466 EKAGGFAPYY GDEPMDFKIN TDEIMTSLKS VNGQIESLIS PDGSRKNPAR NCRDLKFCHP ELKSGEYWVD PNQGCKLDAI KVFCNMETGE TCISANPLNV PRKHWWTDSS AEKKHVWFGE SMDGGFQFSY GNPELPEDVL DVQLAFLRLL SSRASQNITY HCKNSIAYMD QASGNVKKAL KLMGSNEGEF KAEGNSKFTY TVLEDGCTKH TGEWSKTVFE YRTRKAVRLP IVDIAPYDIG GPDQEFGVDV GPVCFL low complexity regions: DUST >gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPCQICVCDSGSV LCDDIICDDQELDCPNPEIPFGECCAVCPQPPTAPTRPPNGQGPQGPKGDPGPPGIPGRN GDPGIPGQPGSPGSPGPPGICESCPTGPQNYSPQYDSYDVKSGVAVGGLAGYPGPAGPPG PPGPPGTSGHPGSPGSPGYQGPPGEPGQAGPSGPPGPPGAIGPSGPAGKDGESGRPGRPG ERGLPGPPGIKGPAGIPGFPGMKGHRGFDGRNGEKGETGAPGLKGENGLPGENGAPGPMG PRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAKGEVGPAGSPG SNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGPAGIPGAPGLMGARGPPGPAG ANGAPGLRGGAGEPGKNGAKGEPGPRGERGEAGIPGVPGAKGEDGKDGSPGEPGANGLPG AAGERGAPGFRGPAGPNGIPGEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPG SPGGPGSDGKPGPPGSQGESGRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPG GPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGLQGLPGTGGPPGENGKPGEPG PKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGPPGPEGGKGAAGPPGPPGAAG TPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGPRGPTGPIGPPGPAGQPGDKG EGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPG VAGPPGGSGPAGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPG KDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIAGITGARGLAG PPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGLPGLAGTAGEPGRDGNPGSDG LPGRDGSPGGKGDRGENGSPGAPGAPGHPGPPGPVGPAGKSGDRGESGPAGPAGAPGPAG SRGAPGPQGPRGDKGETGERGAAGIKGHRGFPGNPGAPGSPGPAGQQGAIGSPGPAGPRG PVGPSGPPGKDGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCCGGV GAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLISPDGSRKNPAR NCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSS AEKKHVWFGESMDGGFQFSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMD QASGNVKKALKLMGSNEGEFKAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLP IVDIAPYDIGGPDQEFGVDVGPVCFL ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for gi|115306|sp|P02461|CA13_HUMAN sequence: 1400 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MMSFVQKGSW LLLALLHPTI ILAQQEAVEG GCSHLGQSYA DRDVWKPEPC QICVCDSGSV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 LCDDIICDDQ ELDCPNPEIP FGECCAVCPQ PPTAPTRPPN GQGPQGPKGD PGPPGIPGRN ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 GDPGIPGQPG SPGSPGPPGI CESCPTGPQN YSPQYDSYDV KSGVAVGGLA GYPGPAGPPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 PPGPPGTSGH PGSPGSPGYQ GPPGEPGQAG PSGPPGPPGA IGPSGPAGKD GESGRPGRPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 ERGLPGPPGI KGPAGIPGFP GMKGHRGFDG RNGEKGETGA PGLKGENGLP GENGAPGPMG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 PRGAPGERGR PGLPGAAGAR GNDGARGSDG QPGPPGPPGT AGFPGSPGAK GEVGPAGSPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 SNGAPGQRGE PGPQGHAGAQ GPPGPPGING SPGGKGEMGP AGIPGAPGLM GARGPPGPAG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 ANGAPGLRGG AGEPGKNGAK GEPGPRGERG EAGIPGVPGA KGEDGKDGSP GEPGANGLPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 AAGERGAPGF RGPAGPNGIP GEKGPAGERG APGPAGPRGA AGEPGRDGVP GGPGMRGMPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 SPGGPGSDGK PGPPGSQGES GRPGPPGPSG PRGQPGVMGF PGPKGNDGAP GKNGERGGPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 GPGPQGPPGK NGETGPQGPP GPTGPGGDKG DTGPPGPQGL QGLPGTGGPP GENGKPGEPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 PKGDAGAPGA PGGKGDAGAP GERGPPGLAG APGLRGGAGP PGPEGGKGAA GPPGPPGAAG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 TPGLQGMPGE RGGLGSPGPK GDKGEPGGPG ADGVPGKDGP RGPTGPIGPP GPAGQPGDKG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 EGGAPGLPGI AGPRGSPGER GETGPPGPAG FPGAPGQNGE PGGKGERGAP GEKGEGGPPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 VAGPPGGSGP AGPPGPQGVK GERGSPGGPG AAGFPGARGL PGPPGSNGNP GPPGPSGSPG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 KDGPPGPAGN TGAPGSPGVS GPKGDAGQPG EKGSPGAQGP PGAPGPLGIA GITGARGLAG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 PPGMPGPRGS PGPQGVKGES GKPGANGLSG ERGPPGPQGL PGLAGTAGEP GRDGNPGSDG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 LPGRDGSPGG KGDRGENGSP GAPGAPGHPG PPGPVGPAGK SGDRGESGPA GPAGAPGPAG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 SRGAPGPQGP RGDKGETGER GAAGIKGHRG FPGNPGAPGS PGPAGQQGAI GSPGPAGPRG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 PVGPSGPPGK DGTSGHPGPI GPPGPRGNRG ERGSEGSPGH PGQPGPPGPP GAPGPCCGGV ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 GAAAIAGIGG EKAGGFAPYY GDEPMDFKIN TDEIMTSLKS VNGQIESLIS PDGSRKNPAR ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 NCRDLKFCHP ELKSGEYWVD PNQGCKLDAI KVFCNMETGE TCISANPLNV PRKHWWTDSS ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 AEKKHVWFGE SMDGGFQFSY GNPELPEDVL DVQLAFLRLL SSRASQNITY HCKNSIAYMD ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~111 1111111111 11111111~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | QASGNVKKAL KLMGSNEGEF ~~~~~~~~~~ ~~~~~~~~~~ ---------- ---------- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** tem15.___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: tem15.___inter___ (1 sequences) MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPC QICVCDSGSVLCDDIICDDQELDCPNPEIPFGECCAVCPQPPTAPTRPPN GQGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPGICESCPTGPQN YSPQYDSYDVKSGVAVGGLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQ GPPGEPGQAGPSGPPGPPGAIGPSGPAGKDGESGRPGRPGERGLPGPPGI KGPAGIPGFPGMKGHRGFDGRNGEKGETGAPGLKGENGLPGENGAPGPMG PRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAK GEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGP AGIPGAPGLMGARGPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERG EAGIPGVPGAKGEDGKDGSPGEPGANGLPGAAGERGAPGFRGPAGPNGIP GEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPGSPGGPGSDGK PGPPGSQGESGRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPG GPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGLQGLPGTGGPP GENGKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP PGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPG ADGVPGKDGPRGPTGPIGPPGPAGQPGDKGEGGAPGLPGIAGPRGSPGER GETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPGVAGPPGGSGP AGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPG KDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIA GITGARGLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGL PGLAGTAGEPGRDGNPGSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPG PPGPVGPAGKSGDRGESGPAGPAGAPGPAGSRGAPGPQGPRGDKGETGER GAAGIKGHRGFPGNPGAPGSPGPAGQQGAIGSPGPAGPRGPVGPSGPPGK DGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCCGGV GAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLIS PDGSRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGE TCISANPLNVPRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPEDVL DVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEF KAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLPIVDIAPYDIG GPDQEFGVDVGPVCFL (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 32 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 5 25 1.102 Certain 2 162 182 0.979 Putative 3 208 228 0.636 Putative 4 708 728 0.675 Putative 5 836 856 0.738 Putative 6 935 955 0.913 Putative 7 1190 1210 1.447 Certain Warning! Only printing 30 out of 32 structures ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 4 5 6 7 Loop length 4 136 25 479 107 78 234 256 K+R profile 2.00 0.00 + + + + + + CYT-EXT prof - - 0.40 0.68 0.10 0.52 0.98 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -1.20 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 3 4 5 6 7 Loop length 4 182 479 107 78 234 256 K+R profile 2.00 + + + + + + CYT-EXT prof - 0.52 0.98 0.68 0.56 0.40 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.54 -> Orientation: N-out ---------------------------------------------------------------------- Structure 3 Transmembrane segments included in this structure: Segment 1 2 4 5 6 7 Loop length 4 136 525 107 78 234 256 K+R profile 2.00 + + + + + + CYT-EXT prof - 0.58 0.98 0.68 0.10 0.40 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.05 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 1.06 -> Orientation: N-out ---------------------------------------------------------------------- Structure 4 Transmembrane segments included in this structure: Segment 1 4 5 6 7 Loop length 4 682 107 78 234 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.40 0.68 0.57 0.98 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.05 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -1.15 -> Orientation: N-in ---------------------------------------------------------------------- Structure 5 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 Loop length 4 136 25 607 78 234 256 K+R profile 2.00 0.00 + + + + + CYT-EXT prof - - 0.98 0.68 0.10 0.51 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.02 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.37 -> Orientation: N-out ---------------------------------------------------------------------- Structure 6 Transmembrane segments included in this structure: Segment 1 3 5 6 7 Loop length 4 182 607 78 234 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.51 0.68 0.56 0.98 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.02 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -1.04 -> Orientation: N-in ---------------------------------------------------------------------- Structure 7 Transmembrane segments included in this structure: Segment 1 2 5 6 7 Loop length 4 136 653 78 234 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.56 0.68 0.10 0.98 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.25 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.52 -> Orientation: N-in ---------------------------------------------------------------------- Structure 8 Transmembrane segments included in this structure: Segment 1 5 6 7 Loop length 4 810 78 234 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.98 0.68 0.55 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.27 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.43 -> Orientation: N-out ---------------------------------------------------------------------- Structure 9 Transmembrane segments included in this structure: Segment 1 2 3 4 6 7 Loop length 4 136 25 479 206 234 256 K+R profile 2.00 0.00 + + + + + CYT-EXT prof - - 0.71 0.68 0.10 0.52 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.09 -> Orientation: N-out ---------------------------------------------------------------------- Structure 10 Transmembrane segments included in this structure: Segment 1 3 4 6 7 Loop length 4 182 479 206 234 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.52 0.68 0.56 0.71 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.76 -> Orientation: N-in ---------------------------------------------------------------------- Structure 11 Transmembrane segments included in this structure: Segment 1 2 4 6 7 Loop length 4 136 525 206 234 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.58 0.68 0.10 0.71 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.14 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.23 -> Orientation: N-in ---------------------------------------------------------------------- Structure 12 Transmembrane segments included in this structure: Segment 1 4 6 7 Loop length 4 682 206 234 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.71 0.68 0.57 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.15 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.14 -> Orientation: N-out ---------------------------------------------------------------------- Structure 13 Transmembrane segments included in this structure: Segment 1 2 3 6 7 Loop length 4 136 25 706 234 256 K+R