analysis of sequence from tem17
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
>gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARESPGHVSEPDRTQLSQDLGGG
TLAMDTLPDNRTRVVEDNHSYYVSRLYGPSEPHSRELWVDVAEANRSQVKIHTILSNTHRQASRVVLSFD
FPFYGHPLRQITIATGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSDNSTVVYFDNGTVFVVQWDHVYL
QGWEDKGSFTFQAALHHDGRIVFAYKEIPMSVPEISSSQHPVKTGLSDAFMILNPSPDVPESRRRSIFEY
HRIELDPSKVTSMSAVEFTPLPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQ
EAEGQDVRGLPGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDTKLNPYAGGDGLQNNLSPKTK
GTPVHLGTIVGIVLAVLLVAAIILAGIYINGHPTSNAALFFIERRPHHWPAMKFRSHPDHSTYAEVEPSG
HEKEGFMEAEQC
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
sec.str. with predator
> gi|9857404|gb|AAG00869.1|AF279144_1
. . . . .
1 MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARE 50
___HHHHHHHHHHHHHHH________________________________
. . . . .
51 SPGHVSEPDRTQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPS 100
__________EEEEE______EEEE_____EEEEE_____EEEEE_____
. . . . .
101 EPHSRELWVDVAEANRSQVKIHTILSNTHRQASRVVLSFDFPFYGHPLRQ 150
____HHHHHHHHHH______EEEEE_________EEEE_________EEE
. . . . .
151 ITIATGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSDNSTVVYFDNGTV 200
EEEE_________HHHHHHHHHHEEEE_____________EEEEE____E
. . . . .
201 FVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEIPMSVPEISSSQH 250
EEEE____EEE_________EEEEE____EEEEEEE______________
. . . . .
251 PVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELDPSKVTSMSAVEFTP 300
________EEEEE_________HHHHHHHHH________EEEEEEEEE__
. . . . .
301 LPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQ 350
_______________________EEEEEE______HHHHHH______HHH
. . . . .
351 EAEGQDVRGLPGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDT 400
HHH__________EEE_____________________EEEEE________
. . . . .
401 KLNPYAGGDGLQNNLSPKTKGTPVHLGTIVGIVLAVLLVAAIILAGIYIN 450
__________________________HHHHHHHHHHHHHHHHHHHHEEE_
. . . . .
451 GHPTSNAALFFIERRPHHWPAMKFRSHPDHSTYAEVEPSGHEKEGFMEAE 500
_____HHHHHHHH____________________EEE______________
501 QC 502
__
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
method : 1
alpha-contents : 7.1 %
beta-contents : 28.1 %
coil-contents : 64.9 %
class : beta
method : 2
alpha-contents : 10.1 %
beta-contents : 21.5 %
coil-contents : 68.3 %
class : beta
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
GPI: learning from metazoa
-27.82 -2.64 -3.62 -1.48 -4.00 0.00 0.00 0.00 -0.59 -7.78 -2.08 -12.00 -12.00 0.00 -12.00 0.00 -86.00
-20.22 -7.71 -3.44 -0.55 -4.00 0.00 -4.00 0.00 0.00 -7.33 -2.08 -12.00 -12.00 0.00 -12.00 0.00 -85.33
ID: gi|9857404|gb|AAG00869.1|AF279144_1 AC: xxx Len: 490 1:I 474 Sc: -85.33 Pv: 8.734346e-01 NO_GPI_SITE
GPI: learning from protozoa
-16.33 -4.02 -0.64 -1.20 -4.00 0.00 -32.00 0.00 0.00 -6.32 -7.89 -12.00 -12.00 0.00 0.00 0.00 -96.41
-8.61 -0.99 -1.38 -1.32 -4.00 0.00 -24.00 0.00 0.00 -6.32 -7.89 -12.00 0.00 0.00 -12.00 0.00 -78.50
ID: gi|9857404|gb|AAG00869.1|AF279144_1 AC: xxx Len: 490 1:I 479 Sc: -78.50 Pv: 4.822081e-01 NO_GPI_SITE
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
# SignalP euk predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|9857404| 0.663 442 Y 0.627 446 Y 0.977 435 Y 0.140 N
# SignalP gram- predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|9857404| 0.382 458 N 0.404 458 Y 0.982 437 Y 0.155 N
# SignalP gram+ predictions
# name Cmax pos ? Ymax pos ? Smax pos ? Smean ?
gi|9857404| 0.804 28 Y 0.391 458 Y 0.982 436 Y 0.189 N
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
low complexity regions: SEG 12 2.2 2.5
>gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
1-3 MRG
elwllvlvlreaaral 4-19
20-428 SPQPGAGHDEGPGSGWAAKGTVRGWNRRAR
ESPGHVSEPDRTQLSQDLGGGTLAMDTLPD
NRTRVVEDNHSYYVSRLYGPSEPHSRELWV
DVAEANRSQVKIHTILSNTHRQASRVVLSF
DFPFYGHPLRQITIATGGFIFMGDVIHRML
TATQYVAPLMANFNPGYSDNSTVVYFDNGT
VFVVQWDHVYLQGWEDKGSFTFQAALHHDG
RIVFAYKEIPMSVPEISSSQHPVKTGLSDA
FMILNPSPDVPESRRRSIFEYHRIELDPSK
VTSMSAVEFTPLPTCLQHRSCDACMSSDLT
FNCSWCHVLQRCSSGFDRYRQEWDGTMGCA
QEAEGQDVRGLPGMRTTTSASPDTSFSPYD
GDLTTTSSSLFIDSLTTEDDTKLNPYAGGD
GLQNNLSPKTKGTPVHLGT
ivgivlavllvaaiilagi 429-447
448-502 YINGHPTSNAALFFIERRPHHWPAMKFRSH
PDHSTYAEVEPSGHEKEGFMEAEQC
low complexity regions: SEG 25 3.0 3.3
>gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
1-364 MRGELWLLVLVLREAARALSPQPGAGHDEG
PGSGWAAKGTVRGWNRRARESPGHVSEPDR
TQLSQDLGGGTLAMDTLPDNRTRVVEDNHS
YYVSRLYGPSEPHSRELWVDVAEANRSQVK
IHTILSNTHRQASRVVLSFDFPFYGHPLRQ
ITIATGGFIFMGDVIHRMLTATQYVAPLMA
NFNPGYSDNSTVVYFDNGTVFVVQWDHVYL
QGWEDKGSFTFQAALHHDGRIVFAYKEIPM
SVPEISSSQHPVKTGLSDAFMILNPSPDVP
ESRRRSIFEYHRIELDPSKVTSMSAVEFTP
LPTCLQHRSCDACMSSDLTFNCSWCHVLQR
CSSGFDRYRQEWDGTMGCAQEAEGQDVRGL
PGMR
tttsaspdtsfspydgdltttssslfidsl 365-400
tteddt
401-428 KLNPYAGGDGLQNNLSPKTKGTPVHLGT
ivgivlavllvaaiilagi 429-447
448-502 YINGHPTSNAALFFIERRPHHWPAMKFRSH
PDHSTYAEVEPSGHEKEGFMEAEQC
low complexity regions: SEG 45 3.4 3.75
>gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
1-358 MRGELWLLVLVLREAARALSPQPGAGHDEG
PGSGWAAKGTVRGWNRRARESPGHVSEPDR
TQLSQDLGGGTLAMDTLPDNRTRVVEDNHS
YYVSRLYGPSEPHSRELWVDVAEANRSQVK
