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= 045686
(885 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 46.2 bits (108), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 43/157 (27%), Positives = 70/157 (44%), Gaps = 23/157 (14%)
Query: 258 VLLLDDVWERLDLSKVGVSDLLDDSSQTGSKIVFTTRSEEVCGE-MGARRRFRVEC-LSP 315
+L+LDDVW+ L + + +I+ TTR + V MG + VE L
Sbjct: 245 LLILDDVWDSWVLK----------AFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGK 294
Query: 316 EAALDLFRYKVGEDVYSSHFEISNLAQTVVEECRGLPLALVTIGHAMASRMGPTQWRYAV 375
E L++ V ++ A ++++EC+G PL + IG + R P +W Y +
Sbjct: 295 EKGLEILSLFVN----MKKADLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEYYL 348
Query: 376 GELQRYPFKFAGMGNS-----VFPILRFSYDSLREDI 407
+LQ FK +S + + S + LREDI
Sbjct: 349 KQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDI 385
>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 = 46.2 bits (108), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 43/157 (27%), Positives = 70/157 (44%), Gaps = 23/157 (14%)
Query: 258 VLLLDDVWERLDLSKVGVSDLLDDSSQTGSKIVFTTRSEEVCGE-MGARRRFRVEC-LSP 315
+L+LDDVW+ L + + +I+ TTR + V MG + VE L
Sbjct: 239 LLILDDVWDSWVLK----------AFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGK 288
Query: 316 EAALDLFRYKVGEDVYSSHFEISNLAQTVVEECRGLPLALVTIGHAMASRMGPTQWRYAV 375
E L++ V ++ A ++++EC+G PL + IG + R P +W Y +
Sbjct: 289 EKGLEILSLFVN----MKKADLPEQAHSIIKECKGSPLVVSLIGALL--RDFPNRWEYYL 342
Query: 376 GELQRYPFKFAGMGNS-----VFPILRFSYDSLREDI 407
+LQ FK +S + + S + LREDI
Sbjct: 343 KQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDI 379
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 52/186 (27%), Positives = 82/186 (44%), Gaps = 30/186 (16%)
Query: 258 VLLLDDVWERLDLSKVGVSDLLDDSSQTGSKIVFTTRSEEVCGE-MGARRRFRVEC-LSP 315
+L+LDDVW+ L D+ Q I+ TTR + V MG + VE L
Sbjct: 239 LLILDDVWDPWVLKA------FDNQCQ----ILLTTRDKSVTDSVMGPKHVVPVESGLGR 288
Query: 316 EAALD---LFRYKVGEDVYSSHFEISNLAQTVVEECRGLPLALVTIGHAMASRMGPTQWR 372
E L+ LF ED+ + A ++++EC+G PL + IG + R P +W
Sbjct: 289 EKGLEILSLFVNMKKEDLPAE-------AHSIIKECKGSPLVVSLIGALL--RDFPNRWA 339
Query: 373 YAVGELQRYPFKFAGMGNS-----VFPILRFSYDSLREDIFKTCFLYCALFPEEHNITKD 427
Y + +LQ FK +S + + S + LREDI K + ++ ++ +
Sbjct: 340 YYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDI-KDYYTDLSILQKDVKVPTK 398
Query: 428 ELIQLW 433
L LW
Sbjct: 399 VLCVLW 404
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 51/186 (27%), Positives = 81/186 (43%), Gaps = 30/186 (16%)
Query: 258 VLLLDDVWERLDLSKVGVSDLLDDSSQTGSKIVFTTRSEEVCGE-MGARRRFRVEC-LSP 315
+L+LDDVW+ L D+ Q I+ TT + V MG + VE L
Sbjct: 246 LLILDDVWDPWVLKA------FDNQCQ----ILLTTSDKSVTDSVMGPKHVVPVESGLGR 295
Query: 316 EAALD---LFRYKVGEDVYSSHFEISNLAQTVVEECRGLPLALVTIGHAMASRMGPTQWR 372
E L+ LF ED+ + A ++++EC+G PL + IG + R P +W
