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