analysis of sequence from tem15
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPCQICVCDSGSVLCDDIICDDQ
ELDCPNPEIPFGECCAVCPQPPTAPTRPPNGQGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPGI
CESCPTGPQNYSPQYDSYDVKSGVAVGGLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQGPPGEPGQAG
PSGPPGPPGAIGPSGPAGKDGESGRPGRPGERGLPGPPGIKGPAGIPGFPGMKGHRGFDGRNGEKGETGA
PGLKGENGLPGENGAPGPMGPRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAK
GEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGPAGIPGAPGLMGARGPPGPAG
ANGAPGLRGGAGEPGKNGAKGEPGPRGERGEAGIPGVPGAKGEDGKDGSPGEPGANGLPGAAGERGAPGF
RGPAGPNGIPGEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPGSPGGPGSDGKPGPPGSQGES
GRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPGGPGPQGPPGKNGETGPQGPPGPTGPGGDKG
DTGPPGPQGLQGLPGTGGPPGENGKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP
PGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGPRGPTGPIGPP
GPAGQPGDKGEGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPG
VAGPPGGSGPAGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPGKDGPPGPAGN
TGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIAGITGARGLAGPPGMPGPRGSPGPQGVKGES
GKPGANGLSGERGPPGPQGLPGLAGTAGEPGRDGNPGSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPG
PPGPVGPAGKSGDRGESGPAGPAGAPGPAGSRGAPGPQGPRGDKGETGERGAAGIKGHRGFPGNPGAPGS
PGPAGQQGAIGSPGPAGPRGPVGPSGPPGKDGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPP
GAPGPCCGGVGAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLISPDGSRKNPAR
NCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSSAEKKHVWFGE
SMDGGFQFSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEF
KAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLPIVDIAPYDIGGPDQEFGVDVGPVCFL
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> gi|115306|sp|P02461|CA13_HUMAN
. . . . .
1 MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPC 50
__________EEE_____HHHHHHHHHH______________________
. . . . .
51 QICVCDSGSVLCDDIICDDQELDCPNPEIPFGECCAVCPQPPTAPTRPPN 100
EEEEE____________________________EEEE_____________
. . . . .
101 GQGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPGICESCPTGPQN 150
__________________________________________________
. . . . .
151 YSPQYDSYDVKSGVAVGGLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQ 200
_____________EEE__________________________________
. . . . .
201 GPPGEPGQAGPSGPPGPPGAIGPSGPAGKDGESGRPGRPGERGLPGPPGI 250
__________________________________________________
. . . . .
251 KGPAGIPGFPGMKGHRGFDGRNGEKGETGAPGLKGENGLPGENGAPGPMG 300
__________________________________________________
. . . . .
301 PRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAK 350
__________________________________________________
. . . . .
351 GEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGP 400
__________________________________________________
. . . . .
401 AGIPGAPGLMGARGPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERG 450
__________________________________________________
. . . . .
451 EAGIPGVPGAKGEDGKDGSPGEPGANGLPGAAGERGAPGFRGPAGPNGIP 500
__________________________________________________
. . . . .
501 GEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPGSPGGPGSDGK 550
__________________________________________________
. . . . .
551 PGPPGSQGESGRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPG 600
__________________________________________________
. . . . .
601 GPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGLQGLPGTGGPP 650
__________________________________________________
. . . . .
651 GENGKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP 700
__________________________________________________
. . . . .
701 PGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPG 750
__________________________________________________
. . . . .
751 ADGVPGKDGPRGPTGPIGPPGPAGQPGDKGEGGAPGLPGIAGPRGSPGER 800
__________________________________________________
. . . . .
801 GETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPGVAGPPGGSGP 850
__________________________________________________
. . . . .
851 AGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPG 900
__________________________________________________
. . . . .
901 KDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIA 950
_______________________________________________EEE
. . . . .
951 GITGARGLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGL 1000
EEE_______________________________________________
. . . . .
1001 PGLAGTAGEPGRDGNPGSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPG 1050
__________________________________________________
. . . . .
1051 PPGPVGPAGKSGDRGESGPAGPAGAPGPAGSRGAPGPQGPRGDKGETGER 1100
_________________________________________________H
. . . . .
1101 GAAGIKGHRGFPGNPGAPGSPGPAGQQGAIGSPGPAGPRGPVGPSGPPGK 1150
HHHH______________________________________________
. . . . .
1151 DGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCCGGV 1200
__________________________________________________
. . . . .
1201 GAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLIS 1250
__EEEE___________________EEEE_____________HHHHHH__
. . . . .
1251 PDGSRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGE 1300
____________HHHHH_________EEE________EEEEEEEE_____
. . . . .
1301 TCISANPLNVPRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPEDVL 1350
EEE____________________EEEEEEE__________________HH
. . . . .
1351 DVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEF 1400
HHHHHHHHHHHHHHHHEEEEE_____________HHHHHHHH________
. . . . .
1401 KAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLPIVDIAPYDIG 1450
______EEEEEEE____________HHHHHHH_______EEEEE______
.
1451 GPDQEFGVDVGPVCFL 1466
_____EEEEE______
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 0.0 %
beta-contents : 0.0 %
coil-contents : 100.0 %
class : irregular
method : 2
alpha-contents : 0.0 %
beta-contents : 0.0 %
coil-contents : 100.0 %
class : irregular
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-15.12 0.00 0.00 0.00 0.00 0.00 0.00 -0.03 -0.39 -6.36 -3.35 -12.00 -12.00 0.00 -12.00 0.00 -61.24
-12.02 -1.74 -1.49 -0.40 0.00 0.00 0.00 0.00 0.00 -4.59 -3.35 -12.00 -12.00 0.00 -12.00 0.00 -59.58
ID: gi|115306|sp|P02461|CA13_HUMAN AC: xxx Len: 1400 1:I 1380 Sc: -59.58 Pv: 3.625512e-01 NO_GPI_SITE
GPI: learning from protozoa
-21.80 0.00 -0.05 -0.27 -4.00 0.00 0.00 -0.10 -0.05 -5.52 -11.49 -12.00 -12.00 0.00 -12.00 0.00 -79.28
-20.41 -0.19 -0.31 0.00 -4.00 0.00 0.00 0.00 0.00 -6.46 -11.49 -12.00 -12.00 0.00 -12.00 0.00 -78.86
ID: gi|115306|sp|P02461|CA13_HUMAN AC: xxx Len: 1400 1:I 1381 Sc: -78.86 Pv: 4.885877e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|115306|s 0.962 24 Y 0.867 24 Y 0.986 10 Y 0.910 Y
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|115306|s 0.553 422 Y 0.586 24 Y 0.982 7 Y 0.706 Y
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|115306|s 0.480 422 Y 0.489 24 Y 0.964 1361 Y 0.796 Y
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
1-10 MMSFVQKGSW
lllall 11-16
17-88 HPTIILAQQEAVEGGCSHLGQSYADRDVWK
PEPCQICVCDSGSVLCDDIICDDQELDCPN
PEIPFGECCAVC
pqpptaptrppngqgpqgpkgdpgppgipg 89-140
rngdpgipgqpgspgspgppgi
141-166 CESCPTGPQNYSPQYDSYDVKSGVAV
gglagypgpagppgppgppgtsghpgspgs 167-228
pgyqgppgepgqagpsgppgppgaigpsgp
ag
229-230 KD
gesgrpgrpgerglpgppgikgpagipgfp 231-261
g
262-293 MKGHRGFDGRNGEKGETGAPGLKGENGLPG
EN
gapgpmgprgapgergrpglpgaagargnd 294-348
gargsdgqpgppgppgtagfpgspg
349-353 AKGEV
gpagspgsngapg 354-366
367-368 QR
gepgpqghagaqgppgppgingspggkg 369-396
397-403 EMGPAGI
pgapglmgargppgpagangapglrggage 404-435
pg
436-437 KN
gakgepgprgergeagipg 438-456
457-476 VPGAKGEDGKDGSPGEPGAN
glpgaagergapgfrgpagpng 477-498
499-499 I
pgekgpagergapgpagprgaagepgrdgv 500-576
pggpgmrgmpgspggpgsdgkpgppgsqge
sgrpgppgpsgprgqpg
577-587 VMGFPGPKGND
gapgkngerggpggpgpqgppgknge 588-613
614-614 T
gpqgppgptgpggdkgdtgppgpqglqglp 615-723
gtggppgengkpgepgpkgdagapgapggk
gdagapgergppglagapglrggagppgpe
ggkgaagppgppgaagtpg
724-734 LQGMPGERGGL
gspgpkgdkgepggpgadgvpgkdgprgpt 735-861
gpigppgpagqpgdkgeggapglpgiagpr
gspgergetgppgpagfpgapgqngepggk
gergapgekgeggppgvagppggsgpagpp
gpqgvkg
862-863 ER
gspggpgaagfpgarglpgppgsngnpgpp 864-918
gpsgspgkdgppgpagntgapgspg
919-932 VSGPKGDAGQPGEK
gspgaqgppgapgplgiagitgarglagpp 933-975
gmpgprgspgpqg
976-992 VKGESGKPGANGLSGER
gppgpqglpglagtag 993-1008
1009-1037 EPGRDGNPGSDGLPGRDGSPGGKGDRGEN
gspgapgapghpgppgpvgpag 1038-1059
1060-1066 KSGDRGE
sgpagpagapgpagsrgapgpqgprg 1067-1092
1093-1109 DKGETGERGAAGIKGHR
gfpgnpgapgspgpagqqgaigspgpagpr 1110-1149
gpvgpsgppg
1150-1151 KD
gtsghpgpigppgprgnrgergsegspghp 1152-1218
gqpgppgppgapgpccggvgaaaiagigge
kaggfap
1219-1353 YYGDEPMDFKINTDEIMTSLKSVNGQIESL
ISPDGSRKNPARNCRDLKFCHPELKSGEYW
VDPNQGCKLDAIKVFCNMETGETCISANPL
NVPRKHWWTDSSAEKKHVWFGESMDGGFQF
SYGNPELPEDVLDVQ
laflrllssras 1354-1365
1366-1466 QNITYHCKNSIAYMDQASGNVKKALKLMGS
NEGEFKAEGNSKFTYTVLEDGCTKHTGEWS
KTVFEYRTRKAVRLPIVDIAPYDIGGPDQE
FGVDVGPVCFL
low complexity regions: SEG 25 3.0 3.3
>gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
1-46 MMSFVQKGSWLLLALLHPTIILAQQEAVEG
GCSHLGQSYADRDVWK
pepcqicvcdsgsvlcddiicddqeldcpn 47-148
peipfgeccavcpqpptaptrppngqgpqg
pkgdpgppgipgrngdpgipgqpgspgspg
ppgicescptgp
149-166 QNYSPQYDSYDVKSGVAV
gglagypgpagppgppgppgtsghpgspgs 167-1218
pgyqgppgepgqagpsgppgppgaigpsgp
agkdgesgrpgrpgerglpgppgikgpagi
pgfpgmkghrgfdgrngekgetgapglkge
nglpgengapgpmgprgapgergrpglpga
agargndgargsdgqpgppgppgtagfpgs
pgakgevgpagspgsngapgqrgepgpqgh
agaqgppgppgingspggkgemgpagipga
pglmgargppgpagangapglrggagepgk
ngakgepgprgergeagipgvpgakgedgk
dgspgepganglpgaagergapgfrgpagp
ngipgekgpagergapgpagprgaagepgr
dgvpggpgmrgmpgspggpgsdgkpgppgs
qgesgrpgppgpsgprgqpgvmgfpgpkgn
dgapgkngerggpggpgpqgppgkngetgp
qgppgptgpggdkgdtgppgpqglqglpgt
ggppgengkpgepgpkgdagapgapggkgd
agapgergppglagapglrggagppgpegg
kgaagppgppgaagtpglqgmpgergglgs
pgpkgdkgepggpgadgvpgkdgprgptgp
igppgpagqpgdkgeggapglpgiagprgs
pgergetgppgpagfpgapgqngepggkge
rgapgekgeggppgvagppggsgpagppgp
qgvkgergspggpgaagfpgarglpgppgs
ngnpgppgpsgspgkdgppgpagntgapgs
pgvsgpkgdagqpgekgspgaqgppgapgp
lgiagitgarglagppgmpgprgspgpqgv
kgesgkpganglsgergppgpqglpglagt
agepgrdgnpgsdglpgrdgspggkgdrge
ngspgapgapghpgppgpvgpagksgdrge
sgpagpagapgpagsrgapgpqgprgdkge
tgergaagikghrgfpgnpgapgspgpagq
qgaigspgpagprgpvgpsgppgkdgtsgh
pgpigppgprgnrgergsegspghpgqpgp
pgppgapgpccggvgaaaiagiggekaggf
ap
1219-1466 YYGDEPMDFKINTDEIMTSLKSVNGQIESL
ISPDGSRKNPARNCRDLKFCHPELKSGEYW
VDPNQGCKLDAIKVFCNMETGETCISANPL
NVPRKHWWTDSSAEKKHVWFGESMDGGFQF
SYGNPELPEDVLDVQLAFLRLLSSRASQNI
TYHCKNSIAYMDQASGNVKKALKLMGSNEG
EFKAEGNSKFTYTVLEDGCTKHTGEWSKTV
FEYRTRKAVRLPIVDIAPYDIGGPDQEFGV
DVGPVCFL
low complexity regions: SEG 45 3.4 3.75
>gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
1-88 MMSFVQKGSWLLLALLHPTIILAQQEAVEG
GCSHLGQSYADRDVWKPEPCQICVCDSGSV
LCDDIICDDQELDCPNPEIPFGECCAVC
pqpptaptrppngqgpqgpkgdpgppgipg 89-1218
rngdpgipgqpgspgspgppgicescptgp
qnyspqydsydvksgvavgglagypgpagp
pgppgppgtsghpgspgspgyqgppgepgq
agpsgppgppgaigpsgpagkdgesgrpgr
pgerglpgppgikgpagipgfpgmkghrgf
dgrngekgetgapglkgenglpgengapgp
mgprgapgergrpglpgaagargndgargs
dgqpgppgppgtagfpgspgakgevgpags
pgsngapgqrgepgpqghagaqgppgppgi
ngspggkgemgpagipgapglmgargppgp
agangapglrggagepgkngakgepgprge
rgeagipgvpgakgedgkdgspgepgangl
pgaagergapgfrgpagpngipgekgpage
rgapgpagprgaagepgrdgvpggpgmrgm
pgspggpgsdgkpgppgsqgesgrpgppgp
sgprgqpgvmgfpgpkgndgapgkngergg
pggpgpqgppgkngetgpqgppgptgpggd
kgdtgppgpqglqglpgtggppgengkpge
pgpkgdagapgapggkgdagapgergppgl
agapglrggagppgpeggkgaagppgppga
agtpglqgmpgergglgspgpkgdkgepgg
pgadgvpgkdgprgptgpigppgpagqpgd
kgeggapglpgiagprgspgergetgppgp
agfpgapgqngepggkgergapgekgeggp
pgvagppggsgpagppgpqgvkgergspgg
pgaagfpgarglpgppgsngnpgppgpsgs
pgkdgppgpagntgapgspgvsgpkgdagq
pgekgspgaqgppgapgplgiagitgargl
agppgmpgprgspgpqgvkgesgkpgangl
sgergppgpqglpglagtagepgrdgnpgs
dglpgrdgspggkgdrgengspgapgapgh
pgppgpvgpagksgdrgesgpagpagapgp
agsrgapgpqgprgdkgetgergaagikgh
rgfpgnpgapgspgpagqqgaigspgpagp
rgpvgpsgppgkdgtsghpgpigppgprgn
rgergsegspghpgqpgppgppgapgpccg
gvgaaaiagiggekaggfap
1219-1466 YYGDEPMDFKINTDEIMTSLKSVNGQIESL
ISPDGSRKNPARNCRDLKFCHPELKSGEYW
VDPNQGCKLDAIKVFCNMETGETCISANPL
NVPRKHWWTDSSAEKKHVWFGESMDGGFQF
SYGNPELPEDVLDVQLAFLRLLSSRASQNI
TYHCKNSIAYMDQASGNVKKALKLMGSNEG
EFKAEGNSKFTYTVLEDGCTKHTGEWSKTV
FEYRTRKAVRLPIVDIAPYDIGGPDQEFGV
DVGPVCFL
low complexity regions: XNU
# Score cutoff = 21, Search from offsets 1 to 4
# both members of each repeat flagged
# lambda = 0.347, K = 0.200, H = 0.664
>gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPCQICVCDSGSV
LCDDIICDDQELDCPNPEIPFGECcavcpqpptaptrppngqgpqgpkgdpgppgipgrn
gdpgipgqpgspgspgppgicescptgpQNYSPQYDSYDVKSGVavgglagypgpagppg
ppgppgtsghpgspgspgyqgppgepgqagpsgppgppgaigpsgpagkdgesgrpgrpg
erglpgppgikgpagipgfpgmkghrgfdgrngekgetgapglkgenglpgengapgpmg
prgapgergrpglpgaagargndgargsdgqpgppgppgtagfpgspgakgevgpagspg
sngapgqrgepgpqghagaqgppgppgingspggkgemgpagipgapglmgargppgpag
angapglrggagepgkngakgepgprgergeagipgvpgakgedgkdgspgepganglpg
aagergapgfrgpagpngipgekgpagergapgpagprgaagepgrdgvpggpgmrgmpg
spggpgsdgkpgppgsqgesgrpgppgpsgprgqpgvmgfpgpkgndgapgkngerggpg
gpgpqgppgkngetgpqgppgptgpggdkgdtgppgpqglqglpgtggppgengkpgepg
pkgdagapgapggkgdagapgergppglagapglrggagppgpeggkgaagppgppgaag
tpglqgmpgergglgspgpkgdkgepggpgadgvpgkdgprgptgpigppgpagqpgdkg
eggapglpgiagprgspgergetgppgpagfpgapgqngepggkgergapgekgeggppg
vagppggsgpagppgpqgvkgergspggpgaagfpgarglpgppgsngnpgppgpsgspg
kdgppgpagntgapgspgvsgpkgdagqpgekgspgaqgppgapgplgiagitgarglag
ppgmpgprgspgpqgvkgesgkpganglsgergppgpqglpglagtagepgrdgnpgsdg
lpgrdgspggkgdrgengspgapgapghpgppgpvgpagksgdrgesgpagpagapgpag
srgapgpqgprgdkgetgergaagikghrgfpgnpgapgspgpagqqgaigspgpagprg
pvgpsgppgkdgtsghpgpigppgprgnrgergsegspghpgqpgppgppgapgpCCggv
gaaaiagiggEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLISPDGSRKNPAR
NCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSS
AEKKHVWFGESMDGGFQFSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMD
QASGNVKKALKLMGSNEGEFKAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLP
IVDIAPYDIGGPDQEFGVDVGPVCFL
1 - 84 MMSFVQKGSW LLLALLHPTI ILAQQEAVEG GCSHLGQSYA DRDVWKPEPC QICVCDSGSV
LCDDIICDDQ ELDCPNPEIP FGEC
85 - 148 cavcpq pptaptrppn gqgpqgpkgd pgppgipgrn gdpgipgqpg spgspgppgi cesc
ptgp
149 - 164 QN YSPQYDSYDV KSGV
165 - 1195 avggla gypgpagppg ppgppgtsgh pgspgspgyq gppgepgqag psgppgppga igps
gpagkd gesgrpgrpg erglpgppgi kgpagipgfp gmkghrgfdg rngekgetga pglk
genglp gengapgpmg prgapgergr pglpgaagar gndgargsdg qpgppgppgt agfp
gspgak gevgpagspg sngapgqrge pgpqghagaq gppgppging spggkgemgp agip
gapglm gargppgpag angapglrgg agepgkngak gepgprgerg eagipgvpga kged
gkdgsp gepganglpg aagergapgf rgpagpngip gekgpagerg apgpagprga agep
grdgvp ggpgmrgmpg spggpgsdgk pgppgsqges grpgppgpsg prgqpgvmgf pgpk
gndgap gkngerggpg gpgpqgppgk ngetgpqgpp gptgpggdkg dtgppgpqgl qglp
gtggpp gengkpgepg pkgdagapga pggkgdagap gergppglag apglrggagp pgpe
ggkgaa gppgppgaag tpglqgmpge rgglgspgpk gdkgepggpg adgvpgkdgp rgpt
gpigpp gpagqpgdkg eggapglpgi agprgspger getgppgpag fpgapgqnge pggk
gergap gekgeggppg vagppggsgp agppgpqgvk gergspggpg aagfpgargl pgpp
gsngnp gppgpsgspg kdgppgpagn tgapgspgvs gpkgdagqpg ekgspgaqgp pgap
gplgia gitgarglag ppgmpgprgs pgpqgvkges gkpganglsg ergppgpqgl pgla
gtagep grdgnpgsdg lpgrdgspgg kgdrgengsp gapgapghpg ppgpvgpagk sgdr
gesgpa gpagapgpag srgapgpqgp rgdkgetger gaagikghrg fpgnpgapgs pgpa
gqqgai gspgpagprg pvgpsgppgk dgtsghpgpi gppgprgnrg ergsegspgh pgqp
gppgpp gapgp
1196 - 1197 CC
1198 - 1210 ggv gaaaiagigg
1211 - 1466 EKAGGFAPYY GDEPMDFKIN TDEIMTSLKS VNGQIESLIS PDGSRKNPAR NCRDLKFCHP
ELKSGEYWVD PNQGCKLDAI KVFCNMETGE TCISANPLNV PRKHWWTDSS AEKKHVWFGE
SMDGGFQFSY GNPELPEDVL DVQLAFLRLL SSRASQNITY HCKNSIAYMD QASGNVKKAL
KLMGSNEGEF KAEGNSKFTY TVLEDGCTKH TGEWSKTVFE YRTRKAVRLP IVDIAPYDIG
GPDQEFGVDV GPVCFL
low complexity regions: DUST
>gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPCQICVCDSGSV
LCDDIICDDQELDCPNPEIPFGECCAVCPQPPTAPTRPPNGQGPQGPKGDPGPPGIPGRN
GDPGIPGQPGSPGSPGPPGICESCPTGPQNYSPQYDSYDVKSGVAVGGLAGYPGPAGPPG
PPGPPGTSGHPGSPGSPGYQGPPGEPGQAGPSGPPGPPGAIGPSGPAGKDGESGRPGRPG
ERGLPGPPGIKGPAGIPGFPGMKGHRGFDGRNGEKGETGAPGLKGENGLPGENGAPGPMG
PRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAKGEVGPAGSPG
SNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGPAGIPGAPGLMGARGPPGPAG
ANGAPGLRGGAGEPGKNGAKGEPGPRGERGEAGIPGVPGAKGEDGKDGSPGEPGANGLPG
AAGERGAPGFRGPAGPNGIPGEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPG
SPGGPGSDGKPGPPGSQGESGRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPG
GPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGLQGLPGTGGPPGENGKPGEPG
PKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGPPGPEGGKGAAGPPGPPGAAG
TPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGPRGPTGPIGPPGPAGQPGDKG
EGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPG
VAGPPGGSGPAGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPG
KDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIAGITGARGLAG
PPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGLPGLAGTAGEPGRDGNPGSDG
LPGRDGSPGGKGDRGENGSPGAPGAPGHPGPPGPVGPAGKSGDRGESGPAGPAGAPGPAG
SRGAPGPQGPRGDKGETGERGAAGIKGHRGFPGNPGAPGSPGPAGQQGAIGSPGPAGPRG
PVGPSGPPGKDGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCCGGV
GAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLISPDGSRKNPAR
NCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSS
AEKKHVWFGESMDGGFQFSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMD
QASGNVKKALKLMGSNEGEFKAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLP
IVDIAPYDIGGPDQEFGVDVGPVCFL
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for gi|115306|sp|P02461|CA13_HUMAN
sequence: 1400 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MMSFVQKGSW LLLALLHPTI ILAQQEAVEG GCSHLGQSYA DRDVWKPEPC QICVCDSGSV
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 120
LCDDIICDDQ ELDCPNPEIP FGECCAVCPQ PPTAPTRPPN GQGPQGPKGD PGPPGIPGRN
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 180
GDPGIPGQPG SPGSPGPPGI CESCPTGPQN YSPQYDSYDV KSGVAVGGLA GYPGPAGPPG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 240
PPGPPGTSGH PGSPGSPGYQ GPPGEPGQAG PSGPPGPPGA IGPSGPAGKD GESGRPGRPG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 300
