BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 039861
(557 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 55/122 (45%), Gaps = 21/122 (17%)
Query: 3 GREIVKKCKGLPLAAKTIASLLRS----------KSTEKEWQNILENEIWELEAIKKGLL 52
I+K+CKG PL I +LLR + K+++ I ++ ++ EA+ +
Sbjct: 310 AHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEA-- 367
Query: 53 APLLLSYNELPSKVKQCFTYCAVFPKDYDIQKEELIELWMAQGYLSEKGAKEMEDIGAEY 112
+ +S L +K +T ++ KD + + L LW + +E+EDI E+
Sbjct: 368 --MSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILW-------DMETEEVEDILQEF 418
Query: 113 FN 114
N
Sbjct: 419 VN 420
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 37.7 bits (86), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 55/122 (45%), Gaps = 21/122 (17%)
Query: 3 GREIVKKCKGLPLAAKTIASLLRS----------KSTEKEWQNILENEIWELEAIKKGLL 52
I+K+CKG PL I +LLR + K+++ I ++ ++ EA+ +
Sbjct: 316 AHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEA-- 373
Query: 53 APLLLSYNELPSKVKQCFTYCAVFPKDYDIQKEELIELWMAQGYLSEKGAKEMEDIGAEY 112
+ +S L +K +T ++ KD + + L LW + +E+EDI E+
Sbjct: 374 --MSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILW-------DMETEEVEDILQEF 424
Query: 113 FN 114
N
Sbjct: 425 VN 426
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 55/122 (45%), Gaps = 21/122 (17%)
Query: 3 GREIVKKCKGLPLAAKTIASLLRS----------KSTEKEWQNILENEIWELEAIKKGLL 52
I+K+CKG PL I +LLR + K+++ I ++ ++ EA+ +
Sbjct: 310 AHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEA-- 367
Query: 53 APLLLSYNELPSKVKQCFTYCAVFPKDYDIQKEELIELWMAQGYLSEKGAKEMEDIGAEY 112
+ +S L +K +T ++ KD + + L LW + +E+EDI E+
Sbjct: 368 --MSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE-------TEEVEDILQEF 418
Query: 113 FN 114
N
Sbjct: 419 VN 420
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 30/122 (24%), Positives = 55/122 (45%), Gaps = 21/122 (17%)
Query: 3 GREIVKKCKGLPLAAKTIASLLRS----------KSTEKEWQNILENEIWELEAIKKGLL 52
I+K+CKG PL I +LLR + K+++ I ++ ++ EA+ +
Sbjct: 317 AHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEA-- 374
Query: 53 APLLLSYNELPSKVKQCFTYCAVFPKDYDIQKEELIELWMAQGYLSEKGAKEMEDIGAEY 112
+ +S L +K +T ++ KD + + L LW + +E+EDI E+
Sbjct: 375 --MSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE-------TEEVEDILQEF 425
Query: 113 FN 114
N
Sbjct: 426 VN 427
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 35.8 bits (81), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 42/140 (30%), Positives = 72/140 (51%), Gaps = 18/140 (12%)
Query: 176 KIRHLMLIVRGRASVPISIWDNVKGLRGLRSFLVKSDEYSWSSEVLPQLFDKLTCLRALN 235
+ +L+L S+P ++D + L+ L LV++ S V FDKLT L LN
Sbjct: 86 NLTYLILTGNQLQSLPNGVFDKLTNLKEL--VLVENQLQSLPDGV----FDKLTNLTYLN 139
Query: 236 LKVRKPWSSVNDIKEIPTNI-EKLLHLKYLNLKSQNKIEKLPETLCE-LHNLERLNVDDC 293
L + N ++ +P + +KL +L L+L S N+++ LPE + + L L+ L +
Sbjct: 140 L-------AHNQLQSLPKGVFDKLTNLTELDL-SYNQLQSLPEGVFDKLTQLKDLRLYQN 191
Query: 294 ENLRELPRGI-GKLRKLMYI 312
+ L+ +P G+ +L L YI
Sbjct: 192 Q-LKSVPDGVFDRLTSLQYI 210
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 39/131 (29%), Positives = 64/131 (48%), Gaps = 15/131 (11%)
Query: 222 PQLFDKLTCLRALNLKVRKPWSSVNDIKEIPTNI-EKLLHLKYLNLKSQNKIEKLPETLC 280