IHTILSNTHRQASRVVLSFDFPFYGHPLRQ
ITIATGGFIFMGDVIHRMLTATQYVAPLMA
NFNPGYSDNSTVVYFDNGTVFVVQWDHVYL
QGWEDKGSFTFQAALHHDGRIVFAYKEIPM
SVPEISSSQHPVKTGLSDAFMILNPSPDVP
ESRRRSIFEYHRIELDPSKVTSMSAVEFTP
LPTCLQHRSCDACMSSDLTFNCSWCHVLQR
CSSGFDRYRQEWDGTMGCAQEAEGQDVR
glpgmrtttsaspdtsfspydgdltttsss 359-459
lfidsltteddtklnpyaggdglqnnlspk
tkgtpvhlgtivgivlavllvaaiilagiy
inghptsnaal
460-502 FFIERRPHHWPAMKFRSHPDHSTYAEVEPS
GHEKEGFMEAEQC
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|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARESPGHVSEPDR
TQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPSEPHSRELWVDVAEANRSQVK
IHTILSNTHRQASRVVLSFDFPFYGHPLRQITIATGGFIFMGDVIHRMLTATQYVAPLMA
NFNPGYSDNSTVVYFDNGTVFVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEIPM
SVPEISSSQHPVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELDPSKVTSMSAVEFTP
LPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQEAEGQDVRGL
PGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDTKLNPYAGGDGLQNNLSPKTK
GTPVHlgtivgivlavllvaaiilagiYINGHPTSNAALFFIERRPHHWPAMKFRSHPDH
STYAEVEPSGHEKEGFMEAEQC
1 - 425 MRGELWLLVL VLREAARALS PQPGAGHDEG PGSGWAAKGT VRGWNRRARE SPGHVSEPDR
TQLSQDLGGG TLAMDTLPDN RTRVVEDNHS YYVSRLYGPS EPHSRELWVD VAEANRSQVK
IHTILSNTHR QASRVVLSFD FPFYGHPLRQ ITIATGGFIF MGDVIHRMLT ATQYVAPLMA
NFNPGYSDNS TVVYFDNGTV FVVQWDHVYL QGWEDKGSFT FQAALHHDGR IVFAYKEIPM
SVPEISSSQH PVKTGLSDAF MILNPSPDVP ESRRRSIFEY HRIELDPSKV TSMSAVEFTP
LPTCLQHRSC DACMSSDLTF NCSWCHVLQR CSSGFDRYRQ EWDGTMGCAQ EAEGQDVRGL
PGMRTTTSAS PDTSFSPYDG DLTTTSSSLF IDSLTTEDDT KLNPYAGGDG LQNNLSPKTK
GTPVH
426 - 447 lgtiv givlavllva aiilagi
448 - 502 YIN GHPTSNAALF FIERRPHHWP AMKFRSHPDH STYAEVEPSG HEKEGFMEAE QC
low complexity regions: DUST
>gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARESPGHVSEPDR
TQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPSEPHSRELWVDVAEANRSQVK
IHTILSNTHRQASRVVLSFDFPFYGHPLRQITIATGGFIFMGDVIHRMLTATQYVAPLMA
NFNPGYSDNSTVVYFDNGTVFVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEIPM
SVPEISSSQHPVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELDPSKVTSMSAVEFTP
LPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQEAEGQDVRGL
PGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDTKLNPYAGGDGLQNNLSPKTK
GTPVHLGTIVGIVLAVLLVAAIILAGIYINGHPTSNAALFFIERRPHHWPAMKFRSHPDH
STYAEVEPSGHEKEGFMEAEQC
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
coiled coil prediction for gi|9857404|gb|AAG00869.1|AF279144_1
sequence: 490 amino acids, 0 residue(s) in coiled coil state
. | . | . | . | . | . 60
MRGELWLLVL VLREAARALS PQPGAGHDEG PGSGWAAKGT VRGWNRRARE SPGHVSEPDR
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
TQLSQDLGGG TLAMDTLPDN RTRVVEDNHS YYVSRLYGPS EPHSRELWVD VAEANRSQVK
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
IHTILSNTHR QASRVVLSFD FPFYGHPLRQ ITIATGGFIF MGDVIHRMLT ATQYVAPLMA
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
NFNPGYSDNS TVVYFDNGTV FVVQWDHVYL QGWEDKGSFT FQAALHHDGR IVFAYKEIPM
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
SVPEISSSQH PVKTGLSDAF MILNPSPDVP ESRRRSIFEY HRIELDPSKV TSMSAVEFTP
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
LPTCLQHRSC DACMSSDLTF NCSWCHVLQR CSSGFDRYRQ EWDGTMGCAQ EAEGQDVRGL
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
PGMRTTTSAS PDTSFSPYDG DLTTTSSSLF IDSLTTEDDT KLNPYAGGDG LQNNLSPKTK
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
GTPVHLGTIV GIVLAVLLVA AIILAGIYIN GHPTSNAALF FIERRPHHWP AMKFRSHPDH
~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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
. |
STYAEVEPSG
~~~~~~~~~~
----------
~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~~~
~~~~~~~~~~
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
prediction of transmembrane regions with toppred2
***********************************
*TOPPREDM with eukaryotic function*
***********************************
tem7.___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: tem7.___inter___
(1 sequences)
MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARE
SPGHVSEPDRTQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPS
EPHSRELWVDVAEANRSQVKIHTILSNTHRQASRVVLSFDFPFYGHPLRQ
ITIATGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSDNSTVVYFDNGTV
FVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEIPMSVPEISSSQH
PVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELDPSKVTSMSAVEFTP
LPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQ
EAEGQDVRGLPGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDT
KLNPYAGGDGLQNNLSPKTKGTPVHLGTIVGIVLAVLLVAAIILAGIYIN
GHPTSNAALFFIERRPHHWPAMKFRSHPDHSTYAEVEPSGHEKEGFMEAE
QC
(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 2 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 146 166 0.741 Putative
2 427 447 2.374 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2
Loop length 145 260 55
K+R profile + 5.00
+
CYT-EXT prof 0.95 -
0.73
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 5.00
Tm probability: 0.35
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 1.00
(NEG-POS)/(NEG+POS): -0.0286
NEG: 17.0000
POS: 18.0000
-> Orientation: N-in
CYT-EXT difference: 0.22
-> Orientation: N-out