ERGLPGPPGI KGPAGIPGFP GMKGHRGFDG RNGEKGETGA PGLKGENGLP GENGAPGPMG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 360
PRGAPGERGR PGLPGAAGAR GNDGARGSDG QPGPPGPPGT AGFPGSPGAK GEVGPAGSPG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 420
SNGAPGQRGE PGPQGHAGAQ GPPGPPGING SPGGKGEMGP AGIPGAPGLM GARGPPGPAG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 480
ANGAPGLRGG AGEPGKNGAK GEPGPRGERG EAGIPGVPGA KGEDGKDGSP GEPGANGLPG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 540
AAGERGAPGF RGPAGPNGIP GEKGPAGERG APGPAGPRGA AGEPGRDGVP GGPGMRGMPG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 600
SPGGPGSDGK PGPPGSQGES GRPGPPGPSG PRGQPGVMGF PGPKGNDGAP GKNGERGGPG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 660
GPGPQGPPGK NGETGPQGPP GPTGPGGDKG DTGPPGPQGL QGLPGTGGPP GENGKPGEPG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 720
PKGDAGAPGA PGGKGDAGAP GERGPPGLAG APGLRGGAGP PGPEGGKGAA GPPGPPGAAG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 780
TPGLQGMPGE RGGLGSPGPK GDKGEPGGPG ADGVPGKDGP RGPTGPIGPP GPAGQPGDKG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 840
EGGAPGLPGI AGPRGSPGER GETGPPGPAG FPGAPGQNGE PGGKGERGAP GEKGEGGPPG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 900
VAGPPGGSGP AGPPGPQGVK GERGSPGGPG AAGFPGARGL PGPPGSNGNP GPPGPSGSPG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 960
KDGPPGPAGN TGAPGSPGVS GPKGDAGQPG EKGSPGAQGP PGAPGPLGIA GITGARGLAG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 1020
PPGMPGPRGS PGPQGVKGES GKPGANGLSG ERGPPGPQGL PGLAGTAGEP GRDGNPGSDG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 1080
LPGRDGSPGG KGDRGENGSP GAPGAPGHPG PPGPVGPAGK SGDRGESGPA GPAGAPGPAG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 1140
SRGAPGPQGP RGDKGETGER GAAGIKGHRG FPGNPGAPGS PGPAGQQGAI GSPGPAGPRG
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 1200
PVGPSGPPGK DGTSGHPGPI GPPGPRGNRG ERGSEGSPGH PGQPGPPGPP GAPGPCCGGV
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 1260
GAAAIAGIGG EKAGGFAPYY GDEPMDFKIN TDEIMTSLKS VNGQIESLIS PDGSRKNPAR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 1320
NCRDLKFCHP ELKSGEYWVD PNQGCKLDAI KVFCNMETGE TCISANPLNV PRKHWWTDSS
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . | . | . | . | . 1380
AEKKHVWFGE SMDGGFQFSY GNPELPEDVL DVQLAFLRLL SSRASQNITY HCKNSIAYMD
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border
---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~111 1111111111 11111111~~ ~~~~~~~~~~ * 21 M'95 +w polar
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif.
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local
. | . |
QASGNVKKAL KLMGSNEGEF
~~~~~~~~~~ ~~~~~~~~~~
---------- ----------
~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~
~~~~~~~~~~ ~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem15.___inter___ is a single sequence
Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale
Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok
Using sequence file: tem15.___inter___
(1 sequences)
MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPC
QICVCDSGSVLCDDIICDDQELDCPNPEIPFGECCAVCPQPPTAPTRPPN
GQGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPGICESCPTGPQN
YSPQYDSYDVKSGVAVGGLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQ
GPPGEPGQAGPSGPPGPPGAIGPSGPAGKDGESGRPGRPGERGLPGPPGI
KGPAGIPGFPGMKGHRGFDGRNGEKGETGAPGLKGENGLPGENGAPGPMG
PRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAK
GEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGP
AGIPGAPGLMGARGPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERG
EAGIPGVPGAKGEDGKDGSPGEPGANGLPGAAGERGAPGFRGPAGPNGIP
GEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPGSPGGPGSDGK
PGPPGSQGESGRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPG
GPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGLQGLPGTGGPP
GENGKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP
PGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPG
ADGVPGKDGPRGPTGPIGPPGPAGQPGDKGEGGAPGLPGIAGPRGSPGER
GETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPGVAGPPGGSGP
AGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPG
KDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIA
GITGARGLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGL
PGLAGTAGEPGRDGNPGSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPG
PPGPVGPAGKSGDRGESGPAGPAGAPGPAGSRGAPGPQGPRGDKGETGER
GAAGIKGHRGFPGNPGAPGSPGPAGQQGAIGSPGPAGPRGPVGPSGPPGK
DGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCCGGV
GAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLIS
PDGSRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGE
TCISANPLNVPRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPEDVL
DVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEF
KAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLPIVDIAPYDIG
GPDQEFGVDVGPVCFL
(p)rokaryotic or (e)ukaryotic: e
Charge-pair energy: 0
Length of full window (odd number!): 21
Length of core window (odd number!): 11
Number of residues to add to each end of helix: 1
Critical length: 60
Upper cutoff for candidates: 1
Lower cutoff for candidates: 0.6
Total of 32 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 5 25 1.102 Certain
2 162 182 0.979 Putative
3 208 228 0.636 Putative
4 708 728 0.675 Putative
5 836 856 0.738 Putative
6 935 955 0.913 Putative
7 1190 1210 1.447 Certain
Warning! Only printing 30 out of 32 structures
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 6 7
Loop length 4 136 25 479 107 78 234 256
K+R profile 2.00 0.00 + +
+ + + +
CYT-EXT prof - - 0.40 0.68
0.10 0.52 0.98 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -1.20
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1 3 4 5 6 7
Loop length 4 182 479 107 78 234 256
K+R profile 2.00 + + +
+ + +
CYT-EXT prof - 0.52 0.98 0.68
0.56 0.40 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.54
-> Orientation: N-out
----------------------------------------------------------------------
Structure 3
Transmembrane segments included in this structure:
Segment 1 2 4 5 6 7
Loop length 4 136 525 107 78 234 256
K+R profile 2.00 + + +
+ + +
CYT-EXT prof - 0.58 0.98 0.68
0.10 0.40 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.05
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 1.06
-> Orientation: N-out
----------------------------------------------------------------------
Structure 4
Transmembrane segments included in this structure:
Segment 1 4 5 6 7
Loop length 4 682 107 78 234 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.40 0.68
0.57 0.98 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.05
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -1.15
-> Orientation: N-in
----------------------------------------------------------------------
Structure 5
Transmembrane segments included in this structure:
Segment 1 2 3 5 6 7
Loop length 4 136 25 607 78 234 256
K+R profile 2.00 0.00 + +
+ + +
CYT-EXT prof - - 0.98 0.68
0.10 0.51 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.02
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.37
-> Orientation: N-out
----------------------------------------------------------------------
Structure 6
Transmembrane segments included in this structure:
Segment 1 3 5 6 7
Loop length 4 182 607 78 234 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.51 0.68
0.56 0.98 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.02
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -1.04
-> Orientation: N-in
----------------------------------------------------------------------
Structure 7
Transmembrane segments included in this structure:
Segment 1 2 5 6 7
Loop length 4 136 653 78 234 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.56 0.68
0.10 0.98 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.25
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.52
-> Orientation: N-in
----------------------------------------------------------------------
Structure 8
Transmembrane segments included in this structure:
Segment 1 5 6 7
Loop length 4 810 78 234 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.98 0.68
0.55 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.27
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.43
-> Orientation: N-out
----------------------------------------------------------------------
Structure 9
Transmembrane segments included in this structure:
Segment 1 2 3 4 6 7
Loop length 4 136 25 479 206 234 256
K+R profile 2.00 0.00 + +
+ + +
CYT-EXT prof - - 0.71 0.68
0.10 0.52 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.01
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.09
-> Orientation: N-out
----------------------------------------------------------------------
Structure 10
Transmembrane segments included in this structure:
Segment 1 3 4 6 7
Loop length 4 182 479 206 234 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.52 0.68
0.56 0.71 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.01
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.76
-> Orientation: N-in
----------------------------------------------------------------------
Structure 11
Transmembrane segments included in this structure:
Segment 1 2 4 6 7
Loop length 4 136 525 206 234 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.58 0.68
0.10 0.71 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.14
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.23
-> Orientation: N-in
----------------------------------------------------------------------
Structure 12
Transmembrane segments included in this structure:
Segment 1 4 6 7
Loop length 4 682 206 234 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.71 0.68
0.57 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.15
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.14
-> Orientation: N-out
----------------------------------------------------------------------
Structure 13
Transmembrane segments included in this structure:
Segment 1 2 3 6 7
Loop length 4 136 25 706 234 256
K+R profile 2.00 0.00 +
+ + +
CYT-EXT prof - - 0.68
0.10 0.59 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.07
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.69
-> Orientation: N-in
----------------------------------------------------------------------
Structure 14
Transmembrane segments included in this structure:
Segment 1 3 6 7
Loop length 4 182 706 234 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.59 0.68
0.56 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.07
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.03
-> Orientation: N-out
----------------------------------------------------------------------
Structure 15
Transmembrane segments included in this structure:
Segment 1 2 6 7
Loop length 4 136 752 234 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.62 0.68
0.10 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.74
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.53
-> Orientation: N-out
----------------------------------------------------------------------
Structure 16
Transmembrane segments included in this structure:
Segment 1 6 7
Loop length 4 909 234 256
K+R profile 2.00 +
+ +
CYT-EXT prof - 0.68
0.61 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.78
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.62
-> Orientation: N-in
----------------------------------------------------------------------
Structure 17
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 7
Loop length 4 136 25 479 107 333 256
K+R profile 2.00 0.00 + +
+ + +
CYT-EXT prof - - 0.40 0.68
0.10 0.52 0.75
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.01
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.28
-> Orientation: N-in
----------------------------------------------------------------------
Structure 18
Transmembrane segments included in this structure:
Segment 1 3 4 5 7
Loop length 4 182 479 107 333 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.52 0.75
0.56 0.40 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.01
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.38
-> Orientation: N-in
----------------------------------------------------------------------
Structure 19
Transmembrane segments included in this structure:
Segment 1 2 4 5 7
Loop length 4 136 525 107 333 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.58 0.75
0.10 0.40 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.06
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.14
-> Orientation: N-out
----------------------------------------------------------------------
Structure 20
Transmembrane segments included in this structure:
Segment 1 4 5 7
Loop length 4 682 107 333 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.40 0.68
0.57 0.75
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.06
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.23
-> Orientation: N-in
----------------------------------------------------------------------
Structure 21
Transmembrane segments included in this structure:
Segment 1 2 3 5 7
Loop length 4 136 25 607 333 256
K+R profile 2.00 0.00 +
+ + +
CYT-EXT prof - - 0.75
0.10 0.51 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.03
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.54
-> Orientation: N-in
----------------------------------------------------------------------
Structure 22
Transmembrane segments included in this structure:
Segment 1 3 5 7
Loop length 4 182 607 333 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.51 0.68
0.56 0.75
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.03
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.12
-> Orientation: N-in
----------------------------------------------------------------------
Structure 23
Transmembrane segments included in this structure:
Segment 1 2 5 7
Loop length 4 136 653 333 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.56 0.68
0.10 0.75
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.33
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.39
-> Orientation: N-out
----------------------------------------------------------------------
Structure 24
Transmembrane segments included in this structure:
Segment 1 5 7
Loop length 4 810 333 256
K+R profile 2.00 +
+ +
CYT-EXT prof - 0.75
0.55 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.34
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.49
-> Orientation: N-in
----------------------------------------------------------------------
Structure 25
Transmembrane segments included in this structure:
Segment 1 2 3 4 7
Loop length 4 136 25 479 461 256
K+R profile 2.00 0.00 +
+ + +
CYT-EXT prof - - 0.69
0.10 0.52 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.02
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.61
-> Orientation: N-in
----------------------------------------------------------------------
Structure 26
Transmembrane segments included in this structure:
Segment 1 3 4 7
Loop length 4 182 479 461 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.52 0.68
0.56 0.69
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.02
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.05
-> Orientation: N-in
----------------------------------------------------------------------
Structure 27
Transmembrane segments included in this structure:
Segment 1 2 4 7
Loop length 4 136 525 461 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.58 0.68
0.10 0.69
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.18
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.48
-> Orientation: N-out
----------------------------------------------------------------------
Structure 28
Transmembrane segments included in this structure:
Segment 1 4 7
Loop length 4 682 461 256
K+R profile 2.00 +
+ +
CYT-EXT prof - 0.69
0.57 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.19
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.57
-> Orientation: N-in
----------------------------------------------------------------------
Structure 29
Transmembrane segments included in this structure:
Segment 1 2 3 7
Loop length 4 136 25 961 256
K+R profile 2.00 0.00 +
+ +
CYT-EXT prof - - 0.68
0.10 0.61
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.09
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.02
-> Orientation: N-in
----------------------------------------------------------------------
Structure 30
Transmembrane segments included in this structure:
Segment 1 3 7
Loop length 4 182 961 256
K+R profile 2.00 +
+ +
CYT-EXT prof - 0.61
0.56 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.09
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.64
-> Orientation: N-in
----------------------------------------------------------------------
"tem15" 1466
5 25 #t 1.10208
162 182 #f 0.979167
208 228 #f 0.636458
708 728 #f 0.675
836 856 #f 0.7375
935 955 #f 0.9125
1190 1210 #t 1.44688
************************************
*TOPPREDM with prokaryotic function*
************************************
tem15.___inter___ is a single sequence
Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale
Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok
Using sequence file: tem15.___inter___
(1 sequences)
MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPC
QICVCDSGSVLCDDIICDDQELDCPNPEIPFGECCAVCPQPPTAPTRPPN
GQGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPGICESCPTGPQN
YSPQYDSYDVKSGVAVGGLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQ
GPPGEPGQAGPSGPPGPPGAIGPSGPAGKDGESGRPGRPGERGLPGPPGI
KGPAGIPGFPGMKGHRGFDGRNGEKGETGAPGLKGENGLPGENGAPGPMG
PRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAK
GEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGP
AGIPGAPGLMGARGPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERG
EAGIPGVPGAKGEDGKDGSPGEPGANGLPGAAGERGAPGFRGPAGPNGIP
GEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPGSPGGPGSDGK
PGPPGSQGESGRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPG
GPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGLQGLPGTGGPP
GENGKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP
PGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPG
ADGVPGKDGPRGPTGPIGPPGPAGQPGDKGEGGAPGLPGIAGPRGSPGER
GETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPGVAGPPGGSGP
AGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPG
KDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIA
GITGARGLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGL
PGLAGTAGEPGRDGNPGSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPG
PPGPVGPAGKSGDRGESGPAGPAGAPGPAGSRGAPGPQGPRGDKGETGER
GAAGIKGHRGFPGNPGAPGSPGPAGQQGAIGSPGPAGPRGPVGPSGPPGK
DGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCCGGV
GAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLIS
PDGSRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGE
TCISANPLNVPRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPEDVL
DVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEF
KAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLPIVDIAPYDIG
GPDQEFGVDVGPVCFL
(p)rokaryotic or (e)ukaryotic: p
Charge-pair energy: 0
Length of full window (odd number!): 21
Length of core window (odd number!): 11
Number of residues to add to each end of helix: 1
Critical length: 60
Upper cutoff for candidates: 1
Lower cutoff for candidates: 0.6
Total of 32 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 5 25 1.102 Certain
2 162 182 0.979 Putative
3 208 228 0.636 Putative
4 708 728 0.675 Putative
5 836 856 0.738 Putative
6 935 955 0.913 Putative
7 1190 1210 1.447 Certain
Warning! Only printing 30 out of 32 structures
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 6 7
Loop length 4 136 25 479 107 78 234 256
K+R profile 2.00 0.00 + +
+ + + +
CYT-EXT prof - - 0.40 0.68
0.10 0.52 0.98 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -1.20
-> Orientation: N-in
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 1 3 4 5 6 7
Loop length 4 182 479 107 78 234 256
K+R profile 2.00 + + +
+ + +
CYT-EXT prof - 0.52 0.98 0.68
0.56 0.40 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.00
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.54
-> Orientation: N-out
----------------------------------------------------------------------
Structure 3
Transmembrane segments included in this structure:
Segment 1 2 4 5 6 7
Loop length 4 136 525 107 78 234 256
K+R profile 2.00 + + +
+ + +
CYT-EXT prof - 0.58 0.98 0.68
0.10 0.40 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.05
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 1.06
-> Orientation: N-out
----------------------------------------------------------------------
Structure 4
Transmembrane segments included in this structure:
Segment 1 4 5 6 7
Loop length 4 682 107 78 234 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.40 0.68
0.57 0.98 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.05
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -1.15
-> Orientation: N-in
----------------------------------------------------------------------
Structure 5
Transmembrane segments included in this structure:
Segment 1 2 3 5 6 7
Loop length 4 136 25 607 78 234 256
K+R profile 2.00 0.00 + +
+ + +
CYT-EXT prof - - 0.98 0.68
0.10 0.51 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.02
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.37
-> Orientation: N-out
----------------------------------------------------------------------
Structure 6
Transmembrane segments included in this structure:
Segment 1 3 5 6 7
Loop length 4 182 607 78 234 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.51 0.68
0.56 0.98 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.02
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -1.04
-> Orientation: N-in
----------------------------------------------------------------------
Structure 7
Transmembrane segments included in this structure:
Segment 1 2 5 6 7
Loop length 4 136 653 78 234 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.56 0.68
0.10 0.98 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.25
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.52
-> Orientation: N-in
----------------------------------------------------------------------
Structure 8
Transmembrane segments included in this structure:
Segment 1 5 6 7
Loop length 4 810 78 234 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.98 0.68
0.55 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.27
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.43
-> Orientation: N-out
----------------------------------------------------------------------
Structure 9
Transmembrane segments included in this structure:
Segment 1 2 3 4 6 7
Loop length 4 136 25 479 206 234 256
K+R profile 2.00 0.00 + +
+ + +
CYT-EXT prof - - 0.71 0.68
0.10 0.52 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.01
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.09
-> Orientation: N-out
----------------------------------------------------------------------
Structure 10
Transmembrane segments included in this structure:
Segment 1 3 4 6 7
Loop length 4 182 479 206 234 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.52 0.68
0.56 0.71 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.01
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.76
-> Orientation: N-in
----------------------------------------------------------------------
Structure 11
Transmembrane segments included in this structure:
Segment 1 2 4 6 7
Loop length 4 136 525 206 234 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.58 0.68
0.10 0.71 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.14
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.23
-> Orientation: N-in
----------------------------------------------------------------------
Structure 12
Transmembrane segments included in this structure:
Segment 1 4 6 7
Loop length 4 682 206 234 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.71 0.68
0.57 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.15
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.14
-> Orientation: N-out
----------------------------------------------------------------------
Structure 13
Transmembrane segments included in this structure:
Segment 1 2 3 6 7
Loop length 4 136 25 706 234 256
K+R profile 2.00 0.00 +
+ + +
CYT-EXT prof - - 0.68
0.10 0.59 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.07
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.69
-> Orientation: N-in
----------------------------------------------------------------------
Structure 14
Transmembrane segments included in this structure:
Segment 1 3 6 7
Loop length 4 182 706 234 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.59 0.68
0.56 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.07
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.03
-> Orientation: N-out
----------------------------------------------------------------------
Structure 15
Transmembrane segments included in this structure:
Segment 1 2 6 7
Loop length 4 136 752 234 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.62 0.68
0.10 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.74
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.53
-> Orientation: N-out
----------------------------------------------------------------------
Structure 16
Transmembrane segments included in this structure:
Segment 1 6 7
Loop length 4 909 234 256
K+R profile 2.00 +
+ +
CYT-EXT prof - 0.68
0.61 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.78
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.62
-> Orientation: N-in
----------------------------------------------------------------------
Structure 17
Transmembrane segments included in this structure:
Segment 1 2 3 4 5 7
Loop length 4 136 25 479 107 333 256
K+R profile 2.00 0.00 + +
+ + +
CYT-EXT prof - - 0.40 0.68
0.10 0.52 0.75
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.01
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.28
-> Orientation: N-in
----------------------------------------------------------------------
Structure 18
Transmembrane segments included in this structure:
Segment 1 3 4 5 7
Loop length 4 182 479 107 333 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.52 0.75
0.56 0.40 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.01
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.38
-> Orientation: N-in
----------------------------------------------------------------------
Structure 19
Transmembrane segments included in this structure:
Segment 1 2 4 5 7
Loop length 4 136 525 107 333 256
K+R profile 2.00 + +
+ + +
CYT-EXT prof - 0.58 0.75
0.10 0.40 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.06
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.14
-> Orientation: N-out
----------------------------------------------------------------------
Structure 20
Transmembrane segments included in this structure:
Segment 1 4 5 7
Loop length 4 682 107 333 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.40 0.68
0.57 0.75
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.06
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.23
-> Orientation: N-in
----------------------------------------------------------------------
Structure 21
Transmembrane segments included in this structure:
Segment 1 2 3 5 7
Loop length 4 136 25 607 333 256
K+R profile 2.00 0.00 +
+ + +
CYT-EXT prof - - 0.75
0.10 0.51 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.03
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.54
-> Orientation: N-in
----------------------------------------------------------------------
Structure 22
Transmembrane segments included in this structure:
Segment 1 3 5 7
Loop length 4 182 607 333 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.51 0.68
0.56 0.75
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.03
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.12
-> Orientation: N-in
----------------------------------------------------------------------
Structure 23
Transmembrane segments included in this structure:
Segment 1 2 5 7
Loop length 4 136 653 333 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.56 0.68
0.10 0.75
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.33
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.39
-> Orientation: N-out
----------------------------------------------------------------------
Structure 24
Transmembrane segments included in this structure:
Segment 1 5 7
Loop length 4 810 333 256
K+R profile 2.00 +
+ +
CYT-EXT prof - 0.75
0.55 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.34
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.49
-> Orientation: N-in
----------------------------------------------------------------------
Structure 25
Transmembrane segments included in this structure:
Segment 1 2 3 4 7
Loop length 4 136 25 479 461 256
K+R profile 2.00 0.00 +
+ + +
CYT-EXT prof - - 0.69
0.10 0.52 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.02
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.61
-> Orientation: N-in
----------------------------------------------------------------------
Structure 26
Transmembrane segments included in this structure:
Segment 1 3 4 7
Loop length 4 182 479 461 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.52 0.68
0.56 0.69
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.02
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.05
-> Orientation: N-in
----------------------------------------------------------------------
Structure 27
Transmembrane segments included in this structure:
Segment 1 2 4 7
Loop length 4 136 525 461 256
K+R profile 2.00 + +
+ +
CYT-EXT prof - 0.58 0.68
0.10 0.69
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.18
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: 0.48
-> Orientation: N-out
----------------------------------------------------------------------
Structure 28
Transmembrane segments included in this structure:
Segment 1 4 7
Loop length 4 682 461 256
K+R profile 2.00 +
+ +
CYT-EXT prof - 0.69
0.57 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.19
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.57
-> Orientation: N-in
----------------------------------------------------------------------
Structure 29
Transmembrane segments included in this structure:
Segment 1 2 3 7
Loop length 4 136 25 961 256
K+R profile 2.00 0.00 +
+ +
CYT-EXT prof - - 0.68
0.10 0.61
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.09
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.02
-> Orientation: N-in
----------------------------------------------------------------------
Structure 30
Transmembrane segments included in this structure:
Segment 1 3 7
Loop length 4 182 961 256
K+R profile 2.00 +
+ +
CYT-EXT prof - 0.61
0.56 0.68
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 2.00
Tm probability: 0.09
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 3.00
(NEG-POS)/(NEG+POS): -1.0000
NEG: 0.0000
POS: 1.0000
-> Orientation: N-in
CYT-EXT difference: -0.64
-> Orientation: N-in
----------------------------------------------------------------------
"tem15" 1466
5 25 #t 1.10208
162 182 #f 0.979167
208 228 #f 0.636458
708 728 #f 0.675
836 856 #f 0.7375
935 955 #f 0.9125
1190 1210 #t 1.44688
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem15.___saps___
SAPS. Version of April 11, 1996.
Date run: Fri Nov 10 14:40:14 2000
File: /people/maria/tem15.___saps___
ID gi|115306|sp|P02461|CA13_HUMAN
DE COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
number of residues: 1466; molecular weight: 138.6 kdal
1 MMSFVQKGSW LLLALLHPTI ILAQQEAVEG GCSHLGQSYA DRDVWKPEPC QICVCDSGSV
61 LCDDIICDDQ ELDCPNPEIP FGECCAVCPQ PPTAPTRPPN GQGPQGPKGD PGPPGIPGRN
121 GDPGIPGQPG SPGSPGPPGI CESCPTGPQN YSPQYDSYDV KSGVAVGGLA GYPGPAGPPG
181 PPGPPGTSGH PGSPGSPGYQ GPPGEPGQAG PSGPPGPPGA IGPSGPAGKD GESGRPGRPG
241 ERGLPGPPGI KGPAGIPGFP GMKGHRGFDG RNGEKGETGA PGLKGENGLP GENGAPGPMG
301 PRGAPGERGR PGLPGAAGAR GNDGARGSDG QPGPPGPPGT AGFPGSPGAK GEVGPAGSPG
361 SNGAPGQRGE PGPQGHAGAQ GPPGPPGING SPGGKGEMGP AGIPGAPGLM GARGPPGPAG
421 ANGAPGLRGG AGEPGKNGAK GEPGPRGERG EAGIPGVPGA KGEDGKDGSP GEPGANGLPG
481 AAGERGAPGF RGPAGPNGIP GEKGPAGERG APGPAGPRGA AGEPGRDGVP GGPGMRGMPG
541 SPGGPGSDGK PGPPGSQGES GRPGPPGPSG PRGQPGVMGF PGPKGNDGAP GKNGERGGPG
601 GPGPQGPPGK NGETGPQGPP GPTGPGGDKG DTGPPGPQGL QGLPGTGGPP GENGKPGEPG
661 PKGDAGAPGA PGGKGDAGAP GERGPPGLAG APGLRGGAGP PGPEGGKGAA GPPGPPGAAG
721 TPGLQGMPGE RGGLGSPGPK GDKGEPGGPG ADGVPGKDGP RGPTGPIGPP GPAGQPGDKG
781 EGGAPGLPGI AGPRGSPGER GETGPPGPAG FPGAPGQNGE PGGKGERGAP GEKGEGGPPG
841 VAGPPGGSGP AGPPGPQGVK GERGSPGGPG AAGFPGARGL PGPPGSNGNP GPPGPSGSPG
901 KDGPPGPAGN TGAPGSPGVS GPKGDAGQPG EKGSPGAQGP PGAPGPLGIA GITGARGLAG
961 PPGMPGPRGS PGPQGVKGES GKPGANGLSG ERGPPGPQGL PGLAGTAGEP GRDGNPGSDG
1021 LPGRDGSPGG KGDRGENGSP GAPGAPGHPG PPGPVGPAGK SGDRGESGPA GPAGAPGPAG
1081 SRGAPGPQGP RGDKGETGER GAAGIKGHRG FPGNPGAPGS PGPAGQQGAI GSPGPAGPRG
1141 PVGPSGPPGK DGTSGHPGPI GPPGPRGNRG ERGSEGSPGH PGQPGPPGPP GAPGPCCGGV
1201 GAAAIAGIGG EKAGGFAPYY GDEPMDFKIN TDEIMTSLKS VNGQIESLIS PDGSRKNPAR
1261 NCRDLKFCHP ELKSGEYWVD PNQGCKLDAI KVFCNMETGE TCISANPLNV PRKHWWTDSS
1321 AEKKHVWFGE SMDGGFQFSY GNPELPEDVL DVQLAFLRLL SSRASQNITY HCKNSIAYMD
1381 QASGNVKKAL KLMGSNEGEF KAEGNSKFTY TVLEDGCTKH TGEWSKTVFE YRTRKAVRLP
1441 IVDIAPYDIG GPDQEFGVDV GPVCFL
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A :115( 7.8%); C : 22( 1.5%); D : 55( 3.8%); E : 74( 5.0%); F- : 23( 1.6%)
G++:413(28.2%); H : 14( 1.0%); I : 36( 2.5%); K : 62( 4.2%); L--: 48( 3.3%)
M : 17( 1.2%); N : 41( 2.8%); P++:281(19.2%); Q : 43( 2.9%); R : 60( 4.1%)
S : 73( 5.0%); T- : 31( 2.1%); V- : 36( 2.5%); W : 7( 0.5%); Y- : 15( 1.0%)
KR : 122 ( 8.3%); ED : 129 ( 8.8%); AGP ++: 809 ( 55.2%);
KRED : 251 ( 17.1%); KR-ED : -7 ( -0.5%); FIKMNY- : 194 ( 13.2%);
LVIFM --: 160 ( 10.9%); ST - : 104 ( 7.1%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 000000+000 0000000000 00000-00-0 0000000000 -+-00+0-00 00000-0000
61 00--000--0 -0-0000-00 00-0000000 000000+000 0000000+0- 00000000+0
121 0-00000000 0000000000 0-00000000 00000-00-0 +000000000 0000000000
181 0000000000 0000000000 0000-00000 0000000000 00000000+- 0-00+00+00
241 -+00000000 +000000000 00+00+00-0 +00-+0-000 000+0-0000 0-00000000
301 0+0000-+0+ 000000000+ 00-00+00-0 0000000000 000000000+ 0-00000000
361 0000000+0- 0000000000 0000000000 0000+0-000 0000000000 00+0000000
421 0000000+00 00-00+000+ 0-000+0-+0 -000000000 +0--0+-000 0-00000000
481 000-+00000 +000000000 0-+0000-+0 0000000+00 00-00+-000 00000+0000
541 0000000-0+ 00000000-0 0+00000000 0+00000000 000+00-000 0+00-+0000
601 000000000+ 00-0000000 0000000-+0 -000000000 0000000000 0-00+00-00
661 0+0-000000 000+0-0000 0-+0000000 0000+00000 000-00+000 0000000000
721 000000000- +00000000+ 0-+0-00000 0-0000+-00 +000000000 0000000-+0
781 -000000000 000+0000-+ 0-00000000 000000000- 000+0-+000 0-+0-00000
841 0000000000 000000000+ 0-+0000000 0000000+00 0000000000 0000000000
901 +-00000000 0000000000 00+0-00000 -+00000000 0000000000 00000+0000
961 0000000+00 000000+0-0 0+00000000 -+00000000 00000000-0 0+-00000-0
1021 000+-00000 +0-+0-0000 0000000000 000000000+ 00-+0-0000 0000000000
1081 0+00000000 +0-+0-00-+ 00000+00+0 0000000000 0000000000 00000000+0
1141 000000000+ -000000000 00000+00+0 -+00-00000 0000000000 0000000000
1201 0000000000 -+00000000 0--00-0+00 0--00000+0 00000-0000 0-00++000+
1261 00+-0+0000 -0+00-000- 00000+0-00 +00000-00- 0000000000 0++0000-00
1321 0-++00000- 00-0000000 000-00--00 -000000+00 00+0000000 00+000000-
1381 000000++00 +00000-0-0 +0-000+000 000--000+0 00-00+000- 0+0++00+00
1441 00-0000-00 00-0-000-0 000000
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 9/30 or 12/45 or 14/60): none
Negative charge clusters (cmin = 9/30 or 12/45 or 15/60):
1) From 56 to 83: DSGSVLCDDIICDDQELDCPNPEIPFGE
-000000--000--0-0-0000-0000-
quartile: 1; size: 28, +count: 0, -count: 9, 0count: 19; t-value: 4.36
E: 3 (10.7%); D: 6 (21.4%); I: 3 (10.7%); P: 3 (10.7%);
C: 3 (10.7%); LVIFM: 7 (25.0%);
