analysis of sequence from tem10
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPAGDRGPRGERGPPGPPGRDGEDGPTGPPGPPGPPGP
PGLGGNFAAQYDGKGVGLGPGPMGLMGPRGPPGAAGAPGPQGFQGPAGEPGEPGQTGPAGARGPAGPPGK
AGEDGHPGKPGRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGAPGVKGEPGAPGENGTP
GQTGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIGSAGPPGFPGAPGPKGEIGAVGNAGPAGPAG
PRGEVGLPGLSGPVGPPGNPGANGLTGAKGAAGLPGVAGAPGLPGPRGIPGPVGAAGATGARGLVGEPGP
AGSKGESGNKGEPGSAGPQGPPGPSGEEGKRGPNGEAGSAGPPGPPGLRGSPGSRGLPGADGRAGVMGPP
GSRGASGPAGVRGPNGDAGRPGEPGLMGPRGLPGSPGNIGPAGKEGPVGLPGIDGRPGPIGPAGARGEPG
NIGFPGPKGPTGDPGKNGDKGHAGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPAGPPGFQGLPGP
SGPAGEVGKPGERGLHGEFGLPGPAGPRGERGPPGESGAAGPTGPIGSRGPSGPPGPDGNKGEPGVVGAV
GTAGPSGPSGLPGERGAAGIPGGKGEKGEPGLRGEIGNPGRDGARGAHGAVGAPGPAGATGDRGEAGAAG
PAGPAGPRGSPGERGEVGPAGPNGFAGPAGAAGQPGAKGERGAKGPKGENGVVGPTGPVGAAGPAGPNGP
PGPAGSRGDGGPPGMTGFPGAAGRTGPPGPSGISGPPGPPGPAGKEGLRGPRGDQGPVGRTGEVGAVGPP
GFAGEKGPSGEAGTAGPPGTPGPQGLLGAPGILGLPGSRGERGLPGVAGAVGEPGPLGIAGPPGARGPPG
AVGSPGVNGAPGEAGRDGNPGNDGPPGRDGQPGHKGERGYPGNIGPVGAAGAPGPHGPVGPAGKHGNRGE
TGPSGPVGPAGAVGPRGPSGPQGIRGDKGEPGEKGPRGLPGLKGHNGLQGLPGIAGHHGDQGAPGSVGPA
GPRGPAGPSGPAGKDGRTGHPGTVGPAGIRGPQGHQGPAGPPGPPGPPGPPGVSGGGYDFGYDGDFYRAD
QPRSAPSLRPKDYEVDATLKSLNNQIETLLTPEGSRKNPARTCRDLRLSHPEWSSGYYWIDPNQGCTMDA
IKVYCDFSTGETCIRAQPENIPAKNWYRSSKDKKHVWLGETINAGSQFEYNVEGVTSKEMATQLAFMRLL
ANYASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVELVAEGNSRFTYTVLVDGCSKKTNEWGKTIIE
YKTNKPSRLPFLDIAPLDIGGADHEFFVDIGPVCFK
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> tem10gi|1418930|emb|CAA98969.1|
. . . . .
1 MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPAGDRGPRGERGPPGPP 50
_____HHHHHHHHHHHHHHHHHHHHHHHH_____________________
. . . . .
51 GRDGEDGPTGPPGPPGPPGPPGLGGNFAAQYDGKGVGLGPGPMGLMGPRG 100
__________________________EEEE____________________
. . . . .
101 PPGAAGAPGPQGFQGPAGEPGEPGQTGPAGARGPAGPPGKAGEDGHPGKP 150
__________________________________________________
. . . . .
151 GRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGAPGVKGE 200
__________________________________________________
. . . . .
201 PGAPGENGTPGQTGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIG 250
______________________EEE_________________________
. . . . .
251 SAGPPGFPGAPGPKGEIGAVGNAGPAGPAGPRGEVGLPGLSGPVGPPGNP 300
________________EEEE_____________EEE______________
. . . . .
301 GANGLTGAKGAAGLPGVAGAPGLPGPRGIPGPVGAAGATGARGLVGEPGP 350
_________________________________________EEE______
. . . . .
351 AGSKGESGNKGEPGSAGPQGPPGPSGEEGKRGPNGEAGSAGPPGPPGLRG 400
__________________________________________________
. . . . .
401 SPGSRGLPGADGRAGVMGPPGSRGASGPAGVRGPNGDAGRPGEPGLMGPR 450
__________________________________________________
. . . . .
451 GLPGSPGNIGPAGKEGPVGLPGIDGRPGPIGPAGARGEPGNIGFPGPKGP 500
__________________________________________________
. . . . .
501 TGDPGKNGDKGHAGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPAG 550
__________________________________________________
. . . . .
551 PPGFQGLPGPSGPAGEVGKPGERGLHGEFGLPGPAGPRGERGPPGESGAA 600
__________________________________________________
. . . . .
601 GPTGPIGSRGPSGPPGPDGNKGEPGVVGAVGTAGPSGPSGLPGERGAAGI 650
_________________________EEEEEE___________________
. . . . .
651 PGGKGEKGEPGLRGEIGNPGRDGARGAHGAVGAPGPAGATGDRGEAGAAG 700
__________________________________________________
. . . . .
701 PAGPAGPRGSPGERGEVGPAGPNGFAGPAGAAGQPGAKGERGAKGPKGEN 750
__________________________________________________
. . . . .
751 GVVGPTGPVGAAGPAGPNGPPGPAGSRGDGGPPGMTGFPGAAGRTGPPGP 800
__________________________________________________
. . . . .
801 SGISGPPGPPGPAGKEGLRGPRGDQGPVGRTGEVGAVGPPGFAGEKGPSG 850
__________________________________________________
. . . . .
851 EAGTAGPPGTPGPQGLLGAPGILGLPGSRGERGLPGVAGAVGEPGPLGIA 900
______________________________________EEE_________
. . . . .
901 GPPGARGPPGAVGSPGVNGAPGEAGRDGNPGNDGPPGRDGQPGHKGERGY 950
__________________________________________________
. . . . .
951 PGNIGPVGAAGAPGPHGPVGPAGKHGNRGETGPSGPVGPAGAVGPRGPSG 1000
__________________________________________________
. . . . .
1001 PQGIRGDKGEPGEKGPRGLPGLKGHNGLQGLPGIAGHHGDQGAPGSVGPA 1050
__________________________________________________
. . . . .
1051 GPRGPAGPSGPAGKDGRTGHPGTVGPAGIRGPQGHQGPAGPPGPPGPPGP 1100
__________________________________________________
. . . . .
1101 PGVSGGGYDFGYDGDFYRADQPRSAPSLRPKDYEVDATLKSLNNQIETLL 1150
________________EEE________________HHHHHHHHHHHHHH_
. . . . .
1151 TPEGSRKNPARTCRDLRLSHPEWSSGYYWIDPNQGCTMDAIKVYCDFSTG 1200
___________HHHHHHH________EEEE_________EEEEEEE____
. . . . .
1201 ETCIRAQPENIPAKNWYRSSKDKKHVWLGETINAGSQFEYNVEGVTSKEM 1250
_EEEE____________________EEE________EEEEE_____HHHH
. . . . .
1251 ATQLAFMRLLANYASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVEL 1300
HHHHHHHHHHHHHH___EEEE_______________EEEEEEE____EEE
. . . . .
1301 VAEGNSRFTYTVLVDGCSKKTNEWGKTIIEYKTNKPSRLPFLDIAPLDIG 1350
EEE____EEEEEEE____________EEEEEE________EEEEE_____
.
1351 GADHEFFVDIGPVCFK 1366
_____EEEEEEEE___
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
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
-16.81 -0.07 0.00 -0.30 -4.00 0.00 -8.00 0.00 -0.11 -6.57 -1.82 -12.00 -12.00 0.00 0.00 0.00 -61.68
-7.25 -0.13 -0.04 -0.06 -4.00 0.00 -16.00 0.00 -0.32 -6.57 -1.82 -12.00 -12.00 0.00 0.00 0.00 -60.19
ID: tem10gi|1418930|emb|CAA98969.1| AC: xxx Len: 1330 1:I 1317 Sc: -60.19 Pv: 3.730853e-01 NO_GPI_SITE
GPI: learning from protozoa
-17.64 0.00 0.00 -0.09 -4.00 0.00 -12.00 0.00 -0.78 -5.70 -7.14 -12.00 -12.00 0.00 0.00 0.00 -71.34
-16.82 -0.04 0.00 0.00 -4.00 0.00 -8.00 0.00 0.00 -5.70 -7.14 -12.00 -12.00 0.00 0.00 0.00 -65.70
ID: tem10gi|1418930|emb|CAA98969.1| AC: xxx Len: 1330 1:I 1315 Sc: -65.70 Pv: 2.885468e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem10gi|141 0.538 23 Y 0.650 23 Y 0.984 9 Y 0.939 Y
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem10gi|141 0.693 732 Y 0.368 27 Y 0.988 9 Y 0.795 Y
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
tem10gi|141 0.643 486 Y 0.392 321 Y 0.996 12 Y 0.143 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
1-8 MLSFVDTR
tllllavtlclatc 9-22
23-32 QSLQEETVRK
gpagdrgprgergppgppgrdgedgptgpp 33-75
gppgppgppglgg
76-82 NFAAQYD
gkgvglgpgpmglmgprgppgaagapgpqg 83-163
fqgpagepgepgqtgpagargpagppgkag
edghpgkpgrpgergvvgpqg
164-218 ARGFPGTPGLPGFKGIRGHNGLDGLKGQPG
APGVKGEPGAPGENGTPGQTGARGL
pgergrvgapgpagargsdgsvgpvgpagp 219-265
igsagppgfpgapgpkg
266-267 EI
gavgnagpagpagprgevglpglsgpvgpp 268-346
gnpgangltgakgaaglpgvagapglpgpr
gipgpvgaagatgarglvg
347-360 EPGPAGSKGESGNK
gepgsagpqgppgpsgeegkrgpngeagsa 361-410
gppgppglrgspgsrglpga
411-417 DGRAGVM
gppgsrgasgpagvrgp 418-434
435-468 NGDAGRPGEPGLMGPRGLPGSPGNIGPAGK
EGPV
glpgidgrpgpigpagargepg 469-490
491-492 NI
gfpgpkgptgdpgkngdkghaglagargap 493-553
gpdgnngaqgppgpqgvqggkgeqgpagpp
g
554-579 FQGLPGPSGPAGEVGKPGERGLHGEF
glpgpagprgergppgesgaagptgpigsr 580-640
gpsgppgpdgnkgepgvvgavgtagpsgps
g
641-642 LP
gergaagipggkgekgepglrge 643-665
666-668 IGN
pgrdgargahgavgapgpagatgdrgeaga 669-739
agpagpagprgspgergevgpagpngfagp
agaagqpgakg
740-750 ERGAKGPKGEN
gvvgptgpvgaagpagpngppgpag 751-775
776-785 SRGDGGPPGM
tgfpgaagrtgppgpsgisgppgppgpag 786-814
815-846 KEGLRGPRGDQGPVGRTGEVGAVGPPGFAG
EK
gpsgeagtagppgtpgpqgllgapgilglp 847-877
g
878-882 SRGER
glpgvagavgepgplgiagppgargppgav 883-922
gspgvngapg
923-924 EA
grdgnpgndgppgrdgqpg 925-943
944-954 HKGERGYPGNI
gpvgaagapgphgpvgpagkhg 955-976
977-981 NRGET
gpsgpvgpagavgprgpsgp 982-1001
1002-1041 QGIRGDKGEPGEKGPRGLPGLKGHNGLQGL
PGIAGHHGDQ
gapgsvgpagprgpagpsgpag 1042-1063
1064-1080 KDGRTGHPGTVGPAGIR
gpqghqgpagppgppgppgppgvsggg 1081-1107
1108-1366 YDFGYDGDFYRADQPRSAPSLRPKDYEVDA
TLKSLNNQIETLLTPEGSRKNPARTCRDLR
LSHPEWSSGYYWIDPNQGCTMDAIKVYCDF
STGETCIRAQPENIPAKNWYRSSKDKKHVW
LGETINAGSQFEYNVEGVTSKEMATQLAFM
RLLANYASQNITYHCKNSIAYMDEETGNLK
KAVILQGSNDVELVAEGNSRFTYTVLVDGC
SKKTNEWGKTIIEYKTNKPSRLPFLDIAPL
DIGGADHEFFVDIGPVCFK
low complexity regions: SEG 25 3.0 3.3
>tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
1-6 MLSFVD
trtllllavtlclatcqslqeetvr 7-31
32-32 K
gpagdrgprgergppgppgrdgedgptgpp 33-1107
gppgppgppglggnfaaqydgkgvglgpgp
mglmgprgppgaagapgpqgfqgpagepge
pgqtgpagargpagppgkagedghpgkpgr
pgergvvgpqgargfpgtpglpgfkgirgh
ngldglkgqpgapgvkgepgapgengtpgq
tgarglpgergrvgapgpagargsdgsvgp
vgpagpigsagppgfpgapgpkgeigavgn
agpagpagprgevglpglsgpvgppgnpga
ngltgakgaaglpgvagapglpgprgipgp
vgaagatgarglvgepgpagskgesgnkge
pgsagpqgppgpsgeegkrgpngeagsagp
pgppglrgspgsrglpgadgragvmgppgs
rgasgpagvrgpngdagrpgepglmgprgl
pgspgnigpagkegpvglpgidgrpgpigp
agargepgnigfpgpkgptgdpgkngdkgh
aglagargapgpdgnngaqgppgpqgvqgg
kgeqgpagppgfqglpgpsgpagevgkpge
rglhgefglpgpagprgergppgesgaagp
tgpigsrgpsgppgpdgnkgepgvvgavgt
agpsgpsglpgergaagipggkgekgepgl
rgeignpgrdgargahgavgapgpagatgd
rgeagaagpagpagprgspgergevgpagp
ngfagpagaagqpgakgergakgpkgengv
vgptgpvgaagpagpngppgpagsrgdggp
pgmtgfpgaagrtgppgpsgisgppgppgp
agkeglrgprgdqgpvgrtgevgavgppgf
agekgpsgeagtagppgtpgpqgllgapgi
lglpgsrgerglpgvagavgepgplgiagp
pgargppgavgspgvngapgeagrdgnpgn
dgppgrdgqpghkgergypgnigpvgaaga
pgphgpvgpagkhgnrgetgpsgpvgpaga
vgprgpsgpqgirgdkgepgekgprglpgl
kghnglqglpgiaghhgdqgapgsvgpagp
rgpagpsgpagkdgrtghpgtvgpagirgp
qghqgpagppgppgppgppgvsggg
1108-1366 YDFGYDGDFYRADQPRSAPSLRPKDYEVDA
TLKSLNNQIETLLTPEGSRKNPARTCRDLR
LSHPEWSSGYYWIDPNQGCTMDAIKVYCDF
STGETCIRAQPENIPAKNWYRSSKDKKHVW
LGETINAGSQFEYNVEGVTSKEMATQLAFM
RLLANYASQNITYHCKNSIAYMDEETGNLK
KAVILQGSNDVELVAEGNSRFTYTVLVDGC
SKKTNEWGKTIIEYKTNKPSRLPFLDIAPL
DIGGADHEFFVDIGPVCFK
low complexity regions: SEG 45 3.4 3.75
>tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
1-30 MLSFVDTRTLLLLAVTLCLATCQSLQEETV
rkgpagdrgprgergppgppgrdgedgptg 31-1107
ppgppgppgppglggnfaaqydgkgvglgp
gpmglmgprgppgaagapgpqgfqgpagep
gepgqtgpagargpagppgkagedghpgkp
grpgergvvgpqgargfpgtpglpgfkgir
ghngldglkgqpgapgvkgepgapgengtp
gqtgarglpgergrvgapgpagargsdgsv
gpvgpagpigsagppgfpgapgpkgeigav
gnagpagpagprgevglpglsgpvgppgnp
gangltgakgaaglpgvagapglpgprgip
gpvgaagatgarglvgepgpagskgesgnk
gepgsagpqgppgpsgeegkrgpngeagsa
gppgppglrgspgsrglpgadgragvmgpp
gsrgasgpagvrgpngdagrpgepglmgpr
glpgspgnigpagkegpvglpgidgrpgpi
gpagargepgnigfpgpkgptgdpgkngdk
ghaglagargapgpdgnngaqgppgpqgvq
ggkgeqgpagppgfqglpgpsgpagevgkp
gerglhgefglpgpagprgergppgesgaa
gptgpigsrgpsgppgpdgnkgepgvvgav
gtagpsgpsglpgergaagipggkgekgep
glrgeignpgrdgargahgavgapgpagat
gdrgeagaagpagpagprgspgergevgpa
gpngfagpagaagqpgakgergakgpkgen
gvvgptgpvgaagpagpngppgpagsrgdg
gppgmtgfpgaagrtgppgpsgisgppgpp
gpagkeglrgprgdqgpvgrtgevgavgpp
gfagekgpsgeagtagppgtpgpqgllgap
gilglpgsrgerglpgvagavgepgplgia
gppgargppgavgspgvngapgeagrdgnp
gndgppgrdgqpghkgergypgnigpvgaa
gapgphgpvgpagkhgnrgetgpsgpvgpa
gavgprgpsgpqgirgdkgepgekgprglp
glkghnglqglpgiaghhgdqgapgsvgpa
gprgpagpsgpagkdgrtghpgtvgpagir
gpqghqgpagppgppgppgppgvsggg
1108-1366 YDFGYDGDFYRADQPRSAPSLRPKDYEVDA
TLKSLNNQIETLLTPEGSRKNPARTCRDLR
LSHPEWSSGYYWIDPNQGCTMDAIKVYCDF
STGETCIRAQPENIPAKNWYRSSKDKKHVW
LGETINAGSQFEYNVEGVTSKEMATQLAFM
RLLANYASQNITYHCKNSIAYMDEETGNLK
KAVILQGSNDVELVAEGNSRFTYTVLVDGC
SKKTNEWGKTIIEYKTNKPSRLPFLDIAPL
DIGGADHEFFVDIGPVCFK
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
>tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPAgdrgprgergppgppgrdgedgptg
ppgppgppgppgLGGNFAAQYDGKGVGLGPgpmglmgprgppgaagapgpqgfqgpagep
gepgqtgpagargpagppgkagedghpgkpgrpgergvvgpqgargfpgtpglpgfkgir
ghngldglkgqpgapgvkgepgapgengtpgqtgarglpgergrvgapgpagargsdgsv
gpvgpagpigsagppgfpgapgpkgeigavgnagpagpagprgevglpglsgpvgppgnp
gangltgakgaaglpgvagapglpgprgipgpvgaagatgarglvgepgpagskgesgnk
gepgsagpqgppgpsgeegkrgpngeagsagppgppglrgspgsrglpgadgragvmgpp
gsrgasgpagvrgpngdagrpgepglmgprglpgspgnigpagkegpvglpgidgrpgpi
gpagargepgnigfpgpkgptgdpgkngdkghaglagargapgpdgnngaqgppgpqgvq
ggkgeqgpagppgfqglpgpsgpagevgkpgerglhgefglpgpagprgergppgesgaa
gptgpigsrgpsgppgpdgnkgepgvvgavgtagpsgpsglpgergaagipggkgekgep
glrgeignpgrdgargahgavgapgpagatgdrgeagaagpagpagprgspgergevgpa
gpngfagpagaagqpgakgergakgpkgengvvgptgpvgaagpagpngppgpagsrgdg
gppgmtgfpgaagrtgppgpsgisgppgppgpagkeglrgprgdqgpvgrtgevgavgpp
gfagekgpsgeagtagppgtpgpqgllgapgilglpgsrgerglpgvagavgepgplgia