profile 2.00 0.00 + + + + CYT-EXT prof - - 0.68 0.10 0.59 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.07 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.69 -> Orientation: N-in ---------------------------------------------------------------------- Structure 14 Transmembrane segments included in this structure: Segment 1 3 6 7 Loop length 4 182 706 234 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.59 0.68 0.56 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.07 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.03 -> Orientation: N-out ---------------------------------------------------------------------- Structure 15 Transmembrane segments included in this structure: Segment 1 2 6 7 Loop length 4 136 752 234 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.62 0.68 0.10 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.74 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.53 -> Orientation: N-out ---------------------------------------------------------------------- Structure 16 Transmembrane segments included in this structure: Segment 1 6 7 Loop length 4 909 234 256 K+R profile 2.00 + + + CYT-EXT prof - 0.68 0.61 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.78 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.62 -> Orientation: N-in ---------------------------------------------------------------------- Structure 17 Transmembrane segments included in this structure: Segment 1 2 3 4 5 7 Loop length 4 136 25 479 107 333 256 K+R profile 2.00 0.00 + + + + + CYT-EXT prof - - 0.40 0.68 0.10 0.52 0.75 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.28 -> Orientation: N-in ---------------------------------------------------------------------- Structure 18 Transmembrane segments included in this structure: Segment 1 3 4 5 7 Loop length 4 182 479 107 333 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.52 0.75 0.56 0.40 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.38 -> Orientation: N-in ---------------------------------------------------------------------- Structure 19 Transmembrane segments included in this structure: Segment 1 2 4 5 7 Loop length 4 136 525 107 333 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.58 0.75 0.10 0.40 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.06 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.14 -> Orientation: N-out ---------------------------------------------------------------------- Structure 20 Transmembrane segments included in this structure: Segment 1 4 5 7 Loop length 4 682 107 333 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.40 0.68 0.57 0.75 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.06 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.23 -> Orientation: N-in ---------------------------------------------------------------------- Structure 21 Transmembrane segments included in this structure: Segment 1 2 3 5 7 Loop length 4 136 25 607 333 256 K+R profile 2.00 0.00 + + + + CYT-EXT prof - - 0.75 0.10 0.51 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.03 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.54 -> Orientation: N-in ---------------------------------------------------------------------- Structure 22 Transmembrane segments included in this structure: Segment 1 3 5 7 Loop length 4 182 607 333 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.51 0.68 0.56 0.75 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.03 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.12 -> Orientation: N-in ---------------------------------------------------------------------- Structure 23 Transmembrane segments included in this structure: Segment 1 2 5 7 Loop length 4 136 653 333 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.56 0.68 0.10 0.75 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.33 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.39 -> Orientation: N-out ---------------------------------------------------------------------- Structure 24 Transmembrane segments included in this structure: Segment 1 5 7 Loop length 4 810 333 256 K+R profile 2.00 + + + CYT-EXT prof - 0.75 0.55 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.34 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.49 -> Orientation: N-in ---------------------------------------------------------------------- Structure 25 Transmembrane segments included in this structure: Segment 1 2 3 4 7 Loop length 4 136 25 479 461 256 K+R profile 2.00 0.00 + + + + CYT-EXT prof - - 0.69 0.10 0.52 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.02 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.61 -> Orientation: N-in ---------------------------------------------------------------------- Structure 26 Transmembrane segments included in this structure: Segment 1 3 4 7 Loop length 4 182 479 461 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.52 0.68 0.56 0.69 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.02 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.05 -> Orientation: N-in ---------------------------------------------------------------------- Structure 27 Transmembrane segments included in this structure: Segment 1 2 4 7 Loop length 4 136 525 461 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.58 0.68 0.10 0.69 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.18 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.48 -> Orientation: N-out ---------------------------------------------------------------------- Structure 28 Transmembrane segments included in this structure: Segment 1 4 7 Loop length 4 682 461 256 K+R profile 2.00 + + + CYT-EXT prof - 0.69 0.57 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.19 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.57 -> Orientation: N-in ---------------------------------------------------------------------- Structure 29 Transmembrane segments included in this structure: Segment 1 2 3 7 Loop length 4 136 25 961 256 K+R profile 2.00 0.00 + + + CYT-EXT prof - - 0.68 0.10 0.61 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.09 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.02 -> Orientation: N-in ---------------------------------------------------------------------- Structure 30 Transmembrane segments included in this structure: Segment 1 3 7 Loop length 4 182 961 256 K+R profile 2.00 + + + CYT-EXT prof - 0.61 0.56 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.09 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.64 -> Orientation: N-in ---------------------------------------------------------------------- "tem15" 1466 5 25 #t 1.10208 162 182 #f 0.979167 208 228 #f 0.636458 708 728 #f 0.675 836 856 #f 0.7375 935 955 #f 0.9125 1190 1210 #t 1.44688 ************************************ *TOPPREDM with prokaryotic function* ************************************ tem15.___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: tem15.___inter___ (1 sequences) MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPC QICVCDSGSVLCDDIICDDQELDCPNPEIPFGECCAVCPQPPTAPTRPPN GQGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPGICESCPTGPQN YSPQYDSYDVKSGVAVGGLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQ GPPGEPGQAGPSGPPGPPGAIGPSGPAGKDGESGRPGRPGERGLPGPPGI KGPAGIPGFPGMKGHRGFDGRNGEKGETGAPGLKGENGLPGENGAPGPMG PRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAK GEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGP AGIPGAPGLMGARGPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERG EAGIPGVPGAKGEDGKDGSPGEPGANGLPGAAGERGAPGFRGPAGPNGIP GEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPGSPGGPGSDGK PGPPGSQGESGRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPG GPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGLQGLPGTGGPP GENGKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP PGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPG ADGVPGKDGPRGPTGPIGPPGPAGQPGDKGEGGAPGLPGIAGPRGSPGER GETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPGVAGPPGGSGP AGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPG KDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIA GITGARGLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGL PGLAGTAGEPGRDGNPGSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPG PPGPVGPAGKSGDRGESGPAGPAGAPGPAGSRGAPGPQGPRGDKGETGER GAAGIKGHRGFPGNPGAPGSPGPAGQQGAIGSPGPAGPRGPVGPSGPPGK DGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCCGGV GAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLIS PDGSRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGE TCISANPLNVPRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPEDVL DVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEF KAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLPIVDIAPYDIG GPDQEFGVDVGPVCFL (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 32 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 5 25 1.102 Certain 2 162 182 0.979 Putative 3 208 228 0.636 Putative 4 708 728 0.675 Putative 5 836 856 0.738 Putative 6 935 955 0.913 Putative 7 1190 1210 1.447 Certain Warning! Only printing 30 out of 32 structures ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 4 5 6 7 Loop length 4 136 25 479 107 78 234 256 K+R profile 2.00 0.00 + + + + + + CYT-EXT prof - - 0.40 0.68 0.10 0.52 0.98 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -1.20 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 3 4 5 6 7 Loop length 4 182 479 107 78 234 256 K+R profile 2.00 + + + + + + CYT-EXT prof - 0.52 0.98 0.68 0.56 0.40 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.54 -> Orientation: N-out ---------------------------------------------------------------------- Structure 3 Transmembrane segments included in this structure: Segment 1 2 4 5 6 7 Loop length 4 136 525 107 78 234 256 K+R profile 2.00 + + + + + + CYT-EXT prof - 0.58 0.98 0.68 0.10 0.40 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.05 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 1.06 -> Orientation: N-out ---------------------------------------------------------------------- Structure 4 Transmembrane segments included in this structure: Segment 1 4 5 6 7 Loop length 4 682 107 78 234 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.40 0.68 0.57 0.98 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.05 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -1.15 -> Orientation: N-in ---------------------------------------------------------------------- Structure 5 Transmembrane segments included in this structure: Segment 1 2 3 5 6 7 Loop length 4 136 25 607 78 234 256 K+R profile 2.00 0.00 + + + + + CYT-EXT prof - - 0.98 0.68 0.10 0.51 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.02 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.37 -> Orientation: N-out ---------------------------------------------------------------------- Structure 6 Transmembrane segments included in this structure: Segment 1 3 5 6 7 Loop length 4 182 607 78 234 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.51 0.68 0.56 0.98 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.02 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -1.04 -> Orientation: N-in ---------------------------------------------------------------------- Structure 7 Transmembrane segments included in this structure: Segment 1 2 5 6 7 Loop length 4 136 653 78 234 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.56 0.68 0.10 0.98 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.25 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.52 -> Orientation: N-in ---------------------------------------------------------------------- Structure 8 Transmembrane segments included in this structure: Segment 1 5 6 7 Loop length 4 810 78 234 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.98 0.68 