Mixed charge clusters (cmin = 14/30 or 19/45 or 23/60): none
B. HIGH SCORING (UN)CHARGED SEGMENTS.
There are no high scoring positive charge segments.
There are no high scoring negative charge segments.
There are no high scoring mixed charge segments.
There are no high scoring uncharged segments.
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 5 | 5 | 7 | 54 | 10 | 10 | 13 | 12 | 12 | 16 | 6 | 8 |
lmin1 6 | 6 | 8 | 65 | 12 | 12 | 15 | 15 | 15 | 19 | 8 | 9 |
lmin2 7 | 7 | 10 | 72 | 13 | 13 | 17 | 17 | 17 | 22 | 9 | 11 |
(Significance level: 0.010000; Minimal displayed length: 6)
(0) 66(1,0,0); at 162- 228: see sequence above
(1. quartile)
G: 23 (34.3%); P: 21 (31.3%);
Run count statistics:
+ runs >= 3: 0
- runs >= 3: 0
* runs >= 4: 0
0 runs >= 36: 1, at 162;
--------------------------------------------------------------------------------
DISTRIBUTION OF OTHER AMINO ACID TYPES
1. HIGH SCORING SEGMENTS.
There are no high scoring hydrophobic segments.
____________________________________
High scoring transmembrane segments:
5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST)
-6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED)
Expected score/letter: -3.568
M_0.01= 48.00; M_0.05= 40.52; M_0.30= 31.63
1) From 1196 to 1210: length= 15, score=33.00
1196 CCGGVGAAAI AGIGG
A: 4(26.7%); G: 6(40.0%); I: 2(13.3%); C: 2(13.3%);
2. SPACINGS OF C.
H2N-31-C-17-C-2-C-1-C-6-C-4-C-6-C-9-C-C-2-C-52-C-2-C-1051-C-C-64-C-5-C-16-C-8-C-7-C-69-C-44-C-46-C-2-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-16-H-14-C-1-H-15-C-2-C-1-C-6-C-4-C-6-C-9-C-C-2-C-52-C-2-C-45-H-74-H-110-H-671-H-59-H-47-H-23-H-15-C-C-64-C-5-C-H-15-C-8-C-7-C-11-H-10-H-45-H-C-44-C-2-H-43-C-2-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 5
Aligned matching blocks:
[ 106- 110]--------[ ]
[ 660- 664]-( -9)-[ 656- 669]
[ 738- 742]--------[ ]
[ 921- 925]-( -9)-[ 917- 930]
[ 106- 110] GPKGD
[ 660- 664] GPKGD
[ 738- 742] GPKGD
[ 921- 925] GPKGD
[ 656- 669] PGEPGPKGDAGAPG
[ 917- 930] PGVSGPKGDAGQPG
______________________________
[ 112- 118] GPPGIPG
[ 174- 181] GPAGPPGP
[ 252- 258] GPAGIPG
[ 354- 360] GPAGSPG
[ 399- 406] GPAGIPGA
[ 450- 456] GEAGIPG
[ 495- 501] GPNGIPG
[ 771- 777] GPAGQPG
[ 807- 814] GPAGFPGA
[ 849- 856] GPAGPPGP
[1071-1078] GPAGAPGP
______________________________
[ 114- 118] PGIPG
[ 123- 127] PGIPG
______________________________
[ 123- 139] PGIPGQPGSPGSPGPPG
[1178-1194] PGHPGQPGPPGPPGAPG
______________________________
[ 123- 124]-( 4)-[ 129- 136]
[ 126- 127]-( 4)-[ 132- 139]
[ 185- 186]-( 4)-[ 191- 198]
[ 533- 534]-( 4)-[ 539- 546]
[ 129- 136] PGSPGSPG
[ 132- 139] PGSPGPPG
[ 191- 198] PGSPGSPG
[ 539- 546] PGSPGGPG
with superset:
[ 129- 133] PGSPG
[ 132- 136] PGSPG
[ 191- 195] PGSPG
[ 194- 198] PGSPG
[ 344- 348] PGSPG
[ 539- 543] PGSPG
[ 914- 918] PGSPG
[1118-1122] PGSPG
______________________________
[ 112- 113]-( 3)-[ 117- 118]-( 4)-[ 123- 124]-( 4)-[ 129- 136]-( -7)-
[ 174- 175]-( 3)-[ 179- 180]-( 4)-[ 185- 186]-( 4)-[ 191- 198]-( -7)-
[ ]--------[ ]--------[ ]--------[ ]--------
[ 130- 134]
[ 192- 196]
[ 357- 361]
[ 129- 136] PGSPGSPG
[ 191- 198] PGSPGSPG
[ 130- 134] GSPGS
[ 192- 196] GSPGS
[ 357- 361] GSPGS
______________________________
[ 170- 192] AGYPGPAGPPGPPGPPGTSGHPG
[1136-1158] AGPRGPVGPSGPPGKDGTSGHPG
______________________________
[ 173- 184] PGPAGPPGPPGP
[1133-1144] PGPAGPRGPVGP
with superset:
[ 174- 178] GPAGP
[ 492- 496] GPAGP
[ 513- 517] GPAGP
[ 849- 853] GPAGP
[1068-1072] GPAGP
[1134-1138] GPAGP
and:
[ 174- 181] GPAGPPGP
[ 849- 856] GPAGPPGP
[1134-1141] GPAGPRGP
______________________________
[ 173- 177]--------[ ]--------[ ]
[ 416- 420]-( -5)-[ 416- 426]-( -11)-[ 416- 424]
[ 512- 516]--------[ ]--------[ 512- 520]
[ 770- 774]--------[ ]--------[ ]
[ 806- 810]-( -5)-[ 806- 816]-( -11)-[ 806- 814]
[ 905- 909]-( -5)-[ 905- 915]-( -11)-[ 905- 913]
[1076-1080]-( -5)-[1076-1086]-( -11)-[1076-1084]
[1121-1125]--------[ ]--------[1121-1129]
[1133-1137]--------[ ]--------[ ]
[ 173- 177] PGPAG
[ 416- 420] PGPAG
[ 512- 516] PGPAG
[ 770- 774] PGPAG
[ 806- 810] PGPAG
[ 905- 909] PGPAG
[1076-1080] PGPAG
[1121-1125] PGPAG
[1133-1137] PGPAG
[ 416- 426] PGPAGANGAPG
[ 806- 816] PGPAGFPGAPG
[ 905- 915] PGPAGNTGAPG
[1076-1086] PGPAGSRGAPG
[ 416- 424] PGPAGANGA
[ 512- 520] PGPAGPRGA
[ 806- 814] PGPAGFPGA
[ 905- 913] PGPAGNTGA
[1076-1084] PGPAGSRGA
[1121-1129] PGPAGQQGA
______________________________
[ 176- 187] AGPPGPPGPPGT
[ 710- 721] AGPPGPPGAAGT
with superset:
[ 176- 180] AGPPG
[ 698- 702] AGPPG
[ 710- 714] AGPPG
[ 842- 846] AGPPG
[ 851- 855] AGPPG
[ 959- 963] AGPPG
and:
[ 176- 183] AGPPGPPG
[ 710- 717] AGPPGPPG
[ 959- 966] AGPPGMPG
______________________________
[ 194- 202] PGSPGYQGP
[ 539- 545] PGSPG__GP
[ 914- 922] PGSPGVSGP
______________________________
[ 197- 205] PGYQGPPGE
[ 644- 652] PGTGGPPGE
______________________________
[ 200- 207] QGPPGEPG
[ 380- 387] QGPPGPPG
[ 938- 945] QGPPGAPG
with superset:
[ 200- 204] QGPPG
[ 380- 384] QGPPG
[ 605- 609] QGPPG
[ 617- 621] QGPPG
[ 938- 942] QGPPG
______________________________
[ 203- 207] PGEPG
[ 470- 474] PGEPG
[ 656- 660] PGEPG
______________________________
[ 210- 214]--------[ ]--------[ 210- 216]
[ 222- 226]-( -5)-[ 222- 237]--------[ ]
[ 567- 571]--------[ ]--------[ ]
[1143-1147]-( -5)-[1143-1158]-( -16)-[1143-1149]
[ 210- 214] GPSGP
[ 222- 226] GPSGP
[ 567- 571] GPSGP
[1143-1147] GPSGP
[ 222- 237] GPSGPAGKDGESGRPG
[1143-1158] GPSGPPGKDGTSGHPG
[ 210- 216] GPSGPPG
[1143-1149] GPSGPPG
______________________________
[ 215- 229] PGPPGAIGPSGPAGK
[1046-1060] PGHPGPPGPVGPAGK
______________________________
[ 216- 223] GPPGAIGP
[ 939- 946] GPPGAPGP
[1188-1195] GPPGAPGP
______________________________
[ 225- 226]-( 4)-[ 231- 240]
[ 300- 301]-( 4)-[ 306- 315]
[ 552- 553]-( 4)-[ 558- 567]
[ 231- 240] GESGRPGRPG
[ 306- 315] GERGRPGLPG
[ 558- 567] GESGRPGPPG
with superset:
[ 231- 237] GESGRPG
[ 306- 312] GERGRPG
[ 558- 564] GESGRPG
[ 978- 984] GESGKPG
______________________________
[ 239- 249] PGERGLPGPPG
[ 305- 315] PGERGRPGLPG
with superset:
[ 239- 243] PGERG
[ 305- 309] PGERG
[ 680- 684] PGERG
[ 728- 732] PGERG
[ 797- 801] PGERG
and:
[ 239- 246] PGERGLPG
[ 305- 312] PGERGRPG
[ 680- 687] PGERGPPG
______________________________
[ 248- 255] PGIKGPAG
[ 500- 507] PGEKGPAG
______________________________
[ 254- 261]-( -8)-[ 254- 264]
[ 401- 408]--------[ ]
[ 452- 459]-( -8)-[ 452- 462]
[ 254- 261] AGIPGFPG
[ 401- 408] AGIPGAPG
[ 452- 459] AGIPGVPG
[ 254- 264] AGIPGFPGMKG
[ 452- 462] AGIPGVPGAKG
______________________________
[ 263- 268] KGHRGF
[1106-1111] KGHRGF
______________________________
[ 275- 279] KGETG
[1094-1098] KGETG
______________________________
[ 278- 282] TGAPG
[ 911- 915] TGAPG
______________________________
[ 281- 282]-( 4)-[ 287- 291]
[ 470- 471]-( 4)-[ 476- 480]
[ 287- 291] NGLPG
[ 476- 480] NGLPG
______________________________
[ 290- 301] PGENGAPGPMGP
[ 650- 661] PGENGKPGEPGP
______________________________
[ 291- 310] GENGAPGPMGPRGAPGERGR
[ 507- 526] GERGAPGPAGPRGAAGEPGR
with superset:
[ 294- 307] GAPGPMGPRGAPGE
[ 510- 523] GAPGPAGPRGAAGE
[1083-1096] GAPGPQGPRGDKGE
______________________________
[ 296- 309] PGPMGPRGAPGERG
[ 788- 801] PGIAGPRGSPGERG
with superset:
[ 300- 306] GPRGAPG
[ 354- 360] GPAGSPG
[ 570- 576] GPRGQPG
[ 792- 798] GPRGSPG
[ 861- 867] GERGSPG
[ 894- 900] GPSGSPG
[ 966- 972] GPRGSPG
______________________________
[ 303- 316] GAPGERGRPGLPGA
[ 678- 691] GAPGERGPPGLAGA
with superset:
[ 303- 307] GAPGE
[ 678- 682] GAPGE
[ 828- 832] GAPGE
______________________________
[ 306- 307]-( 3)-[ 311- 321]
[ 780- 781]-( 3)-[ 785- 795]
[ 311- 321] PGLPGAAGARG
[ 785- 795] PGLPGIAGPRG
______________________________
[ 273- 277]-( 34)-[ 312- 321]-( -8)-[ 314- 318]--------[ ]
[ ]--------[ 477- 486]-( -8)-[ 479- 483]--------[ ]
[ ]--------[ ]--------[ 716- 720]-( -8)-[ 713- 723]
[ 831- 835]--------[ ]--------[ 869- 873]-( -8)-[ 866- 876]
[ 273- 277] GEKGE
[ 831- 835] GEKGE
[ 312- 321] GLPGAAGARG
[ 477- 486] GLPGAAGERG
[ 314- 318] PGAAG
[ 479- 483] PGAAG
[ 716- 720] PGAAG
[ 869- 873] PGAAG
[ 713- 723] PGPPGAAGTPG
[ 866- 876] PGGPGAAGFPG
______________________________
[ 321- 325] GNDGA
[ 585- 589] GNDGA
______________________________
[ 336- 352] GPPGTAGFPGSPGAKGE
[ 804- 820] GPPGPAGFPGAPGQNGE
with superset:
[ 341- 345] AGFPG
[ 809- 813] AGFPG
[ 872- 876] AGFPG
______________________________
[ 341- 355] AGFPGSPGAKGEVGP
[ 431- 445] AGEPGKNGAKGEPGP
with superset:
[ 348- 352] GAKGE
[ 438- 442] GAKGE
[ 459- 463] GAKGE
______________________________
[ ]--------[ 344- 348]--------[ ]
[ 518- 522]-( 16)-[ 539- 543]-( -5)-[ 539- 545]
[ ]--------[ 914- 918]-( -5)-[ 914- 922]
[1100-1104]-( 13)-[1118-1122]--------[ ]
[ 518- 522] RGAAG
[1100-1104] RGAAG
[ 344- 348] PGSPG
[ 539- 543] PGSPG
[ 914- 918] PGSPG
[1118-1122] PGSPG
[ 539- 545] PGSPG__GP
[ 914- 922] PGSPGVSGP
______________________________
[ 345- 349] GSPGA
[ 933- 937] GSPGA
[1038-1042] GSPGA
______________________________
[ 344- 348]-( 4)-[ 353- 357]
[1046-1050]-( 4)-[1055-1059]
[ 344- 348] PGSPG
[1046-1050] PGHPG
[ 353- 357] VGPAG
[1055-1059] VGPAG
______________________________
[ 359- 366] PGSNGAPG
[ 884- 891] PGSNGNPG
______________________________
[ 362- 369] NGAPGQRG
[ 422- 429] NGAPGLRG
with superset:
[ 293- 297] NGAPG
[ 362- 366] NGAPG
[ 422- 426] NGAPG
______________________________
[ 363- 372] GAPGQRGEPG
[ 813- 822] GAPGQNGEPG
______________________________
[ 389- 393] NGSPG
[1037-1041] NGSPG
______________________________
[ ]--------[ 390- 394]
[ 521- 531]-( 8)-[ 540- 546]
[ ]--------[ 864- 870]
[1007-1017]-( 8)-[1026-1030]
[ 521- 531] AGEPGRDGVPG
[1007-1017] AGEPGRDGNPG
with superset:
[ 431- 435] AGEPG
[ 521- 525] AGEPG
[1007-1011] AGEPG
[ 390- 394] GSPGG
[ 540- 546] GSPGGPG
[ 864- 870] GSPGGPG
[1026-1030] GSPGG
______________________________
[ 401- 409]-( -8)-[ 402- 409]
[ 419- 427]-( -8)-[ 420- 427]
[ 482- 489]--------[ ]
[ 506- 514]--------[ ]
[ 515- 523]--------[ ]
[ 665- 672]-( -7)-[ 666- 672]
[ 791- 799]--------[ ]
[ 809- 816]-( -7)-[ 810- 816]
[ 908- 915]-( -4)-[ 912- 918]
[1070-1078]--------[ ]
[1079-1087]--------[ ]
[ 401- 409] AGIPGAPGL
[ 419- 427] AGANGAPGL
[ 482- 489] AGERGAPG
[ 506- 514] AGERGAPGP
[ 515- 523] AGPRGAAGE
[ 665- 672] AGAPGAPG
[ 791- 799] AGPRGSPGE
[ 809- 816] AGFPGAPG
[ 908- 915] AGNTGAPG
[1070-1078] AGPAGAPGP
[1079-1087] AGSRGAPGP
matching also:
[ 402- 409] GIPGAPGL
[ 420- 427] GANGAPGL
[ 666- 672] GAPGAPG
[ 783- 789] GAPGLPG
[ 810- 816] GFPGAPG
[ 912- 918] GAPGSPG
[ 939- 946] GPPGAPGP
[1041-1047] GAPGAPG
[1113-1119] GNPGAPG
[1188-1195] GPPGAPGP
______________________________
[ 369- 373]--------[ ]--------[ 404- 409]
[ 441- 445]--------[ ]--------[ 473- 480]
[ ]--------[ 851- 855]-( 19)-[ 875- 882]
[ ]--------[ 959- 963]-( 19)-[ 983- 988]
matching also:
[ 369- 373] GEPGP
[ 441- 445] GEPGP