gppgargppgavgspgvngapgeagrdgnpgndgppgrdgqpghkgergypgnigpvgaa
gapgphgpvgpagkhgnrgetgpsgpvgpagavgprgpsgpqgirgdkgepgekgprglp
glkghnglqglpgiaghhgdqgapgsvgpagprgpagpsgpagkdgrtghpgtvgpagir
gpqghqgpagppgppgppgppgvsgggydfgydGDFYRADQPRSAPSLRPKDYEVDATLK
SLNNQIETLLTPEGSRKNPARTCRDLRLSHPEWSSGYYWIDPNQGCTMDAIKVYCDFSTG
ETCIRAQPENIPAKNWYRSSKDKKHVWLGETINAGSQFEYNVEGVTSKEMATQLAFMRLL
ANYASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVELVAEGNSRFTYTVLVDGCSKK
TNEWGKTIIEYKTNKPSRLPFLDIAPLDIGGADHEFFVDIGPVCFK
1 - 35 MLSFVDTRTL LLLAVTLCLA TCQSLQEETV RKGPA
36 - 72 gdrgp rgergppgpp grdgedgptg ppgppgppgp pg
73 - 90 LGGNFAAQ YDGKGVGLGP
91 - 1113 gpmglmgprg ppgaagapgp qgfqgpagep gepgqtgpag argpagppgk agedghpgkp
grpgergvvg pqgargfpgt pglpgfkgir ghngldglkg qpgapgvkge pgapgengtp
gqtgarglpg ergrvgapgp agargsdgsv gpvgpagpig sagppgfpga pgpkgeigav
gnagpagpag prgevglpgl sgpvgppgnp gangltgakg aaglpgvaga pglpgprgip
gpvgaagatg arglvgepgp agskgesgnk gepgsagpqg ppgpsgeegk rgpngeagsa
gppgppglrg spgsrglpga dgragvmgpp gsrgasgpag vrgpngdagr pgepglmgpr
glpgspgnig pagkegpvgl pgidgrpgpi gpagargepg nigfpgpkgp tgdpgkngdk
ghaglagarg apgpdgnnga qgppgpqgvq ggkgeqgpag ppgfqglpgp sgpagevgkp
gerglhgefg lpgpagprge rgppgesgaa gptgpigsrg psgppgpdgn kgepgvvgav
gtagpsgpsg lpgergaagi pggkgekgep glrgeignpg rdgargahga vgapgpagat
gdrgeagaag pagpagprgs pgergevgpa gpngfagpag aagqpgakge rgakgpkgen
gvvgptgpvg aagpagpngp pgpagsrgdg gppgmtgfpg aagrtgppgp sgisgppgpp
gpagkeglrg prgdqgpvgr tgevgavgpp gfagekgpsg eagtagppgt pgpqgllgap
gilglpgsrg erglpgvaga vgepgplgia gppgargppg avgspgvnga pgeagrdgnp
gndgppgrdg qpghkgergy pgnigpvgaa gapgphgpvg pagkhgnrge tgpsgpvgpa
gavgprgpsg pqgirgdkge pgekgprglp glkghnglqg lpgiaghhgd qgapgsvgpa
gprgpagpsg pagkdgrtgh pgtvgpagir gpqghqgpag ppgppgppgp pgvsgggydf
gyd
1114 - 1366 GDFYRAD QPRSAPSLRP KDYEVDATLK SLNNQIETLL TPEGSRKNPA RTCRDLRLSH PEW
SSGYYWI DPNQGCTMDA IKVYCDFSTG ETCIRAQPEN IPAKNWYRSS KDKKHVWLGE TIN
AGSQFEY NVEGVTSKEM ATQLAFMRLL ANYASQNITY HCKNSIAYMD EETGNLKKAV ILQ
GSNDVEL VAEGNSRFTY TVLVDGCSKK TNEWGKTIIE YKTNKPSRLP FLDIAPLDIG GAD
HEFFVDI GPVCFK
low complexity regions: DUST
>tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPAGDRGPRGERGPPGPPGRDGEDGPTG
PPGPPGPPGPPGLGGNFAAQYDGKGVGLGPGPMGLMGPRGPPGAAGAPGPQGFQGPAGEP
GEPGQTGPAGARGPAGPPGKAGEDGHPGKPGRPGERGVVGPQGARGFPGTPGLPGFKGIR
GHNGLDGLKGQPGAPGVKGEPGAPGENGTPGQTGARGLPGERGRVGAPGPAGARGSDGSV
GPVGPAGPIGSAGPPGFPGAPGPKGEIGAVGNAGPAGPAGPRGEVGLPGLSGPVGPPGNP
GANGLTGAKGAAGLPGVAGAPGLPGPRGIPGPVGAAGATGARGLVGEPGPAGSKGESGNK
GEPGSAGPQGPPGPSGEEGKRGPNGEAGSAGPPGPPGLRGSPGSRGLPGADGRAGVMGPP
GSRGASGPAGVRGPNGDAGRPGEPGLMGPRGLPGSPGNIGPAGKEGPVGLPGIDGRPGPI
GPAGARGEPGNIGFPGPKGPTGDPGKNGDKGHAGLAGARGAPGPDGNNGAQGPPGPQGVQ
GGKGEQGPAGPPGFQGLPGPSGPAGEVGKPGERGLHGEFGLPGPAGPRGERGPPGESGAA
GPTGPIGSRGPSGPPGPDGNKGEPGVVGAVGTAGPSGPSGLPGERGAAGIPGGKGEKGEP
GLRGEIGNPGRDGARGAHGAVGAPGPAGATGDRGEAGAAGPAGPAGPRGSPGERGEVGPA
GPNGFAGPAGAAGQPGAKGERGAKGPKGENGVVGPTGPVGAAGPAGPNGPPGPAGSRGDG
GPPGMTGFPGAAGRTGPPGPSGISGPPGPPGPAGKEGLRGPRGDQGPVGRTGEVGAVGPP
GFAGEKGPSGEAGTAGPPGTPGPQGLLGAPGILGLPGSRGERGLPGVAGAVGEPGPLGIA
GPPGARGPPGAVGSPGVNGAPGEAGRDGNPGNDGPPGRDGQPGHKGERGYPGNIGPVGAA
GAPGPHGPVGPAGKHGNRGETGPSGPVGPAGAVGPRGPSGPQGIRGDKGEPGEKGPRGLP
GLKGHNGLQGLPGIAGHHGDQGAPGSVGPAGPRGPAGPSGPAGKDGRTGHPGTVGPAGIR
GPQGHQGPAGPPGPPGPPGPPGVSGGGYDFGYDGDFYRADQPRSAPSLRPKDYEVDATLK
SLNNQIETLLTPEGSRKNPARTCRDLRLSHPEWSSGYYWIDPNQGCTMDAIKVYCDFSTG
ETCIRAQPENIPAKNWYRSSKDKKHVWLGETINAGSQFEYNVEGVTSKEMATQLAFMRLL
ANYASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVELVAEGNSRFTYTVLVDGCSKK
TNEWGKTIIEYKTNKPSRLPFLDIAPLDIGGADHEFFVDIGPVCFK
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for tem10gi|1418930|emb|CAA98969.1|
sequence: 1330 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MLSFVDTRTL LLLAVTLCLA TCQSLQEETV RKGPAGDRGP RGERGPPGPP GRDGEDGPTG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
PPGPPGPPGP PGLGGNFAAQ YDGKGVGLGP GPMGLMGPRG PPGAAGAPGP QGFQGPAGEP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GEPGQTGPAG ARGPAGPPGK AGEDGHPGKP GRPGERGVVG PQGARGFPGT PGLPGFKGIR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GHNGLDGLKG QPGAPGVKGE PGAPGENGTP GQTGARGLPG ERGRVGAPGP AGARGSDGSV
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GPVGPAGPIG SAGPPGFPGA PGPKGEIGAV GNAGPAGPAG PRGEVGLPGL SGPVGPPGNP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GANGLTGAKG AAGLPGVAGA PGLPGPRGIP GPVGAAGATG ARGLVGEPGP AGSKGESGNK
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GEPGSAGPQG PPGPSGEEGK RGPNGEAGSA GPPGPPGLRG SPGSRGLPGA DGRAGVMGPP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GSRGASGPAG VRGPNGDAGR PGEPGLMGPR GLPGSPGNIG PAGKEGPVGL PGIDGRPGPI
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GPAGARGEPG NIGFPGPKGP TGDPGKNGDK GHAGLAGARG APGPDGNNGA QGPPGPQGVQ
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GGKGEQGPAG PPGFQGLPGP SGPAGEVGKP GERGLHGEFG LPGPAGPRGE RGPPGESGAA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GPTGPIGSRG PSGPPGPDGN KGEPGVVGAV GTAGPSGPSG LPGERGAAGI PGGKGEKGEP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GLRGEIGNPG RDGARGAHGA VGAPGPAGAT GDRGEAGAAG PAGPAGPRGS PGERGEVGPA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GPNGFAGPAG AAGQPGAKGE RGAKGPKGEN GVVGPTGPVG AAGPAGPNGP PGPAGSRGDG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GPPGMTGFPG AAGRTGPPGP SGISGPPGPP GPAGKEGLRG PRGDQGPVGR TGEVGAVGPP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GFAGEKGPSG EAGTAGPPGT PGPQGLLGAP GILGLPGSRG ERGLPGVAGA VGEPGPLGIA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GPPGARGPPG AVGSPGVNGA PGEAGRDGNP GNDGPPGRDG QPGHKGERGY PGNIGPVGAA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GAPGPHGPVG PAGKHGNRGE TGPSGPVGPA GAVGPRGPSG PQGIRGDKGE PGEKGPRGLP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GLKGHNGLQG LPGIAGHHGD QGAPGSVGPA GPRGPAGPSG PAGKDGRTGH PGTVGPAGIR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GPQGHQGPAG PPGPPGPPGP PGVSGGGYDF GYDGDFYRAD QPRSAPSLRP KDYEVDATLK
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~8888888 * 14 M'95 -w local
. | . | . | . | . | . 1200
SLNNQIETLL TPEGSRKNPA RTCRDLRLSH PEWSSGYYWI DPNQGCTMDA IKVYCDFSTG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
8888888888 6~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 1260
ETCIRAQPEN IPAKNWYRSS KDKKHVWLGE TINAGSQFEY NVEGVTSKEM ATQLAFMRLL
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
ANYASQNITY HCKNSIAYMD EETGNLKKAV ILQGSNDVEL VAEGNSRFTY TVLVDGCSKK
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. |
TNEWGKTIIE
~~~~~~~~~~
----------
~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem10.___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: tem10.___inter___
(1 sequences)
MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPAGDRGPRGERGPPGPP
GRDGEDGPTGPPGPPGPPGPPGLGGNFAAQYDGKGVGLGPGPMGLMGPRG
PPGAAGAPGPQGFQGPAGEPGEPGQTGPAGARGPAGPPGKAGEDGHPGKP
GRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGAPGVKGE
PGAPGENGTPGQTGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIG
SAGPPGFPGAPGPKGEIGAVGNAGPAGPAGPRGEVGLPGLSGPVGPPGNP
GANGLTGAKGAAGLPGVAGAPGLPGPRGIPGPVGAAGATGARGLVGEPGP
AGSKGESGNKGEPGSAGPQGPPGPSGEEGKRGPNGEAGSAGPPGPPGLRG
SPGSRGLPGADGRAGVMGPPGSRGASGPAGVRGPNGDAGRPGEPGLMGPR
GLPGSPGNIGPAGKEGPVGLPGIDGRPGPIGPAGARGEPGNIGFPGPKGP
TGDPGKNGDKGHAGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPAG
PPGFQGLPGPSGPAGEVGKPGERGLHGEFGLPGPAGPRGERGPPGESGAA
GPTGPIGSRGPSGPPGPDGNKGEPGVVGAVGTAGPSGPSGLPGERGAAGI
PGGKGEKGEPGLRGEIGNPGRDGARGAHGAVGAPGPAGATGDRGEAGAAG
PAGPAGPRGSPGERGEVGPAGPNGFAGPAGAAGQPGAKGERGAKGPKGEN
GVVGPTGPVGAAGPAGPNGPPGPAGSRGDGGPPGMTGFPGAAGRTGPPGP
SGISGPPGPPGPAGKEGLRGPRGDQGPVGRTGEVGAVGPPGFAGEKGPSG
EAGTAGPPGTPGPQGLLGAPGILGLPGSRGERGLPGVAGAVGEPGPLGIA
GPPGARGPPGAVGSPGVNGAPGEAGRDGNPGNDGPPGRDGQPGHKGERGY
PGNIGPVGAAGAPGPHGPVGPAGKHGNRGETGPSGPVGPAGAVGPRGPSG
PQGIRGDKGEPGEKGPRGLPGLKGHNGLQGLPGIAGHHGDQGAPGSVGPA
GPRGPAGPSGPAGKDGRTGHPGTVGPAGIRGPQGHQGPAGPPGPPGPPGP
PGVSGGGYDFGYDGDFYRADQPRSAPSLRPKDYEVDATLKSLNNQIETLL
TPEGSRKNPARTCRDLRLSHPEWSSGYYWIDPNQGCTMDAIKVYCDFSTG
ETCIRAQPENIPAKNWYRSSKDKKHVWLGETINAGSQFEYNVEGVTSKEM
ATQLAFMRLLANYASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVEL
VAEGNSRFTYTVLVDGCSKKTNEWGKTIIEYKTNKPSRLPFLDIAPLDIG
GADHEFFVDIGPVCFK
(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 16 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 7 27 1.247 Certain
2 238 258 1.042 Certain
3 306 326 0.850 Putative
4 623 643 1.052 Certain
5 750 770 0.813 Putative
6 858 878 1.015 Certain
7 883 903 0.743 Putative
8 953 973 0.713 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3 4 6 7 8
Loop length 6 210 47 296 214 4 49 393
K+R profile 2.00 3.00 + 5.00
+ + 2.00 +
CYT-EXT prof - - 0.59 -
0.52 0.67 - 0.90
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 8.00
Tm probability: 0.06
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -1.49
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 6 7
Loop length 6 210 47 296 106 87 4 463
K+R profile 2.00 3.00 + 2.00
+ + + +
CYT-EXT prof - - 0.25 -
0.52 0.67 0.70 0.94
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 7.00
Tm probability: 0.12
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -2.57
-> Orientation: N-in
----------------------------------------------------------------------
Structure 3
Transmembrane segments included in this structure:
Segment 1 2 4 5 6 7 8
Loop length 6 210 364 106 87 4 49 393
K+R profile 2.00 + + 5.00
+ + 2.00 +
CYT-EXT prof - 0.72 0.70 -
0.52 0.25 - 0.90
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 5.00
Tm probability: 0.05
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.26
-> Orientation: N-in
----------------------------------------------------------------------
Structure 4
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 6 8
Loop length 6 210 47 296 106 87 74 393
K+R profile 2.00 3.00 + +
+ + + +
CYT-EXT prof - - 0.25 0.69
0.52 0.67 0.70 0.90
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 5.00
Tm probability: 0.09
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -1.84
-> Orientation: N-in
----------------------------------------------------------------------
Structure 5
Transmembrane segments included in this structure:
Segment 1 2 3 4 6 8
Loop length 6 210 47 296 214 74 393
K+R profile 2.00 3.00 + +
+ + +
CYT-EXT prof - - 0.59 0.90
0.52 0.67 0.69
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 5.00
Tm probability: 0.18
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.38
-> Orientation: N-in
----------------------------------------------------------------------
Structure 6
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 6
Loop length 6 210 47 296 106 87 488
K+R profile 2.00 3.00 + +
+ + +
CYT-EXT prof - - 0.25 0.92
0.52 0.67 0.70
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 5.00
Tm probability: 0.33
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.71
-> Orientation: N-in
----------------------------------------------------------------------
Structure 7
Transmembrane segments included in this structure:
Segment 1 2 3 4 6
Loop length 6 210 47 296 214 488
K+R profile 2.00 3.00 +
+ + +
CYT-EXT prof - - 0.59
0.52 0.67 0.92
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 5.00
Tm probability: 0.63
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -1.51
-> Orientation: N-in
----------------------------------------------------------------------
Structure 8
Transmembrane segments included in this structure:
Segment 1 2 4 6 7
Loop length 6 210 364 214 4 463
K+R profile 2.00 + 2.00
+ + +
CYT-EXT prof - 0.72 -
0.52 0.59 0.94
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 4.00
Tm probability: 0.36
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -1.33
-> Orientation: N-in
----------------------------------------------------------------------
Structure 9
Transmembrane segments included in this structure:
Segment 1 2 3 4 6 7
Loop length 6 210 47 296 214 4 463
K+R profile 2.00 3.00 + +
+ + 2.00
CYT-EXT prof - - 0.59 0.94
0.52 0.67 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 3.00
Tm probability: 0.22