P +FD L L+ L L N + +P + + L L L+L + N++ LP +
Sbjct: 57 PGVFDSLINLKELYL-------GSNQLGALPVGVFDSLTQLTVLDLGT-NQLTVLPSAVF 108
Query: 281 E-LHNLERLNVDDCENLRELPRGIGKLRKLMYIDNDDTDSLRYLPVGIGELIRLRRVTK- 338
+ L +L+ L + C L ELPRGI +L L ++ D + L+ +P G + RL +T
Sbjct: 109 DRLVHLKELFMC-CNKLTELPRGIERLTHLTHLALDQ-NQLKSIPHGAFD--RLSSLTHA 164
Query: 339 LVVGGGYDRAC 349
+ G +D C
Sbjct: 165 YLFGNPWDCEC 175
>pdb|1QE3|A Chain A, Pnb Esterase
Length = 489
Score = 33.5 bits (75), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 43/96 (44%), Gaps = 17/96 (17%)
Query: 7 VKKCKGLPLAAKTIASLLRSKSTEKEWQNILENEIWE--LEAIKKGLLAP-----LLLSY 59
V K KG+P A + R K+ E E+WE L+A G + P L LSY
Sbjct: 21 VHKWKGIPYAKPPVGQW-RFKAPEPP-------EVWEDVLDATAYGPICPQPSDLLSLSY 72
Query: 60 NELPSKVKQCFTYCAVFPKDYDIQKEELIELWMAQG 95
ELP + + C Y VF D Q ++ +W+ G
Sbjct: 73 TELPRQSEDCL-YVNVFAPDTPSQNLPVM-VWIHGG 106
>pdb|2O6S|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
pdb|2O6S|B Chain B, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
Length = 208
Score = 33.5 bits (75), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 50/92 (54%), Gaps = 12/92 (13%)
Query: 224 LFDKLTCLRALNLKVRKPWSSVNDIKEIPTNI-EKLLHLKYLNLKSQNKIEKLPETLCE- 281
+F+KLT L LNL S N ++ +P + +KL LK L L + N+++ LP+ + +
Sbjct: 71 VFNKLTSLTYLNL-------STNQLQSLPNGVFDKLTQLKELALNT-NQLQSLPDGVFDK 122
Query: 282 LHNLERLNVDDCENLRELPRGI-GKLRKLMYI 312
L L+ L + L+ +P G+ +L L YI
Sbjct: 123 LTQLKDLRLYQ-NQLKSVPDGVFDRLTSLQYI 153
>pdb|1C7J|A Chain A, Pnb Esterase 56c8
Length = 489
Score = 33.5 bits (75), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 43/96 (44%), Gaps = 17/96 (17%)
Query: 7 VKKCKGLPLAAKTIASLLRSKSTEKEWQNILENEIWE--LEAIKKGLLAP-----LLLSY 59
V K KG+P A + R K+ E E+WE L+A G + P L LSY
Sbjct: 21 VHKWKGIPYAKPPVGQW-RFKAPEPP-------EVWEDVLDATAYGPVCPQPSDLLSLSY 72
Query: 60 NELPSKVKQCFTYCAVFPKDYDIQKEELIELWMAQG 95
ELP + + C Y VF D Q ++ +W+ G
Sbjct: 73 TELPRQSEDCL-YVNVFAPDTPSQNLPVM-VWIHGG 106
>pdb|3S1S|A Chain A, Characterization And Crystal Structure Of The Type Iig
Restriction Endonuclease Bpusi
Length = 878
Score = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 19 TIASLLRSKSTEKEWQNILENEIWELEAIKKGLLAPLLLSYNELPSKVKQCFTYCAVFPK 78
T+++ + + W N +E EL +I+ GLL P L+S N P+ + C++ P+
Sbjct: 338 TVSAGFNNVXPRQIWANDIETLFLELLSIRLGLLFPQLVSSNNAPTITGE--DVCSLNPE 395
Query: 79 DY 80
D+
Sbjct: 396 DF 397
>pdb|4ARN|A Chain A, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor
pdb|4ARN|B Chain B, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor
pdb|4ARN|C Chain C, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor
pdb|4ARN|D Chain D, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor
pdb|4ARR|A Chain A, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor With The Magic Triangle I3c
pdb|4ARR|B Chain B, Crystal Structure Of The N-terminal Domain Of Drosophila
Toll Receptor With The Magic Triangle I3c
Length = 279
Score = 32.7 bits (73), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 39/152 (25%), Positives = 67/152 (44%), Gaps = 34/152 (22%)
Query: 188 ASVPISIWDNVKGLRGLRSFLVKSDEYSWSSEVLPQLFDKLTCLRALNLKVRKPWSSVND 247
PI+ + G+ + + +SD + + Q D+L L+ R+