[ 657- 661] GEPGP
[ 851- 855] AGPPG
[ 959- 963] AGPPG
[ 404- 409] PGAPGL
[ 473- 480] PGANGLPG
[ 875- 882] PGARGLPG
[ 983- 988] PGANGL
______________________________
[ 396- 400]-( 4)-[ 405- 418]
[ 681- 685]-( 4)-[ 690- 703]
[ 396- 400] GEMGP
[ 681- 685] GERGP
[ 405- 418] GAPGLMGARGPPGP
[ 690- 703] GAPGLRGGAGPPGP
with superset:
[ 279- 283] GAPGL
[ 405- 409] GAPGL
[ 423- 427] GAPGL
[ 690- 694] GAPGL
[ 783- 787] GAPGL
and:
[ 405- 412] GAPGL_MGA
[ 423- 431] GAPGLRGGA
[ 690- 698] GAPGLRGGA
______________________________
[ 414- 421] GPPGPAGA
[1068-1075] GPAGPAGA
______________________________
[ 411- 412]-( 4)-[ 417- 418]-( 4)-[ 423- 435]
[ 678- 679]-( 4)-[ 684- 685]-( 4)-[ 690- 702]
[ 423- 435] GAPGLRGGAGEPG
[ 690- 702] GAPGLRGGAGPPG
______________________________
[ 425- 430]-( 3)-[ 434- 435]-( 4)-[ 440- 444]
[ 728- 733]-( 3)-[ 737- 738]-( 4)-[ 743- 747]
[ 425- 430] PGLRGG
[ 728- 733] PGERGG
[ 440- 444] KGEPG
[ 743- 747] KGEPG
______________________________
[ 443- 447]-( -5)-[ 443- 451]
[ 965- 969]--------[ ]
[1163-1167]-( -5)-[1163-1173]
[ 443- 447] PGPRG
[ 965- 969] PGPRG
[1163-1167] PGPRG
[ 443- 451] PGPRGERGE
[1163-1173] PGPRGNRGERG
______________________________
[ 447- 451] GERGE
[ 798- 802] GERGE
______________________________
[ 471- 496] GEPGANGLPGAAGERGAPGFRGPAGP
[ 780- 805] GEGGAPGLPGIAGPRGSPGERGETGP
with superset:
[ 312- 318] GLPGAAG
[ 477- 483] GLPGAAG
[ 714- 720] GPPGAAG
[ 786- 792] GLPGIAG
[ 867- 873] GGPGAAG
[ 999-1005] GLPGLAG
and:
[ 312- 321] GLPGAAGARG
[ 477- 486] GLPGAAGERG
[ 786- 795] GLPGIAGPRG
______________________________
[ 473- 474]-( 4)-[ 479- 489]
[ 770- 771]-( 4)-[ 776- 786]
[ 815- 816]-( 4)-[ 821- 831]
[ 479- 489] PGAAGERGAPG
[ 776- 786] PGDKGEGGAPG
[ 821- 831] PGGKGERGAPG
with superset:
[ 281- 286] PGLKGE
[ 347- 352] PGAKGE
[ 392- 397] PGGKGE
[ 458- 463] PGAKGE
[ 479- 484] PGAAGE
[ 776- 781] PGDKGE
[ 821- 826] PGGKGE
[ 830- 835] PGEKGE
______________________________
[ 480- 484] GAAGE
[ 519- 523] GAAGE
______________________________
[ 482- 493]-( -11)-[ 483- 489]
[ 506- 517]-( -11)-[ 507- 513]
[ ]--------[ 825- 831]
[ ]--------[1098-1102]
[ 482- 493] AGERGAPGFRGP
[ 506- 517] AGERGAPGPAGP
[ 483- 489] GERGAPG
[ 507- 513] GERGAPG
[ 825- 831] GERGAPG
[1098-1102] GERGA
______________________________
[ 485- 489]--------[ ]--------[ 482- 493]
[ 509- 513]-( -10)-[ 504- 523]-( -18)-[ 506- 517]
[ 827- 831]--------[ ]--------[ ]
[1082-1086]-( -10)-[1077-1096]-( -18)-[1079-1090]
[ 485- 489] RGAPG
[ 509- 513] RGAPG
[ 827- 831] RGAPG
[1082-1086] RGAPG
[ 504- 523] GPAGERGAPGPAGPRGAAGE
[1077-1096] GPAGSRGAPGPQGPRGDKGE
[ 482- 493] AGERGAPGFRGP
[ 506- 517] AGERGAPGPAGP
[1079-1090] AGSRGAPGPQGP
______________________________
[ 468- 472]-( 27)-[ 500- 504]
[ 795- 799]-( 30)-[ 830- 834]
[ ]--------[ 929- 933]
[ 468- 472] GSPGE
[ 795- 799] GSPGE
[ 500- 504] PGEKG
[ 830- 834] PGEKG
[ 929- 933] PGEKG
______________________________
[ 467- 471]--------[ ]--------[ 512- 519]-( -7)-[ 513- 517]
[ ]--------[ 848- 853]--------[ ]--------[ 849- 853]
[1025-1029]-( 37)-[1067-1072]--------[ ]--------[1068-1072]
[ ]--------[ ]--------[1133-1140]-( -7)-[1134-1138]
[ 467- 471] DGSPG
[1025-1029] DGSPG
matching also:
[ 224- 228] SGPAG
[ 848- 853] SGPAGP
[1067-1072] SGPAGP
[ 512- 519] PGPAGPRG
[1133-1140] PGPAGPRG
[ 513- 517] GPAGP
[ 849- 853] GPAGP
[1068-1072] GPAGP
[1134-1138] GPAGP
______________________________
[ 524- 537] PGRDGVPGGPGMRG
[ 749- 762] PGADGVPGKDGPRG
______________________________
[ 524- 532] PGRDGVPGG
[1010-1017] PGRDGNPG
[1022-1030] PGRDGSPGG
______________________________
[ 542- 552] PGGPGSDGKPG
[ 746- 756] PGGPGADGVPG
with superset:
[ 530- 534] PGGPG
[ 542- 546] PGGPG
[ 599- 603] PGGPG
[ 746- 750] PGGPG
[ 866- 870] PGGPG
______________________________
[ 539- 540]-( 4)-[ 545- 556]
[1010-1011]-( 4)-[1016-1027]
[ 545- 556] PGSDGKPGPPGS
[1016-1027] PGSDGLPGRDGS
______________________________
[ 581- 591] PGPKGNDGAPG
[ 659- 669] PGPKGDAGAPG
with superset:
[ 581- 585] PGPKG
[ 659- 663] PGPKG
[ 737- 741] PGPKG
______________________________
[ 598- 610] GPGGP_GPQGPPGK
[1137-1150] GPRGPVGPSGPPGK
______________________________
[ 599- 603] PGGPG
[ 746- 751] PGGPGA
[ 866- 871] PGGPGA
______________________________
[ 603- 609] GPQGPPG
[ 615- 621] GPQGPPG
with superset:
[ 103- 107] GPQGP
[ 603- 607] GPQGP
[ 615- 619] GPQGP
[1086-1090] GPQGP
______________________________
[ ]--------[ 590- 595]--------[ ]--------[ 608- 619]-( -6)-
[ 594- 598]-( 9)-[ 608- 613]--------[ ]--------[ ]--------
[ 729- 733]--------[ ]--------[ 741- 750]--------[ ]--------
[ ]--------[ ]--------[ 777- 786]-( 10)-[ 797- 808]-( -6)-
[ 614- 619]-( -6)-[ 614- 622]-( 24)-[ 647- 651]
[ 632- 637]--------[ ]--------[ ]
[ 764- 769]-( -6)-[ 764- 772]--------[ ]
[ 803- 808]--------[ ]--------[ 836- 840]
[ 594- 598] GERGG
[ 729- 733] GERGG
matching also:
[ 434- 438] PGKNG
[ 590- 595] PGKNGE
[ 608- 613] PGKNGE
[ 741- 750] GDKGEPGGPG
[ 777- 786] GDKGEGGAPG
with superset:
[ 741- 745] GDKGE
[ 777- 781] GDKGE
[1092-1096] GDKGE
[ 608- 619] PGKNGETGPQGP
[ 797- 808] PGERGETGPPGP
[ 614- 619] TGPQGP
[ 632- 637] TGPPGP
[ 764- 769] TGPIGP
[ 803- 808] TGPPGP
[ 614- 622] TGPQGPPGP
[ 764- 772] TGPIGPPGP
[ 647- 651] GGPPG
[ 836- 840] GGPPG
______________________________
[ 617- 625] QGPPGPTGP
[ 938- 946] QGPPGAPGP
______________________________
[ 618- 625] GPPGPTGP
[ 759- 766] GPRGPTGP
______________________________
[ 656- 657]-( 4)-[ 662- 669]-( 7)-[ 677- 684]
[ 668- 669]-( 4)-[ 674- 682]-( 6)-[ 689- 696]
[ 917- 918]-( 4)-[ 923- 931]--------[ ]
[ 662- 669] KGDAGAPG
[ 674- 682] KGDAGAPGE
[ 923- 931] KGDAGQPGE
[ 677- 684] AGAPGERG
[ 689- 696] AGAPGLRG
______________________________
[ 636- 637]-( 3)-[ 641- 645]-( 25)-[ 671- 675]--------[ ]
[ ]--------[ ]--------[ 821- 825]-( -5)-[ 821- 828]
[ 993- 994]-( 3)-[ 998-1002]-( 25)-[1028-1032]-( -5)-[1028-1035]
[ 641- 645] QGLPG
[ 998-1002] QGLPG
[ 671- 675] PGGKG
[ 821- 825] PGGKG
[1028-1032] PGGKG
[ 821- 828] PGGKGERG
[1028-1035] PGGKGDRG
______________________________
[ 677- 681] AGAPG
[ 689- 693] AGAPG
[1073-1077] AGAPG
______________________________
[ 680- 688] PGERGPPGL
[ 728- 734] PGERG__GL
______________________________
[ 680- 681]-( 4)-[ 686- 690]
[ 995- 996]-( 4)-[1001-1005]
[ 686- 690] PGLAG
[1001-1005] PGLAG
______________________________
[ 710- 717] AGPPGPPG
[ 959- 966] AGPPGMPG
______________________________
[ 744- 748] GEPGG
[ 819- 823] GEPGG
______________________________
[ 755- 771] PGKDGPRGPTGPIGPPG
[1133-1149] PGPAGPRGPVGPSGPPG
______________________________
[ 746- 750]-( 4)-[ 755- 763]
[ 890- 894]-( 4)-[ 899- 907]
[ 746- 750] PGGPG
[ 890- 894] PGPPG
[ 755- 763] PGKDGPRGP
[ 899- 907] PGKDGPPGP
with superset:
[ 755- 759] PGKDG
[ 899- 903] PGKDG
[1148-1152] PGKDG
______________________________
[ 768- 769]-( 3)-[ 773- 784]
[ 921- 922]-( 3)-[ 926- 937]
[ 773- 784] AGQPGDKGEGGA
[ 926- 937] AGQPGEKGSPGA
______________________________
[ 776- 786] PGDKGEGGAPG
[ 830- 840] PGEKGEGGPPG
______________________________
[ 794- 798] RGSPG
[ 863- 867] RGSPG
[ 968- 972] RGSPG
______________________________
[ 824- 831] KGERGAPG
[ 860- 867] KGERGSPG
______________________________
[ 842- 850] AGPPGGSGP
[ 959- 967] AGPPGMPGP
______________________________
[ 842- 850]-( 3)-[ 854- 862]
[ 959- 967]-( 3)-[ 971- 979]
[ 842- 850] AGPPGGSGP
[ 959- 967] AGPPGMPGP
[ 854- 862] PGPQGVKGE
[ 971- 979] PGPQGVKGE
______________________________
[ 872- 885] AGFPGARGLPGPPG
[ 950- 963] AGITGARGLAGPPG
______________________________
[ 992- 999] RGPPGPQG
[1082-1089] RGAPGPQG
______________________________
[1030-1036] GK_GDRGE
[1059-1066] GKSGDRGE
______________________________
[1046-1057] PGHPGPPGPVGP
[1133-1144] PGPAGPRGPVGP
______________________________
[1046-1057] PGHPGPPGPVGP
[1178-1189] PGHPGQPGPPGP
______________________________
[1112-1119] PGNPGAPG
[1187-1194] PGPPGAPG
______________________________
[1116-1125] GAPGSPGPAG
[1128-1137] GAIGSPGPAG
Highly repetitive regions:
From 106 to 1190 with major motif GPPGPPGPA.
From 109 to 1192 with major motif GQPGPPGPPGP.
From 111 to 1192 with major motif PGPPGP.
From 177 to 1190 with major motif GPPGPP.
From 240 to 997 with major motif GERGPPGP.
From 242 to 1117 with major motif RGLPGPPGP.
B. SEPARATED AND TANDEM REPEATS: 11-letter reduced alphabet.
(i= LVIF; += KR; -= ED; s= AG; o= ST; n= NQ; a= YW; p= P; h= H; m= M; c= C)
Repeat core block length: 9
Aligned matching blocks:
[ 291- 296]-( -2)-[ 295- 316]-( 3)-[ 320- 321]
[ 507- 512]-( 0)-[ 513- 532]-( 3)-[ 536- 537]
[ 291- 296] s-nssp
[ 507- 512] s-+ssp
[ 295- 316] spspmsp+ssps-+s+psipss
[ 513- 532] sps__sp+ssss-ps+-sipss
with superset:
[ 302- 310] +ssps-+s+
[ 428- 436] +ssss-ps+
[ 518- 526] +ssss-ps+
______________________________
[ 785- 793]-( 4)-[ 798- 816]
[1049-1057]-( 4)-[1062-1079]
[ 785- 793] psipsissp
[1049-1057] psppspisp
[ 798- 816] s-+s-osppspssipssps
[1062-1079] s-+s-ospsspsssp_sps
with superset:
[ 627- 637] s-+s-osppsp
[ 798- 808] s-+s-osppsp
[1062-1072] s-+s-ospssp
--------------------------------------------------------------------------------
MULTIPLETS.
A. AMINO ACID ALPHABET.
1. Total number of amino acid multiplets: 94 (Expected range: 121--193) low
1 MM........ LLL.LL...I I..QQ....G G......... .......... ..........
61 ..DDII.DD. .......... ...CC..... PP.....PP. .......... ..PP......
121 .......... ......PP.. .......... .......... ......GG.. .......PP.
181 PP.PP..... .......... .PP....... ...PP.PP.. .......... ..........
241 ......PP.. .......... .......... .......... .......... ..........
301 .......... .....AA... .......... ...PP.PP.. .......... ..........
361 .......... .......... .PP.PP.... ..GG...... .......... ....PP....
421 ........GG .......... .......... .......... .......... ..........
481 AA........ .......... .......... .........A A......... GG........
541 ..GG...... ..PP...... ....PP.... .......... .......... ......GG.G
601 G.....PP.. ........PP .....GG... ...PP..... ......GGPP ..........
661 .......... .GG....... ....PP.... .....GG..P P...GG..AA .PP.PP.AA.
721 .......... .GG....... ......GG.. .......... ........PP ..........
781 .GG....... .......... ....PP.... .......... .GG....... .....GGPP.
841 ...PPGG... ..PP...... ......GG.. AA........ ..PP...... .PP.......
901 ...PP..... .......... .......... .........P P......... ..........
961 PP........ .......... .......... ...PP..... .......... ..........
1021 ........GG .......... .......... PP........ .......... ..........
1081 .......... .......... .AA....... .......... .....QQ... ..........
1141 ......PP.. .......... .PP....... .......... .....PP.PP .....CCGG.
1201 .AAA....GG ...GG...YY .......... .......... .......... ..........
1261 .......... .......... .......... .......... .......... ....WW..SS
1321 ..KK...... ...GG..... .......... ........LL SS........ ..........