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 0.35
-> Orientation: N-out
----------------------------------------------------------------------
Structure 10
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 6 7 8
Loop length 6 210 47 296 106 87 4 49 393
K+R profile 2.00 3.00 + 2.00 +
+ + + 5.00
CYT-EXT prof - - 0.25 - 0.90
0.52 0.67 0.70 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.03
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.73
-> Orientation: N-in
----------------------------------------------------------------------
Structure 11
Transmembrane segments included in this structure:
Segment 1 2 4 5 6 8
Loop length 6 210 364 106 87 74 393
K+R profile 2.00 + + +
+ + +
CYT-EXT prof - 0.72 0.70 0.90
0.52 0.25 0.69
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.15
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 0.85
-> Orientation: N-out
----------------------------------------------------------------------
Structure 12
Transmembrane segments included in this structure:
Segment 1 2 4 6 8
Loop length 6 210 364 214 74 393
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.72 0.69
0.52 0.59 0.90
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.28
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.60
-> Orientation: N-in
----------------------------------------------------------------------
Structure 13
Transmembrane segments included in this structure:
Segment 1 2 4 5 6
Loop length 6 210 364 106 87 488
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.72 0.70
0.52 0.25 0.92
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.53
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.28
-> Orientation: N-in
----------------------------------------------------------------------
Structure 14
Transmembrane segments included in this structure:
Segment 1 2 4 6
Loop length 6 210 364 214 488
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.72 0.92
0.52 0.59
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 0.53
-> Orientation: N-out
----------------------------------------------------------------------
Structure 15
Transmembrane segments included in this structure:
Segment 1 2 4 6 7 8
Loop length 6 210 364 214 4 49 393
K+R profile 2.00 + 2.00 +
+ + 5.00
CYT-EXT prof - 0.72 - 0.90
0.52 0.59 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -1.00
Tm probability: 0.10
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 0.51
-> Orientation: N-out
----------------------------------------------------------------------
Structure 16
Transmembrane segments included in this structure:
Segment 1 2 4 5 6 7
Loop length 6 210 364 106 87 4 463
K+R profile 2.00 + + +
+ + 2.00
CYT-EXT prof - 0.72 0.70 0.94
0.52 0.25 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 0.00
Tm probability: 0.19
-> Orientation: undecided
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 1.58
-> Orientation: N-out
----------------------------------------------------------------------
"tem10" 1366
7 27 #t 1.24687
238 258 #t 1.04167
306 326 #f 0.85
623 643 #t 1.05208
750 770 #f 0.8125
858 878 #t 1.01458
883 903 #f 0.742708
953 973 #f 0.7125
************************************
*TOPPREDM with prokaryotic function*
************************************
tem10.___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: tem10.___inter___
(1 sequences)
MLSFVDTRTLLLLAVTLCLATCQSLQEETVRKGPAGDRGPRGERGPPGPP
GRDGEDGPTGPPGPPGPPGPPGLGGNFAAQYDGKGVGLGPGPMGLMGPRG
PPGAAGAPGPQGFQGPAGEPGEPGQTGPAGARGPAGPPGKAGEDGHPGKP
GRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGAPGVKGE
PGAPGENGTPGQTGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIG
SAGPPGFPGAPGPKGEIGAVGNAGPAGPAGPRGEVGLPGLSGPVGPPGNP
GANGLTGAKGAAGLPGVAGAPGLPGPRGIPGPVGAAGATGARGLVGEPGP
AGSKGESGNKGEPGSAGPQGPPGPSGEEGKRGPNGEAGSAGPPGPPGLRG
SPGSRGLPGADGRAGVMGPPGSRGASGPAGVRGPNGDAGRPGEPGLMGPR
GLPGSPGNIGPAGKEGPVGLPGIDGRPGPIGPAGARGEPGNIGFPGPKGP
TGDPGKNGDKGHAGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPAG
PPGFQGLPGPSGPAGEVGKPGERGLHGEFGLPGPAGPRGERGPPGESGAA
GPTGPIGSRGPSGPPGPDGNKGEPGVVGAVGTAGPSGPSGLPGERGAAGI
PGGKGEKGEPGLRGEIGNPGRDGARGAHGAVGAPGPAGATGDRGEAGAAG
PAGPAGPRGSPGERGEVGPAGPNGFAGPAGAAGQPGAKGERGAKGPKGEN
GVVGPTGPVGAAGPAGPNGPPGPAGSRGDGGPPGMTGFPGAAGRTGPPGP
SGISGPPGPPGPAGKEGLRGPRGDQGPVGRTGEVGAVGPPGFAGEKGPSG
EAGTAGPPGTPGPQGLLGAPGILGLPGSRGERGLPGVAGAVGEPGPLGIA
GPPGARGPPGAVGSPGVNGAPGEAGRDGNPGNDGPPGRDGQPGHKGERGY
PGNIGPVGAAGAPGPHGPVGPAGKHGNRGETGPSGPVGPAGAVGPRGPSG
PQGIRGDKGEPGEKGPRGLPGLKGHNGLQGLPGIAGHHGDQGAPGSVGPA
GPRGPAGPSGPAGKDGRTGHPGTVGPAGIRGPQGHQGPAGPPGPPGPPGP
PGVSGGGYDFGYDGDFYRADQPRSAPSLRPKDYEVDATLKSLNNQIETLL
TPEGSRKNPARTCRDLRLSHPEWSSGYYWIDPNQGCTMDAIKVYCDFSTG
ETCIRAQPENIPAKNWYRSSKDKKHVWLGETINAGSQFEYNVEGVTSKEM
ATQLAFMRLLANYASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVEL
VAEGNSRFTYTVLVDGCSKKTNEWGKTIIEYKTNKPSRLPFLDIAPLDIG
GADHEFFVDIGPVCFK
(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 16 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 7 27 1.247 Certain
2 238 258 1.042 Certain
3 306 326 0.850 Putative
4 623 643 1.052 Certain
5 750 770 0.813 Putative
6 858 878 1.015 Certain
7 883 903 0.743 Putative
8 953 973 0.713 Putative
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3 4 6 7 8
Loop length 6 210 47 296 214 4 49 393
K+R profile 1.00 3.00 + 5.00
+ + 2.00 +
CYT-EXT prof - - 0.59 -
0.52 0.67 - 0.90
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 7.00
Tm probability: 0.06
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -1.49
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 6 7
Loop length 6 210 47 296 106 87 4 463
K+R profile 1.00 3.00 + 2.00
+ + + +
CYT-EXT prof - - 0.25 -
0.52 0.67 0.70 0.94
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 6.00
Tm probability: 0.12
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -2.57
-> Orientation: N-in
----------------------------------------------------------------------
Structure 3
Transmembrane segments included in this structure:
Segment 1 2 4 5 6 7 8
Loop length 6 210 364 106 87 4 49 393
K+R profile 1.00 + + 5.00
+ + 2.00 +
CYT-EXT prof - 0.72 0.70 -
0.52 0.25 - 0.90
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 4.00
Tm probability: 0.05
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.26
-> Orientation: N-in
----------------------------------------------------------------------
Structure 4
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 6 8
Loop length 6 210 47 296 106 87 74 393
K+R profile 1.00 3.00 + +
+ + + +
CYT-EXT prof - - 0.25 0.69
0.52 0.67 0.70 0.90
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 4.00
Tm probability: 0.09
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -1.84
-> Orientation: N-in
----------------------------------------------------------------------
Structure 5
Transmembrane segments included in this structure:
Segment 1 2 3 4 6 8
Loop length 6 210 47 296 214 74 393
K+R profile 1.00 3.00 + +
+ + +
CYT-EXT prof - - 0.59 0.90
0.52 0.67 0.69
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 4.00
Tm probability: 0.18
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.38
-> Orientation: N-in
----------------------------------------------------------------------
Structure 6
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 6
Loop length 6 210 47 296 106 87 488
K+R profile 1.00 3.00 + +
+ + +
CYT-EXT prof - - 0.25 0.92
0.52 0.67 0.70
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 4.00
Tm probability: 0.33
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.71
-> Orientation: N-in
----------------------------------------------------------------------
Structure 7
Transmembrane segments included in this structure:
Segment 1 2 3 4 6
Loop length 6 210 47 296 214 488
K+R profile 1.00 3.00 +
+ + +
CYT-EXT prof - - 0.59
0.52 0.67 0.92
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 4.00
Tm probability: 0.63
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -1.51
-> Orientation: N-in
----------------------------------------------------------------------
Structure 8
Transmembrane segments included in this structure:
Segment 1 2 4 6 7
Loop length 6 210 364 214 4 463
K+R profile 1.00 + 2.00
+ + +
CYT-EXT prof - 0.72 -
0.52 0.59 0.94
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 3.00
Tm probability: 0.36
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -1.33
-> Orientation: N-in
----------------------------------------------------------------------
Structure 9
Transmembrane segments included in this structure:
Segment 1 2 4 6 7 8
Loop length 6 210 364 214 4 49 393
K+R profile 1.00 + 2.00 +
+ + 5.00
CYT-EXT prof - 0.72 - 0.90
0.52 0.59 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -2.00
Tm probability: 0.10
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 0.51
-> Orientation: N-out
----------------------------------------------------------------------
Structure 10
Transmembrane segments included in this structure:
Segment 1 2 3 4 6 7
Loop length 6 210 47 296 214 4 463
K+R profile 1.00 3.00 + +
+ + 2.00
CYT-EXT prof - - 0.59 0.94
0.52 0.67 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.22
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 0.35
-> Orientation: N-out
----------------------------------------------------------------------
Structure 11
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 6 7 8
Loop length 6 210 47 296 106 87 4 49 393
K+R profile 1.00 3.00 + 2.00 +
+ + + 5.00
CYT-EXT prof - - 0.25 - 0.90
0.52 0.67 0.70 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 0.03
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.73
-> Orientation: N-in
----------------------------------------------------------------------
Structure 12
Transmembrane segments included in this structure:
Segment 1 2 4 5 6 8
Loop length 6 210 364 106 87 74 393
K+R profile 1.00 + + +
+ + +
CYT-EXT prof - 0.72 0.70 0.90
0.52 0.25 0.69
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 0.15
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 0.85
-> Orientation: N-out
----------------------------------------------------------------------
Structure 13
Transmembrane segments included in this structure:
Segment 1 2 4 6 8
Loop length 6 210 364 214 74 393
K+R profile 1.00 + +
+ + +
CYT-EXT prof - 0.72 0.69
0.52 0.59 0.90
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 0.28
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.60
-> Orientation: N-in
----------------------------------------------------------------------
Structure 14
Transmembrane segments included in this structure:
Segment 1 2 4 5 6 7
Loop length 6 210 364 106 87 4 463
K+R profile 1.00 + + +
+ + 2.00
CYT-EXT prof - 0.72 0.70 0.94
0.52 0.25 -
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -1.00
Tm probability: 0.19
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 1.58
-> Orientation: N-out
----------------------------------------------------------------------
Structure 15
Transmembrane segments included in this structure:
Segment 1 2 4 5 6
Loop length 6 210 364 106 87 488
K+R profile 1.00 + +
+ + +
CYT-EXT prof - 0.72 0.70
0.52 0.25 0.92
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 0.53
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: -0.28
-> Orientation: N-in
----------------------------------------------------------------------
Structure 16
Transmembrane segments included in this structure:
Segment 1 2 4 6
Loop length 6 210 364 214 488
K+R profile 1.00 + +
+ +
CYT-EXT prof - 0.72 0.92
0.52 0.59
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 1.00
Tm probability: 1.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): -1.00
(NEG-POS)/(NEG+POS): 0.0000
NEG: 1.0000
POS: 1.0000
-> Orientation: N-out
CYT-EXT difference: 0.53
-> Orientation: N-out
----------------------------------------------------------------------
"tem10" 1366
7 27 #t 1.24687
238 258 #t 1.04167
306 326 #f 0.85
623 643 #t 1.05208
750 770 #f 0.8125
858 878 #t 1.01458
883 903 #f 0.742708
953 973 #f 0.7125
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem10.___saps___
SAPS. Version of April 11, 1996.