Sbjct: 296 EKGLEILSLFVNMKKEDLPAE-------AHSIIKECKGSPLVVSLIGALL--RDFPNRWA 346
Query: 373 YAVGELQRYPFKFAGMGNS-----VFPILRFSYDSLREDIFKTCFLYCALFPEEHNITKD 427
Y + +LQ FK +S + + S + LREDI K + ++ ++ +
Sbjct: 347 YYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDI-KDYYTDLSILQKDVKVPTK 405
Query: 428 ELIQLW 433
L LW
Sbjct: 406 VLCVLW 411
>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 = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 49/200 (24%), Positives = 88/200 (44%), Gaps = 18/200 (9%)
Query: 475 NLIRDMALELASENDNKTL--VLQNNVGSNIESINSFDGWHEAVRLSLWGSSI-DFLALV 531
NL + + ++N+ ++ ++ NN S+I+S+ L+L G+ + D AL
Sbjct: 25 NLKKKSVTDAVTQNELNSIDQIIANN--SDIKSVQGIQYLPNVRYLALGGNKLHDISALK 82
Query: 532 EAPSCPQVRTLLARLTMLHTLPIPSRFFDSMDALEVLDLSYNLDLNQLPEEI-GRLKNLH 590
E + + L+ L +LP + FD + L+ L L N L LP+ + +L NL
Sbjct: 83 ELTN---LTYLILTGNQLQSLP--NGVFDKLTNLKELVLVEN-QLQSLPDGVFDKLTNLT 136
Query: 591 HLNLSNTSIGCLPTAXXXXXXXXXXXXXXXQCHLSIPEGVISSLSSLQVFSCFSTELVEL 650
+LNL++ + LP S+PEGV L+ L+ + +L +
Sbjct: 137 YLNLAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRLYQNQLKSV 196
Query: 651 IDPLFNETAILDELNCLEHL 670
D +F D L L+++
Sbjct: 197 PDGVF------DRLTSLQYI 210
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 37.4 bits (85), Expect = 0.035, Method: Composition-based stats.
Identities = 48/201 (23%), Positives = 76/201 (37%), Gaps = 30/201 (14%)
Query: 444 PRDQGEYIIESLKLACLLERGENSEDSVKMHNLIRDMALELASENDNKTLVLQNNVGS-- 501
P D + ++S KL+ L S H L + L L NDNK L +
Sbjct: 36 PADTKKLDLQSNKLSSL--------PSKAFHRLTK---LRLLYLNDNKLQTLPAGIFKEL 84
Query: 502 -NIESINSFDGWHEAVRLSLWGSSIDFLALVEAPSCPQVRTLLARLTMLHTLPIPSRFFD 560
N+E++ D +A+ + ++ ++ L RL +P R FD
Sbjct: 85 KNLETLWVTDNKLQALPIGVFDQLVNLAEL--------------RLDRNQLKSLPPRVFD 130
Query: 561 SMDALEVLDLSYNLDLNQLPEEI-GRLKNLHHLNLSNTSIGCLPTAXXXXXXXXXXXXXX 619
S+ L L L YN +L LP+ + +L +L L L N + +P
Sbjct: 131 SLTKLTYLSLGYN-ELQSLPKGVFDKLTSLKELRLYNNQLKRVPEGAFDKLTELKTLKLD 189
Query: 620 XQCHLSIPEGVISSLSSLQVF 640
+PEG SL L++
Sbjct: 190 NNQLKRVPEGAFDSLEKLKML 210
Score = 30.0 bits (66), Expect = 6.2, Method: Composition-based stats.
Identities = 41/157 (26%), Positives = 64/157 (40%), Gaps = 8/157 (5%)
Query: 538 QVRTLLARLTMLHTLPIPSRFFDSMDALEVLDLSYNLDLNQLPEEI-GRLKNLHHLNLSN 596
++R L L TLP + F + LE L ++ N L LP + +L NL L L
Sbjct: 62 KLRLLYLNDNKLQTLP--AGIFKELKNLETLWVTDN-KLQALPIGVFDQLVNLAELRLDR 118
Query: 597 TSIGCLPTAXXXXXXXXXXXXXXXQCHLSIPEGVISSLSSLQVFSCFSTELVELIDPLFN 656
+ LP S+P+GV L+SL+ ++ +L + + F+
Sbjct: 119 NQLKSLPPRVFDSLTKLTYLSLGYNELQSLPKGVFDKLTSLKELRLYNNQLKRVPEGAFD 178
Query: 657 ETAILDELNCLEHLNDLSLTLFSTEAVDKLLNSPKLQ 693
+ L EL L+ L++ L A D L LQ
Sbjct: 179 K---LTELKTLK-LDNNQLKRVPEGAFDSLEKLKMLQ 211
>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 = 37.4 bits (85), Expect = 0.038, Method: Composition-based stats.