1381 ......KK.. .......... .......... .......... .......... ..........
1441 .........G G......... ......
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 33 (6-10) 15 (11-20) 23 (>=21) 24
3. Clusters of amino acid multiplets (cmin = 11/30 or 14/45 or 17/60): none
4. Significant specific amino acid altplet counts:
Letters Observed (Critical number)
AG 86 (82)
at 170 (l= 2) 176 (l= 2) 209 (l= 2) 219 (l= 2) 227 (l= 2)
254 (l= 2) 279 (l= 2) 294 (l= 2) 303 (l= 2) 315 (l= 2)
317 (l= 3) 324 (l= 2) 341 (l= 2) 348 (l= 2) 356 (l= 2)
363 (l= 2) 377 (l= 3) 401 (l= 2) 405 (l= 2) 411 (l= 2)
419 (l= 3) 423 (l= 2) 430 (l= 3) 438 (l= 2) 452 (l= 2)
459 (l= 2) 474 (l= 2) 480 (l= 2) 482 (l= 2) 486 (l= 2)
494 (l= 2) 506 (l= 2) 510 (l= 2) 515 (l= 2) 519 (l= 2)
521 (l= 2) 588 (l= 2) 665 (l= 3) 669 (l= 2) 677 (l= 3)
689 (l= 3) 697 (l= 3) 708 (l= 2) 710 (l= 2) 717 (l= 2)
719 (l= 2) 750 (l= 2) 773 (l= 2) 783 (l= 2) 791 (l= 2)
809 (l= 2) 813 (l= 2) 828 (l= 2) 842 (l= 2) 851 (l= 2)
870 (l= 2) 872 (l= 2) 876 (l= 2) 908 (l= 2) 912 (l= 2)
926 (l= 2) 936 (l= 2) 942 (l= 2) 950 (l= 2) 954 (l= 2)
959 (l= 2) 984 (l= 2) 1004 (l= 2) 1007 (l= 2) 1041 (l= 2)
1044 (l= 2) 1058 (l= 2) 1070 (l= 2) 1073 (l= 3) 1079 (l= 2)
1083 (l= 2) 1101 (l= 2) 1103 (l= 2) 1116 (l= 2) 1124 (l= 2)
1128 (l= 2) 1136 (l= 2) 1191 (l= 2) 1201 (l= 2) 1206 (l= 2)
1213 (l= 2)
GP 207 (163)
at 103 (l= 2) 106 (l= 2) 111 (l= 3) 114 (l= 2) 117 (l= 2)
123 (l= 2) 126 (l= 2) 129 (l= 2) 132 (l= 2) 135 (l= 3)
138 (l= 2) 147 (l= 2) 173 (l= 3) 177 (l= 2) 179 (l= 3)
182 (l= 3) 185 (l= 2) 191 (l= 2) 194 (l= 2) 197 (l= 2)
201 (l= 2) 203 (l= 2) 206 (l= 2) 210 (l= 2) 213 (l= 2)
215 (l= 3) 218 (l= 2) 222 (l= 2) 225 (l= 2) 236 (l= 2)
239 (l= 2) 245 (l= 3) 248 (l= 2) 252 (l= 2) 257 (l= 2)
260 (l= 2) 281 (l= 2) 290 (l= 2) 296 (l= 3) 300 (l= 2)
305 (l= 2) 311 (l= 2) 314 (l= 2) 332 (l= 3) 335 (l= 3)
338 (l= 2) 344 (l= 2) 347 (l= 2) 354 (l= 2) 359 (l= 2)
365 (l= 2) 371 (l= 3) 381 (l= 2) 383 (l= 3) 386 (l= 2)
392 (l= 2) 399 (l= 2) 404 (l= 2) 407 (l= 2) 414 (l= 2)
416 (l= 3) 425 (l= 2) 434 (l= 2) 443 (l= 3) 455 (l= 2)
458 (l= 2) 470 (l= 2) 473 (l= 2) 479 (l= 2) 488 (l= 2)
492 (l= 2) 495 (l= 2) 500 (l= 2) 504 (l= 2) 512 (l= 3)
516 (l= 2) 524 (l= 2) 530 (l= 2) 532 (l= 3) 539 (l= 2)
542 (l= 2) 544 (l= 3) 551 (l= 3) 554 (l= 2) 563 (l= 3)
566 (l= 3) 570 (l= 2) 575 (l= 2) 581 (l= 3) 590 (l= 2)
598 (l= 3) 601 (l= 4) 606 (l= 2) 608 (l= 2) 615 (l= 2)
618 (l= 2) 620 (l= 3) 624 (l= 3) 633 (l= 2) 635 (l= 3)
644 (l= 2) 648 (l= 2) 650 (l= 2) 656 (l= 2) 659 (l= 3)
668 (l= 2) 671 (l= 2) 680 (l= 2) 684 (l= 2) 686 (l= 2)
692 (l= 2) 699 (l= 2) 7
01 (l= 3) 711 (l= 2) 713 (l= 3)
716 (l= 2) 722 (l= 2) 728 (l= 2) 737 (l= 3) 746 (l= 2)
748 (l= 3) 755 (l= 2) 759 (l= 2) 762 (l= 2) 765 (l= 2)
768 (l= 2) 770 (l= 3) 776 (l= 2) 785 (l= 2) 788 (l= 2)
792 (l= 2) 797 (l= 2) 804 (l= 2) 806 (l= 3) 812 (l= 2)
815 (l= 2) 821 (l= 2) 830 (l= 2) 837 (l= 2) 839 (l= 2)
843 (l= 2) 845 (l= 2) 849 (l= 2) 852 (l= 2) 854 (l= 3)
866 (l= 2) 868 (l= 3) 875 (l= 2) 881 (l= 3) 884 (l= 2)
890 (l= 3) 893 (l= 3) 899 (l= 2) 903 (l= 2) 905 (l= 3)
914 (l= 2) 917 (l= 2) 921 (l= 2) 929 (l= 2) 935 (l= 2)
939 (l= 2) 941 (l= 2) 944 (l= 3) 960 (l= 2) 962 (l= 2)
965 (l= 3) 971 (l= 3) 983 (l= 2) 993 (l= 2) 995 (l= 3)
1001 (l= 2) 1010 (l= 2) 1016 (l= 2) 1022 (l= 2) 1028 (l= 2)
1040 (l= 2) 1043 (l= 2) 1046 (l= 2) 1049 (l= 3) 1052 (l= 3)
1056 (l= 2) 1068 (l= 2) 1071 (l= 2) 1076 (l= 3) 1085 (l= 3)
1089 (l= 2) 1112 (l= 2) 1115 (l= 2) 1118 (l= 2) 1121 (l= 3)
1133 (l= 3) 1137 (l= 2) 1140 (l= 2) 1143 (l= 2) 1146 (l= 2)
1148 (l= 2) 1157 (l= 3) 1161 (l= 2) 1163 (l= 3) 1178 (l= 2)
1181 (l= 2) 1184 (l= 3) 1187 (l= 3) 1190 (l= 2) 1193 (l= 3)
1451 (l= 2) 1461 (l= 2)
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 12 (Expected range: 6-- 33)
5 +plets (f+: 8.3%), 7 -plets (f-: 8.8%)
Total number of charge altplets: 36 (Critical number: 38)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 1 (6-10) 2 (11-20) 1 (>=21) 9
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
89- 109 3 P.. 6 4 1
103- 141 3 G.P 13 13 ! /0/./4/
129- 160 8 P....... 4 4 0
168-1196 3 G.. 343 343 ! 0
1191-1222 8 G....... 4 4 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 7)
Location Period Element Copies Core Errors
63- 87 5 -.000 5 5 /0/./0/1/0/
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
34- 190 (1.) H( 156)H 2 of 15 0.9701 small 2. maximal spacing
39- 151 (1.) Y( 112)Y 2 of 16 0.9996 small 2. maximal spacing
45-1278 (2.) W(1233)W 1 of 8 0.0000 large 1. maximal spacing
144-1196 (2.) C(1052)C 1 of 23 0.0000 large 1. maximal spacing
199-1219 (2.) Y(1020)Y 1 of 16 0.0000 large 1. maximal spacing
308- 310 (1.) R( 2)R 61 of 61 0.0054 large minimal spacing
376-1048 (2.) H( 672)H 1 of 15 0.0027 large 1. maximal spacing
569- 736 (2.) S( 167)S 1 of 74 0.0085 large maximal spacing
1299-1329 (4.) G( 30)G 2 of 414 0.0001 large 2. maximal spacing
1302-1372 (4.) C( 70)C 2 of 23 1.0000 small 2. maximal spacing
1311-1343 (4.) P( 32)P 2 of 282 0.0301 large 2. maximal spacing
1327-1424 (4.) W( 97)W 2 of 8 0.9998 small 2. maximal spacing
1341-1384 (4.) G( 43)G 1 of 414 0.0002 large 1. maximal spacing
1346-1440 (4.) P( 94)P 1 of 282 0.0000 large 1. maximal spacing
1397-1399 (4.) E( 2)E 75 of 75 0.0003 large minimal spacing
1432-1434 (4.) R( 2)R 60 of 61 0.0054 matching minimum
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Pfam (from /data/patterns/pfam)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/pfam/Pfam
Sequence file: tem15
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 949.9 6.8e-282 18
COLFI Fibrillar collagen C-terminal domain 561.6 5.3e-219 1
DNA_pol3_beta DNA polymerase III beta subunit 7.6 0.39 1
CorA CorA-like Mg2+ transporter protein -148.3 24 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Collagen 1/18 82 141 .. 1 60 [] -0.9 0.0034
Collagen 2/18 168 227 .. 1 60 [] 66.5 5.6e-16
Collagen 3/18 234 293 .. 1 60 [] 78.5 1.4e-19
Collagen 4/18 294 353 .. 1 60 [] 68.3 1.6e-16
Collagen 5/18 354 413 .. 1 60 [] 67.2 3.4e-16
Collagen 6/18 414 473 .. 1 60 [] 67.6 2.6e-16
Collagen 7/18 474 533 .. 1 60 [] 63.9 3.5e-15
Collagen 8/18 534 593 .. 1 60 [] 69.3 8.1e-17
Collagen 9/18 594 653 .. 1 60 [] 49.1 9.5e-11
Collagen 10/18 654 713 .. 1 60 [] 46.5 6e-10
Collagen 11/18 714 773 .. 1 60 [] 58.8 1.2e-13
Collagen 12/18 777 836 .. 1 60 [] 58.3 1.7e-13
Collagen 13/18 837 896 .. 1 60 [] 52.6 8.5e-12
Collagen 14/18 897 956 .. 1 60 [] 64.9 1.7e-15
Collagen 15/18 957 1016 .. 1 60 [] 65.2 1.4e-15
Collagen 16/18 1017 1076 .. 1 60 [] 61.0 2.6e-14
Collagen 17/18 1077 1136 .. 1 60 [] 79.3 7.7e-20
Collagen 18/18 1137 1196 .. 1 60 [] 69.7 6.1e-17
DNA_pol3_beta 1/1 1225 1247 .. 1 23 [. 7.6 0.39
CorA 1/1 5 1413 .. 1 324 [] -148.3 24
COLFI 1/1 1248 1465 .. 1 226 [] 561.6 5.3e-219
Alignments of top-scoring domains:
Collagen: domain 1 of 18, from 82 to 141: score -0.9, E = 0.0034
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+ p p+ p+ pp +Gp+G++G+pGppG pG+ G pG pG+
gi|115306| 82 GECCAVCPQPPTAPTRPPNGQGPQGPKGDPGPPGIPGRNGDPGIPGQ 128
pGppGapGapGpp<-*
pG pG pG+pG +
gi|115306| 129 PGSPGSPGPPGIC 141
Collagen: domain 2 of 18, from 168 to 227: score 66.5, E = 5.6e-16
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +G pGp+GppGppGppG G++G+pG+pG +G+pG+PG++Gp Gp
gi|115306| 168 GLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQGPPGEPGQAGPSGP 214
pGppGapGapGpp<-*
pGppGa+G+ Gp+
gi|115306| 215 PGPPGAIGPSGPA 227
Collagen: domain 3 of 18, from 234 to 293: score 78.5, E = 1.4e-19
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+pG++G+pGppG +Gp+G +G+pG++G++G++G+ G +G+ G+
gi|115306| 234 GRPGRPGERGLPGPPGIKGPAGIPGFPGMKGHRGFDGRNGEKGETGA 280
pGppGapGapGpp<-*
pG +G+ G pG++
gi|115306| 281 PGLKGENGLPGEN 293
Collagen: domain 4 of 18, from 294 to 353: score 68.3, E = 1.6e-16
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp+Gp+G+pG++G+pG pG+aGa+G+ G++G +G+PGppGppG
gi|115306| 294 GAPGPMGPRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGT 340
pGppGapGapGpp<-*
+G pG pGa+G++
gi|115306| 341 AGFPGSPGAKGEV 353
Collagen: domain 5 of 18, from 354 to 413: score 67.2, E = 3.4e-16
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G+pG++G+pG++G+pGp+G+aGa+GppGppG +G+PG +G++Gp
gi|115306| 354 GPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGP 400
pGppGapGapGpp<-*
+G pGapG +G++
gi|115306| 401 AGIPGAPGLMGAR 413
Collagen: domain 6 of 18, from 414 to 473: score 67.6, E = 2.6e-16
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+G++G+pG +G +G+pG +Ga+G+pGp+Ge+G+ G pG+pG+
gi|115306| 414 GPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERGEAGIPGVPGA 460
pGppGapGapGpp<-*
+G++G++G+pG+p
gi|115306| 461 KGEDGKDGSPGEP 473
Collagen: domain 7 of 18, from 474 to 533: score 63.9, E = 3.5e-15
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+ G+pG++G++G+pG +Gp+Gp+G pG++Gp+Ge+G+PGp+Gp G+
gi|115306| 474 GANGLPGAAGERGAPGFRGPAGPNGIPGEKGPAGERGAPGPAGPRGA 520
pGppGapGapGpp<-*
+G+pG++G pG p
gi|115306| 521 AGEPGRDGVPGGP 533
Collagen: domain 8 of 18, from 534 to 593: score 69.3, E = 8.1e-17
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +G pG+pG pG +G+pGppG +G+ G pGppG++Gp G+pG++G+
gi|115306| 534 GMRGMPGSPGGPGSDGKPGPPGSQGESGRPGPPGPSGPRGQPGVMGF 580
pGppGapGapGpp<-*
pGp+G++GapG++
gi|115306| 581 PGPKGNDGAPGKN 593
Collagen: domain 9 of 18, from 594 to 653: score 49.1, E = 9.5e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G++G pG+pGp+GppG+ G++Gp+G+pGp Gp G++G GppGp G
gi|115306| 594 GERGGPGGPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGL 640
pGppGapGapGpp<-*
+G pG G+pG++
gi|115306| 641 QGLPGTGGPPGEN 653
Collagen: domain 10 of 18, from 654 to 713: score 46.5, E = 6e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+pGp+G++G+pG+pG +G+aGapG++GppG +G+PG +G +Gp
gi|115306| 654 GKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP 700
pGppGapGapGpp<-*
pGp+G +Ga+Gpp
gi|115306| 701 PGPEGGKGAAGPP 713
Collagen: domain 11 of 18, from 714 to 773: score 58.8, E = 1.2e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppG +G pG++G+pG++G G +G++G++G pG pG++G pG++Gp
gi|115306| 714 GPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGP 760
pGppGapGapGpp<-*
+Gp+G++G+pGp+
gi|115306| 761 RGPTGPIGPPGPA 773
Collagen: domain 12 of 18, from 777 to 836: score 58.3, E = 1.7e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +G+ G+pG+pG +Gp+G pG++G+ GppGp+G+pG+PG+ G+pG
gi|115306| 777 GDKGEGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGG 823
pGppGapGapGpp<-*
+G++GapG++G+
gi|115306| 824 KGERGAPGEKGEG 836
Collagen: domain 13 of 18, from 837 to 896: score 52.6, E = 8.5e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppG +GppG Gp+GppGp+G +G++G+pG pG++G+PG++G pGp
gi|115306| 837 GPPGVAGPPGGSGPAGPPGPQGVKGERGSPGGPGAAGFPGARGLPGP 883
pGppGapGapGpp<-*
pG G+pG+pGp
gi|115306| 884 PGSNGNPGPPGPS 896
Collagen: domain 14 of 18, from 897 to 956: score 64.9, E = 1.7e-15
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pG+ GppGp+G +G+pG pG +G++G++G pGe+G+PG++GppG+
gi|115306| 897 GSPGKDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGA 943
pGppGapGapGpp<-*
pGp G +G G++
gi|115306| 944 PGPLGIAGITGAR 956
Collagen: domain 15 of 18, from 957 to 1016: score 65.2, E = 1.4e-15
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +GppG pGp+G pGp G +G++G+pG +G +Ge+GpPGp+G pG
gi|115306| 957 GLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGLPGL 1003
pGppGapGapGpp<-*
+G +G+pG G p
gi|115306| 1004 AGTAGEPGRDGNP 1016
Collagen: domain 16 of 18, from 1017 to 1076: score 61.0, E = 2.6e-14
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G G+pG+ G pG +G++G+ G +GapG pG+pG+pGp Gp+G+ G
gi|115306| 1017 GSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPGPPGPVGPAGKSGD 1063
pGppGapGapGpp<-*
+G+ G++G++G+p
gi|115306| 1064 RGESGPAGPAGAP 1076
Collagen: domain 17 of 18, from 1077 to 1136: score 79.3, E = 7.7e-20
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G++G+pGp+Gp+G++G++G++Ga+G +G++G+pG PG+pG pGp
gi|115306| 1077 GPAGSRGAPGPQGPRGDKGETGERGAAGIKGHRGFPGNPGAPGSPGP 1123
pGppGapGapGpp<-*
+G++Ga+G+pGp+
gi|115306| 1124 AGQQGAIGSPGPA 1136
Collagen: domain 18 of 18, from 1137 to 1196: score 69.7, E = 6.1e-17
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+Gp Gp GppG +G +G+pGp G+pGp+G++Ge+G+ G+pG+pG+
gi|115306| 1137 GPRGPVGPSGPPGKDGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQ 1183
pGppGapGapGpp<-*
pGppG+pGapGp+
gi|115306| 1184 PGPPGPPGAPGPC 1196
DNA_pol3_beta: domain 1 of 1, from 1225 to 1247: score 7.6, E = 0.39
*->MkFtIeRdaLlkaLqkVarvvsn<-*
M F+I++d+++++L+ V + +++
gi|115306| 1225 MDFKINTDEIMTSLKSVNGQIES 1247
CorA: domain 1 of 1, from 5 to 1413: score -148.3, E = 24
*->iedktvvWidlinePteeemakl.....skafgihpltlediedieq
+ +++ + l+ Pt+ ++ ++++ ++g+++++ + ++
gi|115306| 5 VQKGSWLLLALL-HPTIILAQQEaveggCSHLGQSYADRD--VWKPE 48
raKveedddylfiilhffsvnldeeegvvlar..................