Date run: Tue Oct 31 14:25:59 2000
File: /people/maria/tem10.___saps___
ID tem10gi|1418930|emb|CAA98969.1|
DE prepro-alpha2(I) collagen [Homo sapiens]
number of residues: 1366; molecular weight: 129.3 kdal
1 MLSFVDTRTL LLLAVTLCLA TCQSLQEETV RKGPAGDRGP RGERGPPGPP GRDGEDGPTG
61 PPGPPGPPGP PGLGGNFAAQ YDGKGVGLGP GPMGLMGPRG PPGAAGAPGP QGFQGPAGEP
121 GEPGQTGPAG ARGPAGPPGK AGEDGHPGKP GRPGERGVVG PQGARGFPGT PGLPGFKGIR
181 GHNGLDGLKG QPGAPGVKGE PGAPGENGTP GQTGARGLPG ERGRVGAPGP AGARGSDGSV
241 GPVGPAGPIG SAGPPGFPGA PGPKGEIGAV GNAGPAGPAG PRGEVGLPGL SGPVGPPGNP
301 GANGLTGAKG AAGLPGVAGA PGLPGPRGIP GPVGAAGATG ARGLVGEPGP AGSKGESGNK
361 GEPGSAGPQG PPGPSGEEGK RGPNGEAGSA GPPGPPGLRG SPGSRGLPGA DGRAGVMGPP
421 GSRGASGPAG VRGPNGDAGR PGEPGLMGPR GLPGSPGNIG PAGKEGPVGL PGIDGRPGPI
481 GPAGARGEPG NIGFPGPKGP TGDPGKNGDK GHAGLAGARG APGPDGNNGA QGPPGPQGVQ
541 GGKGEQGPAG PPGFQGLPGP SGPAGEVGKP GERGLHGEFG LPGPAGPRGE RGPPGESGAA
601 GPTGPIGSRG PSGPPGPDGN KGEPGVVGAV GTAGPSGPSG LPGERGAAGI PGGKGEKGEP
661 GLRGEIGNPG RDGARGAHGA VGAPGPAGAT GDRGEAGAAG PAGPAGPRGS PGERGEVGPA
721 GPNGFAGPAG AAGQPGAKGE RGAKGPKGEN GVVGPTGPVG AAGPAGPNGP PGPAGSRGDG
781 GPPGMTGFPG AAGRTGPPGP SGISGPPGPP GPAGKEGLRG PRGDQGPVGR TGEVGAVGPP
841 GFAGEKGPSG EAGTAGPPGT PGPQGLLGAP GILGLPGSRG ERGLPGVAGA VGEPGPLGIA
901 GPPGARGPPG AVGSPGVNGA PGEAGRDGNP GNDGPPGRDG QPGHKGERGY PGNIGPVGAA
961 GAPGPHGPVG PAGKHGNRGE TGPSGPVGPA GAVGPRGPSG PQGIRGDKGE PGEKGPRGLP
1021 GLKGHNGLQG LPGIAGHHGD QGAPGSVGPA GPRGPAGPSG PAGKDGRTGH PGTVGPAGIR
1081 GPQGHQGPAG PPGPPGPPGP PGVSGGGYDF GYDGDFYRAD QPRSAPSLRP KDYEVDATLK
1141 SLNNQIETLL TPEGSRKNPA RTCRDLRLSH PEWSSGYYWI DPNQGCTMDA IKVYCDFSTG
1201 ETCIRAQPEN IPAKNWYRSS KDKKHVWLGE TINAGSQFEY NVEGVTSKEM ATQLAFMRLL
1261 ANYASQNITY HCKNSIAYMD EETGNLKKAV ILQGSNDVEL VAEGNSRFTY TVLVDGCSKK
1321 TNEWGKTIIE YKTNKPSRLP FLDIAPLDIG GADHEFFVDI GPVCFK
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A :130( 9.5%); C : 9( 0.7%); D : 43( 3.1%); E : 66( 4.8%); F : 22( 1.6%)
G++:381(27.9%); H : 17( 1.2%); I : 32( 2.3%); K : 50( 3.7%); L- : 61( 4.5%)
M- : 10( 0.7%); N : 41( 3.0%); P++:230(16.8%); Q : 32( 2.3%); R : 72( 5.3%)
S : 52( 3.8%); T- : 42( 3.1%); V : 55( 4.0%); W : 5( 0.4%); Y : 16( 1.2%)
KR : 122 ( 8.9%); ED : 109 ( 8.0%); AGP ++: 741 ( 54.2%);
KRED : 231 ( 16.9%); KR-ED : 13 ( 1.0%); FIKMNY- : 171 ( 12.5%);
LVIFM - : 180 ( 13.2%); ST - : 94 ( 6.9%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 00000-0+00 0000000000 000000--00 ++0000-+00 +0-+000000 0+-0--0000
61 0000000000 0000000000 0-0+000000 00000000+0 0000000000 00000000-0
121 0-00000000 0+0000000+ 00--0000+0 0+00-+0000 0000+00000 000000+00+
181 00000-00+0 0000000+0- 00000-0000 00000+0000 -+0+000000 000+00-000
241 0000000000 0000000000 000+0-0000 0000000000 0+0-000000 0000000000
301 00000000+0 0000000000 000000+000 0000000000 0+0000-000 000+0-000+
361 0-00000000 000000--0+ +0000-0000 00000000+0 0000+00000 -0+0000000
421 00+0000000 0+0000-00+ 00-000000+ 0000000000 000+-00000 000-0+0000
481 00000+0-00 0000000+00 00-00+00-+ 00000000+0 0000-00000 0000000000
541 00+0-00000 0000000000 00000-00+0 0-+0000-00 0000000+0- +0000-0000
601 00000000+0 0000000-00 +0-0000000 0000000000 000-+00000 000+0-+0-0
661 00+0-00000 +-00+00000 0000000000 0-+0-00000 0000000+00 00-+0-0000
721 0000000000 0000000+0- +00+00+0-0 0000000000 0000000000 000000+0-0
781 0000000000 000+000000 0000000000 0000+-00+0 0+0-00000+ 00-0000000
841 0000-+0000 -000000000 0000000000 00000000+0 -+00000000 00-0000000
901 00000+0000 0000000000 00-00+-000 00-0000+-0 0000+0-+00 0000000000
961 0000000000 000+000+0- 0000000000 00000+0000 0000+0-+0- 00-+00+000
1021 00+0000000 000000000- 0000000000 00+0000000 000+-0+000 000000000+
1081 0000000000 0000000000 00000000-0 00-0-00+0- 00+00000+0 +-0-0-000+
1141 000000-000 00-00++000 +00+-0+000 0-00000000 -0000000-0 0+000-0000
1201 -000+000-0 000+000+00 +-++00000- 00000000-0 00-0000+-0 0000000+00
1261 0000000000 00+000000- --0000++00 000000-0-0 00-000+000 0000-000++
1321 00-00+000- 0+00+00+00 00-0000-00 00-0-000-0 00000+
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 9/30 or 12/45 or 15/60): none
Negative charge clusters (cmin = 9/30 or 11/45 or 14/60): none
Mixed charge clusters (cmin = 14/30 or 18/45 or 23/60): none
B. HIGH SCORING (UN)CHARGED SEGMENTS.
There are no high scoring positive charge segments.
There are no high scoring negative charge segments.
There are no high scoring mixed charge segments.
There are no high scoring uncharged segments.
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 5 | 5 | 7 | 54 | 10 | 10 | 13 | 12 | 12 | 16 | 6 | 8 |
lmin1 6 | 6 | 8 | 65 | 12 | 12 | 15 | 15 | 14 | 19 | 8 | 10 |
lmin2 7 | 7 | 10 | 73 | 14 | 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: 1, at 1280;
* runs >= 4: 1, at 1221;
0 runs >= 36: 0
--------------------------------------------------------------------------------
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-17-C-3-C-1140-C-22-C-8-C-7-C-68-C-44-C-46-C-2-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-17-C-3-C-123-H-35-H-329-H-63-H-101-H-265-H-21-H-8-H-49-H-11-H-H-31-H-14-H-77-C-6-H-15-C-8-C-7-C-21-H-45-H-C-44-C-36-H-9-C-2-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 5
Aligned matching blocks:
[ 38- 46] RGPRGERGP
[ 819- 827] RGPRGDQGP
______________________________
[ 39- 48]-( -5)-[ 44- 48]--------[ ]
[ ]--------[ 99- 103]-( -5)-[ 99- 110]
[ 586- 595]-( -5)-[ 591- 595]-( -5)-[ 591- 602]
[ ]--------[ 906- 910]--------[ ]
[ 39- 48] GPRGERGPPG
[ 586- 595] GPRGERGPPG
with superset:
[ 39- 43] GPRGE
[ 280- 284] GPRGE
[ 586- 590] GPRGE
[ 44- 48] RGPPG
[ 99- 103] RGPPG
[ 591- 595] RGPPG
[ 906- 910] RGPPG
[ 99- 110] RGPPGAAGAPGP
[ 591- 602] RGPPGESGAAGP
______________________________
[ 35- 40]-( 3)-[ 44- 54]
[ 600- 605]-( 3)-[ 609- 619]
[ 35- 40] AGDRGP
[ 600- 605] AGPTGP
[ 44- 54] RGPPGPPGRDG
[ 609- 619] RGPSGPPGPDG
with superset:
[ 44- 49] RGPPGP
[ 132- 137] RGPAGP
[ 609- 614] RGPSGP
[ 996-1001] RGPSGP
[1053-1058] RGPAGP
and:
[ 44- 51] RGPPGPPG
[ 132- 139] RGPAGPPG
[ 609- 616] RGPSGPPG
______________________________
[ 48- 54] GPPGRDG
[ 613- 619] GPPGPDG
[ 667- 673] GNPGRDG
[ 934- 940] GPPGRDG
______________________________
[ 57- 61] GPTGP
[ 601- 605] GPTGP
[ 754- 758] GPTGP
______________________________
[ 59- 67] TGPPGPPGP
[ 981- 989] TGPSGPVGP
with superset:
[ 59- 64] TGPPGP
[ 795- 800] TGPPGP
[ 981- 986] TGPSGP
______________________________
[ 94- 107] GLMGPRGPPGAAGA
[ 322- 335] GLPGPRGIPGPVGA
with superset:
[ 94- 100] GLMGPRG
[ 322- 328] GLPGPRG
[ 445- 451] GLMGPRG
[ 817- 823] GLRGPRG
and:
[ 94- 103] GLMGPRGPPG
[ 322- 331] GLPGPRGIPG
[ 445- 454] GLMGPRGLPG
______________________________
[ 97- 104] GPRGPPGA
[ 214- 221] GARGLPGE
[ 325- 331] GPRGIPG
[ 403- 410] GSRGLPGA
[ 448- 454] GPRGLPG
[ 466- 472] GPVGLPG
[ 637- 644] GPSGLPGE
[ 706- 713] GPRGSPGE
[ 880- 886] GERGLPG
[1015-1021] GPRGLPG
______________________________
[ 100- 110] GPPGAAGAPGP
[ 955- 965] GPVGAAGAPGP
with superset:
[ 103- 107] GAAGA
[ 334- 338] GAAGA
[ 958- 962] GAAGA
______________________________
[ 100- 104] GPPGA
[ 901- 905] GPPGA
[ 907- 911] GPPGA
______________________________
[ 100- 109] GPPGAAGAPG
[ 313- 322] GLPGVAGAPG
[ 913- 922] GSPGVNGAPG
with superset:
[ 100- 107] GPPGAAGA
[ 226- 233] GAPGPAGA
[ 313- 320] GLPGVAGA
[ 622- 629] GEPGVVGA
[ 640- 647] GLPGERGA
[ 682- 689] GAPGPAGA
[ 883- 890] GLPGVAGA
[ 913- 920] GSPGVNGA
______________________________
[ 102- 110] PGAAGAPGP
[ 789- 797] PGAAGRTGP
______________________________
[ 105- 128] AGAPGPQGFQGPAGEPGEPGQTGP
[1077-1100] AGIRGPQGHQGPAGPPGPPGPPGP
______________________________
[ 97- 98]-( 4)-[ 103- 104]-( 3)-[ 108- 119]
[ 523- 524]-( 4)-[ 529- 530]-( 3)-[ 534- 545]
[ 108- 119] PGPQGFQGPAGE
[ 534- 545] PGPQGVQGGKGE
with superset:
[ 108- 112] PGPQG
[ 534- 538] PGPQG
[ 861- 865] PGPQG
______________________________
[ 115- 119] GPAGE
[ 562- 566] GPAGE
______________________________
[ 117- 128] AGEPGEPGQTGP
[ 438- 449] AGRPGEPGLMGP
______________________________
[ 118- 122] GEPGE
[1009-1013] GEPGE
______________________________
[ 118- 119]-( 3)-[ 123- 127]
[ 205- 206]-( 3)-[ 210- 214]
[ 123- 127] PGQTG
[ 210- 214] PGQTG
______________________________
[ 127- 134] GPAGARGP
[ 901- 908] GPPGARGP
______________________________
[ 127- 133] GPAGARG
[ 229- 235] GPAGARG
[ 481- 487] GPAGARG
with superset:
[ 127- 131] GPAGA
[ 229- 233] GPAGA
[ 481- 485] GPAGA
[ 685- 689] GPAGA
[ 727- 731] GPAGA
[ 988- 992] GPAGA
______________________________
[ 151- 155] GRPGE
[ 439- 443] GRPGE
______________________________
[ 154- 161] GERGVVGP
[ 748- 755] GENGVVGP
______________________________
[ 168- 172] PGTPG
[ 858- 862] PGTPG
______________________________
[ 171- 179] PGLPGFKGI
[ 321- 329] PGLPGPRGI
______________________________
[ 181- 188] GHNGLDGL
[1024-1031] GHNGLQGL
______________________________
[ 190- 194] GQPGA
[ 733- 737] GQPGA
______________________________
[ 192- 196]-( -5)-[ 192- 203]
[ 201- 205]--------[ ]
[ 258- 262]-( -5)-[ 258- 269]
[ 192- 196] PGAPG
[ 201- 205] PGAPG
[ 258- 262] PGAPG
[ 192- 203] PGAPGVKGEPGA
[ 258- 269] PGAPGPKGEIGA
______________________________
[ 192- 206] PGAPGVKGEPGAPGE
[ 651- 665] PGGKGEKGEPGLRGE
with superset:
[ 196- 202] GVKGEPG
[ 358- 364] GNKGEPG
[ 619- 625] GNKGEPG
[ 655- 661] GEKGEPG
[1006-1012] GDKGEPG
______________________________
[ 202- 206] GAPGE
[ 919- 923] GAPGE
______________________________
[ 213- 221] TGARGLPGE
[ 339- 347] TGARGLVGE
______________________________
[ 216- 224] RGLPGERGR
[ 405- 413] RGLPGADGR
with superset:
[ 216- 220] RGLPG
[ 405- 409] RGLPG
[ 450- 454] RGLPG
[ 882- 886] RGLPG
[1017-1021] RGLPG
______________________________
[ 216- 230] RGLPGERGRVGAPGP
[ 708- 722] RGSPGERGEVGPAGP
with superset:
[ 151- 160] GRPGERGVVG
[ 217- 226] GLPGERGRVG
[ 709- 718] GSPGERGEVG
______________________________
[ 225- 233] VGAPGPAGA
[ 345- 352] VGEPGPAG
[ 681- 689] VGAPGPAGA
with superset:
[ 225- 230] VGAPGP
[ 345- 350] VGEPGP
[ 681- 686] VGAPGP
[ 891- 896] VGEPGP
______________________________
[ 228- 242] PGPAGARGSDGSVGP
[ 771- 782] PGPAGSRG_DG__GP
with superset:
[ 228- 232] PGPAG
[ 348- 352] PGPAG
[ 582- 586] PGPAG
[ 684- 688] PGPAG
[ 771- 775] PGPAG
[ 810- 814] PGPAG
and:
[ 228- 235] PGPAGARG
[ 582- 589] PGPAGPRG
[ 771- 778] PGPAGSRG
______________________________
[ 231- 235] AGARG
[ 483- 487] AGARG
[ 516- 520] AGARG
______________________________
[ 238- 248] GSVGPVGPAGP
[1045-1055] GSVGPAGPRGP
______________________________
[ 241- 247] GPVGPAG
[ 967- 973] GPVGPAG
[ 985- 991] GPVGPAG