Identities = 30/118 (25%), Positives = 50/118 (42%), Gaps = 8/118 (6%)
Query: 554 IPSRFFDSMDALEVLDLSYNLDLNQLPEEI-GRLKNLHHLNLSNTSIGCLPTAXXXXXXX 612
+P+ FD + +L L L N L LP + +L +L +LNLS + LP
Sbjct: 43 LPNGVFDELTSLTQLYLGGN-KLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQ 101
Query: 613 XXXXXXXXQCHLSIPEGVISSLSSLQVFSCFSTELVELIDPLFNETAILDELNCLEHL 670
S+P+GV L+ L+ + +L + D +F D L L+++
Sbjct: 102 LKELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLKSVPDGVF------DRLTSLQYI 153
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 37.0 bits (84), Expect = 0.043, Method: Composition-based stats.
Identities = 50/200 (25%), Positives = 85/200 (42%), Gaps = 18/200 (9%)
Query: 475 NLIRDMALELASENDNKTL--VLQNNVGSNIESINSFDGWHEAVRLSLWGSSI-DFLALV 531
NL + + ++N+ ++ ++ NN S+I+S+ L+L G+ + D AL
Sbjct: 25 NLKKKSVTDAVTQNELNSIDQIIANN--SDIKSVQGIQYLPNVRYLALGGNKLHDISALK 82
Query: 532 EAPSCPQVRTLLARLTMLHTLPIPSRFFDSMDALEVLDLSYNLDLNQLPEEI-GRLKNLH 590
E + + L+ L +LP + FD + L+ L L N L LP+ + +L NL
Sbjct: 83 ELTN---LTYLILTGNQLQSLP--NGVFDKLTNLKELVLVEN-QLQSLPDGVFDKLTNLT 136
Query: 591 HLNLSNTSIGCLPTAXXXXXXXXXXXXXXXQCHLSIPEGVISSLSSLQVFSCFSTELVEL 650
+L L + + LP S+PEGV L+ L+ S +L +
Sbjct: 137 YLYLYHNQLQSLPKGVFDKLTNLTRLDLDNNQLQSLPEGVFDKLTQLKQLSLNDNQLKSV 196
Query: 651 IDPLFNETAILDELNCLEHL 670
D +F D L L H+
Sbjct: 197 PDGVF------DRLTSLTHI 210
>pdb|3RGX|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
pdb|3RGZ|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
Length = 768
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 542 LLARLTMLHTLPIPSRFFDSMDALEVLDLSYNLDLNQLPEEIGRLKNLHHLNLSNTSI-G 600
+ +R+ HT P FD+ ++ LD+SYN+ +P+EIG + L LNL + I G
Sbjct: 615 ITSRVYGGHTSPT----FDNNGSMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISG 670
Query: 601 CLP 603
+P
Sbjct: 671 SIP 673
>pdb|3RIZ|A Chain A, Crystal Structure Of The Plant Steroid Receptor Bri1
Ectodomain
pdb|3RJ0|A Chain A, Plant Steroid Receptor Bri1 Ectodomain In Complex With
Brassinolide
Length = 772
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 542 LLARLTMLHTLPIPSRFFDSMDALEVLDLSYNLDLNQLPEEIGRLKNLHHLNLSNTSI-G 600
+ +R+ HT P FD+ ++ LD+SYN+ +P+EIG + L LNL + I G
Sbjct: 612 ITSRVYGGHTSPT----FDNNGSMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISG 667
Query: 601 CLP 603
+P
Sbjct: 668 SIP 670
>pdb|1C0M|A Chain A, Crystal Structure Of Rsv Two-Domain Integrase
pdb|1C0M|B Chain B, Crystal Structure Of Rsv Two-Domain Integrase
pdb|1C0M|C Chain C, Crystal Structure Of Rsv Two-Domain Integrase
pdb|1C0M|D Chain D, Crystal Structure Of Rsv Two-Domain Integrase
pdb|1C1A|A Chain A, Crystal Structure Of Rsv Two-Domain Integrase
pdb|1C1A|B Chain B, Crystal Structure Of Rsv Two-Domain Integrase
Length = 238