+ d++ ++ + ++ d+e+ ++++ + ++ +++
gi|115306| 49 PCQICVCDSGSVLCDDI--ICDDQEL-----Dcpnpeipfgeccavcpqp 91
..................................................
++ +++++++++++++++++++++ ++++++++ ++++++++++++++
gi|115306| 92 ptaptrppngqgpqgpkgdpgppgipgrngdpgipgqpgspgspgppgic 141
..................................................
++ ++++++ +++ ++ + +++ ++ + +++ +++++++++++++++
gi|115306| 142 escptgpqnyspqydsydvksgvavgglagypgpagppgppgppgtsghp 191
..................................................
+++++++ +++++++++ ++++++++++ +++++ ++++++++++++++
gi|115306| 192 gspgspgyqgppgepgqagpsgppgppgaigpsgpagkdgesgrpgrpge 241
..................................................
++ +++++ +++ + ++ ++ +++++ +++++++++++ ++ +++++ ++
gi|115306| 242 rglpgppgikgpagipgfpgmkghrgfdgrngekgetgapglkgenglpg 291
..................................................
+++ +++ ++++ ++++++++ ++ + +++++ +++++++++++++++
gi|115306| 292 engapgpmgprgapgergrpglpgaagargndgargsdgqpgppgppgta 341
..................................................
+ +++++ +++ ++ +++++++ ++++++++++++ + ++++++++ +++
gi|115306| 342 gfpgspgakgevgpagspgsngapgqrgepgpqghagaqgppgppgings 391
..................................................
++++++ ++ + ++ ++ + ++++++ + ++ ++ +++ +++++++ ++
gi|115306| 392 pggkgemgpagipgapglmgargppgpagangapglrggagepgkngakg 441
..................................................
++++++++++ + ++ ++ ++++++++++++++ ++ ++ ++++ ++ +
gi|115306| 442 epgprgergeagipgvpgakgedgkdgspgepganglpgaagergapgfr 491
..................................................
++ ++++ ++++++ ++++ +++ ++++ +++++++ +++++ ++ +++
gi|115306| 492 gpagpngipgekgpagergapgpagprgaagepgrdgvpggpgmrgmpgs 541
..................................................
+++++++++++++++++++++++++++++++++++ + ++++++++ ++
gi|115306| 542 pggpgsdgkpgppgsqgesgrpgppgpsgprgqpgvmgfpgpkgndgapg 591
..................................................
++++++++++++++++++++++++++++++++++++++++++++++++ +
gi|115306| 592 kngerggpggpgpqgppgkngetgpqgppgptgpggdkgdtgppgpqglq 641
..................................................
+ +++++++++++++++++++++ + ++ ++++++ + ++++++++ +
gi|115306| 642 glpgtggppgengkpgepgpkgdagapgapggkgdagapgergppglaga 691
..................................................
++ +++ ++++++++++ +++++++ ++++ ++ ++++++ +++++++
gi|115306| 692 pglrggagppgpeggkgaagppgppgaagtpglqgmpgergglgspgpkg 741
..................................................
+++++++++ ++ ++++++++++++ +++++ ++++++++++ ++ ++
gi|115306| 742 dkgepggpgadgvpgkdgprgptgpigppgpagqpgdkgeggapglpgia 791
..................................................
+++++++++++++++++ + ++ ++++++++++++++ +++++++++++
gi|115306| 792 gprgspgergetgppgpagfpgapgqngepggkgergapgekgeggppgv 841
..................................................
++++++++ +++++++ +++++++++++ + ++ ++ +++++++++++
gi|115306| 842 agppggsgpagppgpqgvkgergspggpgaagfpgarglpgppgsngnpg 891
..................................................
++++++++++++++++ ++++ +++++ ++++++ ++++++++++ ++++
gi|115306| 892 ppgpsgspgkdgppgpagntgapgspgvsgpkgdagqpgekgspgaqgpp 941
..................................................
+ +++ + + ++ ++ ++++ +++++++++++ ++++++++ ++ +++
gi|115306| 942 gapgplgiagitgarglagppgmpgprgspgpqgvkgesgkpganglsge 991
..................................................
++++++++ ++ ++ +++++++++++++ ++++++++++++++++++++
gi|115306| 992 rgppgpqglpglagtagepgrdgnpgsdglpgrdgspggkgdrgengspg 1041
..................................................
++ +++++++++ ++ +++++++++++ ++ + +++ ++++ +++++++
gi|115306| 1042 apgapghpgppgpvgpagksgdrgesgpagpagapgpagsrgapgpqgpr 1091
..................................................
++++++++++ + +++++ +++++ ++++++ ++++ +++++ +++++
gi|115306| 1092 gdkgetgergaagikghrgfpgnpgapgspgpagqqgaigspgpagprgp 1141
..................................................
+++++++++++++++++ +++++++++++++++++++++++++++++++
gi|115306| 1142 vgpsgppgkdgtsghpgpigppgprgnrgergsegspghpgqpgppgppg 1191
.........eeleteqvsivlgknfllTiherheidilasvRkRirtkkp
+++ ++ + + + i + + ++a + +
gi|115306| 1192 apgpccggvGAAA------------IAGIGGE-KAGGFAPYYGDEPMD-- 1226
gvlrqkgsdylfyalldaiidsyfpvlekiedeieeLEdqIlagrstpss
++ + +d++ l+ + +ie+L ++ p++
gi|115306| 1227 --FK-------------INTDEIMTSLKSVNGQIESL----IS----PDG 1253
tildeIlslrrelldl.......vtlrralipkrdvlnfllretkepwii
+ +++ ++r + + ++ ++++ ++ + k d+++ + + + i
gi|115306| 1254 SRKNPARNCRDLKFCHpelksgeYWVDPNQGCKLDAIKVFCNMETGETCI 1303
.p....................................qkEvreylrDiy
+ ++ + ++++ ++++ ++++ +++ +++ + + + E+ e++ D++
gi|115306| 1304 sAnplnvprkhwwtdssaekkhvwfgesmdggfqfsygNPELPEDVLDVQ 1353
dHtdqllevietyrellsRsHsNsLmdiylslvvsnrqNeImKilTvvtt
++ll++ ++++ Ns+ +y+++ s ++ +++K +
gi|115306| 1354 LAFLRLLSSRASQNITYH--CKNSI--AYMDQA-SGNVKKALKLM----- 1393
iFiPpTlIaGiYGMN...FkWfMPELnwkyGYpfvlilMvllallmlywF
G N+++Fk E n+k+ Y v
gi|115306| 1394 ------------GSNegeFK---AEGNSKFTY-TV--------------- 1412
rrKgWL<-*
L
gi|115306| 1413 -----L 1413
COLFI: domain 1 of 1, from 1248 to 1465: score 561.6, E = 5.3e-219
*->lksPeGksrknPARtCkDLfLchpefksGeYWiDPNqGCikDAikVf
l+sP+G srknPAR+C+DL++chpe ksGeYW+DPNqGC++DAikVf
gi|115306| 1248 LISPDG-SRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVF 1293
CnkrfetGvgeTCisptpksvpkRiksWykgkskdkKhvWFgetmegGfk
Cn +etG eTCis++p +vp+ k+W++++s++kKhvWFge+m+gGf+
gi|115306| 1294 CN--METG--ETCISANPLNVPR--KHWWTDSSAEKKHVWFGESMDGGFQ 1337
fsYiddelnpeisnvQlTFLRLLSteAsQNiTYhCKNSvAYmDeatGNlk
fsY+++el++++ +vQl+FLRLLS++AsQNiTYhCKNS+AYmD+a+GN+k
gi|115306| 1338 FSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVK 1387
kAlilmgSnDvElsadgnskFtYtvlGeDGCssrtgewgKTViEyeTkKt
kAl lmgSn+ E++a+gnskFtYtvl eDGC+++tgew+KTV+Ey+T+K+
gi|115306| 1388 KALKLMGSNEGEFKAEGNSKFTYTVL-EDGCTKHTGEWSKTVFEYRTRKA 1436
tRLPIvDiApsDiGgedQeFGveiGPVCF<-*
RLPIvDiAp+DiGg+dQeFGv++GPVCF
gi|115306| 1437 VRLPIVDIAPYDIGGPDQEFGVDVGPVCF 1465
//
Start with PfamFrag (from /data/patterns/pfam)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/pfam/PfamFrag
Sequence file: tem15
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copie 938.0 2.5e-278 18
COLFI Fibrillar collagen C-terminal domain 561.6 5.3e-219 1
DNA_pol3_beta DNA polymerase III beta subunit 7.6 0.39 1
FATC FATC domain 2.6 43 1
Fe_dep_repress Iron dependent repressor 1.9 41 1
TILa TILa domain 0.9 85 1
ANATO Anaphylotoxin-like domain -0.9 46 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
TILa 1/1 51 67 .. 23 39 .. 0.9 85
ANATO 1/1 80 85 .. 32 37 .] -0.9 46
Fe_dep_repress 1/1 81 91 .. 120 132 .] 1.9 41
Collagen 1/18 102 139 .. 12 49 .. 20.6 0.00035
Collagen 2/18 168 227 .. 1 60 [] 64.5 3e-16
Collagen 3/18 234 293 .. 1 60 [] 76.5 1.6e-19
Collagen 4/18 294 353 .. 1 60 [] 66.4 9.5e-17
Collagen 5/18 354 413 .. 1 60 [] 65.2 1.9e-16
Collagen 6/18 414 473 .. 1 60 [] 65.6 1.5e-16
Collagen 7/18 474 533 .. 1 60 [] 61.9 1.6e-15
Collagen 8/18 534 593 .. 1 60 [] 67.3 5.2e-17
Collagen 9/18 594 653 .. 1 60 [] 47.2 1.8e-11
Collagen 10/18 654 713 .. 1 60 [] 44.5 9.7e-11
Collagen 11/18 714 773 .. 1 60 [] 56.8 4e-14
Collagen 12/18 777 836 .. 1 60 [] 56.3 5.6e-14
Collagen 13/18 837 896 .. 1 60 [] 50.6 2e-12
Collagen 14/18 897 956 .. 1 60 [] 62.9 8.3e-16
Collagen 15/18 957 1016 .. 1 60 [] 63.2 6.9e-16
Collagen 16/18 1017 1076 .. 1 60 [] 59.0 1e-14
Collagen 17/18 1077 1136 .. 1 60 [] 77.4 9.1e-20
Collagen 18/18 1137 1196 .. 1 60 [] 67.7 4e-17
DNA_pol3_beta 1/1 1225 1247 .. 1 23 [. 7.6 0.39
FATC 1/1 1237 1250 .. 1 14 [. 2.6 43
COLFI 1/1 1248 1465 .. 1 226 [] 561.6 5.3e-219
Alignments of top-scoring domains:
TILa: domain 1 of 1, from 51 to 67: score 0.9, E = 85
*->qsCaCtgGaiqCqnFqC<-*
q C+C G++ C + C
gi|115306| 51 QICVCDSGSVLCDDIIC 67
ANATO: domain 1 of 1, from 80 to 85: score -0.9, E = 46
*->aFlqCC<-*
+F +CC
gi|115306| 80 PFGECC 85
Fe_dep_repress: domain 1 of 1, from 81 to 91: score 1.9, E = 41
*->peecPhgkpdWIP<-*
++ec++++p +P
gi|115306| 81 FGECCAVCP--QP 91
Collagen: domain 1 of 18, from 102 to 139: score 20.6, E = 0.00035
*->pGppGppGppGpaGapGppGppGepGpPGppGppGppG<-*
+Gp Gp+G pGp+G pG +G+pG pG+PG+pG pGppG
gi|115306| 102 QGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPG 139
Collagen: domain 2 of 18, from 168 to 227: score 64.5, E = 3e-16
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +G pGp+GppGppGppG G++G+pG+pG +G+pG+PG++Gp Gp
gi|115306| 168 GLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQGPPGEPGQAGPSGP 214
pGppGapGapGpp<-*
pGppGa+G+ Gp+
gi|115306| 215 PGPPGAIGPSGPA 227
Collagen: domain 3 of 18, from 234 to 293: score 76.5, E = 1.6e-19
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+pG++G+pGppG +Gp+G +G+pG++G++G++G+ G +G+ G+
gi|115306| 234 GRPGRPGERGLPGPPGIKGPAGIPGFPGMKGHRGFDGRNGEKGETGA 280
pGppGapGapGpp<-*
pG +G+ G pG++
gi|115306| 281 PGLKGENGLPGEN 293
Collagen: domain 4 of 18, from 294 to 353: score 66.4, E = 9.5e-17
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp+Gp+G+pG++G+pG pG+aGa+G+ G++G +G+PGppGppG
gi|115306| 294 GAPGPMGPRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGT 340
pGppGapGapGpp<-*
+G pG pGa+G++
gi|115306| 341 AGFPGSPGAKGEV 353
Collagen: domain 5 of 18, from 354 to 413: score 65.2, E = 1.9e-16
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G+pG++G+pG++G+pGp+G+aGa+GppGppG +G+PG +G++Gp
gi|115306| 354 GPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGP 400
pGppGapGapGpp<-*
+G pGapG +G++
gi|115306| 401 AGIPGAPGLMGAR 413
Collagen: domain 6 of 18, from 414 to 473: score 65.6, E = 1.5e-16
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+G++G+pG +G +G+pG +Ga+G+pGp+Ge+G+ G pG+pG+
gi|115306| 414 GPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERGEAGIPGVPGA 460
pGppGapGapGpp<-*
+G++G++G+pG+p
gi|115306| 461 KGEDGKDGSPGEP 473
Collagen: domain 7 of 18, from 474 to 533: score 61.9, E = 1.6e-15
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+ G+pG++G++G+pG +Gp+Gp+G pG++Gp+Ge+G+PGp+Gp G+
gi|115306| 474 GANGLPGAAGERGAPGFRGPAGPNGIPGEKGPAGERGAPGPAGPRGA 520
pGppGapGapGpp<-*
+G+pG++G pG p
gi|115306| 521 AGEPGRDGVPGGP 533
Collagen: domain 8 of 18, from 534 to 593: score 67.3, E = 5.2e-17
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +G pG+pG pG +G+pGppG +G+ G pGppG++Gp G+pG++G+
gi|115306| 534 GMRGMPGSPGGPGSDGKPGPPGSQGESGRPGPPGPSGPRGQPGVMGF 580
pGppGapGapGpp<-*
pGp+G++GapG++
gi|115306| 581 PGPKGNDGAPGKN 593
Collagen: domain 9 of 18, from 594 to 653: score 47.2, E = 1.8e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G++G pG+pGp+GppG+ G++Gp+G+pGp Gp G++G GppGp G
gi|115306| 594 GERGGPGGPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGL 640
pGppGapGapGpp<-*
+G pG G+pG++
gi|115306| 641 QGLPGTGGPPGEN 653
Collagen: domain 10 of 18, from 654 to 713: score 44.5, E = 9.7e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+pGp+G++G+pG+pG +G+aGapG++GppG +G+PG +G +Gp
gi|115306| 654 GKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGP 700
pGppGapGapGpp<-*
pGp+G +Ga+Gpp
gi|115306| 701 PGPEGGKGAAGPP 713
Collagen: domain 11 of 18, from 714 to 773: score 56.8, E = 4e-14
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppG +G pG++G+pG++G G +G++G++G pG pG++G pG++Gp
gi|115306| 714 GPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGP 760
pGppGapGapGpp<-*
+Gp+G++G+pGp+
gi|115306| 761 RGPTGPIGPPGPA 773
Collagen: domain 12 of 18, from 777 to 836: score 56.3, E = 5.6e-14
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +G+ G+pG+pG +Gp+G pG++G+ GppGp+G+pG+PG+ G+pG
gi|115306| 777 GDKGEGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGG 823
pGppGapGapGpp<-*
+G++GapG++G+
gi|115306| 824 KGERGAPGEKGEG 836
Collagen: domain 13 of 18, from 837 to 896: score 50.6, E = 2e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppG +GppG Gp+GppGp+G +G++G+pG pG++G+PG++G pGp
gi|115306| 837 GPPGVAGPPGGSGPAGPPGPQGVKGERGSPGGPGAAGFPGARGLPGP 883
pGppGapGapGpp<-*
pG G+pG+pGp
gi|115306| 884 PGSNGNPGPPGPS 896
Collagen: domain 14 of 18, from 897 to 956: score 62.9, E = 8.3e-16
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pG+ GppGp+G +G+pG pG +G++G++G pGe+G+PG++GppG+
gi|115306| 897 GSPGKDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGA 943
pGppGapGapGpp<-*
pGp G +G G++
gi|115306| 944 PGPLGIAGITGAR 956
Collagen: domain 15 of 18, from 957 to 1016: score 63.2, E = 6.9e-16
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G +GppG pGp+G pGp G +G++G+pG +G +Ge+GpPGp+G pG
gi|115306| 957 GLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGLPGL 1003
pGppGapGapGpp<-*
+G +G+pG G p
gi|115306| 1004 AGTAGEPGRDGNP 1016
Collagen: domain 16 of 18, from 1017 to 1076: score 59.0, E = 1e-14