0.55 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.27 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.43 -> Orientation: N-out ---------------------------------------------------------------------- Structure 9 Transmembrane segments included in this structure: Segment 1 2 3 4 6 7 Loop length 4 136 25 479 206 234 256 K+R profile 2.00 0.00 + + + + + CYT-EXT prof - - 0.71 0.68 0.10 0.52 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.09 -> Orientation: N-out ---------------------------------------------------------------------- Structure 10 Transmembrane segments included in this structure: Segment 1 3 4 6 7 Loop length 4 182 479 206 234 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.52 0.68 0.56 0.71 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.76 -> Orientation: N-in ---------------------------------------------------------------------- Structure 11 Transmembrane segments included in this structure: Segment 1 2 4 6 7 Loop length 4 136 525 206 234 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.58 0.68 0.10 0.71 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.14 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.23 -> Orientation: N-in ---------------------------------------------------------------------- Structure 12 Transmembrane segments included in this structure: Segment 1 4 6 7 Loop length 4 682 206 234 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.71 0.68 0.57 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.15 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.14 -> Orientation: N-out ---------------------------------------------------------------------- Structure 13 Transmembrane segments included in this structure: Segment 1 2 3 6 7 Loop length 4 136 25 706 234 256 K+R profile 2.00 0.00 + + + + CYT-EXT prof - - 0.68 0.10 0.59 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.07 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.69 -> Orientation: N-in ---------------------------------------------------------------------- Structure 14 Transmembrane segments included in this structure: Segment 1 3 6 7 Loop length 4 182 706 234 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.59 0.68 0.56 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.07 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.03 -> Orientation: N-out ---------------------------------------------------------------------- Structure 15 Transmembrane segments included in this structure: Segment 1 2 6 7 Loop length 4 136 752 234 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.62 0.68 0.10 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.74 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.53 -> Orientation: N-out ---------------------------------------------------------------------- Structure 16 Transmembrane segments included in this structure: Segment 1 6 7 Loop length 4 909 234 256 K+R profile 2.00 + + + CYT-EXT prof - 0.68 0.61 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.78 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.62 -> Orientation: N-in ---------------------------------------------------------------------- Structure 17 Transmembrane segments included in this structure: Segment 1 2 3 4 5 7 Loop length 4 136 25 479 107 333 256 K+R profile 2.00 0.00 + + + + + CYT-EXT prof - - 0.40 0.68 0.10 0.52 0.75 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.28 -> Orientation: N-in ---------------------------------------------------------------------- Structure 18 Transmembrane segments included in this structure: Segment 1 3 4 5 7 Loop length 4 182 479 107 333 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.52 0.75 0.56 0.40 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.01 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.38 -> Orientation: N-in ---------------------------------------------------------------------- Structure 19 Transmembrane segments included in this structure: Segment 1 2 4 5 7 Loop length 4 136 525 107 333 256 K+R profile 2.00 + + + + + CYT-EXT prof - 0.58 0.75 0.10 0.40 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.06 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.14 -> Orientation: N-out ---------------------------------------------------------------------- Structure 20 Transmembrane segments included in this structure: Segment 1 4 5 7 Loop length 4 682 107 333 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.40 0.68 0.57 0.75 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.06 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.23 -> Orientation: N-in ---------------------------------------------------------------------- Structure 21 Transmembrane segments included in this structure: Segment 1 2 3 5 7 Loop length 4 136 25 607 333 256 K+R profile 2.00 0.00 + + + + CYT-EXT prof - - 0.75 0.10 0.51 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.03 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.54 -> Orientation: N-in ---------------------------------------------------------------------- Structure 22 Transmembrane segments included in this structure: Segment 1 3 5 7 Loop length 4 182 607 333 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.51 0.68 0.56 0.75 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.03 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.12 -> Orientation: N-in ---------------------------------------------------------------------- Structure 23 Transmembrane segments included in this structure: Segment 1 2 5 7 Loop length 4 136 653 333 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.56 0.68 0.10 0.75 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.33 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.39 -> Orientation: N-out ---------------------------------------------------------------------- Structure 24 Transmembrane segments included in this structure: Segment 1 5 7 Loop length 4 810 333 256 K+R profile 2.00 + + + CYT-EXT prof - 0.75 0.55 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.34 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.49 -> Orientation: N-in ---------------------------------------------------------------------- Structure 25 Transmembrane segments included in this structure: Segment 1 2 3 4 7 Loop length 4 136 25 479 461 256 K+R profile 2.00 0.00 + + + + CYT-EXT prof - - 0.69 0.10 0.52 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.02 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.61 -> Orientation: N-in ---------------------------------------------------------------------- Structure 26 Transmembrane segments included in this structure: Segment 1 3 4 7 Loop length 4 182 479 461 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.52 0.68 0.56 0.69 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.02 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.05 -> Orientation: N-in ---------------------------------------------------------------------- Structure 27 Transmembrane segments included in this structure: Segment 1 2 4 7 Loop length 4 136 525 461 256 K+R profile 2.00 + + + + CYT-EXT prof - 0.58 0.68 0.10 0.69 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.18 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: 0.48 -> Orientation: N-out ---------------------------------------------------------------------- Structure 28 Transmembrane segments included in this structure: Segment 1 4 7 Loop length 4 682 461 256 K+R profile 2.00 + + + CYT-EXT prof - 0.69 0.57 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.19 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.57 -> Orientation: N-in ---------------------------------------------------------------------- Structure 29 Transmembrane segments included in this structure: Segment 1 2 3 7 Loop length 4 136 25 961 256 K+R profile 2.00 0.00 + + + CYT-EXT prof - - 0.68 0.10 0.61 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.09 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.02 -> Orientation: N-in ---------------------------------------------------------------------- Structure 30 Transmembrane segments included in this structure: Segment 1 3 7 Loop length 4 182 961 256 K+R profile 2.00 + + + CYT-EXT prof - 0.61 0.56 0.68 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 Tm probability: 0.09 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 1.0000 -> Orientation: N-in CYT-EXT difference: -0.64 -> Orientation: N-in ---------------------------------------------------------------------- "tem15" 1466 5 25 #t 1.10208 162 182 #f 0.979167 208 228 #f 0.636458 708 728 #f 0.675 836 856 #f 0.7375 935 955 #f 0.9125 1190 1210 #t 1.44688 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem15.___saps___ SAPS. Version of April 11, 1996. Date run: Fri Nov 10 14:40:14 2000 File: /people/maria/tem15.___saps___ ID gi|115306|sp|P02461|CA13_HUMAN DE COLLAGEN ALPHA 1(III) CHAIN PRECURSOR number of residues: 1466; molecular weight: 138.6 kdal 1 MMSFVQKGSW LLLALLHPTI ILAQQEAVEG GCSHLGQSYA DRDVWKPEPC QICVCDSGSV 61 LCDDIICDDQ ELDCPNPEIP FGECCAVCPQ PPTAPTRPPN GQGPQGPKGD PGPPGIPGRN 121 GDPGIPGQPG SPGSPGPPGI CESCPTGPQN YSPQYDSYDV KSGVAVGGLA GYPGPAGPPG 181 PPGPPGTSGH PGSPGSPGYQ GPPGEPGQAG PSGPPGPPGA IGPSGPAGKD GESGRPGRPG 241 ERGLPGPPGI KGPAGIPGFP GMKGHRGFDG RNGEKGETGA PGLKGENGLP GENGAPGPMG 301 PRGAPGERGR PGLPGAAGAR GNDGARGSDG QPGPPGPPGT AGFPGSPGAK GEVGPAGSPG 361 SNGAPGQRGE PGPQGHAGAQ GPPGPPGING SPGGKGEMGP AGIPGAPGLM GARGPPGPAG 421 ANGAPGLRGG AGEPGKNGAK GEPGPRGERG EAGIPGVPGA KGEDGKDGSP GEPGANGLPG 481 AAGERGAPGF RGPAGPNGIP GEKGPAGERG APGPAGPRGA AGEPGRDGVP GGPGMRGMPG 541 SPGGPGSDGK PGPPGSQGES GRPGPPGPSG PRGQPGVMGF PGPKGNDGAP GKNGERGGPG 601 GPGPQGPPGK NGETGPQGPP GPTGPGGDKG DTGPPGPQGL QGLPGTGGPP GENGKPGEPG 661 PKGDAGAPGA PGGKGDAGAP GERGPPGLAG APGLRGGAGP PGPEGGKGAA GPPGPPGAAG 721 TPGLQGMPGE RGGLGSPGPK GDKGEPGGPG ADGVPGKDGP RGPTGPIGPP GPAGQPGDKG 781 EGGAPGLPGI AGPRGSPGER GETGPPGPAG FPGAPGQNGE PGGKGERGAP GEKGEGGPPG 841 VAGPPGGSGP AGPPGPQGVK GERGSPGGPG AAGFPGARGL PGPPGSNGNP GPPGPSGSPG 901 KDGPPGPAGN TGAPGSPGVS GPKGDAGQPG EKGSPGAQGP PGAPGPLGIA GITGARGLAG 961 PPGMPGPRGS PGPQGVKGES GKPGANGLSG ERGPPGPQGL PGLAGTAGEP GRDGNPGSDG 1021 LPGRDGSPGG KGDRGENGSP GAPGAPGHPG PPGPVGPAGK SGDRGESGPA GPAGAPGPAG 1081 SRGAPGPQGP RGDKGETGER GAAGIKGHRG FPGNPGAPGS PGPAGQQGAI GSPGPAGPRG 1141 PVGPSGPPGK DGTSGHPGPI GPPGPRGNRG ERGSEGSPGH PGQPGPPGPP GAPGPCCGGV 1201 GAAAIAGIGG EKAGGFAPYY GDEPMDFKIN TDEIMTSLKS VNGQIESLIS PDGSRKNPAR 1261 NCRDLKFCHP ELKSGEYWVD PNQGCKLDAI KVFCNMETGE TCISANPLNV PRKHWWTDSS 1321 AEKKHVWFGE SMDGGFQFSY GNPELPEDVL DVQLAFLRLL SSRASQNITY HCKNSIAYMD 1381 QASGNVKKAL KLMGSNEGEF KAEGNSKFTY TVLEDGCTKH TGEWSKTVFE YRTRKAVRLP 1441 IVDIAPYDIG GPDQEFGVDV GPVCFL -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A :115( 7.8%); C : 22( 1.5%); D : 55( 3.8%); E : 74( 5.0%); F- : 23( 1.6%) G++:413(28.2%); H : 14( 1.0%); I : 36( 2.5%); K : 62( 4.2%); L--: 48( 3.3%) M : 17( 1.2%); N : 41( 2.8%); P++:281(19.2%); Q : 43( 2.9%); R : 60( 4.1%) S : 73( 5.0%); T- : 31( 2.1%); V- : 36( 2.5%); W : 7( 0.5%); Y- : 15( 1.0%) KR : 122 ( 8.3%); ED : 129 ( 8.8%); AGP ++: 809 ( 55.2%); KRED : 251 ( 17.1%); KR-ED : -7 ( -0.5%); FIKMNY- : 194 ( 13.2%); LVIFM --: 160 ( 10.9%); ST - : 104 ( 7.1%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 000000+000 0000000000 00000-00-0 0000000000 -+-00+0-00 00000-0000 61 00--000--0 -0-0000-00 00-0000000 000000+000 0000000+0- 00000000+0 121 0-00000000 0000000000 0-00000000 00000-00-0 +000000000 0000000000 181 0000000000 0000000000 0000-00000 0000000000 00000000+- 0-00+00+00 241 -+00000000 +000000000 00+00+00-0 +00-+0-000 000+0-0000 0-00000000 301 0+0000-+0+ 000000000+ 00-00+00-0 0000000000 000000000+ 0-00000000 361 0000000+0- 0000000000 0000000000 0000+0-000 0000000000 00+0000000 421 0000000+00 00-00+000+ 0-000+0-+0 -000000000 +0--0+-000 0-00000000 481 000-+00000 +000000000 0-+0000-+0 0000000+00 00-00+-000 00000+0000 541 0000000-0+ 00000000-0 0+00000000 0+00000000 000+00-000 0+00-+0000 601 000000000+ 00-0000000 0000000-+0 -000000000 0000000000 0-00+00-00 661 0+0-000000 000+0-0000 0-+0000000 0000+00000 000-00+000 0000000000 721 000000000- +00000000+ 0-+0-00000 0-0000+-00 +000000000 0000000-+0 781 -000000000 000+0000-+ 0-00000000 000000000- 000+0-+000 0-+0-00000 841 0000000000 000000000+ 0-+0000000 0000000+00 0000000000 0000000000 901 +-00000000 0000000000 00+0-00000 -+00000000 0000000000 00000+0000 961 0000000+00 000000+0-0 0+00000000 -+00000000 00000000-0 0+-00000-0 1021 000+-00000 +0-+0-0000 0000000000 000000000+ 00-+0-0000 0000000000 1081 0+00000000 +0-+0-00-+ 00000+00+0 0000000000 0000000000 00000000+0 1141 000000000+ -000000000 00000+00+0 -+00-00000 0000000000 0000000000 1201 0000000000 -+00000000 0--00-0+00 0--00000+0 00000-0000 0-00++000+ 1261 00+-0+0000 -0+00-000- 00000+0-00 +00000-00- 0000000000 0++0000-00 1321 0-++00000- 00-0000000 000-00--00 -000000+00 00+0000000 00+000000- 1381 000000++00 +00000-0-0 +0-000+000 000--000+0 00-00+000- 0+0++00+00 1441 00-0000-00 00-0-000-0 000000 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 9/30 or 12/45 or 14/60): none Negative charge clusters (cmin = 9/30 or 12/45 or 15/60): 1) From 56 to 83: DSGSVLCDDIICDDQELDCPNPEIPFGE -000000--000--0-0-0000-0000- quartile: 1; size: 28, +count: 0, -count: 9, 0count: 19; t-value: 4.36 E: 3 (10.7%); D: 6 (21.4%); I: 3 (10.7%); P: 3 (10.7%); C: 3 (10.7%); LVIFM: 7 (25.0%); 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 | 7 | 54 | 10 | 10 | 13 | 12 | 12 | 16 | 6 | 8 | lmin1 6 | 6 | 8 | 65 | 12 | 12 | 15 | 15 | 15 | 19 | 8 | 9 | lmin2 7 | 7 | 10 | 72 | 13 | 13 | 17 | 17 | 17 | 22 | 9 | 11 | (Significance level: 0.010000; Minimal displayed length: 6) (0) 66(1,0,0); at 162- 228: see sequence above (1. quartile) G: 23 (34.3%); P: 21 (31.3%); Run count statistics: + runs >= 3: 0 - runs >= 3: 0 * runs >= 4: 0 0 runs >= 36: 1, at 162; -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. There are no high scoring hydrophobic segments. ____________________________________ High scoring transmembrane segments: 5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST) -6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED) Expected score/letter: -3.568 M_0.01= 48.00; M_0.05= 40.52; M_0.30= 31.63 1) From 1196 to 1210: length= 15, score=33.00 1196 CCGGVGAAAI AGIGG A: 4(26.7%); G: 6(40.0%); I: 2(13.3%); C: 2(13.3%); 2. SPACINGS OF C. H2N-31-C-17-C-2-C-1-C-6-C-4-C-6-C-9-C-C-2-C-52-C-2-C-1051-C-C-64-C-5-C-16-C-8-C-7-C-69-C-44-C-46-C-2-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-16-H-14-C-1-H-15-C-2-C-1-C-6-C-4-C-6-C-9-C-C-2-C-52-C-2-C-45-H-74-H-110-H-671-H-59-H-47-H-23-H-15-C-C-64-C-5-C-H-15-C-8-C-7-C-11-H-10-H-45-H-C-44-C-2-H-43-C-2-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 5 Aligned matching blocks: [ 106- 110]--------[ ] [ 660- 664]-( -9)-[ 656- 669] [ 738- 742]--------[ ] [ 921- 925]-( -9)-[ 917- 930] [ 106- 110] GPKGD [ 660- 664] GPKGD [ 738- 742] GPKGD [ 921- 925] GPKGD [ 656- 669] PGEPGPKGDAGAPG [ 917- 930] PGVSGPKGDAGQPG ______________________________ [ 112- 118] GPPGIPG [ 174- 181] GPAGPPGP [ 252- 258] GPAGIPG [ 354- 360] GPAGSPG [ 399- 406] GPAGIPGA [ 450- 456] GEAGIPG [ 495- 501] GPNGIPG [ 771- 777] GPAGQPG [ 807- 814] GPAGFPGA [ 849- 856] GPAGPPGP [1071-1078] GPAGAPGP ______________________________ [ 114- 118] PGIPG [ 123- 127] PGIPG ______________________________ [ 123- 139] PGIPGQPGSPGSPGPPG [1178-1194] PGHPGQPGPPGPPGAPG ______________________________ [ 123- 124]-( 4)-[ 129- 136] [ 126- 127]-( 4)-[ 132- 139] [ 185- 186]-( 4)-[ 191- 198] [ 533- 534]-( 4)-[ 539- 546] [ 129- 136] PGSPGSPG [ 132- 139] PGSPGPPG [ 191- 198] PGSPGSPG [ 539- 546] PGSPGGPG with superset: [ 129- 133] PGSPG [ 132- 136] PGSPG [ 191- 195] PGSPG [ 194- 198] PGSPG [ 344- 348] PGSPG [ 539- 543] PGSPG [ 914- 918] PGSPG [1118-1122] PGSPG ______________________________ [ 112- 113]-( 3)-[ 117- 118]-( 4)-[ 123- 124]-( 4)-[ 129- 136]-( -7)- [ 174- 175]-( 3)-[ 179- 180]-( 4)-[ 185- 186]-( 4)-[ 191- 198]-( -7)- [ ]--------[ ]--------[ ]--------[ ]-------- [ 130- 134] [ 192- 196] [ 357- 361] [ 129- 136] PGSPGSPG [ 191- 198] PGSPGSPG [ 130- 134] GSPGS [ 192- 196] GSPGS [ 357- 361] GSPGS ______________________________ [ 170- 192] AGYPGPAGPPGPPGPPGTSGHPG [1136-1158] AGPRGPVGPSGPPGKDGTSGHPG ______________________________ [ 173- 184] PGPAGPPGPPGP [1133-1144] PGPAGPRGPVGP with superset: [ 174- 178] GPAGP [ 492- 496] GPAGP [ 513- 517] GPAGP [ 849- 853] GPAGP [1068-1072] GPAGP [1134-1138] GPAGP and: [ 174- 181] GPAGPPGP [ 849- 856] GPAGPPGP [1134-1141] GPAGPRGP ______________________________ [ 173- 177]--------[ ]--------[ ] [ 416- 420]-( -5)-[ 416- 426]-( -11)-[ 416- 424] [ 512- 516]--------[ ]--------[ 512- 520] [ 770- 774]--------[ ]--------[ ] [ 806- 810]-( -5)-[ 806- 816]-( -11)-[ 806- 814] [ 905- 909]-( -5)-[ 905- 915]-( -11)-[ 905- 913] [1076-1080]-( -5)-[1076-1086]-( -11)-[1076-1084] [1121-1125]--------[ ]--------[1121-1129] [1133-1137]--------[ ]--------[ ] [ 173- 177] PGPAG [ 416- 420] PGPAG [ 512- 516] PGPAG [ 770- 774] PGPAG [ 806- 810] PGPAG [ 905- 909] PGPAG [1076-1080] PGPAG [1121-1125] PGPAG [1133-1137] PGPAG [ 416- 426] PGPAGANGAPG [ 806- 816] PGPAGFPGAPG [ 905- 915] PGPAGNTGAPG [1076-1086] PGPAGSRGAPG [ 416- 424] PGPAGANGA [ 512- 520] PGPAGPRGA [ 806- 814] PGPAGFPGA [ 905- 913] PGPAGNTGA [1076-1084] PGPAGSRGA [1121-1129] PGPAGQQGA ______________________________ [ 176- 187] AGPPGPPGPPGT [ 710- 721] AGPPGPPGAAGT with superset: [ 176- 180] AGPPG [ 698- 702] AGPPG [ 710- 714] AGPPG [ 842- 846] AGPPG [ 851- 855] AGPPG [ 959- 963] AGPPG and: [ 176- 183] AGPPGPPG [ 710- 717] AGPPGPPG [ 959- 966] AGPPGMPG ______________________________ [ 194- 202] PGSPGYQGP [ 539- 545] PGSPG__GP [ 914- 922] PGSPGVSGP ______________________________ [ 197- 205] PGYQGPPGE [ 644- 652] PGTGGPPGE ______________________________ [ 200- 207] QGPPGEPG [ 380- 387] QGPPGPPG [ 938- 945] QGPPGAPG with superset: [ 200- 204] QGPPG [ 380- 384] QGPPG [ 605- 609] QGPPG [ 617- 621] QGPPG [ 938- 942] QGPPG ______________________________ [ 203- 207] PGEPG [ 470- 474] PGEPG [ 656- 660] PGEPG ______________________________ [ 210- 214]--------[ ]--------[ 210- 216] [ 222- 226]-( -5)-[ 222- 237]--------[ ] [ 567- 571]--------[ ]--------[ ] [1143-1147]-( -5)-[1143-1158]-( -16)-[1143-1149] [ 210- 214] GPSGP [ 222- 226] GPSGP [ 567- 571] GPSGP [1143-1147] GPSGP [ 222- 237] GPSGPAGKDGESGRPG [1143-1158] GPSGPPGKDGTSGHPG [ 210- 216] GPSGPPG [1143-1149] GPSGPPG ______________________________ [ 215- 229] PGPPGAIGPSGPAGK [1046-1060] PGHPGPPGPVGPAGK ______________________________ [ 216- 223] GPPGAIGP [ 939- 946] GPPGAPGP [1188-1195] GPPGAPGP ______________________________ [ 225- 226]-( 4)-[ 231- 240] [ 300- 301]-( 4)-[ 306- 315] [ 552- 553]-( 4)-[ 558- 567] [ 231- 240] GESGRPGRPG [ 306- 315] GERGRPGLPG [ 558- 567] GESGRPGPPG with superset: [ 231- 237] GESGRPG [ 306- 312] GERGRPG [ 558- 564] GESGRPG [ 978- 984] GESGKPG ______________________________ [ 239- 249] PGERGLPGPPG [ 305- 315] PGERGRPGLPG with superset: [ 239- 243] PGERG [ 305- 309] PGERG [ 680- 684] PGERG [ 728- 732] PGERG [ 797- 801] PGERG and: [ 239- 246] PGERGLPG [ 305- 312] PGERGRPG [ 680- 687] PGERGPPG ______________________________ [ 248- 255] PGIKGPAG [ 500- 507] PGEKGPAG ______________________________ [ 254- 261]-( -8)-[ 254- 264] [ 401- 408]--------[ ] [ 452- 459]-( -8)-[ 452- 462] [ 254- 261] AGIPGFPG [ 401- 408] AGIPGAPG [ 452- 459] AGIPGVPG [ 254- 264] AGIPGFPGMKG [ 452- 462] AGIPGVPGAKG ______________________________ [ 263- 268] KGHRGF [1106-1111] KGHRGF ______________________________ [ 275- 279] KGETG [1094-1098] KGETG ______________________________ [ 278- 282] TGAPG [ 911- 915] TGAPG ______________________________ [ 281- 282]-( 4)-[ 287- 291] [ 470- 471]-( 4)-[ 476- 480] [ 287- 291] NGLPG [ 476- 480] NGLPG ______________________________ [ 290- 301] PGENGAPGPMGP [ 650- 661] PGENGKPGEPGP ______________________________ [ 291- 310] GENGAPGPMGPRGAPGERGR [ 507- 526] GERGAPGPAGPRGAAGEPGR with superset: [ 294- 307] GAPGPMGPRGAPGE [ 510- 523] GAPGPAGPRGAAGE [1083-1096] GAPGPQGPRGDKGE ______________________________ [ 296- 309] PGPMGPRGAPGERG [ 788- 801] PGIAGPRGSPGERG with superset: [ 300- 306] GPRGAPG [ 354- 360] GPAGSPG [ 570- 576] GPRGQPG [ 792- 798] GPRGSPG [ 861- 867] GERGSPG [ 894- 900] GPSGSPG [ 966- 972] GPRGSPG ______________________________ [ 303- 316] GAPGERGRPGLPGA [ 678- 691] GAPGERGPPGLAGA with superset: [ 303- 307] GAPGE [ 678- 682] GAPGE [ 828- 832] GAPGE ______________________________ [ 306- 307]-( 3)-[ 311- 321] [ 780- 781]-( 3)-[ 785- 795] [ 311- 321] PGLPGAAGARG [ 785- 795] PGLPGIAGPRG ______________________________ [ 273- 277]-( 34)-[ 312- 321]-( -8)-[ 314- 318]--------[ ] [ ]--------[ 477- 486]-( -8)-[ 479- 483]--------[ ] [ ]--------[ ]--------[ 716- 720]-( -8)-[ 713- 723] [ 831- 835]--------[ ]--------[ 869- 873]-( -8)-[ 866- 876] [ 273- 277] GEKGE [ 831- 835] GEKGE [ 312- 321] GLPGAAGARG [ 477- 486] GLPGAAGERG [ 314- 318] PGAAG [ 479- 483] PGAAG [ 716- 720] PGAAG [ 869- 873] PGAAG [ 713- 723] PGPPGAAGTPG [ 866- 876] PGGPGAAGFPG ______________________________ [ 321- 325] GNDGA [ 585- 589] GNDGA ______________________________ [ 336- 352] GPPGTAGFPGSPGAKGE [ 804- 820] GPPGPAGFPGAPGQNGE with superset: [ 341- 345] AGFPG [ 809- 813] AGFPG [ 872- 876] AGFPG ______________________________ [ 341- 355] AGFPGSPGAKGEVGP [ 431- 445] AGEPGKNGAKGEPGP with superset: [ 348- 352] GAKGE [ 438- 442] GAKGE [ 459- 463] GAKGE ______________________________ [ ]--------[ 344- 348]--------[ ] [ 518- 522]-( 16)-[ 539- 543]-( -5)-[ 539- 545] [ ]--------[ 914- 918]-( -5)-[ 914- 922] [1100-1104]-( 13)-[1118-1122]--------[ ] [ 518- 522] RGAAG [1100-1104] RGAAG [ 344- 348] PGSPG [ 539- 543] PGSPG [ 914- 918] PGSPG [1118-1122] PGSPG [ 539- 545] PGSPG__GP [ 914- 922] PGSPGVSGP ______________________________ [ 345- 349] GSPGA [ 933- 937] GSPGA [1038-1042] GSPGA ______________________________ [ 344- 348]-( 4)-[ 353- 357] [1046-1050]-( 4)-[1055-1059] [ 344- 348] PGSPG [1046-1050] PGHPG [ 353- 357] VGPAG [1055-1059] VGPAG ______________________________ [ 359- 366] PGSNGAPG [ 884- 891] PGSNGNPG ______________________________ [ 362- 369] NGAPGQRG [ 422- 429] NGAPGLRG with superset: [ 293- 297] NGAPG [ 362- 366] NGAPG [ 422- 426] NGAPG ______________________________ [ 363- 372] GAPGQRGEPG [ 813- 822] GAPGQNGEPG ______________________________ [ 389- 393] NGSPG [1037-1041] NGSPG ______________________________ [ ]--------[ 390- 394] [ 521- 531]-( 8)-[ 540- 546] [ ]--------[ 864- 870] [1007-1017]-( 8)-[1026-1030] [ 521- 531] AGEPGRDGVPG [1007-1017] AGEPGRDGNPG with superset: [ 431- 435] AGEPG [ 521- 525] AGEPG [1007-1011] AGEPG [ 390- 394] GSPGG [ 540- 546] GSPGGPG [ 864- 870] GSPGGPG [1026-1030] GSPGG ______________________________ [ 401- 409]-( -8)-[ 402- 409] [ 419- 427]-( -8)-[ 420- 427] [ 482- 489]--------[ ] [ 506- 514]--------[ ] [ 515- 523]--------[ ] [ 665- 672]-( -7)-[ 666- 672] [ 791- 799]--------[ ] [ 809- 816]-( -7)-[ 810- 816] [ 908- 915]-( -4)-[ 912- 918] [1070-1078]--------[ ] [1079-1087]--------[ ] [ 401- 409] AGIPGAPGL [ 419- 427] AGANGAPGL [ 482- 489] AGERGAPG [ 506- 514] AGERGAPGP [ 515- 523] AGPRGAAGE [ 665- 672] AGAPGAPG [ 791- 799] AGPRGSPGE [ 809- 816] AGFPGAPG [ 908- 915] AGNTGAPG [1070-1078] AGPAGAPGP [1079-1087] AGSRGAPGP matching also: [ 402- 409] GIPGAPGL [ 420- 427] GANGAPGL [ 666- 672] GAPGAPG [ 783- 789] GAPGLPG [ 810- 816] GFPGAPG [ 912- 918] GAPGSPG [ 939- 946] GPPGAPGP [1041-1047] GAPGAPG [1113-1119] GNPGAPG [1188-1195] GPPGAPGP ______________________________ [ 369- 373]--------[ ]--------[ 404- 409] [ 441- 445]--------[ ]--------[ 473- 480] [ ]--------[ 851- 855]-( 19)-[ 875- 882] [ ]--------[ 959- 963]-( 19)-[ 983- 988] matching also: [ 369- 373] GEPGP [ 441- 445] GEPGP [ 657- 661] GEPGP [ 851- 855] AGPPG [ 959- 963] AGPPG [ 404- 409] PGAPGL [ 473- 480] PGANGLPG [ 875- 882] PGARGLPG [ 983- 988] PGANGL ______________________________ [ 396- 400]-( 4)-[ 405- 418] [ 681- 685]-( 4)-[ 690- 703] [ 396- 400] GEMGP [ 681- 685] GERGP [ 405- 418] GAPGLMGARGPPGP [ 690- 703] GAPGLRGGAGPPGP with superset: [ 279- 283] GAPGL [ 405- 409] GAPGL [ 423- 427] GAPGL [ 690- 694] GAPGL [ 783- 787] GAPGL and: [ 405- 412] GAPGL_MGA [ 423- 431] GAPGLRGGA [ 690- 698] GAPGLRGGA ______________________________ [ 414- 421] GPPGPAGA [1068-1075] GPAGPAGA ______________________________ [ 411- 412]-( 4)-[ 417- 418]-( 4)-[ 423- 435] [ 678- 679]-( 4)-[ 684- 685]-( 4)-[ 690- 702] [ 423- 435] GAPGLRGGAGEPG [ 690- 702] GAPGLRGGAGPPG ______________________________ [ 425- 430]-( 3)-[ 434- 435]-( 4)-[ 440- 444] [ 728- 733]-( 3)-[ 737- 738]-( 4)-[ 743- 747] [ 425- 430] PGLRGG [ 728- 733] PGERGG [ 440- 444] KGEPG [ 743- 747] KGEPG ______________________________ [ 443- 447]-( -5)-[ 443- 451] [ 965- 969]--------[ ] [1163-1167]-( -5)-[1163-1173] [ 443- 447] PGPRG [ 965- 969] PGPRG [1163-1167] PGPRG [ 443- 451] PGPRGERGE [1163-1173] PGPRGNRGERG ______________________________ [ 447- 451] GERGE [ 798- 802] GERGE ______________________________ [ 471- 496] GEPGANGLPGAAGERGAPGFRGPAGP [ 780- 805] GEGGAPGLPGIAGPRGSPGERGETGP with superset: [ 312- 318] GLPGAAG [ 477- 483] GLPGAAG [ 714- 720] GPPGAAG [ 786- 792] GLPGIAG [ 867- 873] GGPGAAG [ 999-1005] GLPGLAG and: [ 312- 321] GLPGAAGARG [ 477- 486] GLPGAAGERG [ 786- 795] GLPGIAGPRG ______________________________ [ 473- 474]-( 4)-[ 479- 489] [ 770- 771]-( 4)-[ 776- 786] [ 815- 816]-( 4)-[ 821- 831] [ 479- 489] PGAAGERGAPG [ 776- 786] PGDKGEGGAPG [ 821- 831] PGGKGERGAPG with superset: [ 281- 286] PGLKGE [ 347- 352] PGAKGE [ 392- 397] PGGKGE [ 458- 463] PGAKGE [ 479- 484] PGAAGE [ 776- 781] PGDKGE [ 821- 826] PGGKGE [ 830- 835] PGEKGE ______________________________ [ 480- 484] GAAGE [ 519- 523] GAAGE ______________________________ [ 482- 493]-( -11)-[ 483- 489] [ 506- 517]-( -11)-[ 507- 513] [ ]--------[ 825- 831] [ ]--------[1098-1102] [ 482- 493] AGERGAPGFRGP [ 506- 517] AGERGAPGPAGP [ 483- 489] GERGAPG [ 507- 513] GERGAPG [ 825- 831] GERGAPG [1098-1102] GERGA ______________________________ [ 485- 489]--------[ ]--------[ 482- 493] [ 509- 513]-( -10)-[ 504- 523]-( -18)-[ 506- 517] [ 827- 831]--------[ ]--------[ ] [1082-1086]-( -10)-[1077-1096]-( -18)-[1079-1090] [ 485- 489] RGAPG [ 509- 513] RGAPG [ 827- 831] RGAPG [1082-1086] RGAPG [ 504- 523] GPAGERGAPGPAGPRGAAGE [1077-1096] GPAGSRGAPGPQGPRGDKGE [ 482- 493] AGERGAPGFRGP [ 506- 517] AGERGAPGPAGP [1079-1090] AGSRGAPGPQGP ______________________________ [ 468- 472]-( 27)-[ 500- 504] [ 795- 799]-( 30)-[ 830- 834] [ ]--------[ 929- 933] [ 468- 472] GSPGE [ 795- 799] GSPGE [ 500- 504] PGEKG [ 830- 834] PGEKG [ 929- 933] PGEKG ______________________________ [ 467- 471]--------[ ]--------[ 512- 519]-( -7)-[ 513- 517] [ ]--------[ 848- 853]--------[ ]--------[ 849- 853] [1025-1029]-( 37)-[1067-1072]--------[ ]--------[1068-1072] [ ]--------[ ]--------[1133-1140]-( -7)-[1134-1138] [ 467- 471] DGSPG [1025-1029] DGSPG matching also: [ 224- 228] SGPAG [ 848- 853] SGPAGP [1067-1072] SGPAGP [ 512- 519] PGPAGPRG [1133-1140] PGPAGPRG [ 513- 517] GPAGP [ 849- 853] GPAGP [1068-1072] GPAGP [1134-1138] GPAGP ______________________________ [ 524- 537] PGRDGVPGGPGMRG [ 749- 762] PGADGVPGKDGPRG ______________________________ [ 524- 532] PGRDGVPGG [1010-1017] PGRDGNPG [1022-1030] PGRDGSPGG ______________________________ [ 542- 552] PGGPGSDGKPG [ 746- 756] PGGPGADGVPG with superset: [ 530- 534] PGGPG [ 542- 546] PGGPG [ 599- 603] PGGPG [ 746- 750] PGGPG [ 866- 870] PGGPG ______________________________ [ 539- 540]-( 4)-[ 545- 556] [1010-1011]-( 4)-[1016-1027] [ 545- 556] PGSDGKPGPPGS [1016-1027] PGSDGLPGRDGS ______________________________ [ 581- 591] PGPKGNDGAPG [ 659- 669] PGPKGDAGAPG with superset: [ 581- 585] PGPKG [ 659- 663] PGPKG [ 737- 741] PGPKG ______________________________ [ 598- 610] GPGGP_GPQGPPGK [1137-1150] GPRGPVGPSGPPGK ______________________________ [ 599- 603] PGGPG [ 746- 751] PGGPGA [ 866- 871] PGGPGA ______________________________ [ 603- 609] GPQGPPG [ 615- 621] GPQGPPG with superset: [ 103- 107] GPQGP [ 603- 607] GPQGP [ 615- 619] GPQGP [1086-1090] GPQGP ______________________________ [ ]--------[ 590- 595]--------[ ]--------[ 608- 619]-( -6)- [ 594- 598]-( 9)-[ 608- 613]--------[ ]--------[ ]-------- [ 729- 733]--------[ ]--------[ 741- 750]--------[ ]-------- [ ]--------[ ]--------[ 777- 786]-( 10)-[ 797- 808]-( -6)- [ 614- 619]-( -6)-[ 614- 622]-( 24)-[ 647- 651] [ 632- 637]--------[ ]--------[ ] [ 764- 769]-( -6)-[ 764- 772]--------[ ] [ 803- 808]--------[ ]--------[ 836- 840] [ 594- 598] GERGG [ 729- 733] GERGG matching also: [ 434- 438] PGKNG [ 590- 595] PGKNGE [ 608- 613] PGKNGE [ 741- 750] GDKGEPGGPG [ 777- 786] GDKGEGGAPG with superset: [ 741- 745] GDKGE [ 777- 781] GDKGE [1092-1096] GDKGE [ 608- 619] PGKNGETGPQGP [ 797- 808] PGERGETGPPGP [ 614- 619] TGPQGP [ 632- 637] TGPPGP [ 764- 769] TGPIGP [ 803- 808] TGPPGP [ 614- 622] TGPQGPPGP [ 764- 772] TGPIGPPGP [ 647- 651] GGPPG [ 836- 840] GGPPG ______________________________ [ 617- 625] QGPPGPTGP [ 938- 946] QGPPGAPGP ______________________________ [ 618- 625] GPPGPTGP [ 759- 766] GPRGPTGP ______________________________ [ 656- 657]-( 4)-[ 662- 669]-( 7)-[ 677- 684] [ 668- 669]-( 4)-[ 674- 682]-( 6)-[ 689- 696] [ 917- 918]-( 4)-[ 923- 931]--------[ ] [ 662- 669] KGDAGAPG [ 674- 682] KGDAGAPGE [ 923- 931] KGDAGQPGE [ 677- 684] AGAPGERG [ 689- 696] AGAPGLRG ______________________________ [ 636- 637]-( 3)-[ 641- 645]-( 25)-[ 671- 675]--------[ ] [ ]--------[ ]--------[ 821- 825]-( -5)-[ 821- 828] [ 993- 994]-( 3)-[ 998-1002]-( 25)-[1028-1032]-( -5)-[1028-1035] [ 641- 645] QGLPG [ 998-1002] QGLPG [ 671- 675] PGGKG [ 821- 825] PGGKG [1028-1032] PGGKG [ 821- 828] PGGKGERG [1028-1035] PGGKGDRG ______________________________ [ 677- 681] AGAPG [ 689- 693] AGAPG [1073-1077] AGAPG ______________________________ [ 680- 688] PGERGPPGL [ 728- 734] PGERG__GL ______________________________ [ 680- 681]-( 4)-[ 686- 690] [ 995- 996]-( 4)-[1001-1005] [ 686- 690] PGLAG [1001-1005] PGLAG ______________________________ [ 710- 717] AGPPGPPG [ 959- 966] AGPPGMPG ______________________________ [ 744- 748] GEPGG [ 819- 823] GEPGG ______________________________ [ 755- 771] PGKDGPRGPTGPIGPPG [1133-1149] PGPAGPRGPVGPSGPPG ______________________________ [ 746- 750]-( 4)-[ 755- 763] [ 890- 894]-( 4)-[ 899- 907] [ 746- 750] PGGPG [ 890- 894] PGPPG [ 755- 763] PGKDGPRGP [ 899- 907] PGKDGPPGP with superset: [ 755- 759] PGKDG [ 899- 903] PGKDG [1148-1152] PGKDG ______________________________ [ 768- 769]-( 3)-[ 773- 784] [ 921- 922]-( 3)-[ 926- 937] [ 773- 784] AGQPGDKGEGGA [ 926- 937] AGQPGEKGSPGA ______________________________ [ 776- 786] PGDKGEGGAPG [ 830- 840] PGEKGEGGPPG ______________________________ [ 794- 798] RGSPG [ 863- 867] RGSPG [ 968- 972] RGSPG ______________________________ [ 824- 831] KGERGAPG [ 860- 867] KGERGSPG ______________________________ [ 842- 850] AGPPGGSGP [ 959- 967] AGPPGMPGP ______________________________ [ 842- 850]-( 3)-[ 854- 862] [ 959- 967]-( 3)-[ 971- 979] [ 842- 850] AGPPGGSGP [ 959- 967] AGPPGMPGP [ 854- 862] PGPQGVKGE [ 971- 979] PGPQGVKGE ______________________________ [ 872- 885] AGFPGARGLPGPPG [ 950- 963] AGITGARGLAGPPG ______________________________ [ 992- 999] RGPPGPQG [1082-1089] RGAPGPQG ______________________________ [1030-1036] GK_GDRGE [1059-1066] GKSGDRGE ______________________________ [1046-1057] PGHPGPPGPVGP [1133-1144] PGPAGPRGPVGP ______________________________ [1046-1057] PGHPGPPGPVGP [1178-1189] PGHPGQPGPPGP ______________________________ [1112-1119] PGNPGAPG [1187-1194] PGPPGAPG ______________________________ [1116-1125] GAPGSPGPAG [1128-1137] GAIGSPGPAG Highly repetitive regions: From 106 to 1190 with major motif GPPGPPGPA. From 109 to 1192 with major motif GQPGPPGPPGP. From 111 to 1192 with major motif PGPPGP. From 177 to 1190 with major motif GPPGPP. From 240 to 997 with major motif GERGPPGP. From 242 to 1117 with major motif RGLPGPPGP. 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: [ 291- 296]-( -2)-[ 295- 316]-( 3)-[ 320- 321] [ 507- 512]-( 0)-[ 513- 532]-( 3)-[ 536- 537] [ 291- 296] s-nssp [ 507- 512] s-+ssp [ 295- 316] spspmsp+ssps-+s+psipss [ 513- 532] sps__sp+ssss-ps+-sipss with superset: [ 302- 310] +ssps-+s+ [ 428- 436] +ssss-ps+ [ 518- 526] +ssss-ps+ ______________________________ [ 785- 793]-( 4)-[ 798- 816] [1049-1057]-( 4)-[1062-1079] [ 785- 793] psipsissp [1049-1057] psppspisp [ 798- 816] s-+s-osppspssipssps [1062-1079] s-+s-ospsspsssp_sps with superset: [ 627- 637] s-+s-osppsp [ 798- 808] s-+s-osppsp [1062-1072] s-+s-ospssp -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 94 (Expected range: 121--193) low 1 MM........ LLL.LL...I I..QQ....G G......... .......... .......... 61 ..DDII.DD. .......... ...CC..... PP.....PP. .......... ..PP...... 121 .......... ......PP.. .......... .......... ......GG.. .......PP. 181 PP.PP..... .......... .PP....... ...PP.PP.. .......... .......... 241 ......PP.. .......... .......... .......... .......... .......... 301 .......... .....AA... .......... ...PP.PP.. .......... .......... 361 .......... .......... .PP.PP.... ..GG...... .......... ....PP.... 421 ........GG .......... .......... .......... .......... .......... 481 AA........ .......... .......... .........A A......... GG........ 541 ..GG...... ..PP...... ....PP.... .......... .......... ......GG.G 601 G.....PP.. ........PP .....GG... ...PP..... ......GGPP .......... 661 .......... .GG....... ....PP.... .....GG..P P...GG..AA .PP.PP.AA. 721 .......... .GG....... ......GG.. .......... ........PP .......... 781 .GG....... .......... ....PP.... .......... .GG....... .....GGPP. 841 ...PPGG... ..PP...... ......GG.. AA........ ..PP...... .PP....... 901 ...PP..... .......... .......... .........P P......... .......... 961 PP........ .......... .......... ...PP..... .......... .......... 1021 ........GG .......... .......... PP........ .......... .......... 1081 .......... .......... .AA....... .......... .....QQ... .......... 1141 ......PP.. .......... .PP....... .......... .....PP.PP .....CCGG. 1201 .AAA....GG ...GG...YY .......... .......... .......... .......... 1261 .......... .......... .......... .......... .......... ....WW..SS 1321 ..KK...... ...GG..... .......... ........LL SS........ .......... 1381 ......KK.. .......... .......... .......... .......... .......... 1441 .........G G......... ...... 