______________________________
[ 244- 254] GPAGPIGSAGP
[ 601- 611] GPTGPIGSRGP
______________________________
[ 250- 254]--------[ ]--------[ 250- 259]
[ 364- 368]-( -8)-[ 361- 373]--------[ ]
[ 388- 392]-( -8)-[ 385- 397]-( -10)-[ 388- 397]
[ 250- 254] GSAGP
[ 364- 368] GSAGP
[ 388- 392] GSAGP
[ 361- 373] GEPGSAGPQGPPG
[ 385- 397] GEAGSAGPPGPPG
[ 250- 259] GSAGPPGFPG
[ 388- 397] GSAGPPGPPG
______________________________
[ 252- 263] AGPPGFPGAPGP
[1089-1100] AGPPGPPGPPGP
with superset:
[ 135- 139] AGPPG
[ 252- 256] AGPPG
[ 390- 394] AGPPG
[ 549- 553] AGPPG
[ 855- 859] AGPPG
[ 900- 904] AGPPG
[1089-1093] AGPPG
and:
[ 252- 259] AGPPGFPG
[ 390- 397] AGPPGPPG
[ 855- 862] AGPPGTPG
[1089-1096] AGPPGPPG
______________________________
[ 253- 257]--------[ ]
[ 550- 554]-( 33)-[ 588- 599]
[ 838- 842]-( 36)-[ 879- 890]
[ 253- 257] GPPGF
[ 550- 554] GPPGF
[ 838- 842] GPPGF
[ 588- 599] RGERGPPGESGA
[ 879- 890] RGERGLPGVAGA
with superset:
[ 41- 48] RGERGPPG
[ 588- 595] RGERGPPG
[ 879- 886] RGERGLPG
______________________________
[ 256- 260] GFPGA
[ 787- 791] GFPGA
______________________________
[ 259- 266] GAPGPKGE
[ 742- 749] GAKGPKGE
______________________________
[ 259- 263] GAPGP
[ 520- 524] GAPGP
[ 682- 686] GAPGP
[ 961- 965] GAPGP
______________________________
[ 255- 256]-( 4)-[ 261- 265]
[ 489- 490]-( 4)-[ 495- 499]
[ 261- 265] PGPKG
[ 495- 499] PGPKG
______________________________
[ 273- 283] AGPAGPAGPRG
[ 699- 709] AGPAGPAGPRG
______________________________
[ 273- 279] AGPAGPA
[ 366- 372] AGPQGPP
[ 390- 396] AGPPGPP
[ 600- 605] AGPTGP
[ 633- 638] AGPSGP
[ 699- 705] AGPAGPA
[ 762- 767] AGPAGP
[1050-1056] AGPRGPA
[1056-1062] AGPSGPA
[1089-1095] AGPPGPP
______________________________
[ 282- 286] RGEVG
[ 714- 718] RGEVG
______________________________
[ 277- 280]-( 4)-[ 285- 289]
[ 460- 463]-( 4)-[ 468- 472]
[ 277- 280] GPAG
[ 460- 463] GPAG
[ 285- 289] VGLPG
[ 468- 472] VGLPG
______________________________
[ 286- 290] GLPGL
[1018-1022] GLPGL
______________________________
[ 291- 298] SGPVGPPG
[ 804- 811] SGPPGPPG
______________________________
[ 294- 298] VGPPG
[ 837- 841] VGPPG
______________________________
[ 318- 326] AGAPGLPGP
[ 960- 968] AGAPGPHGP
with superset:
[ 105- 109] AGAPG
[ 318- 322] AGAPG
[ 960- 964] AGAPG
______________________________
[ 336- 343] AGATGARG
[ 687- 694] AGATGDRG
______________________________
[ 360- 364]-( -5)-[ 360- 368]-( 27)-[ 396- 400]
[ 621- 625]--------[ ]--------[ 660- 664]
[ 657- 661]--------[ ]--------[ ]
[1008-1012]-( -5)-[1008-1016]--------[ ]
[ 360- 364] KGEPG
[ 621- 625] KGEPG
[ 657- 661] KGEPG
[1008-1012] KGEPG
[ 360- 368] KGEPGSAGP
[1008-1016] KGEPGEKGP
[ 396- 400] PGLRG
[ 660- 664] PGLRG
______________________________
[ 369- 376] QGPPGPSG
[ 555- 562] QGLPGPSG
with superset:
[ 369- 374] QGPPGP
[ 531- 536] QGPPGP
[ 546- 551] QGPAGP
[ 555- 560] QGLPGP
[1086-1091] QGPAGP
______________________________
[ 372- 376] PGPSG
[ 558- 562] PGPSG
[ 798- 802] PGPSG
______________________________
[ 375- 376]-( 4)-[ 381- 388]
[ 426- 427]-( 4)-[ 432- 439]
[ 381- 388] RGPNGEAG
[ 432- 439] RGPNGDAG
______________________________
[ 390- 397] AGPPGPPG
[ 855- 863] AGPPGTPGP
[1089-1097] AGPPGPPGP
______________________________
[ 385- 395]-( 3)-[ 399- 406]
[ 694- 704]-( 3)-[ 708- 715]
[ 385- 395] GEAGSAGPPGP
[ 694- 704] GEAGAAGPAGP
[ 399- 406] RGSPGSRG
[ 708- 715] RGSPGERG
______________________________
[ 373- 377]-( 24)-[ 402- 406]
[ ]--------[ 420- 424]
[ 847- 851]-( 24)-[ 876- 880]
[ 373- 377] GPSGE
[ 847- 851] GPSGE
[ 402- 406] PGSRG
[ 420- 424] PGSRG
[ 876- 880] PGSRG
______________________________
[ 426- 430] SGPAG
[ 561- 565] SGPAG
[1059-1063] SGPAG
______________________________
[ 442- 446] GEPGL
[ 658- 662] GEPGL
______________________________
[ 444- 445]-( 4)-[ 450- 454]
[ 876- 877]-( 4)-[ 882- 886]
[1011-1012]-( 4)-[1017-1021]
[ 450- 454] RGLPG
[ 882- 886] RGLPG
[1017-1021] RGLPG
______________________________
[ 451- 455] GLPGS
[ 874- 878] GLPGS
______________________________
[ 456- 463] PGNIGPAG
[ 477- 484] PGPIGPAG
______________________________
[ 456- 461]-( 21)-[ 483- 490]
[ 489- 493]-( 22)-[ 516- 523]
[ 951- 956]--------[ ]
[ 456- 461] PGNIGP
[ 489- 493] PGNIG
[ 951- 956] PGNIGP
[ 483- 490] AGARGEPG
[ 516- 523] AGARGAPG
______________________________
[ 460- 464]-( -9)-[ 456- 466]--------[ ]
[ 811- 815]-( -9)-[ 807- 817]-( 17)-[ 835- 839]
[ 970- 974]--------[ ]--------[ 991- 995]
[1060-1064]--------[ ]--------[ ]
[ 460- 464] GPAGK
[ 811- 815] GPAGK
[ 970- 974] GPAGK
[1060-1064] GPAGK
[ 456- 466] PGNIGPAGKEG
[ 807- 817] PGPPGPAGKEG
[ 835- 839] GAVGP
[ 991- 995] GAVGP
______________________________
[ 469- 473] GLPGI
[1030-1034] GLPGI
______________________________
[ 517- 521] GARGA
[ 673- 677] GARGA
______________________________
[ 522- 527] PGPDGN
[ 615- 620] PGPDGN
______________________________
[ 531- 541] QGPPGPQGVQG
[ 546- 556] QGPAGPPGFQG
with superset:
[ 114- 121] QGPAGEPG
[ 369- 376] QGPPGPSG
[ 531- 538] QGPPGPQG
[ 546- 553] QGPAGPPG
[1086-1093] QGPAGPPG
______________________________
[ 541- 545] GGKGE
[ 652- 656] GGKGE
______________________________
[ 549- 553]--------[ ]--------[ ]--------[ 571- 575]
[ 855- 859]--------[ ]--------[ 855- 863]-( 16)-[ 880- 884]
[ 900- 904]-( -5)-[ 900- 910]-( -11)-[ 900- 908]--------[ ]
[1089-1093]-( -5)-[1089-1099]-( -11)-[1089-1097]--------[ ]
[ 549- 553] AGPPG
[ 855- 859] AGPPG
[ 900- 904] AGPPG
[1089-1093] AGPPG
[ 900- 910] AGPPGARGPPG
[1089-1099] AGPPGPPGPPG
[ 855- 863] AGPPGTPGP
[ 900- 908] AGPPGARGP
[1089-1097] AGPPGPPGP
[ 571- 575] GERGL
[ 880- 884] GERGL
______________________________
[ 556- 566] GLPGPSGPAGE
[ 580- 590] GLPGPAGPRGE
______________________________
[ 559- 565] GPSGPAG
[1057-1063] GPSGPAG
______________________________
[ 582- 595] PGPAGPRGERGPPG
[ 771- 784] PGPAGSRGDGGPPG
______________________________
[ 598- 605]--------[ ]--------[ 643- 647]
[ 697- 704]-( -8)-[ 697- 707]-( 31)-[ 739- 743]
[ 760- 767]-( -8)-[ 760- 770]--------[ ]
[ 598- 605] GAAGPTGP
[ 697- 704] GAAGPAGP
[ 760- 767] GAAGPAGP
[ 697- 707] GAAGPAGPAGP
[ 760- 770] GAAGPAGPNGP
[ 643- 647] GERGA
[ 739- 743] GERGA
______________________________
[ 610- 617] GPSGPPGP
[ 982- 989] GPSGPVGP
with superset:
[ 610- 614] GPSGP
[ 634- 638] GPSGP
[ 982- 986] GPSGP
[ 997-1001] GPSGP
[1057-1061] GPSGP
______________________________
[ 627- 631] VGAVG
[ 834- 838] VGAVG
______________________________
[ 631- 635] GTAGP
[ 853- 857] GTAGP
______________________________
[ 684- 692] PGPAGATGD
[ 771- 779] PGPAGSRGD
______________________________
[ 685- 689] GPAGA
[ 727- 731] GPAGA
[ 988- 992] GPAGA
______________________________
[ ]--------[ 702- 707]
[ 696- 700]-( 25)-[ 726- 730]
[ 729- 733]-( 28)-[ 762- 767]
[ 696- 700] AGAAG
[ 729- 733] AGAAG
[ 702- 707] AGPAGP
[ 726- 730] AGPAG
[ 762- 767] AGPAGP
______________________________
[ 727- 728]-( 4)-[ 733- 742]
[ 934- 935]-( 4)-[ 940- 949]
[ 733- 742] GQPGAKGERG
[ 940- 949] GQPGHKGERG
______________________________
[ 757- 775] GPVGAAGPAGPNGPPGPAG
[ 955- 973] GPVGAAGAPGPHGPVGPAG
with superset:
[ 100- 106] GPPGAAG
[ 241- 247] GPVGPAG
[ 331- 337] GPVGAAG
[ 727- 733] GPAGAAG
[ 757- 763] GPVGAAG
[ 955- 961] GPVGAAG
[ 967- 973] GPVGPAG
[ 985- 991] GPVGPAG
and:
[ 100- 110] GPPGAAGAPGP
[ 757- 767] GPVGAAGPAGP
[ 955- 965] GPVGAAGAPGP
[ 985- 995] GPVGPAGAVGP
and:
[ 757- 773] GPVGAAGPAGPNGPPGP
[ 955- 971] GPVGAAGAPGPHGPVGP
[ 985-1001] GPVGPAGAVGPRGPSGP
______________________________
[ 844- 848] GEKGP
[1012-1016] GEKGP
______________________________
[ 888- 896] AGAVGEPGP
[ 990- 998] AGAVGPRGP
______________________________
[ 987-1001] VGPAGAVGPRGPSGP
[1047-1061] VGPAGPRGPAGPSGP
Highly repetitive regions:
From 45 to 1101 with major motif GPPGPP.
From 133 to 1092 with major motif GPAGPR.
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:
[ 247- 265] spisossppsipsspsp+s
[ 694- 709] s_-ssssspsspssp__+s
with superset:
[ 247- 256] spisosspps
[ 361- 370] s-psosspns
[ 385- 394] s-ssosspps
[ 544- 553] s-nspsspps
[ 694- 703] s-ssssspss
[ 850- 859] s-ssosspps
and:
[ 247- 259] spisossppsips
[ 361- 373] s-psosspnspps
[ 385- 397] s-ssossppspps
[ 694- 705] s-ss_ssspssps
[ 850- 862] s-ssossppsops
______________________________
[ 573- 592] +sihs-isipspssp+s-+s
[ 675- 694] +sshssisspspsssos-+s
with superset:
[ 348- 356] pspsso+s-
[ 582- 590] pspssp+s-
[ 615- 623] psp-sn+s-
[ 684- 692] pspsssos-
[ 771- 779] pspsso+s-
______________________________
[1044-1063] psoispssp+spsspospss
[1071-1090] psoispssi+spnshnspss
with superset:
[ 33- 42] spss-+sp+s
[ 127- 136] spsss+spss
[ 427- 436] spssi+spns
[1048-1057] spssp+spss
[1075-1084] spssi+spns
and:
[ 33- 46] spss-+sp+s-+sp
[1048-1061] spssp+spssposp
[1075-1088] spssi+spnshnsp
--------------------------------------------------------------------------------
MULTIPLETS.
A. AMINO ACID ALPHABET.
1. Total number of amino acid multiplets: 70 (Expected range: 107--175) low
1 .........L LLL....... ......EE.. .......... .....PP.PP ..........
61 PP.PP.PP.P P..GG..AA. .......... .......... PP.AA..... ..........
121 .......... ......PP.. .......... .......VV. .......... ..........
181 .......... .......... .......... .......... .......... ..........
241 .......... ...PP..... .......... .......... .......... .....PP...
301 .......... AA........ .......... ....AA.... .......... ..........
361 .......... PP....EE.. .......... .PP.PP.... .......... ........PP
421 .......... .......... .......... .......... .......... ..........
481 .......... .......... .......... .......... ......NN.. ..PP......
541 GG........ PP........ .......... .......... .......... ..PP....AA
601 .......... ...PP..... .....VV... .......... ......AA.. .GG.......
661 .......... .......... .......... .......AA. .......... ..........
721 .......... AA........ .......... .VV....... AA.......P P........G
781 GPP....... AA....PP.. .....PP.PP .......... .......... ........PP
841 .......... ......PP.. .....LL... .......... .......... ..........
901 .PP....PP. .......... .......... ....PP.... .......... ........AA
961 .......... .......... .......... .......... .......... ..........
1021 .......... ......HH.. .......... .......... .......... ..........
1081 .......... PP.PP.PP.P P...GGG... .......... .......... ..........
1141 ..NN....LL .......... .......... ...SS.YY.. .......... ..........
1201 .......... ........SS ..KK...... .......... .......... ........LL
1261 .......... .......... EE....KK.. .......... .......... ........KK
1321 .......II. .......... .........G G....FF... ......