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G G+pG+ G pG +G++G+ G +GapG pG+pG+pGp Gp+G+ G
gi|115306| 1017 GSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPGPPGPVGPAGKSGD 1063
pGppGapGapGpp<-*
+G+ G++G++G+p
gi|115306| 1064 RGESGPAGPAGAP 1076
Collagen: domain 17 of 18, from 1077 to 1136: score 77.4, E = 9.1e-20
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G++G+pGp+Gp+G++G++G++Ga+G +G++G+pG PG+pG pGp
gi|115306| 1077 GPAGSRGAPGPQGPRGDKGETGERGAAGIKGHRGFPGNPGAPGSPGP 1123
pGppGapGapGpp<-*
+G++Ga+G+pGp+
gi|115306| 1124 AGQQGAIGSPGPA 1136
Collagen: domain 18 of 18, from 1137 to 1196: score 67.7, E = 4e-17
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+Gp Gp GppG +G +G+pGp G+pGp+G++Ge+G+ G+pG+pG+
gi|115306| 1137 GPRGPVGPSGPPGKDGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQ 1183
pGppGapGapGpp<-*
pGppG+pGapGp+
gi|115306| 1184 PGPPGPPGAPGPC 1196
DNA_pol3_beta: domain 1 of 1, from 1225 to 1247: score 7.6, E = 0.39
*->MkFtIeRdaLlkaLqkVarvvsn<-*
M F+I++d+++++L+ V + +++
gi|115306| 1225 MDFKINTDEIMTSLKSVNGQIES 1247
FATC: domain 1 of 1, from 1237 to 1250: score 2.6, E = 43
*->epLsvegqvndLIq<-*
+ +sv+gq+++LI+
gi|115306| 1237 SLKSVNGQIESLIS 1250
COLFI: domain 1 of 1, from 1248 to 1465: score 561.6, E = 5.3e-219
*->lksPeGksrknPARtCkDLfLchpefksGeYWiDPNqGCikDAikVf
l+sP+G srknPAR+C+DL++chpe ksGeYW+DPNqGC++DAikVf
gi|115306| 1248 LISPDG-SRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVF 1293
CnkrfetGvgeTCisptpksvpkRiksWykgkskdkKhvWFgetmegGfk
Cn +etG eTCis++p +vp+ k+W++++s++kKhvWFge+m+gGf+
gi|115306| 1294 CN--METG--ETCISANPLNVPR--KHWWTDSSAEKKHVWFGESMDGGFQ 1337
fsYiddelnpeisnvQlTFLRLLSteAsQNiTYhCKNSvAYmDeatGNlk
fsY+++el++++ +vQl+FLRLLS++AsQNiTYhCKNS+AYmD+a+GN+k
gi|115306| 1338 FSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVK 1387
kAlilmgSnDvElsadgnskFtYtvlGeDGCssrtgewgKTViEyeTkKt
kAl lmgSn+ E++a+gnskFtYtvl eDGC+++tgew+KTV+Ey+T+K+
gi|115306| 1388 KALKLMGSNEGEFKAEGNSKFTYTVL-EDGCTKHTGEWSKTVFEYRTRKA 1436
tRLPIvDiApsDiGgedQeFGveiGPVCF<-*
RLPIvDiAp+DiGg+dQeFGv++GPVCF
gi|115306| 1437 VRLPIVDIAPYDIGGPDQEFGVDVGPVCF 1465
//
Start with Repeat Library (from /data/patterns/repeats-Miguel-Andrade/hmm)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/repeats-Miguel-Andrade/hmm/repeats.hmm-lib
Sequence file: tem15
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Prosite
---------------------------------------------------------
| ppsearch (c) 1994 EMBL Data Library |
| based on MacPattern (c) 1990-1994 R. Fuchs |
---------------------------------------------------------
PROSITE pattern search started: Fri Nov 10 14:43:09 2000
Sequence file: tem15
----------------------------------------
Sequence gi|115306|sp|P02461|CA13_HUMAN (1466 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
1367: NITY
Total matches: 1
Matching pattern PS00005 PKC_PHOSPHO_SITE:
233: SGR
560: SGR
980: SGK
1237: SLK
1254: SRK
1361: SSR
1433: TRK
Total matches: 7
Matching pattern PS00006 CK2_PHOSPHO_SITE:
38: SYAD
469: SPGE
556: SQGE
796: SPGE
1006: TAGE
1319: SSAE
1411: TVLE
1427: TVFE
Total matches: 8
Matching pattern PS00008 MYRISTYL:
36: GQSYAD
58: GSVLCD
139: GICESC
163: GVAVGG
167: GGLAGY
312: GLPGAA
315: GAAGAR
318: GARGND
321: GNDGAR
324: GARGSD
345: GSPGAK
357: GSPGSN
390: GSPGGK
408: GLMGAR
426: GLRGGA
456: GVPGAK
477: GLPGAA
543: GGPGSD
626: GGDKGD
642: GLPGTG
647: GGPPGE
669: GAPGGK
693: GLRGGA
705: GGKGAA
747: GGPGAD
782: GGAPGL
836: GGPPGV
847: GSGPAG
867: GGPGAA
933: GSPGAQ
951: GITGAR
1002: GLAGTA
1014: GNPGSD
1026: GSPGGK
1125: GQQGAI
1198: GGVGAA
1199: GVGAAA
1209: GGEKAG
1243: GQIESL
1394: GSNEGE
Total matches: 40
Matching pattern PS00343 GRAM_POS_ANCHORING:
643: LPGTGG
Total matches: 1
Matching pattern PS00016 RGD:
1091: RGD
Total matches: 1
Matching pattern PS01208 VWFC:
50: CQICVCDSGSVLCDDIICDDQELDCPNPEIPFGECCAVC
Total matches: 1
Total no of hits in this sequence: 59
========================================
1314 pattern(s) searched in 1 sequence(s), 1466 residues.
Total no of hits in all sequences: 59.
Search time: 00:00 min
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Start with Profile Search
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Start with motif search against own library
***** bioMotif : Version V41a DB, 1999 Nov 11 *****
argv[1]=P
argv[2]=-m /data/patterns/own/motif.fa
argv[4]=-seq tem15
***** bioMotif : Version V41a DB, 1999 Nov 11 *****
SeqTyp=2 : PROTEIN search;
>APC D-Box is the MOTIF name
>STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 1466 units
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Start with HMM-search search against own library
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/own/own-hmm.lib
Sequence file: tem15
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/own/own-hmm-f.lib
Sequence file: tem15
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN PRECURSOR
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
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L. Aravind's signalling DB
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN
PRECURSOR
(1466 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
POZ Pox virus Zinc finger domain (Also called BTB domain; a... 35 7e-04
PCNA Proliferating Cell nuclear antigen like domain 31 0.008
BRIGHT BRIGHT domain (Alpha helical DNA binding domain) 27 0.15
14-3-3 14-3-3 protein alpha Helical domain 25 0.74
UBA Ubiquitin pathway associated domain 24 1.8
MATH The Meprin associated TRAF homology domain 23 2.1
FYVE Zinc Finger domain involved in PtdIns(3)P binding 23 3.5
>POZ Pox virus Zinc finger domain (Also called BTB domain; a protein-protein interaction domain)
Length = 229
Score = 34.9 bits (79), Expect = 7e-04
Identities = 23/248 (9%), Positives = 44/248 (17%), Gaps = 55/248 (22%)
Query: 1230 NTDEIMTSLKSVNGQIESLISPDGSRKNPAR---NCRDLKF--------CHPE-----LK 1273
+ D L +G L G N + H
Sbjct: 2 SGDTC---LCPASGAKPKLSGFKGGGLGNKYVQLNVGGSLYYTTVRALTRHDTMLKAMFS 58
Query: 1274 SG--EYWVDPNQGCKLDAI------KVFCNMETGETCISANPLNVPR-----KHWWTDSS 1320
+G L + + + N + K++
Sbjct: 59 GRMEVL--TDKEGWILIDRCGKHFGTILNYLRDDTITLPQNRQEIKELMAEAKYYLIQ-G 115
Query: 1321 AEKKHVWFGESMDGGFQFSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMD 1380
+ + P + + + S +
Sbjct: 116 LVNMCQSALQDKK--------DSYQPVCNIPIITSLKEEERLIESSTKPVVKLLYNRSNN 167
Query: 1381 QASGNVKK-ALKLMGSNEGE---FKAEGNSKF--TYTVLEDGCTKHTGEWSKTVFEYRTR 1434
+ S L + + G F E C WS +
Sbjct: 168 KYSYTSNSDDHLLKNIELFDKLSLRFNGRVLFIKDVIGDEICC------WSFYGQGRKLA 221
Query: 1435 KAVRLPIV 1442
+ IV
Sbjct: 222 EVCCTSIV 229
>PCNA Proliferating Cell nuclear antigen like domain
Length = 280
Score = 31.5 bits (71), Expect = 0.008
Identities = 7/32 (21%), Positives = 14/32 (42%), Gaps = 1/32 (3%)
Query: 1212 KAGGFAPY-YGDEPMDFKINTDEIMTSLKSVN 1242
+A F + +E + F+IN ++ L
Sbjct: 66 QADVFQEFVIQEESVTFRINLTILLDCLSIFG 97
>BRIGHT BRIGHT domain (Alpha helical DNA binding domain)
Length = 172
Score = 27.3 bits (60), Expect = 0.15
Identities = 6/31 (19%), Positives = 7/31 (22%)
Query: 886 SNGNPGPPGPSGSPGKDGPPGPAGNTGAPGS 916
G G + P P PG
Sbjct: 130 REGRRSSYGQYEAMHNQMPMTPISRPSLPGG 160
Score = 23.0 bits (49), Expect = 2.7
Identities = 11/40 (27%), Positives = 14/40 (34%), Gaps = 3/40 (7%)
Query: 367 QRGEPGPQGHAGA---QGPPGPPGINGSPGGKGEMGPAGI 403
+ G G A Q P P PGG +M P +
Sbjct: 130 REGRRSSYGQYEAMHNQMPMTPISRPSLPGGMQQMSPLAL 169
>14-3-3 14-3-3 protein alpha Helical domain
Length = 270
Score = 25.0 bits (54), Expect = 0.74
Identities = 6/24 (25%), Positives = 9/24 (37%)
Query: 362 NGAPGQRGEPGPQGHAGAQGPPGP 385
+ A G Q +A + P G
Sbjct: 240 SAAAAGGNTEGAQENAPSNAPEGE 263
Score = 23.0 bits (49), Expect = 2.9
Identities = 7/27 (25%), Positives = 8/27 (28%)
Query: 818 NGEPGGKGERGAPGEKGEGGPPGVAGP 844
+ G GA P G A P
Sbjct: 240 SAAAAGGNTEGAQENAPSNAPEGEAEP 266
Score = 21.5 bits (45), Expect = 8.9
Identities = 3/25 (12%), Positives = 4/25 (16%)
Query: 463 EDGKDGSPGEPGANGLPGAAGERGA 487
GA + G
Sbjct: 239 YSAAAAGGNTEGAQENAPSNAPEGE 263
>UBA Ubiquitin pathway associated domain
Length = 255
Score = 23.5 bits (50), Expect = 1.8
Identities = 15/52 (28%), Positives = 21/52 (39%)
Query: 338 PGTAGFPGSPGAKGEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGIN 389
P TA A+ ++ + G N + G G G A GPPG G+
Sbjct: 80 PSTAATTAEQPAEDDLFAQAAQGGNASSGALGTTGGATDAAQGGPPGSIGLT 131
Score = 22.7 bits (48), Expect = 3.2
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 814 APGQNGEPGGKGERGAPGEKGEGGPPGVAG 843
A G N G G G + +GGPPG G
Sbjct: 100 AQGGNASSGALGTTGGATDAAQGGPPGSIG 129
Score = 22.3 bits (47), Expect = 4.4
Identities = 11/34 (32%), Positives = 14/34 (40%)
Query: 584 KGNDGAPGKNGERGGPGGPGPQGPPGKNGETGPQ 617
+G + + G G GG GPPG G T
Sbjct: 101 QGGNASSGALGTTGGATDAAQGGPPGSIGLTVED 134
Score = 21.6 bits (45), Expect = 8.6
Identities = 12/28 (42%), Positives = 14/28 (49%)
Query: 531 GGPGMRGMPGSPGGPGSDGKPGPPGSQG 558
GG G G+ GG + GPPGS G
Sbjct: 102 GGNASSGALGTTGGATDAAQGGPPGSIG 129
Score = 21.2 bits (44), Expect = 9.5
Identities = 19/72 (26%), Positives = 24/72 (32%), Gaps = 1/72 (1%)
Query: 896 SGSPGKDGPPGPAGNTGAPG-SPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIAGITG 954
G P P P T A P + + + + AQG + G LG G
Sbjct: 58 MGIPENLRQPEPQQQTAAAAEQPSTAATTAEQPAEDDLFAQAAQGGNASSGALGTTGGAT 117
Query: 955 ARGLAGPPGMPG 966
GPPG G
Sbjct: 118 DAAQGGPPGSIG 129
>MATH The Meprin associated TRAF homology domain
Length = 209
Score = 23.3 bits (50), Expect = 2.1
Identities = 5/23 (21%), Positives = 6/23 (25%)
Query: 124 GIPGQPGSPGSPGPPGICESCPT 146
+P P P C T
Sbjct: 3 RVPSPPPPAEMSSGPVAESWCYT 25
>FYVE Zinc Finger domain involved in PtdIns(3)P binding
Length = 99
Score = 22.8 bits (48), Expect = 3.5
Identities = 12/34 (35%), Positives = 16/34 (46%), Gaps = 4/34 (11%)
Query: 58 GSVLCDDIICDDQELDCPNPEIPFGECCAVCPQP 91
G ++C D+ C E PE +CC C QP
Sbjct: 10 GKLMCWDMNCKRVET----PEWKTSDCCQKCNQP 39
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 7
Number of calls to ALIGN: 14
Length of query: 1466
Total length of test sequences: 20182
Effective length of test sequences: 16738.0
Effective search space size: 23993297.2
Initial X dropoff for ALIGN: 25.0 bits
Y. Wolf's SCOP PSSM
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= gi|115306|sp|P02461|CA13_HUMAN COLLAGEN ALPHA 1(III) CHAIN
PRECURSOR
(1466 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|1173357 [36..558] Periplasmic binding protein-like II 28 0.72
gi|421277 [11..339] NAD(P)-binding Rossmann-fold domains 28 1.4
gi|2496947 [316..429] Protein kinases (PK), catalytic core 27 2.5
gi|2497951 [161..384] Creatinase/methionine aminopeptidase 25 6.8
>gi|1173357 [36..558] Periplasmic binding protein-like II
Length = 523
Score = 28.5 bits (63), Expect = 0.72
Identities = 14/82 (17%), Positives = 23/82 (27%), Gaps = 9/82 (10%)
Query: 1339 SYGNPELPEDVLDVQLAFLRLLSSR-------ASQNITYHCKNSIAYMDQASGNVKKALK 1391
+ P + DV + R+L A N+TY + +QA
Sbjct: 75 PWFTPTRDFNAEDVVFSINRVLGGHNTYLPTLAETNVTYSNPQYRVFHEQARKVRFPYFD 134
Query: 1392 LMGSNEGEF--KAEGNSKFTYT 1411
+ NE A +
Sbjct: 135 SIKLNEKIKSVTALSPYQVKIE 156
>gi|421277 [11..339] NAD(P)-binding Rossmann-fold domains
Length = 329
Score = 27.7 bits (60), Expect = 1.4
Identities = 6/87 (6%), Positives = 15/87 (16%), Gaps = 7/87 (8%)
Query: 1293 FCNMETGETCISANPLNV-----PRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPE 1347
+ G + NV + +
Sbjct: 169 ANYGQHGTAVATVRAGNVIGGGDWALDRIVPDILRAFEQSQPVIIRNPHAI--RPWQHVL 226
Query: 1348 DVLDVQLAFLRLLSSRASQNITYHCKN 1374
+ L L + L + ++
Sbjct: 227 EPLSGYLLLAQKLYTDGAEYAEGWNFG 253
>gi|2496947 [316..429] Protein kinases (PK), catalytic core
Length = 114
Score = 26.9 bits (58), Expect = 2.5
Identities = 4/79 (5%), Positives = 16/79 (20%)
Query: 1262 CRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSSA 1321
K ++KS ++ + ++ + V ++
Sbjct: 14 LHKHKVAQRDMKSDNILLEYDFDDEIPQLVVADFGCALACDNWQVDYESDEVSLGGNAKT 73
Query: 1322 EKKHVWFGESMDGGFQFSY 1340
+ +
Sbjct: 74 KAPEIATAVPGKNVKVNFE 92
>gi|2497951 [161..384] Creatinase/methionine aminopeptidase
Length = 224
Score = 25.3 bits (55), Expect = 6.8
Identities = 5/30 (16%), Positives = 5/30 (16%)
Query: 1183 QPGPPGPPGAPGPCCGGVGAAAIAGIGGEK 1212
G G A C E
Sbjct: 50 TNGKAGTDLASMYFCSSPRTGTCHIRWSED 79
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 4
Number of calls to ALIGN: 4
Length of query: 1466
Total length of test sequences: 256703
Effective length of test sequences: 211865.0
Effective search space size: 302552198.5
Initial X dropoff for ALIGN: 25.0 bits