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 2
Loop length 426 55
K+R profile +
5.00
CYT-EXT prof 0.93
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -5.00
Tm probability: 1.00
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): 2.00
(NEG-POS)/(NEG+POS): 0.1395
NEG: 49.0000
POS: 37.0000
-> Orientation: N-in
CYT-EXT difference: 0.93
-> Orientation: N-out
----------------------------------------------------------------------
"tem7" 502
146 166 #f 0.740625
427 447 #t 2.37396
************************************
*TOPPREDM with prokaryotic function*
************************************
tem7.___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: tem7.___inter___
(1 sequences)
MRGELWLLVLVLREAARALSPQPGAGHDEGPGSGWAAKGTVRGWNRRARE
SPGHVSEPDRTQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPS
EPHSRELWVDVAEANRSQVKIHTILSNTHRQASRVVLSFDFPFYGHPLRQ
ITIATGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSDNSTVVYFDNGTV
FVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEIPMSVPEISSSQH
PVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELDPSKVTSMSAVEFTP
LPTCLQHRSCDACMSSDLTFNCSWCHVLQRCSSGFDRYRQEWDGTMGCAQ
EAEGQDVRGLPGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDT
KLNPYAGGDGLQNNLSPKTKGTPVHLGTIVGIVLAVLLVAAIILAGIYIN
GHPTSNAALFFIERRPHHWPAMKFRSHPDHSTYAEVEPSGHEKEGFMEAE
QC
(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 2 structures are to be tested
Candidate membrane-spanning segments:
Helix Begin End Score Certainity
1 146 166 0.741 Putative
2 427 447 2.374 Certain
----------------------------------------------------------------------
Structure 1
Transmembrane segments included in this structure:
Segment 1 2
Loop length 145 260 55
K+R profile + 5.00
+
CYT-EXT prof 0.95 -
0.73
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: 5.00
Tm probability: 0.35
-> Orientation: N-in
Charge-difference over N-terminal Tm (+-15 residues): 1.00
(NEG-POS)/(NEG+POS): -0.0286
NEG: 17.0000
POS: 18.0000
-> Orientation: N-in
CYT-EXT difference: 0.22
-> Orientation: N-out
----------------------------------------------------------------------
Structure 2
Transmembrane segments included in this structure:
Segment 2
Loop length 426 55
K+R profile +
5.00
CYT-EXT prof 0.93
-
For CYT-EXT profile neg. values indicate cytoplasmic preference.
K+R difference: -5.00
Tm probability: 1.00
-> Orientation: N-out
Charge-difference over N-terminal Tm (+-15 residues): 2.00
(NEG-POS)/(NEG+POS): 0.1395
NEG: 49.0000
POS: 37.0000
-> Orientation: N-in
CYT-EXT difference: 0.93
-> Orientation: N-out
----------------------------------------------------------------------
"tem7" 502
146 166 #f 0.740625
427 447 #t 2.37396
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem7.___saps___
SAPS. Version of April 11, 1996.
Date run: Thu Oct 12 13:37:47 2000
File: /people/maria/tem7.___saps___
ID gi|9857404|gb|AAG00869.1|AF279144_1
DE tumor endothelial marker 7 precursor [Homo sapiens]
number of residues: 502; molecular weight: 55.6 kdal
1 MRGELWLLVL VLREAARALS PQPGAGHDEG PGSGWAAKGT VRGWNRRARE SPGHVSEPDR
61 TQLSQDLGGG TLAMDTLPDN RTRVVEDNHS YYVSRLYGPS EPHSRELWVD VAEANRSQVK
121 IHTILSNTHR QASRVVLSFD FPFYGHPLRQ ITIATGGFIF MGDVIHRMLT ATQYVAPLMA
181 NFNPGYSDNS TVVYFDNGTV FVVQWDHVYL QGWEDKGSFT FQAALHHDGR IVFAYKEIPM
241 SVPEISSSQH PVKTGLSDAF MILNPSPDVP ESRRRSIFEY HRIELDPSKV TSMSAVEFTP
301 LPTCLQHRSC DACMSSDLTF NCSWCHVLQR CSSGFDRYRQ EWDGTMGCAQ EAEGQDVRGL
361 PGMRTTTSAS PDTSFSPYDG DLTTTSSSLF IDSLTTEDDT KLNPYAGGDG LQNNLSPKTK
421 GTPVHLGTIV GIVLAVLLVA AIILAGIYIN GHPTSNAALF FIERRPHHWP AMKFRSHPDH
481 STYAEVEPSG HEKEGFMEAE QC
--------------------------------------------------------------------------------
COMPOSITIONAL ANALYSIS (extremes relative to: swp23s)
A : 34( 6.8%); C : 8( 1.6%); D : 30( 6.0%); E : 27( 5.4%); F : 22( 4.4%)
G : 40( 8.0%); H+ : 22( 4.4%); I : 20( 4.0%); K : 11( 2.2%); L : 39( 7.8%)
M : 13( 2.6%); N : 16( 3.2%); P : 32( 6.4%); Q : 18( 3.6%); R : 31( 6.2%)
S : 46( 9.2%); T : 35( 7.0%); V : 34( 6.8%); W : 9( 1.8%); Y : 15( 3.0%)
KR : 42 ( 8.4%); ED : 57 ( 11.4%); AGP : 106 ( 21.1%);
KRED : 99 ( 19.7%); KR-ED : -15 ( -3.0%); FIKMNY : 97 ( 19.3%);
LVIFM : 128 ( 25.5%); ST : 81 ( 16.1%).
--------------------------------------------------------------------------------
CHARGE DISTRIBUTIONAL ANALYSIS
1 0+0-000000 00+-00+000 0000000--0 0000000+00 0+000++0+- 000000-0-+
61 00000-0000 0000-000-0 +0+00--000 0000+00000 -000+-000- 00-00+000+
121 000000000+ 000+00000- 00000000+0 0000000000 00-000+000 0000000000
181 0000000-00 00000-0000 00000-0000 000--+0000 0000000-0+ 00000+-000
241 000-000000 00+0000-00 0000000-00 -0+++000-0 0+0-0-00+0 000000-000
301 0000000+00 -00000-000 000000000+ 00000-+0+0 -0-0000000 -0-00-0+00
361 000+000000 0-000000-0 -000000000 0-0000---0 +0000000-0 0000000+0+
421 0000000000 0000000000 0000000000 0000000000 00-++00000 00+0+000-0
481 0000-0-000 0-+-000-0- 00
A. CHARGE CLUSTERS.
Positive charge clusters (cmin = 8/30 or 11/45 or 13/60): none
Negative charge clusters (cmin = 10/30 or 13/45 or 16/60): none
Mixed charge clusters (cmin = 14/30 or 19/45 or 24/60): 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.