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 33 (6-10) 15 (11-20) 23 (>=21) 24 3. Clusters of amino acid multiplets (cmin = 11/30 or 14/45 or 17/60): none 4. Significant specific amino acid altplet counts: Letters Observed (Critical number) AG 86 (82) at 170 (l= 2) 176 (l= 2) 209 (l= 2) 219 (l= 2) 227 (l= 2) 254 (l= 2) 279 (l= 2) 294 (l= 2) 303 (l= 2) 315 (l= 2) 317 (l= 3) 324 (l= 2) 341 (l= 2) 348 (l= 2) 356 (l= 2) 363 (l= 2) 377 (l= 3) 401 (l= 2) 405 (l= 2) 411 (l= 2) 419 (l= 3) 423 (l= 2) 430 (l= 3) 438 (l= 2) 452 (l= 2) 459 (l= 2) 474 (l= 2) 480 (l= 2) 482 (l= 2) 486 (l= 2) 494 (l= 2) 506 (l= 2) 510 (l= 2) 515 (l= 2) 519 (l= 2) 521 (l= 2) 588 (l= 2) 665 (l= 3) 669 (l= 2) 677 (l= 3) 689 (l= 3) 697 (l= 3) 708 (l= 2) 710 (l= 2) 717 (l= 2) 719 (l= 2) 750 (l= 2) 773 (l= 2) 783 (l= 2) 791 (l= 2) 809 (l= 2) 813 (l= 2) 828 (l= 2) 842 (l= 2) 851 (l= 2) 870 (l= 2) 872 (l= 2) 876 (l= 2) 908 (l= 2) 912 (l= 2) 926 (l= 2) 936 (l= 2) 942 (l= 2) 950 (l= 2) 954 (l= 2) 959 (l= 2) 984 (l= 2) 1004 (l= 2) 1007 (l= 2) 1041 (l= 2) 1044 (l= 2) 1058 (l= 2) 1070 (l= 2) 1073 (l= 3) 1079 (l= 2) 1083 (l= 2) 1101 (l= 2) 1103 (l= 2) 1116 (l= 2) 1124 (l= 2) 1128 (l= 2) 1136 (l= 2) 1191 (l= 2) 1201 (l= 2) 1206 (l= 2) 1213 (l= 2) GP 207 (163) at 103 (l= 2) 106 (l= 2) 111 (l= 3) 114 (l= 2) 117 (l= 2) 123 (l= 2) 126 (l= 2) 129 (l= 2) 132 (l= 2) 135 (l= 3) 138 (l= 2) 147 (l= 2) 173 (l= 3) 177 (l= 2) 179 (l= 3) 182 (l= 3) 185 (l= 2) 191 (l= 2) 194 (l= 2) 197 (l= 2) 201 (l= 2) 203 (l= 2) 206 (l= 2) 210 (l= 2) 213 (l= 2) 215 (l= 3) 218 (l= 2) 222 (l= 2) 225 (l= 2) 236 (l= 2) 239 (l= 2) 245 (l= 3) 248 (l= 2) 252 (l= 2) 257 (l= 2) 260 (l= 2) 281 (l= 2) 290 (l= 2) 296 (l= 3) 300 (l= 2) 305 (l= 2) 311 (l= 2) 314 (l= 2) 332 (l= 3) 335 (l= 3) 338 (l= 2) 344 (l= 2) 347 (l= 2) 354 (l= 2) 359 (l= 2) 365 (l= 2) 371 (l= 3) 381 (l= 2) 383 (l= 3) 386 (l= 2) 392 (l= 2) 399 (l= 2) 404 (l= 2) 407 (l= 2) 414 (l= 2) 416 (l= 3) 425 (l= 2) 434 (l= 2) 443 (l= 3) 455 (l= 2) 458 (l= 2) 470 (l= 2) 473 (l= 2) 479 (l= 2) 488 (l= 2) 492 (l= 2) 495 (l= 2) 500 (l= 2) 504 (l= 2) 512 (l= 3) 516 (l= 2) 524 (l= 2) 530 (l= 2) 532 (l= 3) 539 (l= 2) 542 (l= 2) 544 (l= 3) 551 (l= 3) 554 (l= 2) 563 (l= 3) 566 (l= 3) 570 (l= 2) 575 (l= 2) 581 (l= 3) 590 (l= 2) 598 (l= 3) 601 (l= 4) 606 (l= 2) 608 (l= 2) 615 (l= 2) 618 (l= 2) 620 (l= 3) 624 (l= 3) 633 (l= 2) 635 (l= 3) 644 (l= 2) 648 (l= 2) 650 (l= 2) 656 (l= 2) 659 (l= 3) 668 (l= 2) 671 (l= 2) 680 (l= 2) 684 (l= 2) 686 (l= 2) 692 (l= 2) 699 (l= 2) 7 01 (l= 3) 711 (l= 2) 713 (l= 3) 716 (l= 2) 722 (l= 2) 728 (l= 2) 737 (l= 3) 746 (l= 2) 748 (l= 3) 755 (l= 2) 759 (l= 2) 762 (l= 2) 765 (l= 2) 768 (l= 2) 770 (l= 3) 776 (l= 2) 785 (l= 2) 788 (l= 2) 792 (l= 2) 797 (l= 2) 804 (l= 2) 806 (l= 3) 812 (l= 2) 815 (l= 2) 821 (l= 2) 830 (l= 2) 837 (l= 2) 839 (l= 2) 843 (l= 2) 845 (l= 2) 849 (l= 2) 852 (l= 2) 854 (l= 3) 866 (l= 2) 868 (l= 3) 875 (l= 2) 881 (l= 3) 884 (l= 2) 890 (l= 3) 893 (l= 3) 899 (l= 2) 903 (l= 2) 905 (l= 3) 914 (l= 2) 917 (l= 2) 921 (l= 2) 929 (l= 2) 935 (l= 2) 939 (l= 2) 941 (l= 2) 944 (l= 3) 960 (l= 2) 962 (l= 2) 965 (l= 3) 971 (l= 3) 983 (l= 2) 993 (l= 2) 995 (l= 3) 1001 (l= 2) 1010 (l= 2) 1016 (l= 2) 1022 (l= 2) 1028 (l= 2) 1040 (l= 2) 1043 (l= 2) 1046 (l= 2) 1049 (l= 3) 1052 (l= 3) 1056 (l= 2) 1068 (l= 2) 1071 (l= 2) 1076 (l= 3) 1085 (l= 3) 1089 (l= 2) 1112 (l= 2) 1115 (l= 2) 1118 (l= 2) 1121 (l= 3) 1133 (l= 3) 1137 (l= 2) 1140 (l= 2) 1143 (l= 2) 1146 (l= 2) 1148 (l= 2) 1157 (l= 3) 1161 (l= 2) 1163 (l= 3) 1178 (l= 2) 1181 (l= 2) 1184 (l= 3) 1187 (l= 3) 1190 (l= 2) 1193 (l= 3) 1451 (l= 2) 1461 (l= 2) B. CHARGE ALPHABET. 1. Total number of charge multiplets: 12 (Expected range: 6-- 33) 5 +plets (f+: 8.3%), 7 -plets (f-: 8.8%) Total number of charge altplets: 36 (Critical number: 38) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 1 (6-10) 2 (11-20) 1 (>=21) 9 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 89- 109 3 P.. 6 4 1 103- 141 3 G.P 13 13 ! /0/./4/ 129- 160 8 P....... 4 4 0 168-1196 3 G.. 343 343 ! 0 1191-1222 8 G....... 4 4 0 B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 7) Location Period Element Copies Core Errors 63- 87 5 -.000 5 5 /0/./0/1/0/ -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 34- 190 (1.) H( 156)H 2 of 15 0.9701 small 2. maximal spacing 39- 151 (1.) Y( 112)Y 2 of 16 0.9996 small 2. maximal spacing 45-1278 (2.) W(1233)W 1 of 8 0.0000 large 1. maximal spacing 144-1196 (2.) C(1052)C 1 of 23 0.0000 large 1. maximal spacing 199-1219 (2.) Y(1020)Y 1 of 16 0.0000 large 1. maximal spacing 308- 310 (1.) R( 2)R 61 of 61 0.0054 large minimal spacing 376-1048 (2.) H( 672)H 1 of 15 0.0027 large 1. maximal spacing 569- 736 (2.) S( 167)S 1 of 74 0.0085 large maximal spacing 1299-1329 (4.) G( 30)G 2 of 414 0.0001 large 2. maximal spacing 1302-1372 (4.) C( 70)C 2 of 23 1.0000 small 2. maximal spacing 1311-1343 (4.) P( 32)P 2 of 282 0.0301 large 2. maximal spacing 1327-1424 (4.) W( 97)W 2 of 8 0.9998 small 2. maximal spacing 1341-1384 (4.) G( 43)G 1 of 414 0.0002 large 1. maximal spacing 1346-1440 (4.) P( 94)P 1 of 282 0.0000 large 1. maximal spacing 1397-1399 (4.) E( 2)E 75 of 75 0.0003 large minimal spacing 1432-1434 (4.) R( 2)R 60 of 61 0.0054 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: tem15 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Collagen Collagen triple helix repeat (20 copies 949.9 6.8e-282 18 COLFI Fibrillar collagen C-terminal domain 561.6 5.3e-219 1 DNA_pol3_beta DNA polymerase III beta subunit 7.6 0.39 1 CorA CorA-like Mg2+ transporter protein -148.3 24 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Collagen 1/18 82 141 .. 1 60 [] -0.9 0.0034 Collagen 2/18 168 227 .. 1 60 [] 66.5 5.6e-16 Collagen 3/18 234 293 .. 1 60 [] 78.5 1.4e-19 Collagen 4/18 294 353 .. 1 60 [] 68.3 1.6e-16 Collagen 5/18 354 413 .. 1 60 [] 67.2 3.4e-16 Collagen 6/18 414 473 .. 1 60 [] 67.6 2.6e-16 Collagen 7/18 474 533 .. 1 60 [] 63.9 3.5e-15 Collagen 8/18 534 593 .. 1 60 [] 69.3 8.1e-17 Collagen 9/18 594 653 .. 1 60 [] 49.1 9.5e-11 Collagen 10/18 654 713 .. 1 60 [] 46.5 6e-10 Collagen 11/18 714 773 .. 1 60 [] 58.8 1.2e-13 Collagen 12/18 777 836 .. 1 60 [] 58.3 1.7e-13 Collagen 13/18 837 896 .. 1 60 [] 52.6 8.5e-12 Collagen 14/18 897 956 .. 1 60 [] 64.9 1.7e-15 Collagen 15/18 957 1016 .. 1 60 [] 65.2 1.4e-15 Collagen 16/18 1017 1076 .. 1 60 [] 61.0 2.6e-14 Collagen 17/18 1077 1136 .. 1 60 [] 79.3 7.7e-20 Collagen 18/18 1137 1196 .. 1 60 [] 69.7 6.1e-17 DNA_pol3_beta 1/1 1225 1247 .. 1 23 [. 7.6 0.39 CorA 1/1 5 1413 .. 1 324 [] -148.3 24 COLFI 1/1 1248 1465 .. 1 226 [] 561.6 5.3e-219 Alignments of top-scoring domains: Collagen: domain 1 of 18, from 82 to 141: score -0.9, E = 0.0034 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+ p p+ p+ pp +Gp+G++G+pGppG pG+ G pG pG+ gi|115306| 82 GECCAVCPQPPTAPTRPPNGQGPQGPKGDPGPPGIPGRNGDPGIPGQ 128 pGppGapGapGpp<-* pG pG pG+pG + gi|115306| 129 PGSPGSPGPPGIC 141 Collagen: domain 2 of 18, from 168 to 227: score 66.5, E = 5.6e-16 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G pGp+GppGppGppG G++G+pG+pG +G+pG+PG++Gp Gp gi|115306| 168 GLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQGPPGEPGQAGPSGP 214 pGppGapGapGpp<-* pGppGa+G+ Gp+ gi|115306| 215 PGPPGAIGPSGPA 227 Collagen: domain 3 of 18, from 234 to 293: score 78.5, E = 1.4e-19 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pG+pG++G+pGppG +Gp+G +G+pG++G++G++G+ G +G+ G+ gi|115306| 234 GRPGRPGERGLPGPPGIKGPAGIPGFPGMKGHRGFDGRNGEKGETGA 280 pGppGapGapGpp<-* pG +G+ G pG++ gi|115306| 281 PGLKGENGLPGEN 293 Collagen: domain 4 of 18, from 294 to 353: score 68.3, E = 1.6e-16 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pGp+Gp+G+pG++G+pG pG+aGa+G+ G++G +G+PGppGppG gi|115306| 294 GAPGPMGPRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGT 340 pGppGapGapGpp<-* +G pG pGa+G++ gi|115306| 341 AGFPGSPGAKGEV 353 Collagen: domain 5 of 18, from 354 to 413: score 67.2, E = 3.4e-16 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp Gp+G+pG++G+pG++G+pGp+G+aGa+GppGppG +G+PG +G++Gp gi|115306| 354 GPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGP 400 pGppGapGapGpp<-* +G pGapG +G++ gi|115306| 401 AGIPGAPGLMGAR 413 Collagen: domain 6 of 18, from 414 to 473: score 67.6, E = 2.6e-16 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp GppGp+G++G+pG +G +G+pG +Ga+G+pGp+Ge+G+ G pG+pG+ gi|115306| 414 GPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERGEAGIPGVPGA 460 pGppGapGapGpp<-* +G++G++G+pG+p gi|115306| 461 KGEDGKDGSPGEP 473 Collagen: domain 7 of 18, from 474 to 533: score 63.9, E = 3.5e-15 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+ G+pG++G++G+pG +Gp+Gp+G pG++Gp+Ge+G+PGp+Gp G+ gi|115306| 474 GANGLPGAAGERGAPGFRGPAGPNGIPGEKGPAGERGAPGPAGPRGA 520 pGppGapGapGpp<-* +G+pG++G pG p gi|115306| 521 AGEPGRDGVPGGP 533 Collagen: domain 8 of 18, from 534 to 593: score 69.3, E = 8.1e-17 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G pG+pG pG +G+pGppG +G+ G pGppG++Gp G+pG++G+ gi|115306| 534 GMRGMPGSPGGPGSDGKPGPPGSQGESGRPGPPGPSGPRGQPGVMGF 580 pGppGapGapGpp<-* pGp+G++GapG++ gi|115306| 581 PGPKGNDGAPGKN 593 Collagen: domain 9 of 18, from 594 to 653: score 49.1, E = 9.5e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G++G pG+pGp+GppG+ G++Gp+G+pGp Gp G++G GppGp G gi|115306| 594 GERGGPGGPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGL 640 pGppGapGapGpp<-* +G pG G+pG++ gi|115306| 641 QGLPGTGGPPGEN 653 Collagen: domain 10 of 18, from 654 to 713: score 46.5, E = 6e-10 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pG+pGp+G++G+pG+pG +G+aGapG++GppG +G+PG +G +Gp gi|115306| 654 GKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP 700 pGppGapGapGpp<-* pGp+G +Ga+Gpp gi|115306| 701 PGPEGGKGAAGPP 713 Collagen: domain 11 of 18, from 714 to 773: score 58.8, E = 1.2e-13 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp GppG +G pG++G+pG++G G +G++G++G pG pG++G pG++Gp gi|115306| 714 GPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGP 760 pGppGapGapGpp<-* +Gp+G++G+pGp+ gi|115306| 761 RGPTGPIGPPGPA 773 Collagen: domain 12 of 18, from 777 to 836: score 58.3, E = 1.7e-13 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G+ G+pG+pG +Gp+G pG++G+ GppGp+G+pG+PG+ G+pG gi|115306| 777 GDKGEGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGG 823 pGppGapGapGpp<-* +G++GapG++G+ gi|115306| 824 KGERGAPGEKGEG 836 Collagen: domain 13 of 18, from 837 to 896: score 52.6, E = 8.5e-12 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp GppG +GppG Gp+GppGp+G +G++G+pG pG++G+PG++G pGp gi|115306| 837 GPPGVAGPPGGSGPAGPPGPQGVKGERGSPGGPGAAGFPGARGLPGP 883 pGppGapGapGpp<-* pG G+pG+pGp gi|115306| 884 PGSNGNPGPPGPS 896 Collagen: domain 14 of 18, from 897 to 956: score 64.9, E = 1.7e-15 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G pG+ GppGp+G +G+pG pG +G++G++G pGe+G+PG++GppG+ gi|115306| 897 GSPGKDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGA 943 pGppGapGapGpp<-* pGp G +G G++ gi|115306| 944 PGPLGIAGITGAR 956 Collagen: domain 15 of 18, from 957 to 1016: score 65.2, E = 1.4e-15 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +GppG pGp+G pGp G +G++G+pG +G +Ge+GpPGp+G pG gi|115306| 957 GLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGLPGL 1003 pGppGapGapGpp<-* +G +G+pG G p gi|115306| 1004 AGTAGEPGRDGNP 1016 Collagen: domain 16 of 18, from 1017 to 1076: score 61.0, E = 2.6e-14 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G G+pG+ G pG +G++G+ G +GapG pG+pG+pGp Gp+G+ G gi|115306| 1017 GSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPGPPGPVGPAGKSGD 1063 pGppGapGapGpp<-* +G+ G++G++G+p gi|115306| 1064 RGESGPAGPAGAP 1076 Collagen: domain 17 of 18, from 1077 to 1136: score 79.3, E = 7.7e-20 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp Gp+G++G+pGp+Gp+G++G++G++Ga+G +G++G+pG PG+pG pGp gi|115306| 1077 GPAGSRGAPGPQGPRGDKGETGERGAAGIKGHRGFPGNPGAPGSPGP 1123 pGppGapGapGpp<-* +G++Ga+G+pGp+ gi|115306| 1124 AGQQGAIGSPGPA 1136 Collagen: domain 18 of 18, from 1137 to 1196: score 69.7, E = 6.1e-17 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp Gp+Gp Gp GppG +G +G+pGp G+pGp+G++Ge+G+ G+pG+pG+ gi|115306| 1137 GPRGPVGPSGPPGKDGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQ 1183 pGppGapGapGpp<-* pGppG+pGapGp+ gi|115306| 1184 PGPPGPPGAPGPC 1196 DNA_pol3_beta: domain 1 of 1, from 1225 to 1247: score 7.6, E = 0.39 *->MkFtIeRdaLlkaLqkVarvvsn<-* M F+I++d+++++L+ V + +++ gi|115306| 1225 MDFKINTDEIMTSLKSVNGQIES 1247 CorA: domain 1 of 1, from 5 to 1413: score -148.3, E = 24 *->iedktvvWidlinePteeemakl.....skafgihpltlediedieq + +++ + l+ Pt+ ++ ++++ ++g+++++ + ++ gi|115306| 5 VQKGSWLLLALL-HPTIILAQQEaveggCSHLGQSYADRD--VWKPE 48 raKveedddylfiilhffsvnldeeegvvlar.................. + d++ ++ + ++ d+e+ ++++ + ++ +++ gi|115306| 49 PCQICVCDSGSVLCDDI--ICDDQEL-----Dcpnpeipfgeccavcpqp 91 .................................................. ++ +++++++++++++++++++++ ++++++++ ++++++++++++++ gi|115306| 92 ptaptrppngqgpqgpkgdpgppgipgrngdpgipgqpgspgspgppgic 141 .................................................. ++ ++++++ +++ ++ + +++ ++ + +++ +++++++++++++++ gi|115306| 142 escptgpqnyspqydsydvksgvavgglagypgpagppgppgppgtsghp 191 .................................................. +++++++ +++++++++ ++++++++++ +++++ ++++++++++++++ gi|115306| 192 gspgspgyqgppgepgqagpsgppgppgaigpsgpagkdgesgrpgrpge 241 .................................................. ++ +++++ +++ + ++ ++ +++++ +++++++++++ ++ +++++ ++ gi|115306| 242 rglpgppgikgpagipgfpgmkghrgfdgrngekgetgapglkgenglpg 291 .................................................. +++ +++ ++++ ++++++++ ++ + +++++ +++++++++++++++ gi|115306| 292 engapgpmgprgapgergrpglpgaagargndgargsdgqpgppgppgta 341 .................................................. + +++++ +++ ++ +++++++ ++++++++++++ + ++++++++ +++ gi|115306| 342 gfpgspgakgevgpagspgsngapgqrgepgpqghagaqgppgppgings 391 .................................................. ++++++ ++ + ++ ++ + ++++++ + ++ ++ +++ +++++++ ++ gi|115306| 392 pggkgemgpagipgapglmgargppgpagangapglrggagepgkngakg 441 .................................................. ++++++++++ + ++ ++ ++++++++++++++ ++ ++ ++++ ++ + gi|115306| 442 epgprgergeagipgvpgakgedgkdgspgepganglpgaagergapgfr 491 .................................................. ++ ++++ ++++++ ++++ +++ ++++ +++++++ +++++ ++ +++ gi|115306| 492 gpagpngipgekgpagergapgpagprgaagepgrdgvpggpgmrgmpgs 541 .................................................. +++++++++++++++++++++++++++++++++++ + ++++++++ ++ gi|115306| 542 pggpgsdgkpgppgsqgesgrpgppgpsgprgqpgvmgfpgpkgndgapg 591 .................................................. ++++++++++++++++++++++++++++++++++++++++++++++++ + gi|115306| 592 kngerggpggpgpqgppgkngetgpqgppgptgpggdkgdtgppgpqglq 641 .................................................. + +++++++++++++++++++++ + ++ ++++++ + ++++++++ + gi|115306| 642 glpgtggppgengkpgepgpkgdagapgapggkgdagapgergppglaga 691 .................................................. ++ +++ ++++++++++ +++++++ ++++ ++ ++++++ +++++++ gi|115306| 692 pglrggagppgpeggkgaagppgppgaagtpglqgmpgergglgspgpkg 741 .................................................. +++++++++ ++ ++++++++++++ +++++ ++++++++++ ++ ++ gi|115306| 742 dkgepggpgadgvpgkdgprgptgpigppgpagqpgdkgeggapglpgia 791 .................................................. +++++++++++++++++ + ++ ++++++++++++++ +++++++++++ gi|115306| 792 gprgspgergetgppgpagfpgapgqngepggkgergapgekgeggppgv 841 .................................................. ++++++++ +++++++ +++++++++++ + ++ ++ +++++++++++ gi|115306| 842 agppggsgpagppgpqgvkgergspggpgaagfpgarglpgppgsngnpg 891 .................................................. ++++++++++++++++ ++++ +++++ ++++++ ++++++++++ ++++ gi|115306| 892 ppgpsgspgkdgppgpagntgapgspgvsgpkgdagqpgekgspgaqgpp 941 .................................................. + +++ + + ++ ++ ++++ +++++++++++ ++++++++ ++ +++ gi|115306| 942 gapgplgiagitgarglagppgmpgprgspgpqgvkgesgkpganglsge 991 .................................................. ++++++++ ++ ++ +++++++++++++ ++++++++++++++++++++ gi|115306| 992 rgppgpqglpglagtagepgrdgnpgsdglpgrdgspggkgdrgengspg 1041 .................................................. ++ +++++++++ ++ +++++++++++ ++ + +++ ++++ +++++++ gi|115306| 1042 apgapghpgppgpvgpagksgdrgesgpagpagapgpagsrgapgpqgpr 1091 .................................................. ++++++++++ + +++++ +++++ ++++++ ++++ +++++ +++++ gi|115306| 1092 gdkgetgergaagikghrgfpgnpgapgspgpagqqgaigspgpagprgp 1141 .................................................. +++++++++++++++++ +++++++++++++++++++++++++++++++ gi|115306| 1142 vgpsgppgkdgtsghpgpigppgprgnrgergsegspghpgqpgppgppg 1191 .........eeleteqvsivlgknfllTiherheidilasvRkRirtkkp +++ ++ + + + i + + ++a + + gi|115306| 1192 apgpccggvGAAA------------IAGIGGE-KAGGFAPYYGDEPMD-- 1226 gvlrqkgsdylfyalldaiidsyfpvlekiedeieeLEdqIlagrstpss ++ + +d++ l+ + +ie+L ++ p++ gi|115306| 1227 --FK-------------INTDEIMTSLKSVNGQIESL----IS----PDG 1253 tildeIlslrrelldl.......vtlrralipkrdvlnfllretkepwii + +++ ++r + + ++ ++++ ++ + k d+++ + + + i gi|115306| 1254 SRKNPARNCRDLKFCHpelksgeYWVDPNQGCKLDAIKVFCNMETGETCI 1303 .p....................................qkEvreylrDiy + ++ + ++++ ++++ ++++ +++ +++ + + + E+ e++ D++ gi|115306| 1304 sAnplnvprkhwwtdssaekkhvwfgesmdggfqfsygNPELPEDVLDVQ 1353 dHtdqllevietyrellsRsHsNsLmdiylslvvsnrqNeImKilTvvtt ++ll++ ++++ Ns+ +y+++ s ++ +++K + gi|115306| 1354 LAFLRLLSSRASQNITYH--CKNSI--AYMDQA-SGNVKKALKLM----- 1393 iFiPpTlIaGiYGMN...FkWfMPELnwkyGYpfvlilMvllallmlywF G N+++Fk E n+k+ Y v gi|115306| 1394 ------------GSNegeFK---AEGNSKFTY-TV--------------- 1412 rrKgWL<-* L gi|115306| 1413 -----L 1413 COLFI: domain 1 of 1, from 1248 to 1465: score 561.6, E = 5.3e-219 *->lksPeGksrknPARtCkDLfLchpefksGeYWiDPNqGCikDAikVf l+sP+G srknPAR+C+DL++chpe ksGeYW+DPNqGC++DAikVf gi|115306| 1248 LISPDG-SRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVF 1293 CnkrfetGvgeTCisptpksvpkRiksWykgkskdkKhvWFgetmegGfk Cn +etG eTCis++p +vp+ k+W++++s++kKhvWFge+m+gGf+ gi|115306| 1294 CN--METG--ETCISANPLNVPR--KHWWTDSSAEKKHVWFGESMDGGFQ 1337 fsYiddelnpeisnvQlTFLRLLSteAsQNiTYhCKNSvAYmDeatGNlk fsY+++el++++ +vQl+FLRLLS++AsQNiTYhCKNS+AYmD+a+GN+k gi|115306| 1338 FSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVK 1387 kAlilmgSnDvElsadgnskFtYtvlGeDGCssrtgewgKTViEyeTkKt kAl lmgSn+ E++a+gnskFtYtvl eDGC+++tgew+KTV+Ey+T+K+ gi|115306| 1388 KALKLMGSNEGEFKAEGNSKFTYTVL-EDGCTKHTGEWSKTVFEYRTRKA 1436 tRLPIvDiApsDiGgedQeFGveiGPVCF<-* RLPIvDiAp+DiGg+dQeFGv++GPVCF gi|115306| 1437 VRLPIVDIAPYDIGGPDQEFGVDVGPVCF 1465 // 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: tem15 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Collagen Collagen triple helix repeat (20 copie 938.0 2.5e-278 18 COLFI Fibrillar collagen C-terminal domain 561.6 5.3e-219 1 DNA_pol3_beta DNA polymerase III beta subunit 7.6 0.39 1 FATC FATC domain 2.6 43 1 Fe_dep_repress Iron dependent repressor 1.9 41 1 TILa TILa domain 0.9 85 1 ANATO Anaphylotoxin-like domain -0.9 46 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TILa 1/1 51 67 .. 23 39 .. 0.9 85 ANATO 1/1 80 85 .. 32 37 .] -0.9 46 Fe_dep_repress 1/1 81 91 .. 120 132 .] 1.9 41 Collagen 1/18 102 139 .. 12 49 .. 20.6 0.00035 Collagen 2/18 168 227 .. 1 60 [] 64.5 3e-16 Collagen 3/18 234 293 .. 1 60 [] 76.5 1.6e-19 Collagen 4/18 294 353 .. 1 60 [] 66.4 9.5e-17 Collagen 5/18 354 413 .. 1 60 [] 65.2 1.9e-16 Collagen 6/18 414 473 .. 1 60 [] 65.6 1.5e-16 Collagen 7/18 474 533 .. 1 60 [] 61.9 1.6e-15 Collagen 8/18 534 593 .. 1 60 [] 67.3 5.2e-17 Collagen 9/18 594 653 .. 1 60 [] 47.2 1.8e-11 Collagen 10/18 654 713 .. 1 60 [] 44.5 9.7e-11 Collagen 11/18 714 773 .. 1 60 [] 56.8 4e-14 Collagen 12/18 777 836 .. 1 60 [] 56.3 5.6e-14 Collagen 13/18 837 896 .. 1 60 [] 50.6 2e-12 Collagen 14/18 897 956 .. 1 60 [] 62.9 8.3e-16 Collagen 15/18 957 1016 .. 1 60 [] 63.2 6.9e-16 Collagen 16/18 1017 1076 .. 1 60 [] 59.0 1e-14 Collagen 17/18 1077 1136 .. 1 60 [] 77.4 9.1e-20 Collagen 18/18 1137 1196 .. 1 60 [] 67.7 4e-17 DNA_pol3_beta 1/1 1225 1247 .. 1 23 [. 7.6 0.39 FATC 1/1 1237 1250 .. 1 14 [. 2.6 43 COLFI 1/1 1248 1465 .. 1 226 [] 561.6 5.3e-219 Alignments of top-scoring domains: TILa: domain 1 of 1, from 51 to 67: score 0.9, E = 85 *->qsCaCtgGaiqCqnFqC<-* q C+C G++ C + C gi|115306| 51 QICVCDSGSVLCDDIIC 67 ANATO: domain 1 of 1, from 80 to 85: score -0.9, E = 46 *->aFlqCC<-* +F +CC gi|115306| 80 PFGECC 85 Fe_dep_repress: domain 1 of 1, from 81 to 91: score 1.9, E = 41 *->peecPhgkpdWIP<-* ++ec++++p +P gi|115306| 81 FGECCAVCP--QP 91 Collagen: domain 1 of 18, from 102 to 139: score 20.6, E = 0.00035 *->pGppGppGppGpaGapGppGppGepGpPGppGppGppG<-* +Gp Gp+G pGp+G pG +G+pG pG+PG+pG pGppG gi|115306| 102 QGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPG 139 Collagen: domain 2 of 18, from 168 to 227: score 64.5, E = 3e-16 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G pGp+GppGppGppG G++G+pG+pG +G+pG+PG++Gp Gp gi|115306| 168 GLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQGPPGEPGQAGPSGP 214 pGppGapGapGpp<-* pGppGa+G+ Gp+ gi|115306| 215 PGPPGAIGPSGPA 227 Collagen: domain 3 of 18, from 234 to 293: score 76.5, E = 1.6e-19 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pG+pG++G+pGppG +Gp+G +G+pG++G++G++G+ G +G+ G+ gi|115306| 234 GRPGRPGERGLPGPPGIKGPAGIPGFPGMKGHRGFDGRNGEKGETGA 280 pGppGapGapGpp<-* pG +G+ G pG++ gi|115306| 281 PGLKGENGLPGEN 293 Collagen: domain 4 of 18, from 294 to 353: score 66.4, E = 9.5e-17 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pGp+Gp+G+pG++G+pG pG+aGa+G+ G++G +G+PGppGppG gi|115306| 294 GAPGPMGPRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGT 340 pGppGapGapGpp<-* +G pG pGa+G++ gi|115306| 341 AGFPGSPGAKGEV 353 Collagen: domain 5 of 18, from 354 to 413: score 65.2, E = 1.9e-16 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp Gp+G+pG++G+pG++G+pGp+G+aGa+GppGppG +G+PG +G++Gp gi|115306| 354 GPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGP 400 pGppGapGapGpp<-* +G pGapG +G++ gi|115306| 401 AGIPGAPGLMGAR 413 Collagen: domain 6 of 18, from 414 to 473: score 65.6, E = 1.5e-16 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp GppGp+G++G+pG +G +G+pG +Ga+G+pGp+Ge+G+ G pG+pG+ gi|115306| 414 GPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERGEAGIPGVPGA 460 pGppGapGapGpp<-* +G++G++G+pG+p gi|115306| 461 KGEDGKDGSPGEP 473 Collagen: domain 7 of 18, from 474 to 533: score 61.9, E = 1.6e-15 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+ G+pG++G++G+pG +Gp+Gp+G pG++Gp+Ge+G+PGp+Gp G+ gi|115306| 474 GANGLPGAAGERGAPGFRGPAGPNGIPGEKGPAGERGAPGPAGPRGA 520 pGppGapGapGpp<-* +G+pG++G pG p gi|115306| 521 AGEPGRDGVPGGP 533 Collagen: domain 8 of 18, from 534 to 593: score 67.3, E = 5.2e-17 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G pG+pG pG +G+pGppG +G+ G pGppG++Gp G+pG++G+ gi|115306| 534 GMRGMPGSPGGPGSDGKPGPPGSQGESGRPGPPGPSGPRGQPGVMGF 580 pGppGapGapGpp<-* pGp+G++GapG++ gi|115306| 581 PGPKGNDGAPGKN 593 Collagen: domain 9 of 18, from 594 to 653: score 47.2, E = 1.8e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G++G pG+pGp+GppG+ G++Gp+G+pGp Gp G++G GppGp G gi|115306| 594 GERGGPGGPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGL 640 pGppGapGapGpp<-* +G pG G+pG++ gi|115306| 641 QGLPGTGGPPGEN 653 Collagen: domain 10 of 18, from 654 to 713: score 44.5, E = 9.7e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pG+pGp+G++G+pG+pG +G+aGapG++GppG +G+PG +G +Gp gi|115306| 654 GKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP 700 pGppGapGapGpp<-* pGp+G +Ga+Gpp gi|115306| 701 PGPEGGKGAAGPP 713 Collagen: domain 11 of 18, from 714 to 773: score 56.8, E = 4e-14 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp GppG +G pG++G+pG++G G +G++G++G pG pG++G pG++Gp gi|115306| 714 GPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGP 760 pGppGapGapGpp<-* +Gp+G++G+pGp+ gi|115306| 761 RGPTGPIGPPGPA 773 Collagen: domain 12 of 18, from 777 to 836: score 56.3, E = 5.6e-14 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +G+ G+pG+pG +Gp+G pG++G+ GppGp+G+pG+PG+ G+pG gi|115306| 777 GDKGEGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGG 823 pGppGapGapGpp<-* +G++GapG++G+ gi|115306| 824 KGERGAPGEKGEG 836 Collagen: domain 13 of 18, from 837 to 896: score 50.6, E = 2e-12 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp GppG +GppG Gp+GppGp+G +G++G+pG pG++G+PG++G pGp gi|115306| 837 GPPGVAGPPGGSGPAGPPGPQGVKGERGSPGGPGAAGFPGARGLPGP 883 pGppGapGapGpp<-* pG G+pG+pGp gi|115306| 884 PGSNGNPGPPGPS 896 Collagen: domain 14 of 18, from 897 to 956: score 62.9, E = 8.3e-16 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G pG+ GppGp+G +G+pG pG +G++G++G pGe+G+PG++GppG+ gi|115306| 897 GSPGKDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGA 943 pGppGapGapGpp<-* pGp G +G G++ gi|115306| 944 PGPLGIAGITGAR 