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 25 (6-10) 11 (11-20) 11 (>=21) 24
3. Clusters of amino acid multiplets (cmin = 10/30 or 13/45 or 15/60): none
4. Significant specific amino acid altplet counts:
Letters Observed (Critical number)
AG 98 (89)
at 35 (l= 2) 103 (l= 2) 105 (l= 3) 117 (l= 2) 129 (l= 3)
135 (l= 2) 141 (l= 2) 163 (l= 2) 193 (l= 2) 202 (l= 2)
214 (l= 2) 226 (l= 2) 231 (l= 3) 246 (l= 2) 252 (l= 2)
259 (l= 2) 268 (l= 2) 273 (l= 2) 276 (l= 2) 279 (l= 2)
301 (l= 2) 307 (l= 2) 310 (l= 2) 312 (l= 2) 318 (l= 3)
334 (l= 2) 336 (l= 3) 340 (l= 2) 351 (l= 2) 366 (l= 2)
387 (l= 2) 390 (l= 2) 409 (l= 2) 414 (l= 2) 424 (l= 2)
429 (l= 2) 438 (l= 2) 462 (l= 2) 483 (l= 3) 513 (l= 2)
516 (l= 3) 520 (l= 2) 529 (l= 2) 549 (l= 2) 564 (l= 2)
585 (l= 2) 598 (l= 2) 600 (l= 2) 628 (l= 2) 633 (l= 2)
646 (l= 2) 648 (l= 2) 673 (l= 2) 676 (l= 2) 679 (l= 2)
682 (l= 2) 687 (l= 3) 696 (l= 3) 699 (l= 2) 702 (l= 2)
705 (l= 2) 720 (l= 2) 726 (l= 2) 729 (l= 3) 732 (l= 2)
736 (l= 2) 742 (l= 2) 760 (l= 2) 762 (l= 2) 765 (l= 2)
774 (l= 2) 790 (l= 2) 792 (l= 2) 813 (l= 2) 835 (l= 2)
843 (l= 2) 852 (l= 2) 855 (l= 2) 868 (l= 2) 888 (l= 3)
900 (l= 2) 904 (l= 2) 910 (l= 2) 919 (l= 2) 924 (l= 2)
958 (l= 2) 960 (l= 3) 972 (l= 2) 990 (l= 3) 1035 (l= 2)
1042 (l= 2) 1050 (l= 2) 1056 (l= 2) 1062 (l= 2) 1077 (l= 2)
1089 (l= 2) 1234 (l= 2) 1351 (l= 2)
GP 187 (139)
at 33 (l= 2) 39 (l= 2) 45 (l= 2) 47 (l= 3) 50 (l= 2)
57 (l= 2) 60 (l= 2) 62 (l= 3) 65 (l= 3) 68 (l= 3)
71 (l= 2) 89 (l= 4) 97 (l= 2) 100 (l= 2) 102 (l= 2)
108 (l= 3) 115 (l= 2) 120 (l= 2) 123 (l= 2) 127 (l= 2)
133 (l= 2) 136 (l= 2) 138 (l= 2) 147 (l= 2) 150 (l= 2)
153 (l= 2) 160 (l= 2) 168 (l= 2) 171 (l= 2) 174 (l= 2)
192 (l= 2) 195 (l= 2) 201 (l= 2) 204 (l= 2) 210 (l= 2)
219 (l= 2) 228 (l= 3) 241 (l= 2) 244 (l= 2) 247 (l= 2)
253 (l= 2) 255 (l= 2) 258 (l= 2) 261 (l= 3) 274 (l= 2)
277 (l= 2) 280 (l= 2) 288 (l= 2) 292 (l= 2) 295 (l= 2)
297 (l= 2) 300 (l= 2) 315 (l= 2) 321 (l= 2) 324 (l= 3)
330 (l= 3) 348 (l= 3) 363 (l= 2) 367 (l= 2) 370 (l= 2)
372 (l= 3) 382 (l= 2) 391 (l= 2) 393 (l= 3) 396 (l= 2)
402 (l= 2) 408 (l= 2) 418 (l= 2) 420 (l= 2) 427 (l= 2)
433 (l= 2) 441 (l= 2) 444 (l= 2) 448 (l= 2) 453 (l= 2)
456 (l= 2) 460 (l= 2) 466 (l= 2) 471 (l= 2) 477 (l= 3)
481 (l= 2) 489 (l= 2) 495 (l= 3) 499 (l= 2) 504 (l= 2)
522 (l= 3) 532 (l= 2) 534 (l= 3) 547 (l= 2) 550 (l= 2)
552 (l= 2) 558 (l= 3) 562 (l= 2) 570 (l= 2) 582 (l= 3)
586 (l= 2) 592 (l= 2) 594 (l= 2) 601 (l= 2) 604 (l= 2)
610 (l= 2) 613 (l= 2) 615 (l= 3) 624 (l= 2) 634 (l= 2)
637 (l= 2) 642 (l= 2) 651 (l= 2) 660 (l= 2) 669 (l= 2)
684 (l= 3) 700 (l= 2) 703 (l= 2) 706 (l= 2) 711 (l= 2)
718 (l= 2) 721 (l= 2) 727 (l= 2) 735 (l= 2) 745 (l= 2)
754 (l= 2) 757 (l= 2) 763 (l= 2) 766 (l= 2) 769 (l= 2)
771 (l= 3) 781 (l= 2) 783 (l= 2) 789 (l= 2) 796 (l= 2)
798 (l= 3) 805 (l= 2) 807 (l= 3) 810 (l= 3) 820 (l= 2)
826 (l= 2) 838 (l= 2) 840 (l= 2) 847 (l= 2) 856 (l= 2)
858 (l= 2) 861 (l= 3) 870 (l= 2) 876 (l= 2) 885 (l= 2)
894 (l= 3) 901 (l= 2) 903 (l= 2) 907 (l= 2) 909 (l= 2)
915 (l= 2) 921 (l= 2) 930 (l= 2) 934 (l= 2) 936 (l= 2)
942 (l= 2) 951 (l= 2) 955 (l= 2) 963 (l= 3) 967 (l= 2)
970 (l= 2) 982 (l= 2) 985 (l= 2) 988 (l= 2) 994 (l= 2)
997 (l= 2) 1000 (l= 2) 1011 (l= 2) 1015 (l= 2) 1020 (l= 2)
1032 (l= 2) 1044 (l= 2) 1048 (l= 2) 1051 (l= 2) 1054 (l= 2)
1057 (l= 2) 1060 (l= 2) 1071 (l= 2) 1075 (l= 2) 1081 (l= 2)
1087 (l= 2) 1090 (l= 2) 1092 (l= 3) 1095 (l= 3) 1098 (l= 3)
1101 (l= 2) 1361 (l= 2)
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 11 (Expected range: 5-- 31)
6 +plets (f+: 8.9%), 5 -plets (f-: 8.0%)
Total number of charge altplets: 28 (Critical number: 35)
2. Histogram of spacings between consecutive charge
multiplets:
(1-5) 3 (6-10) 0 (11-20) 0 (>=21) 9
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
10- 13 1 L 4 4 0
33- 77 3 G.. 15 15 ! 0
83- 92 2 G. 5 5 ! 0
91-1116 3 G.. 341 339 ! 1
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
There are no periodicities of the prescribed length.
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
0-1173 (2.) W(1173)W 1 of 6 0.0003 large 1. maximal spacing
22-1163 (2.) C(1141)C 1 of 10 0.0000 large 1. maximal spacing
24- 236 (1.) S( 212)S 1 of 53 0.0068 large maximal spacing
81- 950 (2.) Y( 869)Y 1 of 17 0.0000 large maximal spacing
222- 224 (1.) R( 2)R 73 of 73 0.0003 large minimal spacing
519- 573 (2.) R( 54)R 1 of 73 0.9955 small 1. maximal spacing
1114-1154 (4.) G( 40)G 2 of 382 0.0000 large 2. maximal spacing
1203-1272 (4.) C( 69)C 2 of 10 1.0000 small 2. maximal spacing
1212-1336 (4.) P( 124)P 1 of 231 0.0000 large maximal spacing
1227-1324 (4.) W( 97)W 2 of 6 0.9987 small 2. maximal spacing
1244-1284 (4.) G( 40)G 1 of 382 0.0006 large 1. maximal spacing
1258-1307 (4.) R( 49)R 2 of 73 0.9931 small 2. maximal spacing
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
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: tem10
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copi 730.0 1.1e-215 18
COLFI Fibrillar collagen C-terminal domain 538.4 6.3e-210 1
adenylatekinase Adenylate kinase 1.8 23 1
G6PD Glucose-6-phosphate dehydrogenase -2.3 59 1
prion Prion protein -107.8 63 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Collagen 1/18 25 83 .. 1 60 [] 12.6 0.00069
Collagen 2/18 89 147 .. 1 60 [] 39.8 6.3e-08
Collagen 3/18 148 207 .. 1 60 [] 61.9 1.4e-14
Collagen 4/18 208 267 .. 1 60 [] 50.5 3.6e-11
Collagen 5/18 268 327 .. 1 60 [] 54.4 2.5e-12
Collagen 6/18 328 387 .. 1 60 [] 56.7 4.9e-13
adenylatekinase 1/1 416 422 .. 1 7 [. 1.8 23
Collagen 7/18 388 447 .. 1 60 [] 47.2 3.6e-10
Collagen 8/18 448 507 .. 1 60 [] 45.4 1.3e-09
Collagen 9/18 508 567 .. 1 60 [] 50.4 3.9e-11
G6PD 1/1 605 611 .. 475 481 .] -2.3 59
Collagen 10/18 568 627 .. 1 60 [] 49.1 1e-10
Collagen 11/18 628 687 .. 1 60 [] 51.2 2.3e-11
Collagen 12/18 691 750 .. 1 60 [] 63.7 4e-15
Collagen 13/18 751 810 .. 1 60 [] 47.7 2.6e-10
Collagen 14/18 811 870 .. 1 60 [] 44.8 1.9e-09
Collagen 15/18 871 930 .. 1 60 [] 49.4 8.1e-11
Collagen 16/18 931 990 .. 1 60 [] 49.4 7.7e-11
Collagen 17/18 991 1050 .. 1 60 [] 53.5 4.5e-12
Collagen 18/18 1051 1110 .. 1 60 [] 38.2 1.9e-07
prion 1/1 1059 1315 .. 1 244 [] -107.8 63
COLFI 1/1 1149 1365 .. 1 226 [] 538.4 6.3e-210
Alignments of top-scoring domains:
Collagen: domain 1 of 18, from 25 to 83: score 12.6, E = 0.00069
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
+ ++Gp+G +Gp+G+ Gp+G+pG G G+ GpPGppGppGp
tem10gi|14 25 -LQEETVRKGPAGDRGPRGERGPPGPPGRDGEDGPTGPPGPPGPPGP 70
pGppGapGapGpp<-*
pG G+ a
tem10gi|14 71 PGLGGNFAAQYDG 83
Collagen: domain 2 of 18, from 89 to 147: score 39.8, E = 6.3e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
pGp+G Gp+GppG++G+pGp+G++Gp+G pGepG+ Gp+G+ Gp
tem10gi|14 89 -GPGPMGLMGPRGPPGAAGAPGPQGFQGPAGEPGEPGQTGPAGARGP 134
pGppGapGapGpp<-*
+GppG++G+ G p
tem10gi|14 135 AGPPGKAGEDGHP 147
Collagen: domain 3 of 18, from 148 to 207: score 61.9, E = 1.4e-14
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+pG++G Gp G++G+pG +G pG +G +G +G +G +G+pG+
tem10gi|14 148 GKPGRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGA 194
pGppGapGapGpp<-*
pG +G+pGapG++
tem10gi|14 195 PGVKGEPGAPGEN 207
Collagen: domain 4 of 18, from 208 to 267: score 50.5, E = 3.6e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pG+ G++G+pG++G+ G+pGpaGa+G+ G G+ Gp Gp G +Gp
tem10gi|14 208 GTPGQTGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIGSAGP 254
pGppGapGapGpp<-*
pG pGapG++G+
tem10gi|14 255 PGFPGAPGPKGEI 267
Collagen: domain 5 of 18, from 268 to 327: score 54.4, E = 2.5e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+ G +Gp+Gp+Gp+G+ G pG +G+ GppG+pG++G G++G++G
tem10gi|14 268 GAVGNAGPAGPAGPRGEVGLPGLSGPVGPPGNPGANGLTGAKGAAGL 314
pGppGapGapGpp<-*
pG +GapG pGp+
tem10gi|14 315 PGVAGAPGLPGPR 327
Collagen: domain 6 of 18, from 328 to 387: score 56.7, E = 4.9e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pGp G++G++G++G G+pGpaG++G+ G++GepG+ Gp+GppGp
tem10gi|14 328 GIPGPVGAAGATGARGLVGEPGPAGSKGESGNKGEPGSAGPQGPPGP 374
pGppGapGapGpp<-*
G++G+ G+ G++
tem10gi|14 375 SGEEGKRGPNGEA 387
adenylatekinase: domain 1 of 1, from 416 to 422: score 1.8, E = 23
*->LlGpPGa<-*
++GpPG+
tem10gi|14 416 VMGPPGS 422
Collagen: domain 7 of 18, from 388 to 447: score 47.2, E = 3.6e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +GppGppG++G pG +G pG++G +G GppG +G+ Gp+G+ Gp
tem10gi|14 388 GSAGPPGPPGLRGSPGSRGLPGADGRAGVMGPPGSRGASGPAGVRGP 434
pGppGapGapGpp<-*
G +G+pG+pG
tem10gi|14 435 NGDAGRPGEPGLM 447
Collagen: domain 8 of 18, from 448 to 507: score 45.4, E = 1.3e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G+pG+pG Gp+G+ Gp G +G G pGp G++G+ G pG G+
tem10gi|14 448 GPRGLPGSPGNIGPAGKEGPVGLPGIDGRPGPIGPAGARGEPGNIGF 494
pGppGapGapGpp<-*
pGp+G+ G+pG++
tem10gi|14 495 PGPKGPTGDPGKN 507
Collagen: domain 9 of 18, from 508 to 567: score 50.4, E = 3.9e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +G +G +G++G+pGp G G++G+pGp+G +G +G++Gp+GppG+
tem10gi|14 508 GDKGHAGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPAGPPGF 554
pGppGapGapGpp<-*
+G pG++G++G++
tem10gi|14 555 QGLPGPSGPAGEV 567
G6PD: domain 1 of 1, from 605 to 611: score -2.3, E = 59
*->eyGSrGP<-*
+ GSrGP
tem10gi|14 605 PIGSRGP 611
Collagen: domain 10 of 18, from 568 to 627: score 49.1, E = 1e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG++G G+ G pGp+Gp G++G+pG+ G++G+ Gp G++Gp Gp
tem10gi|14 568 GKPGERGLHGEFGLPGPAGPRGERGPPGESGAAGPTGPIGSRGPSGP 614
pGppGapGapGpp<-*
pGp+G++G+pG +
tem10gi|14 615 PGPDGNKGEPGVV 627
Collagen: domain 11 of 18, from 628 to 687: score 51.2, E = 2.3e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+ G +Gp Gp G pG++G++G +G++G++G pG +G+ G pG++G+
tem10gi|14 628 GAVGTAGPSGPSGLPGERGAAGIPGGKGEKGEPGLRGEIGNPGRDGA 674
pGppGapGapGpp<-*
+G Ga GapGp+
tem10gi|14 675 RGAHGAVGAPGPA 687
Collagen: domain 12 of 18, from 691 to 750: score 63.7, E = 4e-15
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +G++G++Gp+Gp+Gp+G pG++G+ Gp+Gp G++Gp G++G+pG+
tem10gi|14 691 GDRGEAGAAGPAGPAGPRGSPGERGEVGPAGPNGFAGPAGAAGQPGA 737
pGppGapGapGpp<-*
+G++Ga+G++G++
tem10gi|14 738 KGERGAKGPKGEN 750
Collagen: domain 13 of 18, from 751 to 810: score 47.7, E = 2.6e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G Gp Gp G++Gp+Gp GppGpaG++G+ GppG G+PG++G+ Gp
tem10gi|14 751 GVVGPTGPVGAAGPAGPNGPPGPAGSRGDGGPPGMTGFPGAAGRTGP 797
pGppGapGapGpp<-*
pGp G +G+pGpp
tem10gi|14 798 PGPSGISGPPGPP 810
Collagen: domain 14 of 18, from 811 to 870: score 44.8, E = 1.9e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G+ G +Gp+G Gp G +G+ Ga GppG +Ge+Gp G +G +Gp
tem10gi|14 811 GPAGKEGLRGPRGDQGPVGRTGEVGAVGPPGFAGEKGPSGEAGTAGP 857
pGppGapGapGpp<-*
pG pG+ G G+p
tem10gi|14 858 PGTPGPQGLLGAP 870
Collagen: domain 15 of 18, from 871 to 930: score 49.4, E = 8.1e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G G+pG++G++G pG +G+ G++G+ G +GppG++GpPG+ G pG
tem10gi|14 871 GILGLPGSRGERGLPGVAGAVGEPGPLGIAGPPGARGPPGAVGSPGV 917
pGppGapGapGpp<-*
G pG++G G p
tem10gi|14 918 NGAPGEAGRDGNP 930
Collagen: domain 16 of 18, from 931 to 990: score 49.4, E = 7.7e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G GppG+ G pG +G++G pG+ G+ G +G+pG+ Gp Gp+G+ G
tem10gi|14 931 GNDGPPGRDGQPGHKGERGYPGNIGPVGAAGAPGPHGPVGPAGKHGN 977
pGppGapGapGpp<-*
+G++G++G+ Gp+
tem10gi|14 978 RGETGPSGPVGPA 990
Collagen: domain 17 of 18, from 991 to 1050: score 53.5, E = 4.5e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+ Gp+Gp Gp+G +G++G+pG++G++G pG +G +G +G pG +G
tem10gi|14 991 GAVGPRGPSGPQGIRGDKGEPGEKGPRGLPGLKGHNGLQGLPGIAGH 1037
pGppGapGapGpp<-*
G +GapG+ Gp+
tem10gi|14 1038 HGDQGAPGSVGPA 1050
Collagen: domain 18 of 18, from 1051 to 1110: score 38.2, E = 1.9e-07