________________________________
High scoring uncharged segments:
score= 1.00 frequency= 0.803 ( LAGSVTIPNFQYHMCW )
score= 0.00 frequency= 0.000 ( BZX )
score= -8.00 frequency= 0.197 ( KEDR )
Expected score/letter: -0.775
M_0.01= 50.04; M_0.05= 40.22
1) From 421 to 462: length= 42, score=42.00 *
421 GTPVHLGTIV GIVLAVLLVA AIILAGIYIN GHPTSNAALF FI
L: 6(14.3%); A: 6(14.3%); G: 5(11.9%); V: 5(11.9%);
I: 7(16.7%);
C. CHARGE RUNS AND PATTERNS.
pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)|
lmin0 4 | 5 | 7 | 42 | 9 | 10 | 12 | 11 | 12 | 15 | 8 | 10 |
lmin1 6 | 6 | 8 | 51 | 11 | 12 | 15 | 13 | 14 | 18 | 9 | 12 |
lmin2 7 | 7 | 9 | 56 | 12 | 13 | 17 | 15 | 16 | 20 | 11 | 14 |
(Significance level: 0.010000; Minimal displayed length: 6)
(0) 42(0,0,0); at 421- 462: GTPVHLGTIVGIVLAVLLVAAIILAGIYINGHPTSNAALFFI
(4. quartile) 000000000000000000000000000000000000000000
L: 6 (14.3%); A: 6 (14.3%); G: 5 (11.9%); V: 5 (11.9%);
I: 7 (16.7%); LVIFM: 20 (47.6%);
Run count statistics:
+ runs >= 3: 1, at 273;
- runs >= 3: 1, at 397;
* runs >= 4: 0
0 runs >= 28: 1, at 421;
------------
--------------------------------------------------------------------
DISTRIBUTION OF OTHER AMINO ACID TYPES
1. HIGH SCORING SEGMENTS.
__________________________________
High scoring hydrophobic segments:
2.00 (LVIFM) 1.00 (AGYCW) 0.00 (BZX) -2.00 (PH) -4.00 (STNQ)
-8.00 (KEDR)
Expected score/letter: -1.988
M_0.01= 23.24; M_0.05= 19.29
1) From 429 to 449: length= 21, score=35.00 **
429 IVGIVLAVLL VAAIILAGIY I
L: 4(19.0%); A: 4(19.0%); V: 4(19.0%); I: 6(28.6%);
____________________________________
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: -3.574
M_0.01= 55.42; M_0.05= 45.67; M_0.30= 34.07
1) From 426 to 449: length= 24, score=86.00 **
426 LGTIVGIVLA VLLVAAIILA GIYI
L: 5(20.8%); A: 4(16.7%); G: 3(12.5%); V: 4(16.7%);
I: 6(25.0%);
2. SPACINGS OF C.
H2N-303-C-5-C-2-C-8-C-2-C-5-C-16-C-153-C-0-COOH
2*. SPACINGS OF C and H. (additional deluxe function for ALEX)
H2N-26-H-26-H-34-H-13-H-18-H-6-H-16-H-19-H-40-H-18-H-H-22-H-30-H-22-C-2-H-2-C-2-C-8-C-2-C-H-4-C-16-C-76-H-26-H-14-H-H-8-H-2-H-10-H-10-C-0-COOH
--------------------------------------------------------------------------------
REPETITIVE STRUCTURES.
A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet.
Repeat core block length: 5
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
--------------------------------------------------------------------------------
MULTIPLETS.
A. AMINO ACID ALPHABET.
1. Total number of amino acid multiplets: 31 (Expected range: 12-- 44)
2. Histogram of spacings between consecutive amino acid multiplets:
(1-5) 9 (6-10) 7 (11-20) 8 (>=21) 8
3. Clusters of amino acid multiplets (cmin = 11/30 or 14/45 or 17/60): none
B. CHARGE ALPHABET.
1. Total number of charge multiplets: 7 (Expected range: 0-- 18)
3 +plets (f+: 8.4%), 4 -plets (f-: 11.4%)
Total number of charge altplets: 9 (Critical number: 21)
2. Histogram of spacings between consecutive charge multiplets:
(1-5) 0 (6-10) 0 (11-20) 1 (>=21) 7
--------------------------------------------------------------------------------
PERIODICITY ANALYSIS.
A. AMINO ACID ALPHABET (core: 4; !-core: 5)
Location Period Element Copies Core Errors
304- 339 9 C........ 4 4 0
430- 441 3 V.. 4 4 0
B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6)
and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9)
Location Period Element Copies Core Errors
7- 12 1 i 6 6 0
261- 308 8 i..0..0. 6 6 /0/././1/././2/./
424- 453 5 i00.. 6 6 /0/1/2/././
--------------------------------------------------------------------------------
SPACING ANALYSIS.