956 Collagen: domain 15 of 18, from 957 to 1016: score 63.2, E = 6.9e-16 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G +GppG pGp+G pGp G +G++G+pG +G +Ge+GpPGp+G pG gi|115306| 957 GLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGLPGL 1003 pGppGapGapGpp<-* +G +G+pG G p gi|115306| 1004 AGTAGEPGRDGNP 1016 Collagen: domain 16 of 18, from 1017 to 1076: score 59.0, E = 1e-14 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G G+pG+ G pG +G++G+ G +GapG pG+pG+pGp Gp+G+ G gi|115306| 1017 GSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPGPPGPVGPAGKSGD 1063 pGppGapGapGpp<-* +G+ G++G++G+p gi|115306| 1064 RGESGPAGPAGAP 1076 Collagen: domain 17 of 18, from 1077 to 1136: score 77.4, E = 9.1e-20 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp Gp+G++G+pGp+Gp+G++G++G++Ga+G +G++G+pG PG+pG pGp gi|115306| 1077 GPAGSRGAPGPQGPRGDKGETGERGAAGIKGHRGFPGNPGAPGSPGP 1123 pGppGapGapGpp<-* +G++Ga+G+pGp+ gi|115306| 1124 AGQQGAIGSPGPA 1136 Collagen: domain 18 of 18, from 1137 to 1196: score 67.7, E = 4e-17 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp Gp+Gp Gp GppG +G +G+pGp G+pGp+G++Ge+G+ G+pG+pG+ gi|115306| 1137 GPRGPVGPSGPPGKDGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQ 1183 pGppGapGapGpp<-* pGppG+pGapGp+ gi|115306| 1184 PGPPGPPGAPGPC 1196 DNA_pol3_beta: domain 1 of 1, from 1225 to 1247: score 7.6, E = 0.39 *->MkFtIeRdaLlkaLqkVarvvsn<-* M F+I++d+++++L+ V + +++ gi|115306| 1225 MDFKINTDEIMTSLKSVNGQIES 1247 FATC: domain 1 of 1, from 1237 to 1250: score 2.6, E = 43 *->epLsvegqvndLIq<-* + +sv+gq+++LI+ gi|115306| 1237 SLKSVNGQIESLIS 1250 COLFI: domain 1 of 1, from 1248 to 1465: score 561.6, E = 5.3e-219 *->lksPeGksrknPARtCkDLfLchpefksGeYWiDPNqGCikDAikVf l+sP+G srknPAR+C+DL++chpe ksGeYW+DPNqGC++DAikVf gi|115306| 1248 LISPDG-SRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVF 1293 CnkrfetGvgeTCisptpksvpkRiksWykgkskdkKhvWFgetmegGfk Cn +etG eTCis++p +vp+ k+W++++s++kKhvWFge+m+gGf+ gi|115306| 1294 CN--METG--ETCISANPLNVPR--KHWWTDSSAEKKHVWFGESMDGGFQ 1337 fsYiddelnpeisnvQlTFLRLLSteAsQNiTYhCKNSvAYmDeatGNlk fsY+++el++++ +vQl+FLRLLS++AsQNiTYhCKNS+AYmD+a+GN+k gi|115306| 1338 FSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVK 1387 kAlilmgSnDvElsadgnskFtYtvlGeDGCssrtgewgKTViEyeTkKt kAl lmgSn+ E++a+gnskFtYtvl eDGC+++tgew+KTV+Ey+T+K+ gi|115306| 1388 KALKLMGSNEGEFKAEGNSKFTYTVL-EDGCTKHTGEWSKTVFEYRTRKA 1436 tRLPIvDiApsDiGgedQeFGveiGPVCF<-* RLPIvDiAp+DiGg+dQeFGv++GPVCF gi|115306| 1437 VRLPIVDIAPYDIGGPDQEFGVDVGPVCF 1465 // 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: tem15 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) 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: Fri Nov 10 14:43:09 2000 Sequence file: tem15 ---------------------------------------- Sequence gi|115306|sp|P02461|CA13_HUMAN (1466 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 1367: NITY Total matches: 1 Matching pattern PS00005 PKC_PHOSPHO_SITE: 233: SGR 560: SGR 980: SGK 1237: SLK 1254: SRK 1361: SSR 1433: TRK Total matches: 7 Matching pattern PS00006 CK2_PHOSPHO_SITE: 38: SYAD 469: SPGE 556: SQGE 796: SPGE 1006: TAGE 1319: SSAE 1411: TVLE 1427: TVFE Total matches: 8 Matching pattern PS00008 MYRISTYL: 36: GQSYAD 58: GSVLCD 139: GICESC 163: GVAVGG 167: GGLAGY 312: GLPGAA 315: GAAGAR 318: GARGND 321: GNDGAR 324: GARGSD 345: GSPGAK 357: GSPGSN 390: GSPGGK 408: GLMGAR 426: GLRGGA 456: GVPGAK 477: GLPGAA 543: GGPGSD 626: GGDKGD 642: GLPGTG 647: GGPPGE 669: GAPGGK 693: GLRGGA 705: GGKGAA 747: GGPGAD 782: GGAPGL 836: GGPPGV 847: GSGPAG 867: GGPGAA 933: GSPGAQ 951: GITGAR 1002: GLAGTA 1014: GNPGSD 1026: GSPGGK 1125: GQQGAI 1198: GGVGAA 1199: GVGAAA 1209: GGEKAG 1243: GQIESL 1394: GSNEGE Total matches: 40 Matching pattern PS00343 GRAM_POS_ANCHORING: 643: LPGTGG Total matches: 1 Matching pattern PS00016 RGD: 1091: RGD Total matches: 1 Matching pattern PS01208 VWFC: 50: CQICVCDSGSVLCDDIICDDQELDCPNPEIPFGECCAVC Total matches: 1 Total no of hits in this sequence: 59 ======================================== 1314 pattern(s) searched in 1 sequence(s), 1466 residues. Total no of hits in all sequences: 59. 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 tem15 ***** 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, 1466 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: tem15 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) 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: tem15 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) 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= gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR (1466 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value POZ Pox virus Zinc finger domain (Also called BTB domain; a... 35 7e-04 PCNA Proliferating Cell nuclear antigen like domain 31 0.008 BRIGHT BRIGHT domain (Alpha helical DNA binding domain) 27 0.15 14-3-3 14-3-3 protein alpha Helical domain 25 0.74 UBA Ubiquitin pathway associated domain 24 1.8 MATH The Meprin associated TRAF homology domain 23 2.1 FYVE Zinc Finger domain involved in PtdIns(3)P binding 23 3.5 >POZ Pox virus Zinc finger domain (Also called BTB domain; a protein-protein interaction domain) Length = 229 Score = 34.9 bits (79), Expect = 7e-04 Identities = 23/248 (9%), Positives = 44/248 (17%), Gaps = 55/248 (22%) Query: 1230 NTDEIMTSLKSVNGQIESLISPDGSRKNPAR---NCRDLKF--------CHPE-----LK 1273 + D L +G L G N + H Sbjct: 2 SGDTC---LCPASGAKPKLSGFKGGGLGNKYVQLNVGGSLYYTTVRALTRHDTMLKAMFS 58 Query: 1274 SG--EYWVDPNQGCKLDAI------KVFCNMETGETCISANPLNVPR-----KHWWTDSS 1320 +G L + + + N + K++ Sbjct: 59 GRMEVL--TDKEGWILIDRCGKHFGTILNYLRDDTITLPQNRQEIKELMAEAKYYLIQ-G 115 Query: 1321 AEKKHVWFGESMDGGFQFSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMD 1380 + + P + + + S + Sbjct: 116 LVNMCQSALQDKK--------DSYQPVCNIPIITSLKEEERLIESSTKPVVKLLYNRSNN 167 Query: 1381 QASGNVKK-ALKLMGSNEGE---FKAEGNSKF--TYTVLEDGCTKHTGEWSKTVFEYRTR 1434 + S L + + G F E C WS + Sbjct: 168 KYSYTSNSDDHLLKNIELFDKLSLRFNGRVLFIKDVIGDEICC------WSFYGQGRKLA 221 Query: 1435 KAVRLPIV 1442 + IV Sbjct: 222 EVCCTSIV 229 >PCNA Proliferating Cell nuclear antigen like domain Length = 280 Score = 31.5 bits (71), Expect = 0.008 Identities = 7/32 (21%), Positives = 14/32 (42%), Gaps = 1/32 (3%) Query: 1212 KAGGFAPY-YGDEPMDFKINTDEIMTSLKSVN 1242 +A F + +E + F+IN ++ L Sbjct: 66 QADVFQEFVIQEESVTFRINLTILLDCLSIFG 97 >BRIGHT BRIGHT domain (Alpha helical DNA binding domain) Length = 172 Score = 27.3 bits (60), Expect = 0.15 Identities = 6/31 (19%), Positives = 7/31 (22%) Query: 886 SNGNPGPPGPSGSPGKDGPPGPAGNTGAPGS 916 G G + P P PG Sbjct: 130 REGRRSSYGQYEAMHNQMPMTPISRPSLPGG 160 Score = 23.0 bits (49), Expect = 2.7 Identities = 11/40 (27%), Positives = 14/40 (34%), Gaps = 3/40 (7%) Query: 367 QRGEPGPQGHAGA---QGPPGPPGINGSPGGKGEMGPAGI 403 + G G A Q P P PGG +M P + Sbjct: 130 REGRRSSYGQYEAMHNQMPMTPISRPSLPGGMQQMSPLAL 169 >14-3-3 14-3-3 protein alpha Helical domain Length = 270 Score = 25.0 bits (54), Expect = 0.74 Identities = 6/24 (25%), Positives = 9/24 (37%) Query: 362 NGAPGQRGEPGPQGHAGAQGPPGP 385 + A G Q +A + P G Sbjct: 240 SAAAAGGNTEGAQENAPSNAPEGE 263 Score = 23.0 bits (49), Expect = 2.9 Identities = 7/27 (25%), Positives = 8/27 (28%) Query: 818 NGEPGGKGERGAPGEKGEGGPPGVAGP 844 + G GA P G A P Sbjct: 240 SAAAAGGNTEGAQENAPSNAPEGEAEP 266 Score = 21.5 bits (45), Expect = 8.9 Identities = 3/25 (12%), Positives = 4/25 (16%) Query: 463 EDGKDGSPGEPGANGLPGAAGERGA 487 GA + G Sbjct: 239 YSAAAAGGNTEGAQENAPSNAPEGE 263 >UBA Ubiquitin pathway associated domain Length = 255 Score = 23.5 bits (50), Expect = 1.8 Identities = 15/52 (28%), Positives = 21/52 (39%) Query: 338 PGTAGFPGSPGAKGEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGIN 389 P TA A+ ++ + G N + G G G A GPPG G+ Sbjct: 80 PSTAATTAEQPAEDDLFAQAAQGGNASSGALGTTGGATDAAQGGPPGSIGLT 131 Score = 22.7 bits (48), Expect = 3.2 Identities = 12/30 (40%), Positives = 14/30 (46%) Query: 814 APGQNGEPGGKGERGAPGEKGEGGPPGVAG 843 A G N G G G + +GGPPG G Sbjct: 100 AQGGNASSGALGTTGGATDAAQGGPPGSIG 129 Score = 22.3 bits (47), Expect = 4.4 Identities = 11/34 (32%), Positives = 14/34 (40%) Query: 584 KGNDGAPGKNGERGGPGGPGPQGPPGKNGETGPQ 617 +G + + G G GG GPPG G T Sbjct: 101 QGGNASSGALGTTGGATDAAQGGPPGSIGLTVED 134 Score = 21.6 bits (45), Expect = 8.6 Identities = 12/28 (42%), Positives = 14/28 (49%) Query: 531 GGPGMRGMPGSPGGPGSDGKPGPPGSQG 558 GG G G+ GG + GPPGS G Sbjct: 102 GGNASSGALGTTGGATDAAQGGPPGSIG 129 Score = 21.2 bits (44), Expect = 9.5 Identities = 19/72 (26%), Positives = 24/72 (32%), Gaps = 1/72 (1%) Query: 896 SGSPGKDGPPGPAGNTGAPG-SPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIAGITG 954 G P P P T A P + + + + AQG + G LG G Sbjct: 58 MGIPENLRQPEPQQQTAAAAEQPSTAATTAEQPAEDDLFAQAAQGGNASSGALGTTGGAT 117 Query: 955 ARGLAGPPGMPG 966 GPPG G Sbjct: 118 DAAQGGPPGSIG 129 >MATH The Meprin associated TRAF homology domain Length = 209 Score = 23.3 bits (50), Expect = 2.1 Identities = 5/23 (21%), Positives = 6/23 (25%) Query: 124 GIPGQPGSPGSPGPPGICESCPT 146 +P P P C T Sbjct: 3 RVPSPPPPAEMSSGPVAESWCYT 25 >FYVE Zinc Finger domain involved in PtdIns(3)P binding Length = 99 Score = 22.8 bits (48), Expect = 3.5 Identities = 12/34 (35%), Positives = 16/34 (46%), Gaps = 4/34 (11%) Query: 58 GSVLCDDIICDDQELDCPNPEIPFGECCAVCPQP 91 G ++C D+ C E PE +CC C QP Sbjct: 10 GKLMCWDMNCKRVET----PEWKTSDCCQKCNQP 39 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 7 Number of calls to ALIGN: 14 Length of query: 1466 Total length of test sequences: 20182 Effective length of test sequences: 16738.0 Effective search space size: 23993297.2 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= gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR (1466 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|1173357 [36..558] Periplasmic binding protein-like II 28 0.72 gi|421277 [11..339] NAD(P)-binding Rossmann-fold domains 28 1.4 gi|2496947 [316..429] Protein kinases (PK), catalytic core 27 2.5 gi|2497951 [161..384] Creatinase/methionine aminopeptidase 25 6.8 >gi|1173357 [36..558] Periplasmic binding protein-like II Length = 523 Score = 28.5 bits (63), Expect = 0.72 Identities = 14/82 (17%), Positives = 23/82 (27%), Gaps = 9/82 (10%) Query: 1339 SYGNPELPEDVLDVQLAFLRLLSSR-------ASQNITYHCKNSIAYMDQASGNVKKALK 1391 + P + DV + R+L A N+TY + +QA Sbjct: 75 PWFTPTRDFNAEDVVFSINRVLGGHNTYLPTLAETNVTYSNPQYRVFHEQARKVRFPYFD 134 Query: 1392 LMGSNEGEF--KAEGNSKFTYT 1411 + NE A + Sbjct: 135 SIKLNEKIKSVTALSPYQVKIE 156 >gi|421277 [11..339] NAD(P)-binding Rossmann-fold domains Length = 329 Score = 27.7 bits (60), Expect = 1.4 Identities = 6/87 (6%), Positives = 15/87 (16%), Gaps = 7/87 (8%) Query: 1293 FCNMETGETCISANPLNV-----PRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPE 1347 + G + NV + + Sbjct: 169 ANYGQHGTAVATVRAGNVIGGGDWALDRIVPDILRAFEQSQPVIIRNPHAI--RPWQHVL 226 Query: 1348 DVLDVQLAFLRLLSSRASQNITYHCKN 1374 + L L + L + ++ Sbjct: 227 EPLSGYLLLAQKLYTDGAEYAEGWNFG 253 >gi|2496947 [316..429] Protein kinases (PK), catalytic core Length = 114 Score = 26.9 bits (58), Expect = 2.5 Identities = 4/79 (5%), Positives = 16/79 (20%) Query: 1262 CRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSSA 1321 K ++KS ++ + ++ + V ++ Sbjct: 14 LHKHKVAQRDMKSDNILLEYDFDDEIPQLVVADFGCALACDNWQVDYESDEVSLGGNAKT 73 Query: 1322 EKKHVWFGESMDGGFQFSY 1340 + + Sbjct: 74 KAPEIATAVPGKNVKVNFE 92 >gi|2497951 [161..384] Creatinase/methionine aminopeptidase Length = 224 Score = 25.3 bits (55), Expect = 6.8 Identities = 5/30 (16%), Positives = 5/30 (16%) Query: 1183 QPGPPGPPGAPGPCCGGVGAAAIAGIGGEK 1212 G G A C E Sbjct: 50 TNGKAGTDLASMYFCSSPRTGTCHIRWSED 79 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 4 Number of calls to ALIGN: 4 Length of query: 1466 Total length of test sequences: 256703 Effective length of test sequences: 211865.0 Effective search space size: 302552198.5 Initial X dropoff for ALIGN: 25.0 bits