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+Gp+Gp Gp+G +G+ G+pG G++G +Gp+G Gp GppGppGp
tem10gi|14 1051 GPRGPAGPSGPAGKDGRTGHPGTVGPAGIRGPQGHQGPAGPPGPPGP 1097
pGppGapGapGpp<-*
pGppG +G
tem10gi|14 1098 PGPPGVSGGGYDF 1110
prion: domain 1 of 1, from 1059 to 1315: score -107.8, E = 63
*->KKRPKPGGgWntGGsRYPGqgsPGGnRYPPqggggwgqphG..GtWG
P G G PG P G R Pqg g + p G++G G
tem10gi|14 1059 ---SGPAG--KDGRTGHPGTVGPAGIR-GPQGHQGPAGPPGppGPPG 1099
qPHG.gGGWGqPHGGGW...GqPHGGGWGqPHGgGGWGqGGGtHnqWnKP
P +gGG+ G + + qP P nq
tem10gi|14 1100 PPGVsGGGYDFGYDGDFyraDQPRSAPSLRPKDYEVDATLKSLNNQIETL 1149
sKPKtnmKHvAGAAAAGAvvG...GLGGYmL....GsAmsRPliHFGnDy
P K A ++ G Y +++++G m +
tem10gi|14 1150 LTPEGSRKNPARTCRDLRLSHpewSSGYYWIdpnqGCTMDAIKVYCDFST 1199
EDRYYREnmyRYPnqvYYRPvDqYsnqnnFvHDCvnitiK.qHtvttttK
+ R + P + +YR + + + + +n + + v t
tem10gi|14 1200 GETCIRAQPENIPAKNWYRSSK--DKKHVWLGETINAGSQfEYNVEGVTS 1247
GEnFtEtDiKimERvvEqmCitqYqkEsqAYYqgrRgs...svvLFssPP
E t + it k s AY + g +++v+L s
tem10gi|14 1248 KEMATQLAFMRLLANYASQNITYHCKNSIAYMDEETGNlkkAVILQGSND 1297
viLLis....FLiflivG<-*
v L+ ++++F ++v
tem10gi|14 1298 VELVAEgnsrFTYTVLVD 1315
COLFI: domain 1 of 1, from 1149 to 1365: score 538.4, E = 6.3e-210
*->lksPeGksrknPARtCkDLfLchpefksGeYWiDPNqGCikDAikVf
l++PeG srknPARtC+DL+L+hpe++sG+YWiDPNqGC++DAikV+
tem10gi|14 1149 LLTPEG-SRKNPARTCRDLRLSHPEWSSGYYWIDPNQGCTMDAIKVY 1194
CnkrfetGvgeTCisptpksvpkRiksWykgkskdkKhvWFgetmegGfk
C+ f tG eTCi+++p+++p+ k+Wy+++ kdkKhvW get+++G++
tem10gi|14 1195 CD--FSTG--ETCIRAQPENIPA--KNWYRSS-KDKKHVWLGETINAGSQ 1237
fsYiddelnpeisnvQlTFLRLLSteAsQNiTYhCKNSvAYmDeatGNlk
f+Y++++++++++++Ql+F+RLL+++AsQNiTYhCKNS+AYmDe+tGNlk
tem10gi|14 1238 FEYNVEGVTSKEMATQLAFMRLLANYASQNITYHCKNSIAYMDEETGNLK 1287
kAlilmgSnDvElsadgnskFtYtvlGeDGCssrtgewgKTViEyeTkKt
kA+il+gSnDvEl+a+gns+FtYtvl +DGCs++t+ewgKT+iEy+T+K+
tem10gi|14 1288 KAVILQGSNDVELVAEGNSRFTYTVL-VDGCSKKTNEWGKTIIEYKTNKP 1336
tRLPIvDiApsDiGgedQeFGveiGPVCF<-*
+RLP++DiAp+DiGg+d+eF+v+iGPVCF
tem10gi|14 1337 SRLPFLDIAPLDIGGADHEFFVDIGPVCF 1365
//
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: tem10
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copi 728.4 3.1e-215 19
COLFI Fibrillar collagen C-terminal domain 538.4 6.3e-210 1
PPR PPR repeat 6.5 3.8 1
adenylatekinase Adenylate kinase 1.8 23 1
Mu_DNA_bind Mu DNA-binding domain -0.1 91 1
G6PD Glucose-6-phosphate dehydrogenase -2.3 59 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Collagen 1/19 33 72 .. 1 40 [. 26.5 8.5e-06
Collagen 2/19 90 147 .. 3 60 .] 42.7 3.1e-10
Collagen 3/19 148 207 .. 1 60 [] 59.9 5.6e-15
Collagen 4/19 208 267 .. 1 60 [] 48.5 7.5e-12
Mu_DNA_bind 1/1 309 317 .. 1 9 [. -0.1 91
Collagen 5/19 268 327 .. 1 60 [] 52.4 6.6e-13
Collagen 6/19 328 387 .. 1 60 [] 54.7 1.5e-13
Collagen 7/19 388 415 .. 1 28 [. 19.4 0.00075
adenylatekinase 1/1 416 422 .. 1 7 [. 1.8 23
Collagen 8/19 418 465 .. 13 60 .] 40.7 1.1e-09
Collagen 9/19 469 528 .. 1 60 [] 55.7 8.3e-14
Collagen 10/19 529 567 .. 22 60 .] 30.1 8.6e-07
G6PD 1/1 605 611 .. 475 481 .] -2.3 59
Collagen 11/19 568 627 .. 1 60 [] 47.1 1.9e-11
Collagen 12/19 628 687 .. 1 60 [] 49.2 4.9e-12
Collagen 13/19 691 750 .. 1 60 [] 61.7 1.8e-15
Collagen 14/19 751 810 .. 1 60 [] 45.7 4.5e-11
Collagen 15/19 811 870 .. 1 60 [] 42.9 2.7e-10
Collagen 16/19 874 933 .. 1 60 [] 60.0 5.3e-15
Collagen 17/19 934 990 .. 4 60 .] 41.1 8.1e-10
Collagen 18/19 991 1050 .. 1 60 [] 51.6 1.1e-12
Collagen 19/19 1051 1105 .. 1 55 [. 40.4 1.3e-09
PPR 1/1 1308 1320 .. 1 13 [. 6.5 3.8
COLFI 1/1 1149 1365 .. 1 226 [] 538.4 6.3e-210
Alignments of top-scoring domains:
Collagen: domain 1 of 19, from 33 to 72: score 26.5, E = 8.5e-06
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPG<-*
Gp+G +Gp+G++GppGppG G++G+ GppGppG+pGpPG
tem10gi|14 33 GPAGDRGPRGERGPPGPPGRDGEDGPTGPPGPPGPPGPPG 72
Collagen: domain 2 of 19, from 90 to 147: score 42.7, E = 3.1e-10
*->pGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGppG
pGp+G Gp+GppG++G+pGp+G++Gp+G pGepG+ Gp+G+ Gp+G
tem10gi|14 90 PGPMGLMGPRGPPGAAGAPGPQGFQGPAGEPGEPGQTGPAGARGPAG 136
ppGapGapGpp<-*
ppG++G+ G p
tem10gi|14 137 PPGKAGEDGHP 147
Collagen: domain 3 of 19, from 148 to 207: score 59.9, E = 5.6e-15
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+pG++G Gp G++G+pG +G pG +G +G +G +G +G+pG+
tem10gi|14 148 GKPGRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGA 194
pGppGapGapGpp<-*
pG +G+pGapG++
tem10gi|14 195 PGVKGEPGAPGEN 207
Collagen: domain 4 of 19, from 208 to 267: score 48.5, E = 7.5e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pG+ G++G+pG++G+ G+pGpaGa+G+ G G+ Gp Gp G +Gp
tem10gi|14 208 GTPGQTGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIGSAGP 254
pGppGapGapGpp<-*
pG pGapG++G+
tem10gi|14 255 PGFPGAPGPKGEI 267
Mu_DNA_bind: domain 1 of 1, from 309 to 317: score -0.1, E = 91
*->kelaGlPGl<-*
k +aGlPG+
tem10gi|14 309 KGAAGLPGV 317
Collagen: domain 5 of 19, from 268 to 327: score 52.4, E = 6.6e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+ G +Gp+Gp+Gp+G+ G pG +G+ GppG+pG++G G++G++G
tem10gi|14 268 GAVGNAGPAGPAGPRGEVGLPGLSGPVGPPGNPGANGLTGAKGAAGL 314
pGppGapGapGpp<-*
pG +GapG pGp+
tem10gi|14 315 PGVAGAPGLPGPR 327
Collagen: domain 6 of 19, from 328 to 387: score 54.7, E = 1.5e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pGp G++G++G++G G+pGpaG++G+ G++GepG+ Gp+GppGp
tem10gi|14 328 GIPGPVGAAGATGARGLVGEPGPAGSKGESGNKGEPGSAGPQGPPGP 374
pGppGapGapGpp<-*
G++G+ G+ G++
tem10gi|14 375 SGEEGKRGPNGEA 387
Collagen: domain 7 of 19, from 388 to 415: score 19.4, E = 0.00075
*->GppGppGppGppGppGppGppGpaGapG<-*
G +GppGppG++G pG +G pG++G +G
tem10gi|14 388 GSAGPPGPPGLRGSPGSRGLPGADGRAG 415
adenylatekinase: domain 1 of 1, from 416 to 422: score 1.8, E = 23
*->LlGpPGa<-*
++GpPG+
tem10gi|14 416 VMGPPGS 422
Collagen: domain 8 of 19, from 418 to 465: score 40.7, E = 1.1e-09
*->GppGppGppGpaGapGppGppGepGpPGppGppGppGppGapGapGp
GppG +G+ GpaG +Gp+G++G pG+PG Gp G pG pG++G++G+
tem10gi|14 418 GPPGSRGASGPAGVRGPNGDAGRPGEPGLMGPRGLPGSPGNIGPAGK 464
p<-*
tem10gi|14 465 E 465
Collagen: domain 9 of 19, from 469 to 528: score 55.7, E = 8.3e-14
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pG G+pGp Gp+G++G+pG+ G+pGp+Gp G+pG G +G++G
tem10gi|14 469 GLPGIDGRPGPIGPAGARGEPGNIGFPGPKGPTGDPGKNGDKGHAGL 515
pGppGapGapGpp<-*
+G +GapG+ G +
tem10gi|14 516 AGARGAPGPDGNN 528
Collagen: domain 10 of 19, from 529 to 567: score 30.1, E = 8.6e-07
*->GpaGapGppGppGepGpPGppGppGppGppGapGapGpp<-*
G++G+pGp+G +G +G++Gp+GppG++G pG++G++G++
tem10gi|14 529 GAQGPPGPQGVQGGKGEQGPAGPPGFQGLPGPSGPAGEV 567
G6PD: domain 1 of 1, from 605 to 611: score -2.3, E = 59
*->eyGSrGP<-*
+ GSrGP
tem10gi|14 605 PIGSRGP 611
Collagen: domain 11 of 19, from 568 to 627: score 47.1, E = 1.9e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG++G G+ G pGp+Gp G++G+pG+ G++G+ Gp G++Gp Gp
tem10gi|14 568 GKPGERGLHGEFGLPGPAGPRGERGPPGESGAAGPTGPIGSRGPSGP 614
pGppGapGapGpp<-*
pGp+G++G+pG +
tem10gi|14 615 PGPDGNKGEPGVV 627
Collagen: domain 12 of 19, from 628 to 687: score 49.2, E = 4.9e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+ G +Gp Gp G pG++G++G +G++G++G pG +G+ G pG++G+
tem10gi|14 628 GAVGTAGPSGPSGLPGERGAAGIPGGKGEKGEPGLRGEIGNPGRDGA 674
pGppGapGapGpp<-*
+G Ga GapGp+
tem10gi|14 675 RGAHGAVGAPGPA 687
Collagen: domain 13 of 19, from 691 to 750: score 61.7, E = 1.8e-15
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +G++G++Gp+Gp+Gp+G pG++G+ Gp+Gp G++Gp G++G+pG+
tem10gi|14 691 GDRGEAGAAGPAGPAGPRGSPGERGEVGPAGPNGFAGPAGAAGQPGA 737
pGppGapGapGpp<-*
+G++Ga+G++G++
tem10gi|14 738 KGERGAKGPKGEN 750
Collagen: domain 14 of 19, from 751 to 810: score 45.7, E = 4.5e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G Gp Gp G++Gp+Gp GppGpaG++G+ GppG G+PG++G+ Gp
tem10gi|14 751 GVVGPTGPVGAAGPAGPNGPPGPAGSRGDGGPPGMTGFPGAAGRTGP 797
pGppGapGapGpp<-*
pGp G +G+pGpp
tem10gi|14 798 PGPSGISGPPGPP 810
Collagen: domain 15 of 19, from 811 to 870: score 42.9, E = 2.7e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G+ G +Gp+G Gp G +G+ Ga GppG +Ge+Gp G +G +Gp
tem10gi|14 811 GPAGKEGLRGPRGDQGPVGRTGEVGAVGPPGFAGEKGPSGEAGTAGP 857
pGppGapGapGpp<-*
pG pG+ G G+p
tem10gi|14 858 PGTPGPQGLLGAP 870
Collagen: domain 16 of 19, from 874 to 933: score 60.0, E = 5.3e-15
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pG++G++G+pG +G+ G+pGp G +GppG++G+pG+ G+pG++G+
tem10gi|14 874 GLPGSRGERGLPGVAGAVGEPGPLGIAGPPGARGPPGAVGSPGVNGA 920
pGppGapGapGpp<-*
pG++G++G pG
tem10gi|14 921 PGEAGRDGNPGND 933
Collagen: domain 17 of 19, from 934 to 990: score 41.1, E = 8.1e-10
*->GppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGppGp
GppG+ G pG +G++G pG+ G+ G +G+pG+ Gp Gp+G+ G +G+
tem10gi|14 934 GPPGRDGQPGHKGERGYPGNIGPVGAAGAPGPHGPVGPAGKHGNRGE 980
pGapGapGpp<-*
+G++G+ Gp+
tem10gi|14 981 TGPSGPVGPA 990
Collagen: domain 18 of 19, from 991 to 1050: score 51.6, E = 1.1e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+ Gp+Gp Gp+G +G++G+pG++G++G pG +G +G +G pG +G
tem10gi|14 991 GAVGPRGPSGPQGIRGDKGEPGEKGPRGLPGLKGHNGLQGLPGIAGH 1037
pGppGapGapGpp<-*
G +GapG+ Gp+
tem10gi|14 1038 HGDQGAPGSVGPA 1050
Collagen: domain 19 of 19, from 1051 to 1105: score 40.4, E = 1.3e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+Gp+Gp Gp+G +G+ G+pG G++G +Gp+G Gp GppGppGp
tem10gi|14 1051 GPRGPAGPSGPAGKDGRTGHPGTVGPAGIRGPQGHQGPAGPPGPPGP 1097
pGppGapG<-*
pGppG +G
tem10gi|14 1098 PGPPGVSG 1105
PPR: domain 1 of 1, from 1308 to 1320: score 6.5, E = 3.8
*->vtYntlIsgycka<-*
+tY++l++g++k+
tem10gi|14 1308 FTYTVLVDGCSKK 1320
COLFI: domain 1 of 1, from 1149 to 1365: score 538.4, E = 6.3e-210
*->lksPeGksrknPARtCkDLfLchpefksGeYWiDPNqGCikDAikVf
l++PeG srknPARtC+DL+L+hpe++sG+YWiDPNqGC++DAikV+
tem10gi|14 1149 LLTPEG-SRKNPARTCRDLRLSHPEWSSGYYWIDPNQGCTMDAIKVY 1194
CnkrfetGvgeTCisptpksvpkRiksWykgkskdkKhvWFgetmegGfk
C+ f tG eTCi+++p+++p+ k+Wy+++ kdkKhvW get+++G++
tem10gi|14 1195 CD--FSTG--ETCIRAQPENIPA--KNWYRSS-KDKKHVWLGETINAGSQ 1237
fsYiddelnpeisnvQlTFLRLLSteAsQNiTYhCKNSvAYmDeatGNlk
f+Y++++++++++++Ql+F+RLL+++AsQNiTYhCKNS+AYmDe+tGNlk
tem10gi|14 1238 FEYNVEGVTSKEMATQLAFMRLLANYASQNITYHCKNSIAYMDEETGNLK 1287
kAlilmgSnDvElsadgnskFtYtvlGeDGCssrtgewgKTViEyeTkKt
kA+il+gSnDvEl+a+gns+FtYtvl +DGCs++t+ewgKT+iEy+T+K+
tem10gi|14 1288 KAVILQGSNDVELVAEGNSRFTYTVL-VDGCSKKTNEWGKTIIEYKTNKP 1336
tRLPIvDiApsDiGgedQeFGveiGPVCF<-*
+RLP++DiAp+DiGg+d+eF+v+iGPVCF
tem10gi|14 1337 SRLPFLDIAPLDIGGADHEFFVDIGPVCF 1365
//
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: tem10
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
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 14:29:31 2000
Sequence file: tem10
----------------------------------------
Sequence tem10gi|1418930|emb|CAA98969.1| (1366 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
1267: NITY
Total matches: 1
Matching pattern PS00005 PKC_PHOSPHO_SITE:
29: TVR
1127: SLR
1138: TLK
1155: SRK
1162: TCR
1219: SSK
1246: TSK
1318: SKK
1333: TNK
Total matches: 9
Matching pattern PS00006 CK2_PHOSPHO_SITE:
3: SFVD
24: SLQE
353: SKGE
375: SGEE
710: SPGE
776: SRGD
878: SRGE
1162: TCRD
1169: SHPE
1198: STGE
1219: SSKD
1236: SQFE
1246: TSKE
1327: TIIE
Total matches: 14
Matching pattern PS00008 MYRISTYL:
72: GLGGNF
74: GGNFAA
75: GNFAAQ
211: GQTGAR
232: GARGSD
235: GSDGSV
268: GAVGNA
298: GNPGAN
304: GLTGAK
307: GAKGAA
334: GAAGAT
337: GATGAR
400: GSPGSR
406: GLPGAD
421: GSRGAS
454: GSPGNI
514: GLAGAR
526: GNNGAQ
538: GVQGGK
625: GVVGAV
628: GAVGTA
649: GIPGGK
673: GARGAH
676: GAHGAV
733: GQPGAK
780: GGPPGM
874: GLPGSR
886: GVAGAV
928: GNPGND
1042: GAPGSV
1102: GVSGGG
Total matches: 31
Matching pattern PS00009 AMIDATION:
378: EGKR
Total matches: 1
Matching pattern PS00016 RGD:
777: RGD
822: RGD
1005: RGD
Total matches: 3
Total no of hits in this sequence: 59
========================================
1314 pattern(s) searched in 1 sequence(s), 1366 residues.