Location (Quartile) Spacing Rank P-value Interpretation
0- 304 (2.) C( 304)C 1 of 9 0.0048 large 1. maximal spacing
348- 502 (4.) C( 154)C 2 of 9 0.0164 large 2. maximal spacing
420- 463 (4.) *( 43)* 1 of 100 0.0049 large maximal spacing
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Pfam (from /data/patterns/pfam)
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/pfam/Pfam
Sequence file: tem7
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Plexin_repeat Plexin repeat 20.0 0.021 1
ART NAD:arginine ADP-ribosyltransferase 0.1 42 1
Peptidase_M45 D-ala-D-ala dipeptidase -0.6 1e+02 1
Syndecan Syndecan domain -2.0 51 1
Zn_clus Fungal Zn(2)-Cys(6) binuclear cluster d -16.6 90 1
Como_SCP Small coat protein -121.5 86 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
ART 1/1 1 20 [. 1 22 [. 0.1 42
Syndecan 1/1 2 23 .. 1 22 [. -2.0 51
Como_SCP 1/1 11 153 .. 1 178 [] -121.5 86
Zn_clus 1/1 308 339 .. 1 43 [] -16.6 90
Peptidase_M45 1/1 332 342 .. 183 193 .. -0.6 1e+02
Plexin_repeat 1/1 303 349 .. 1 67 [] 20.0 0.021
Alignments of top-scoring domains:
ART: domain 1 of 1, from 1 to 20: score 0.1, E = 42
*->mpalhfvLllSVglllstqals<-*
m +++L+l +l+++ +als
gi|9857404 1 MRGELWLLVL--VLREAARALS 20
Syndecan: domain 1 of 1, from 2 to 23: score -2.0, E = 51
*->rkllllallllllslqaalaQr<-*
r+ l+l++l l +++a+++Q+
gi|9857404 2 RGELWLLVLVLREAARALSPQP 23
Como_SCP: domain 1 of 1, from 11 to 153: score -121.5, E = 86
*->VyspiwrvrTPladtakqnfasFslDLlggtistDgsgsnWnfviin
V + +r+ P + a + + g++ + g+ ++Wn +
gi|9857404 11 VLREAARALSPQ-PGAGHDEGP------GSGWAAKGTVRGWNRRARE 50
SP..ivNLLrtAAWKrGTLhvklvm.rGkaaVKRsdWastvqldLrnsen
SP++++ rt +l ++G ++ +d + ++ +n
gi|9857404 51 SPghVSEPDRT----------QLSQdLG-GGTLAMDTLPDNRTRVVE-DN 88
tesydArtwvisePhsgeleFsiEicGPNnGFESMwnssWanQtsWyLev
++y r + sePhs el +++ E an +++
gi|9857404 89 HSYYVSRLYGPSEPHSRELW--VDVA------E-------ANRSQVKIHT 123
vigNpkQstiFevymrldenFevAGNtLmPPflL<-*
+N + ++ +v l+ +F + G L + +
gi|9857404 124 ILSNTHRQASRVV---LSFDFPFYGHPLRQ-ITI 153
Zn_clus: domain 1 of 1, from 308 to 339: score -16.6, E = 90
*->tACdrCRkrKvKCdgskkPapCsrCikngkleCtiysrksrks<-*
++Cd+C d + Cs C + C s + r++
gi|9857404 308 RSCDACMSS----DL-TFN--CSWCHVLQ--RCS--SGFDRYR 339
Peptidase_M45: domain 1 of 1, from 332 to 342: score -0.6, E = 1e+02
*->sgGFlrysgEW<-*
s+GF ry+ EW
gi|9857404 332 SSGFDRYRQEW 342
Plexin_repeat: domain 1 of 1, from 303 to 349: score 20.0, E = 0.021
*->nCsqhRqsCssClsapdpfgCgWCvsrkrCtrreaygpsfpygeCsr
+C qh sC +C+s++ f+C WC+ ++rC++ + r
gi|9857404 303 TCLQH-RSCDACMSSDLTFNCSWCHVLQRCSSGF---------DRYR 339
gekpedNswlgwsqsseqCp<-*
+e + + C
gi|9857404 340 QE----------WDGTMGCA 349
//
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: tem7
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Plexin_repeat Plexin repeat 24.0 1.4e-06 1
RADICAL_ACTIVATING Radical activating enzymes 5.8 5.8 1
Herpes_glycop_D Herpesvirus glycoprotein D 3.3 6.7 1
ART NAD:arginine ADP-ribosyltransferas 0.1 42 1
Peptidase_M45 D-ala-D-ala dipeptidase -0.6 1e+02 1
Syndecan Syndecan domain -2.0 51 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
ART 1/1 1 20 [. 1 22 [. 0.1 42
Syndecan 1/1 2 23 .. 1 22 [. -2.0 51
RADICAL_ACTIVATING 1/1 319 326 .. 30 37 .] 5.8 5.8
Plexin_repeat 1/1 303 333 .. 1 32 [. 24.0 1.4e-06
Peptidase_M45 1/1 332 342 .. 183 193 .. -0.6 1e+02
Herpes_glycop_D 1/1 416 448 .. 353 390 .. 3.3 6.7
Alignments of top-scoring domains:
ART: domain 1 of 1, from 1 to 20: score 0.1, E = 42
*->mpalhfvLllSVglllstqals<-*
m +++L+l +l+++ +als
gi|9857404 1 MRGELWLLVL--VLREAARALS 20
Syndecan: domain 1 of 1, from 2 to 23: score -2.0, E = 51
*->rkllllallllllslqaalaQr<-*
r+ l+l++l l +++a+++Q+
gi|9857404 2 RGELWLLVLVLREAARALSPQP 23
RADICAL_ACTIVATING: domain 1 of 1, from 319 to 326: score 5.8, E = 5.8
*->nlrCpyCh<-*
+++C++Ch
gi|9857404 319 TFNCSWCH 326
Plexin_repeat: domain 1 of 1, from 303 to 333: score 24.0, E = 1.4e-06
*->nCsqhRqsCssClsapdpfgCgWCvsrkrCtr<-*
+C qh sC +C+s++ f+C WC+ ++rC++
gi|9857404 303 TCLQH-RSCDACMSSDLTFNCSWCHVLQRCSS 333
Peptidase_M45: domain 1 of 1, from 332 to 342: score -0.6, E = 1e+02
*->sgGFlrysgEW<-*
s+GF ry+ EW
gi|9857404 332 SSGFDRYRQEW 342
Herpes_glycop_D: domain 1 of 1, from 416 to 448: score 3.3, E = 6.7
*->pspppatpaNpdakvtsviigivvlalligaiivgvvy<-*
++ ++ tp++ ++i+giv ++ll +aii++++y
gi|9857404 416 SPKTKGTPVH-----LGTIVGIVLAVLLVAAIILAGIY 448
//
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: tem7
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Prosite
---------------------------------------------------------
| ppsearch (c) 1994 EMBL Data Library |
| based on MacPattern (c) 1990-1994 R. Fuchs |
---------------------------------------------------------
PROSITE pattern search started: Thu Oct 12 13:39:53 2000
Sequence file: tem7
----------------------------------------
Sequence gi|9857404|gb|AAG00869.1|AF279144_1 (502 residues):
Matching pattern PS00001 ASN_GLYCOSYLATION:
80: NRTR
88: NHSY
115: NRSQ
189: NSTV
197: NGTV
321: NCSW
Total matches: 6
Matching pattern PS00004 CAMP_PHOSPHO_SITE:
273: RRRS
Total matches: 1
Matching pattern PS00005 PKC_PHOSPHO_SITE:
40: TVR
128: THR
272: SRR
416: SPK
Total matches: 4
Matching pattern PS00006 CK2_PHOSPHO_SITE:
56: SEPD
76: TLPD
241: SVPE
276: SIFE
294: SAVE
333: SGFD
376: SPYD
395: TTED
396: TEDD
476: SHPD
482: TYAE
489: SGHE
Total matches: 12
Matching pattern PS00007 TYR_PHOSPHO_SITE:
83: RVVEDNHSY
475: RSHPDHSTY
Total matches: 2
Matching pattern PS00008 MYRISTYL:
32: GSGWAA
39: GTVRGW
69: GGTLAM
255: GLSDAF
344: GTMGCA
362: GMRTTT
410: GLQNNL
427: GTIVGI
431: GIVLAV
446: GIYING
Total matches: 10
Total no of hits in this sequence: 35
========================================
1314 pattern(s) searched in 1 sequence(s), 502 residues.