Sbjct: 84 GHTPIASILDYLGIVSPTTLIFESDNLGMN--ITRQHLDRLHGLKRFRFTTRR------- 134
Query: 248 IKEIPTNI-EKLLHLKYLNLKSQNKIEKLPETLCELHNLERLNVDDCENL---------- 296
+ IP N+ + +L +L L++ IE++P L DD ENL
Sbjct: 135 LTHIPANLLTDMRNLSHLELRA--NIEEMPSHL----------FDDLENLESIEFGSNKL 182
Query: 297 RELPRGI-GKLRKLMYIDNDDTDSLRYLPVGI 327
R++PRGI GK+ KL + N ++ L+ +P GI
Sbjct: 183 RQMPRGIFGKMPKLKQL-NLASNQLKSVPDGI 213
>pdb|1C7I|A Chain A, Thermophylic Pnb Esterase
Length = 489
Score = 32.3 bits (72), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 43/96 (44%), Gaps = 17/96 (17%)
Query: 7 VKKCKGLPLAAKTIASLLRSKSTEKEWQNILENEIWE--LEAIKKGLLAP-----LLLSY 59
V K KG+P A + R K+ E E+WE L+A G + P L LSY
Sbjct: 21 VHKWKGIPYAKPPVGQW-RFKAPEPP-------EVWEDVLDATVYGPVCPQPSDLLSLSY 72
Query: 60 NELPSKVKQCFTYCAVFPKDYDIQKEELIELWMAQG 95
ELP + + C Y VF D Q ++ +W+ G
Sbjct: 73 KELPRQSEDCL-YVNVFAPDTPSQNLPVM-VWIHGG 106
>pdb|2HOE|A Chain A, Crystal Structure Of N-Acetylglucosamine Kinase (Tm1224)
From Thermotoga Maritima At 2.46 A Resolution
Length = 380
Score = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 301 RGIGKLRKLMYIDNDDTDSLRYLPVGIGELIRLRRVTKLVVGGGY 345
R G +R Y D D RY +G+ LI L ++K+V+GG +
Sbjct: 284 RDSGDVRVKEYFD----DIARYFSIGLLNLIHLFGISKIVIGGFF 324
>pdb|4H1Z|A Chain A, Crystal Structure Of Putative Isomerase From Sinorhizobium
Meliloti, Open Loop Conformation (Target Efi-502104)
pdb|4H1Z|B Chain B, Crystal Structure Of Putative Isomerase From Sinorhizobium
Meliloti, Open Loop Conformation (Target Efi-502104)
pdb|4H1Z|C Chain C, Crystal Structure Of Putative Isomerase From Sinorhizobium
Meliloti, Open Loop Conformation (Target Efi-502104)
pdb|4H1Z|D Chain D, Crystal Structure Of Putative Isomerase From Sinorhizobium
Meliloti, Open Loop Conformation (Target Efi-502104)
pdb|4H1Z|E Chain E, Crystal Structure Of Putative Isomerase From Sinorhizobium
Meliloti, Open Loop Conformation (Target Efi-502104)
pdb|4H1Z|F Chain F, Crystal Structure Of Putative Isomerase From Sinorhizobium
Meliloti, Open Loop Conformation (Target Efi-502104)
pdb|4H1Z|G Chain G, Crystal Structure Of Putative Isomerase From Sinorhizobium
Meliloti, Open Loop Conformation (Target Efi-502104)
pdb|4H1Z|H Chain H, Crystal Structure Of Putative Isomerase From Sinorhizobium
Meliloti, Open Loop Conformation (Target Efi-502104)
Length = 412
Score = 28.9 bits (63), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 71 TYCAVFPKDYDIQKEELIELWMAQGYLSEKGAKEMEDIG-AEYFNILASR 119
Y + P+D ++ EL W A+G+ S K A + D G A+ IL R
Sbjct: 179 AYISGLPEDTRAKRAELAAAWQAKGFSSFKFASPVADDGVAKEMEILRER 228
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.139 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,104,855
Number of Sequences: 62578
Number of extensions: 656154
Number of successful extensions: 1599
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1583
Number of HSP's gapped (non-prelim): 38
length of query: 557
length of database: 14,973,337
effective HSP length: 104
effective length of query: 453
effective length of database: 8,465,225
effective search space: 3834746925
effective search space used: 3834746925
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)