Score = 33.9 bits (76), Expect = 0.39, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 416 ALFPEEHNITKDELIQLWIGEGFLNGISPRDQGEYIIESLKLACLLERGENSEDSVKMH 474
A+ + + KD + L G+GF+ I QGE + +++ ERGEN++ ++ H
Sbjct: 106 AMVERANRLLKDRIRVLAEGDGFMKRIPTSKQGELLAKAMYALNHKERGENTKTPIQKH 164
>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 = 0.95, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 26/86 (30%)
Query: 554 IPSRFFDSMDALEVLDLSYNLDLNQLPEEI-GRLKNLHHLNLSNTSIGCLPTAXXXXXXX 612
+PS FD ++ LE ++ N L Q+P I G++ L LNL++ +
Sbjct: 161 MPSHLFDDLENLESIEFGSN-KLRQMPRGIFGKMPKLKQLNLASNQLK------------ 207
Query: 613 XXXXXXXXQCHLSIPEGVISSLSSLQ 638
S+P+G+ L+SLQ
Sbjct: 208 ------------SVPDGIFDRLTSLQ 221
>pdb|3V47|A Chain A, Crystal Structure Of The N-Tetminal Fragment Of Zebrafish
Tlr5 In Complex With Salmonella Flagellin
pdb|3V47|B Chain B, Crystal Structure Of The N-Tetminal Fragment Of Zebrafish
Tlr5 In Complex With Salmonella Flagellin
Length = 455
Score = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 36/85 (42%), Gaps = 24/85 (28%)
Query: 554 IPSRFFDSMDALEVLDLSYNLDLNQLPEEIGRLKNLHHLNLSNTSIGCLPTAXXXXXXXX 613
I SR F+++D LEVLDLSYN I L + L L N L T
Sbjct: 338 IDSRMFENLDKLEVLDLSYN--------HIRALGDQSFLGLPNLKELALDTNQLK----- 384
Query: 614 XXXXXXXQCHLSIPEGVISSLSSLQ 638
S+P+G+ L+SLQ
Sbjct: 385 -----------SVPDGIFDRLTSLQ 398
>pdb|1CXQ|A Chain A, Atomic Resolution Asv Integrase Core Domain From Ammonium
Sulfate
pdb|1CXU|A Chain A, 1.42a Resolution Asv Integrase Core Domain From Citrate
pdb|1CZB|A Chain A, Atomic Resolution Asv Integrase Core Domain From Hepes
Length = 162
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 31/56 (55%)
Query: 416 ALFPEEHNITKDELIQLWIGEGFLNGISPRDQGEYIIESLKLACLLERGENSEDSV 471
A+ + + KD++ L G+GF+ I QGE + +++ ERGEN++ ++
Sbjct: 107 AMVERANRLLKDKIRVLAEGDGFMKRIPTSKQGELLAKAMYALNHFERGENTKTNL 162
>pdb|1ASV|A Chain A, Avian Sarcoma Virus Integrase Catalytic Core Domain
Length = 162
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 31/56 (55%)
Query: 416 ALFPEEHNITKDELIQLWIGEGFLNGISPRDQGEYIIESLKLACLLERGENSEDSV 471
A+ + + KD++ L G+GF+ I QGE + +++ ERGEN++ ++
Sbjct: 107 AMVERANRLLKDKIRVLAEGDGFMKRIPTSKQGELLAKAMYALNHFERGENTKTNL 162
>pdb|1A5V|A Chain A, Asv Integrase Core Domain With Hiv-1 Integrase Inhibitor
Y3 And Mn Cation
pdb|1A5W|A Chain A, Asv Integrase Core Domain With Hiv-1 Integrase Inhibitor
Y3
pdb|1A5X|A Chain A, Asv Integrase Core Domain With Hiv-1 Integrase Inhibitor
Y3
Length = 158
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 31/56 (55%)
Query: 416 ALFPEEHNITKDELIQLWIGEGFLNGISPRDQGEYIIESLKLACLLERGENSEDSV 471
A+ + + KD++ L G+GF+ I QGE + +++ ERGEN++ ++
Sbjct: 103 AMVERANRLLKDKIRVLAEGDGFMKRIPTSKQGELLAKAMYALNHFERGENTKTNL 158