Total no of hits in all sequences: 35.
Search time: 00:00 min
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with Profile Search
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
Start with motif search against own library
***** bioMotif : Version V41a DB, 1999 Nov 11 *****
argv[1]=P
argv[2]=-m /data/patterns/own/motif.fa
argv[4]=-seq tem7
***** 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, 502 units
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~ ~~~
Start with HMM-search search against own library
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/own/own-hmm.lib
Sequence file: tem7
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /data/patterns/own/own-hmm-f.lib
Sequence file: tem7
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7 precursor [Homo sapiens]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
[no hits above thresholds]
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
[no hits above thresholds]
Alignments of top-scoring domains:
[no hits above thresholds]
//
~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~
L. Aravind's signalling DB
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7
precursor [Homo sapiens]
(502 letters)
Searching..................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
HOG HOG- intein(HINT) like domain 24 0.56
PAIRED Paired domain (A HTH domain) 22 1.5
MYND MYND domain (A zinc coordinating Cysteine rich domain) 22 1.8
ww 22 2.0
ACTIN Actin ATPase/ Cytoskeletal ATPase domain 22 2.4
RASGAP RAS-type GTPase GTP hydrolysis activating protein 21 2.8
LON The LON serine protease domain 21 4.3
HISDAC Histone deacetylase domain 20 5.6
ARR Arrestin domain 21 5.6
SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chrom... 20 6.0
AN1 AN1 like cysteine rich zinc coordinating domain 20 6.5
14-3-3 14-3-3 protein alpha Helical domain 20 6.7
PH Pleckstrin homology domain (lipid and protein interactio... 20 6.7
KIN Protein kinase domain 20 9.1
PUM Pumilio repeat RNA binding domain 20 9.5
>HOG HOG- intein(HINT) like domain
Length = 389
Score = 23.8 bits (51), Expect = 0.56
Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 204 QWDHVYL---QGWEDKGSFTFQAALHHDGRIV 232
+W + L + W++ Q +LH++GR V
Sbjct: 94 EWPGIRLLVTESWDEDY-HHGQESLHYEGRAV 124
>PAIRED Paired domain (A HTH domain)
Length = 127
Score = 22.4 bits (47), Expect = 1.5
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 444 LAGIYINGHPTSNA 457
L G+++NG P NA
Sbjct: 8 LGGVFVNGRPLPNA 21
>MYND MYND domain (A zinc coordinating Cysteine rich domain)
Length = 107
Score = 22.1 bits (46), Expect = 1.8
Identities = 8/26 (30%), Positives = 9/26 (33%), Gaps = 1/26 (3%)
Query: 308 RSCDACMSSDLTFNCSWCHVLQRCSS 333
+ C C L CS C CS
Sbjct: 50 KKCANCNREAL-AECSLCRKTPYCSE 74
>ww
Length = 38
Score = 22.1 bits (47), Expect = 2.0
Identities = 7/38 (18%), Positives = 14/38 (36%), Gaps = 1/38 (2%)
Query: 177 PLMANFNPGYSDNSTVVYFDNGTVFVVQWDHVYLQGWE 214
P+ + Y + + D+ + WD L+ E
Sbjct: 2 PMPQGWEMCYDSDGVRYFKDHNSK-TTTWDDPRLKQQE 38
>ACTIN Actin ATPase/ Cytoskeletal ATPase domain
Length = 376
Score = 21.7 bits (46), Expect = 2.4
Identities = 8/30 (26%), Positives = 12/30 (39%)
Query: 361 PGMRTTTSASPDTSFSPYDGDLTTTSSSLF 390
M+ A P+ +S + G S S F
Sbjct: 324 SSMKIKVVAPPERKYSVWIGGSILASLSTF 353
>RASGAP RAS-type GTPase GTP hydrolysis activating protein
Length = 292
Score = 21.3 bits (44), Expect = 2.8
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 284 ELDPSKVTSMSAVE 297
E+DPSK+ SAV+
Sbjct: 135 EIDPSKIKDRSAVD 148
>LON The LON serine protease domain
Length = 132
Score = 20.9 bits (44), Expect = 4.3
Identities = 9/43 (20%), Positives = 16/43 (36%), Gaps = 8/43 (18%)
Query: 235 YKEIPMSVP---EISSSQHPVKTGLSDAFMILNPSPDVPESRR 274
+EIP +V +I HPVK + + + +
Sbjct: 92 LEEIPDNVIADLDI----HPVKR-IEEVLTLALQNEPSGMQVV 129
>HISDAC Histone deacetylase domain
Length = 433
Score = 20.2 bits (42), Expect = 5.6
Identities = 10/55 (18%), Positives = 17/55 (30%), Gaps = 7/55 (12%)
Query: 135 VVLSFDF-PFYGHPLRQITIATGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSD 188
VVL G L ++ G + + + P+M GY+
Sbjct: 267 VVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVK------SFGIPMMVVGGGGYTM 315
>ARR Arrestin domain
Length = 454
Score = 20.6 bits (43), Expect = 5.6
Identities = 14/60 (23%), Positives = 16/60 (26%), Gaps = 10/60 (16%)
Query: 361 PGMRTTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDTKLN----PYAGGDGLQNNLS 416
G R SP+ + Y G FID D N P G L
Sbjct: 8 SGTRVFKKTSPNGKITTYLG------KRDFIDRGDYVDLIGENKGTEPQNVGFILTGLSH 61
>SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chromatin associated domain)
Length = 219