Total no of hits in all sequences: 59.
Search time: 00:00 min
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Profile Search
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with motif search against own library
***** bioMotif : Version V41a DB, 1999 Nov 11 *****
argv[1]=P
argv[2]=-m /data/patterns/own/motif.fa
argv[4]=-seq tem10
***** 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, 1366 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: tem10
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
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: tem10
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo sapiens]
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= tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo
sapiens]
(1366 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
DNASE1 DNASE-1/Sphingomyelinase like domain 25 0.72
BRIGHT BRIGHT domain (Alpha helical DNA binding domain) 24 1.4
AAA AAA+ ATPase Module 24 1.5
SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chrom... 24 1.6
UBA Ubiquitin pathway associated domain 23 2.9
ARR Arrestin domain 23 3.1
MATH The Meprin associated TRAF homology domain 22 5.0
14-3-3 14-3-3 protein alpha Helical domain 22 5.5
DNAJ DNAJ co-chaperone domain (Hsp70 cofactors) 22 6.1
>DNASE1 DNASE-1/Sphingomyelinase like domain
Length = 388
Score = 24.8 bits (53), Expect = 0.72
Identities = 10/91 (10%), Positives = 21/91 (22%), Gaps = 7/91 (7%)
Query: 1114 GDFYRA--DQPRSAPSLRPKDYEVDATLKSLNNQIETLLT--PEGSRKNPARTCRDLRLS 1169
GDF ++ + + L S + + E T + T D
Sbjct: 280 GDFNADPTEEVYKRFASSSLNLNSAYKLLSEDGESEPPYTTWKIRTTGESCHTL-DYIWY 338
Query: 1170 HPEWSSGYYWIDPNQGCTMDA--IKVYCDFS 1198
+ + + + S
Sbjct: 339 SQHALRVNAALGLPTEEQIGPNRLPSFNYPS 369
>BRIGHT BRIGHT domain (Alpha helical DNA binding domain)
Length = 172
Score = 23.8 bits (51), Expect = 1.4
Identities = 8/29 (27%), Positives = 8/29 (27%)
Query: 41 RGERGPPGPPGRDGEDGPTGPPGPPGPPG 69
G R G P P P PG
Sbjct: 131 EGRRSSYGQYEAMHNQMPMTPISRPSLPG 159
Score = 21.5 bits (45), Expect = 7.0
Identities = 7/28 (25%), Positives = 8/28 (28%)
Query: 793 GRTGPPGPSGISGPPGPPGPAGKEGLRG 820
GR G P P + L G
Sbjct: 132 GRRSSYGQYEAMHNQMPMTPISRPSLPG 159
Score = 21.5 bits (45), Expect = 8.2
Identities = 7/30 (23%), Positives = 10/30 (33%)
Query: 377 EEGKRGPNGEAGSAGPPGPPGLRGSPGSRG 406
EG+R G+ + P P G
Sbjct: 130 REGRRSSYGQYEAMHNQMPMTPISRPSLPG 159
>AAA AAA+ ATPase Module
Length = 298
Score = 23.7 bits (50), Expect = 1.5
Identities = 20/138 (14%), Positives = 41/138 (29%), Gaps = 12/138 (8%)
Query: 1222 DKKHVWLGETINAGSQFEYNVEGVTSKEMATQLAFMRLLANYASQNITYHCKNSIAYMDE 1281
D V A Y + + L + ++ + TY I +D+
Sbjct: 1 DINDV-TPNCRVALRNDSYTLHKI-LPNKVDPLVSLMMVEKVP--DSTY---EMIGGLDK 53
Query: 1282 ETGNLKKAVILQGSNDVELVAEGNSRFTYTVLVDGCSKKTNEWGKTIIEYKTNKPSRLPF 1341
+ +K+ + L E VL+ G T GKT++ + F
Sbjct: 54 QIKEIKEVIELP-VKHPEHFEALGIAQPKGVLLYG-PPGT---GKTLLARAVAHHTDCTF 108
Query: 1342 LDIAPLDIGGADHEFFVD 1359
+ ++ ++
Sbjct: 109 IRVSGSELVQKFIGEGAR 126
Score = 22.5 bits (47), Expect = 3.9
Identities = 8/25 (32%), Positives = 10/25 (40%)
Query: 380 KRGPNGEAGSAGPPGPPGLRGSPGS 404
K + EA P L G PG+
Sbjct: 67 KHPEHFEALGIAQPKGVLLYGPPGT 91
Score = 21.8 bits (45), Expect = 6.2
Identities = 5/11 (45%), Positives = 7/11 (63%)
Query: 894 PGPLGIAGPPG 904
P + + GPPG
Sbjct: 80 PKGVLLYGPPG 90
>SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chromatin associated domain)
Length = 219
Score = 23.8 bits (51), Expect = 1.6
Identities = 11/72 (15%), Positives = 19/72 (26%), Gaps = 9/72 (12%)
Query: 1217 YRSSKDKKH-VWLGETINAGSQF-EYNVEGVTSKEMATQLAFMRLLANYASQNITYHCKN 1274
+ + V+ E+I A S EY + +Y +
Sbjct: 91 CWINSYVGYGVFARESIPAWSYIGEYTGILRRRQA------LWLDENDYCFRYPVPRYSF 144
Query: 1275 SIAYMD-EETGN 1285
+D GN
Sbjct: 145 RYFTIDSGMQGN 156
>UBA Ubiquitin pathway associated domain
Length = 255
Score = 22.7 bits (48), Expect = 2.9
Identities = 15/47 (31%), Positives = 20/47 (41%)
Query: 729 AGAAGQPGAKGERGAKGPKGENGVVGPTGPVGAAGPAGPNGPPGPAG 775
A + A+ + A+ +G N G G G A A GPPG G
Sbjct: 83 AATTAEQPAEDDLFAQAAQGGNASSGALGTTGGATDAAQGGPPGSIG 129
Score = 21.6 bits (45), Expect = 6.9
Identities = 16/52 (30%), Positives = 22/52 (41%)
Query: 347 EPGPAGSKGESGNKGEPGSAGPQGPPGPSGEEGKRGPNGEAGSAGPPGPPGL 398
+P A + E + + + QG SG G G +A GPPG GL
Sbjct: 79 QPSTAATTAEQPAEDDLFAQAAQGGNASSGALGTTGGATDAAQGGPPGSIGL 130
Score = 21.2 bits (44), Expect = 8.3
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 674 ARGAHGAVGAPGPAGATGDRGEAGAAGPAGPAG 706
A+ A G + G G TG +A GP G G
Sbjct: 97 AQAAQGGNASSGALGTTGGATDAAQGGPPGSIG 129
Score = 21.2 bits (44), Expect = 9.9
Identities = 12/40 (30%), Positives = 15/40 (37%)
Query: 225 VGAPGPAGARGSDGSVGPVGPAGPIGSAGPPGFPGAPGPK 264
+ A G S G++G G A GPPG G
Sbjct: 95 LFAQAAQGGNASSGALGTTGGATDAAQGGPPGSIGLTVED 134
>ARR Arrestin domain
Length = 454
Score = 22.9 bits (49), Expect = 3.1
Identities = 5/21 (23%), Positives = 6/21 (27%), Gaps = 4/21 (19%)
Query: 551 PPGFQGLPGPSGPAGEVGKPG 571
P P + GKP
Sbjct: 149 ASSVTLQPAPG----DTGKPC 165
>MATH The Meprin associated TRAF homology domain
Length = 209
Score = 22.1 bits (47), Expect = 5.0
Identities = 6/16 (37%), Positives = 7/16 (43%)
Query: 803 ISGPPGPPGPAGKEGL 818
+S P PP PA
Sbjct: 1 MSRVPSPPPPAEMSSG 16
Score = 22.1 bits (47), Expect = 5.2
Identities = 6/14 (42%), Positives = 7/14 (49%)
Query: 1095 PGPPGPPGVSGGGY 1108
P PP P +S G
Sbjct: 5 PSPPPPAEMSSGPV 18
Score = 21.4 bits (45), Expect = 7.4
Identities = 9/71 (12%), Positives = 22/71 (30%), Gaps = 17/71 (23%)
Query: 1148 TLLTPEGSRKNPARTCRDLRLSHPEWSSGYYW---------IDPNQGCTM-DAIKVYCDF 1197
++L +G + R R + + + +D G D + ++C+
Sbjct: 105 SILNAKGEETKAMESQRAYRFVQGK---DWGFKKFIRRDFLLDEANGLLPDDKLTLFCEV 161
Query: 1198 S----TGETCI 1204
S +
Sbjct: 162 SVVQDSVNISG 172
Score = 21.0 bits (44), Expect = 9.7
Identities = 4/18 (22%), Positives = 6/18 (33%)
Query: 855 AGPPGTPGPQGLLGAPGI 872
+ P P P + P
Sbjct: 2 SRVPSPPPPAEMSSGPVA 19
>14-3-3 14-3-3 protein alpha Helical domain
Length = 270
Score = 21.9 bits (46), Expect = 5.5
Identities = 6/34 (17%), Positives = 10/34 (28%)
Query: 831 TGEVGAVGPPGFAGEKGPSGEAGTAGPPGTPGPQ 864
T + +G A + P G P+
Sbjct: 234 TSDAEYSAAAAGGNTEGAQENAPSNAPEGEAEPK 267
>DNAJ DNAJ co-chaperone domain (Hsp70 cofactors)
Length = 75
Score = 21.7 bits (46), Expect = 6.1
Identities = 7/28 (25%), Positives = 10/28 (35%)
Query: 1126 PSLRPKDYEVDATLKSLNNQIETLLTPE 1153
P D E +A K + E L +
Sbjct: 33 PDRNQGDKEAEAKFKEIKEAYEVLTDSQ 60
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 9
Number of calls to ALIGN: 19
Length of query: 1366
Total length of test sequences: 20182
Effective length of test sequences: 16637.0
Effective search space size: 22175247.6
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= tem10gi|1418930|emb|CAA98969.1| prepro-alpha2(I) collagen [Homo
sapiens]
(1366 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|1815643 [227..431] Metzincin-like 27 1.6
gi|2780210 [404..848] beta/alpha (TIM)-barrel 26 3.2
gi|137178 [233..498] Ligand-binding domain of nuclear recept... 26 3.9
gi|585620 [104..580] Periplasmic binding protein-like II 26 4.0
gi|538698 [52..502] Periplasmic binding protein-like II 26 4.4
gi|227130 [11..85] Cytochrome c oxidase subunit h 26 4.9
>gi|1815643 [227..431] Metzincin-like
Length = 205
Score = 27.2 bits (60), Expect = 1.6
Identities = 9/43 (20%), Positives = 15/43 (33%), Gaps = 2/43 (4%)
Query: 73 LGGNFAAQYDGKGVGLGPGPMGLMGPR--GPPGAAGAPGPQGF 113
+G ++D P P +M + G G+P F
Sbjct: 139 IGHLLGLEHDTTACSCEPSPECVMRQQPGRVGGGGGSPFSWQF 181
>gi|2780210 [404..848] beta/alpha (TIM)-barrel
Length = 445
Score = 26.4 bits (57), Expect = 3.2
Identities = 18/163 (11%), Positives = 31/163 (18%), Gaps = 17/163 (10%)
Query: 1111 GYDGDFYRADQPRSAPSLRPKDYEVDATLKSLNNQIETLLTPEGSRKNPARTCRDLRLSH 1170
GY + P + N I + D +
Sbjct: 155 GYTLYDCQWPSPT---------SGMFPKALYHNCWIGNWEGEDSRSCWLHEDLADFNTEN 205
Query: 1171 PE-----WSSGYYWID-PNQGCTMDAIKVYCDFSTGETCIRAQPENIPAKNWYRSSKDKK 1224
P+ + +ID G +D + + K
Sbjct: 206 PQVQNYLIGAYDKYIDMGVDGFRVDTAVHIPRT--TWNRRFLPAIQERVAQQHGAEAAKN 263
Query: 1225 HVWLGETINAGSQFEYNVEGVTSKEMATQLAFMRLLANYASQN 1267
GE + S + T A+ A
Sbjct: 264 FFVFGEVAAFVNDKWNRGSVTHSAQFYTWKERKEYSADDAKAA 306
>gi|137178 [233..498] Ligand-binding domain of nuclear receptor
Length = 266
Score = 26.3 bits (57), Expect = 3.9
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 1102 GVSGGGYDFGYDGDFYRADQPRSAPSLRPK 1131
G GGG G+DG F R +P L+P+
Sbjct: 106 GAGGGGGGLGHDGSF-----ERRSPGLQPQ 130
>gi|585620 [104..580] Periplasmic binding protein-like II
Length = 477
Score = 26.1 bits (57), Expect = 4.0
Identities = 20/148 (13%), Positives = 44/148 (29%), Gaps = 28/148 (18%)
Query: 1213 AKNWYRSSKDKKHVWLGETINAGSQFEYNVEGVTSKEMATQLAFMRLLANYASQNITYHC 1272
A + K+ K + T+ ++ E VT+K+ + Y S T
Sbjct: 5 AADV-ALDKESKTATI--TLRKDLKWSDGSE-VTAKDYEFTYETI-ANPAYGSDRWTDS- 58
Query: 1273 KNSIAYMDEETGNLKKAVILQGSNDVELVAEGNSRFTYTVLVDGCSKK-------TNEWG 1325
+I + + + + + + + V K +
Sbjct: 59 LANIVGLSDY--------HTGKAKTISGITFPDGENGKVIKVQFKEMKPGMTQSGNGYFL 110
Query: 1326 KTIIEYKTNKPSRLPFLDIAPLDIGGAD 1353
+T+ Y+ D+AP D+ +
Sbjct: 111 ETVAPYQ-------YLKDVAPKDLASSP 131
>gi|538698 [52..502] Periplasmic binding protein-like II
Length = 451
Score = 26.1 bits (57), Expect = 4.4
Identities = 16/105 (15%), Positives = 26/105 (24%), Gaps = 13/105 (12%)
Query: 1088 PAGPPGPPGPPG-PPGVSGGGYD----------FGYDGDFYRADQPRSAPSLRPKDYE-V 1135
PAG P P Y+ GYDG + + +
Sbjct: 276 PAGFNFPNYGETFDPKRKAMEYNVEEAKRLVKESGYDGTPITYHTMGNYYANAMPALMMM 335
Query: 1136 DATLKSLNNQIETLLTPEGSRKNPARTCRDLRLSHPEWSSGYYWI 1180
K + + + T P S+ +W + Y
Sbjct: 336 IEMWKQIGVNVV-MKTYAPGSFPPDNQTWMRNWSNGQWMTDAYAT 379
>gi|227130 [11..85] Cytochrome c oxidase subunit h
Length = 75
Score = 25.6 bits (55), Expect = 4.9
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 1182 PNQGCTMDAIKVYCDFSTGETCIRAQPENIPAKNWYR 1218
PNQ T + + Y DF E + A+ ++ WYR
Sbjct: 11 PNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYR 47
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 6
Number of calls to ALIGN: 6
Length of query: 1366
Total length of test sequences: 256703
Effective length of test sequences: 210706.0
Effective search space size: 279679373.4
Initial X dropoff for ALIGN: 25.0 bits