Score = 20.3 bits (42), Expect = 6.0
Identities = 5/23 (21%), Positives = 7/23 (29%)
Query: 362 GMRTTTSASPDTSFSPYDGDLTT 384
G+ S + Y G L
Sbjct: 100 GVFARESIPAWSYIGEYTGILRR 122
>AN1 AN1 like cysteine rich zinc coordinating domain
Length = 57
Score = 20.4 bits (42), Expect = 6.5
Identities = 5/19 (26%), Positives = 7/19 (36%), Gaps = 2/19 (10%)
Query: 309 SCDACMS--SDLTFNCSWC 325
S C + + L C C
Sbjct: 9 SFAKCTASTTTLGQFCMHC 27
>14-3-3 14-3-3 protein alpha Helical domain
Length = 270
Score = 20.3 bits (42), Expect = 6.7
Identities = 19/62 (30%), Positives = 28/62 (44%), Gaps = 14/62 (22%)
Query: 234 AYKEIPMSVPEISSSQ----HPVKTGLSDAFM-----ILNPSPDVPESRRRSIFEYHRIE 284
YK EI++++ HP++ GL+ F ILN SPD + F+ E
Sbjct: 153 GYKA----ASEIATAELAPTHPIRLGLALNFSVFYYEILN-SPDRACYLAKQAFDEAISE 207
Query: 285 LD 286
LD
Sbjct: 208 LD 209
>PH Pleckstrin homology domain (lipid and protein interaction domain)
Length = 138
Score = 20.0 bits (41), Expect = 6.7
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 3/64 (4%)
Query: 62 QLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPSEPHSRELWVDVAEANRSQVKI 121
+L G L + RVVE NH Y + P++ ++ W+ +A S
Sbjct: 78 ELYIPNNKGQLIKACKTEADGRVVEGNHMVYR--ISAPTQ-EEKDEWIKSIQAAVSVDPF 134
Query: 122 HTIL 125
+ +L
Sbjct: 135 YEML 138
>KIN Protein kinase domain
Length = 313
Score = 19.6 bits (40), Expect = 9.1
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 8/68 (11%)
Query: 187 SDNSTVVYFDNGTVFVV--QWDHVYLQGWEDKGSF--TFQAALHHDGRIVFAYKEIPMSV 242
+ N + YF G+ F V ++ V G G++ A + G V A K+I +
Sbjct: 11 NFNDNISYFVYGSQFTVPRRYSIVKCIG---HGAYGVVCSAKDNLTGEKV-AIKKISKAF 66
Query: 243 PEISSSQH 250
+ ++
Sbjct: 67 DNLKDTKR 74
>PUM Pumilio repeat RNA binding domain
Length = 337
Score = 19.8 bits (41), Expect = 9.5
Identities = 12/51 (23%), Positives = 22/51 (42%), Gaps = 15/51 (29%)
Query: 281 HRIELDPSKVTSMSAVEFTPLPTCLQHRSCDACMSSDLTFNCSWCHVLQRC 331
+I+L + + EFT + + + +DL N HV+Q+C
Sbjct: 112 VQIDL----IIKGFSQEFTSIEQVVT-------LINDLNGN----HVIQKC 147
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 105
Number of sequences better than 10.0: 15
Number of calls to ALIGN: 15
Length of query: 502
Total length of test sequences: 20182
Effective length of test sequences: 16637.0
Effective search space size: 7789758.6
Initial X dropoff for ALIGN: 25.0 bits
Y. Wolf's SCOP PSSM
IMPALA version 1.1 [20-December-1999]
Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting,
Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999),
"IMPALA: Matching a Protein Sequence Against a Collection of
"PSI-BLAST-Constructed Position-Specific Score Matrices",
Bioinformatics 15:1000-1011.
Query= gi|9857404|gb|AAG00869.1|AF279144_1 tumor endothelial marker 7
precursor [Homo sapiens]
(502 letters)
Searching.................................................done
Results from profile search
Score E
Sequences producing significant alignments: (bits) Value
gi|2392378 [1..380] Periplasmic binding protein-like II 28 0.32
gi|2209100 [9..467] PLP-dependent transferases 26 1.6
gi|1581788 [38..194] Hedgehog/DD-peptidase 25 4.2
gi|420193 [185..357] Integrin A (or I) domain 25 4.2
gi|629488 [18..291] Ribosome inactivating proteins (RIP) 24 5.8
gi|1421437 [1..65] A DNA topoisomerase I domain 24 7.2
gi|728990 [311..529] Periplasmic binding protein-like II 23 8.3
gi|1469051 [197..455] (Phosphotyrosine) protein phosphatases... 23 9.0
gi|2292739 [32..255] Zn metallo-beta-lactamase 23 9.2
gi|461959 [221..583] DNA/RNA polymerases 23 9.2
gi|1170097 [1..85] Thioredoxin-like 23 9.2
>gi|2392378 [1..380] Periplasmic binding protein-like II
Length = 380
Score = 28.1 bits (62), Expect = 0.32
Identities = 18/179 (10%), Positives = 44/179 (24%), Gaps = 32/179 (17%)
Query: 65 QDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYG------------PSEPHSRELWVDVA 112
++ D L V N + P+ P + E D
Sbjct: 77 AEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPDPQ 136
Query: 113 EANRSQVKIHTILSNTHRQASRVVLSFDFPFYGHPLRQITIATGGFIFMGDV-------- 164
+ + S ++ + P++ + A GG+ F +
Sbjct: 137 DPRVRGLY--FPAGGLDPGKSALMFNLQEPYF---TWPLIAADGGYAFKYENGKYDIKDV 191
Query: 165 ---IHRMLTATQYVAPLMANFNPGYSDNSTVVY--FDNGTV-FVVQWDHVYLQGWEDKG 217
++ L+ N + + ++ F+ G + + +
Sbjct: 192 GVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAW-SNIDTSK 249
>gi|2209100 [9..467] PLP-dependent transferases
Length = 459
Score = 26.0 bits (56), Expect = 1.6
Identities = 26/281 (9%), Positives = 50/281 (17%), Gaps = 40/281 (14%)
Query: 12 LREAARALSPQPGAGHDEGPGSGWAA-----KGTVRGWNRRARESPGHV------SEPDR 60
A+A+ G + G A + R +
Sbjct: 72 YYALAKAVKDIFGYEYTIPTHQGRGAEQIYIPVLIAKREREKGLDRSKMVVFSNYFFDTT 131
Query: 61 TQLSQDLGGGTLAMDTLPDNRTRVVEDNHSYYVSRLYGPSEPHSRELWVDVAEANRSQVK 120
SQ G + T + + N +
Sbjct: 132 QGHSQINGATVRNVYIKEAFDTTAKHPFK-------GNFDLEKLEKGIQEAGAHNVPYIV 184
Query: 121 IHTILSNTHRQASRVVLSFDFPFYGHPLRQIT--IATGGFIFMGDVIHRMLTATQYVAPL 178
++ A +S L+ + + D A
Sbjct: 185 CTITCNS----AGGQPVSIAN------LKGMYEIARKYDIPVIMDSA--------RFAEN 226
Query: 179 MANFNPGYSDNSTVVYFDNGTVFVVQWDHVYLQGWEDKGSFTFQAALHHDGRIVFAYKEI 238
D + + +D D + Y E
Sbjct: 227 AYFVQQREEAYKDWTIEQITYESYRYADGLAMSAKKDAMVPMGGILAFKDKSMEEVYHEC 286
Query: 239 --PMSVPEISSSQHPVKTGLSDAFMILNPSPDVPESRRRSI 277
V E + ++ G + + E I
Sbjct: 287 RTLCVVQEGFPTYGGLEGGAMERLAVGLHDGMRQEWLAYRI 327
>gi|1581788 [38..194] Hedgehog/DD-peptidase
Length = 157
Score = 24.5 bits (52), Expect = 4.2
Identities = 12/32 (37%), Positives = 19/32 (58%), Gaps = 4/32 (12%)
Query: 204 QWDHVYL---QGWEDKGSFTFQAALHHDGRIV 232
QW V L +GW++ G + +LH++GR V
Sbjct: 79 QWPGVKLRVTEGWDEDG-HHSEESLHYEGRAV 109
>gi|420193 [185..357] Integrin A (or I) domain
Length = 173
Score = 24.6 bits (53), Expect = 4.2
Identities = 8/64 (12%), Positives = 22/64 (33%), Gaps = 1/64 (1%)
Query: 98 GPSEPHSRELWVDVAEANRSQVKIHTILSN-THRQASRVVLSFDFPFYGHPLRQITIATG 156
G + H+ +V + + + + + + V++ L +I++
Sbjct: 102 GGARRHAELSFVFLTDGVTGNDSLEESVHSMRKQNVVPTVVAVGGDVDMDVLTKISLGDR 161
Query: 157 GFIF 160
IF
Sbjct: 162 AAIF 165
>gi|629488 [18..291] Ribosome inactivating proteins (RIP)
Length = 274
Score = 24.1 bits (52), Expect = 5.8
Identities = 20/97 (20%), Positives = 31/97 (31%), Gaps = 4/97 (4%)
Query: 365 TTTSASPDTSFSPYDGDLTTTSSSLFIDSLTTEDDTKLNPYAGGDGLQNNLSPKTKGTPV 424
T AS + F + T + S F+ SL K G + L+ + K V
Sbjct: 2 LTPPASSNIVFDV--ENATPETYSNFLTSLREAVKDKKLTCHGMI-MATTLTEQPKYVLV 58
Query: 425 HLGTIVGIVLAVLLVAAIILAGIYINGHPTSNAALFF 461
L G + + L G Y + + F
Sbjct: 59 DLKFGSGTFTLAIRRGNLYLEG-YSDIYNGKCRYRIF 94
>gi|1421437 [1..65] A DNA topoisomerase I domain
Length = 65
Score = 23.6 bits (50), Expect = 7.2
Identities = 14/51 (27%), Positives = 25/51 (48%), Gaps = 4/51 (7%)
Query: 236 KEIPMSVPEI----SSSQHPVKTGLSDAFMILNPSPDVPESRRRSIFEYHR 282
KE P+ +PE+ S + ++ G + F+ N P E+R + E +R
Sbjct: 9 KEDPVPLPELPCEKSDAYFVLRDGAAGVFLAANTFPKSRETRAPLVEELYR 59
>gi|728990 [311..529] Periplasmic binding protein-like II
Length = 219
Score = 23.4 bits (50), Expect = 8.3
Identities = 14/79 (17%), Positives = 25/79 (30%), Gaps = 3/79 (3%)
Query: 191 TVVYFDNGTVFVVQWDHVYLQGWEDKGSFTFQAALH--HDGRIVFAYKEIPMSVPE-ISS 247
+ Y NG V V + D + T + + Y + + + S
Sbjct: 77 SRPYVRNGMVIVTRQDPDAPVDADHLDGRTVALVRNSAAIPLLQRRYPQAKVVTADNPSE 136
Query: 248 SQHPVKTGLSDAFMILNPS 266
+ V G +DA + S
Sbjct: 137 AMLMVANGQADAVVQTQIS 155
>gi|1469051 [197..455] (Phosphotyrosine) protein phosphatases II
Length = 259
Score = 23.5 bits (50), Expect = 9.0
Identities = 12/72 (16%), Positives = 22/72 (29%), Gaps = 13/72 (18%)
Query: 228 DGRIVFA-YKEIPMSVPEISSSQHPVKTGLSDAFMILNPSPDVPESRRRSIFEYHRIELD 286
D I ++++ +P V M N DV ++ ++ L
Sbjct: 2 DANIAANDFEQVVSYIP------PSVTKHQFVKNMHKNRFADVI------CLDHSKVHLS 49
Query: 287 PSKVTSMSAVEF 298
S S +E
Sbjct: 50 DSSYIHASYLEL 61
>gi|2292739 [32..255] Zn metallo-beta-lactamase
Length = 224
Score = 23.5 bits (50), Expect = 9.2
Identities = 18/158 (11%), Positives = 41/158 (25%), Gaps = 17/158 (10%)
Query: 98 GPSEPHSRELWVDVAEANRSQVKIHTILSNTHR---QASRVVLSFDFPFYGHPLRQITIA 154
+ +REL + +R V I +N H + S + +
Sbjct: 37 TWTPDTARELHKLIKRVSRKPVL-EVINTNYHTDRAGGNAYWKSIGAKVISTRQTRDLMK 95
Query: 155 TGGFIFMGDVIHRMLTATQYVAPLMANFNPGYSDNSTVVYFDNGTVFVVQWDHVYLQG-- 212
+ + + L + ++ N G + +
Sbjct: 96 SDWAEIVAF-TRKGLPEYPDLPLVLPNVVHE-----GDFTLQEGKLRAFYLGPAHSPDGI 149
Query: 213 ---WEDKGS-FTFQAALHHDGRIVFAY-KEIPMSVPEI 245
+ D+ + G + FA K P ++ +
Sbjct: 150 FVYFPDQQVLYGNCILKEKLGNLSFADVKAYPQTLERL 187
>gi|461959 [221..583] DNA/RNA polymerases
Length = 363
Score = 23.3 bits (50), Expect = 9.2
Identities = 9/47 (19%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 120 KIHTILSNTHRQASRVVLSF----DFPFYGHPLRQITIATGGFIFMG 162
+ HT ++ + SR+ ++ P +R+ IA G +
Sbjct: 123 RCHTFINPLQARTSRMSITGIPAQTLPSSDWIVRRCFIAEPGDVMAS 169
>gi|1170097 [1..85] Thioredoxin-like
Length = 85
Score = 23.3 bits (50), Expect = 9.2
Identities = 10/60 (16%), Positives = 20/60 (32%), Gaps = 15/60 (25%)
Query: 230 RIVFAYKEIPMSV--------PEISSSQHPVKTGLSDAFMILNPSPDVP--ESRRRSIFE 279
R++ Y + P+ SQ L++ F + P++P I +
Sbjct: 18 RLLLEYTDSSYVEKKYTMGDAPDYDRSQW-----LNEKFKLGLDFPNLPYLIDGAHKITQ 72
Underlying Matrix: BLOSUM62
Number of sequences tested against query: 1187
Number of sequences better than 10.0: 11
Number of calls to ALIGN: 11
Length of query: 502
Total length of test sequences: 256703
Effective length of test sequences: 209547.0
Effective search space size: 96839557.8
Initial X dropoff for ALIGN: 25.0 bits