>pdb|1ASU|A Chain A, Avian Sarcoma Virus Integrase Catalytic Core Domain
Crystallized From 2% Peg 400, 2m Ammonium Sulfate, Hepes
Ph 7.5
Length = 162
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 31/56 (55%)
Query: 416 ALFPEEHNITKDELIQLWIGEGFLNGISPRDQGEYIIESLKLACLLERGENSEDSV 471
A+ + + KD++ L G+GF+ I QGE + +++ ERGEN++ ++
Sbjct: 107 AMVERANRLLKDKIRVLAEGDGFMKRIPTSKQGELLAKAMYALNHFERGENTKTNL 162
>pdb|1CZ9|A Chain A, Atomic Resolution Asv Integrase Core Domain (D64n) From
Citrate
Length = 162
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 31/56 (55%)
Query: 416 ALFPEEHNITKDELIQLWIGEGFLNGISPRDQGEYIIESLKLACLLERGENSEDSV 471
A+ + + KD++ L G+GF+ I QGE + +++ ERGEN++ ++
Sbjct: 107 AMVERANRLLKDKIRVLAEGDGFMKRIPTSKQGELLAKAMYALNHFERGENTKTNL 162
>pdb|2NAC|A Chain A, High Resolution Structures Of Holo And Apo Formate
Dehydrogenase
pdb|2NAC|B Chain B, High Resolution Structures Of Holo And Apo Formate
Dehydrogenase
pdb|2NAD|A Chain A, High Resolution Structures Of Holo And Apo Formate
Dehydrogenase
pdb|2NAD|B Chain B, High Resolution Structures Of Holo And Apo Formate
Dehydrogenase
Length = 393
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 10/84 (11%)
Query: 353 LALVTIGHAMASRMGPTQWRYAVGELQRYPFKFAGMGNSVFPILRFSYDSLREDIFKTC- 411
+A IG A+ R+ P + R P SV L ++ + RED++ C
Sbjct: 197 VAAGRIGLAVLRRLAPFDVHLHYTDRHRLP-------ESVEKELNLTWHATREDMYPVCD 249
Query: 412 --FLYCALFPEEHNITKDELIQLW 433
L C L PE ++ DE ++L+
Sbjct: 250 VVTLNCPLHPETEHMINDETLKLF 273
>pdb|2GO1|A Chain A, Nad-Dependent Formate Dehydrogenase From Pseudomonas
Sp.101
Length = 401
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 10/84 (11%)
Query: 353 LALVTIGHAMASRMGPTQWRYAVGELQRYPFKFAGMGNSVFPILRFSYDSLREDIFKTC- 411
+A IG A+ R+ P + R P SV L ++ + RED++ C
Sbjct: 198 VAAGRIGLAVLRRLAPFDVHLHYTDRHRLP-------ESVEKELNLTWHATREDMYPVCD 250
Query: 412 --FLYCALFPEEHNITKDELIQLW 433
L C L PE ++ DE ++L+
Sbjct: 251 VVTLNCPLHPETEHMINDETLKLF 274
>pdb|2GUG|A Chain A, Nad-dependent Formate Dehydrogenase From Pseudomonas
Sp.101 In Complex With Formate
pdb|2GUG|B Chain B, Nad-dependent Formate Dehydrogenase From Pseudomonas
Sp.101 In Complex With Formate
pdb|2GUG|C Chain C, Nad-dependent Formate Dehydrogenase From Pseudomonas
Sp.101 In Complex With Formate
pdb|2GUG|D Chain D, Nad-dependent Formate Dehydrogenase From Pseudomonas
Sp.101 In Complex With Formate
Length = 401
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 10/84 (11%)
Query: 353 LALVTIGHAMASRMGPTQWRYAVGELQRYPFKFAGMGNSVFPILRFSYDSLREDIFKTC- 411
+A IG A+ R+ P + R P SV L ++ + RED++ C
Sbjct: 198 VAAGRIGLAVLRRLAPFDVHLHYTDRHRLP-------ESVEKELNLTWHATREDMYPVCD 250
Query: 412 --FLYCALFPEEHNITKDELIQLW 433
L C L PE ++ DE ++L+
Sbjct: 251 VVTLNCPLHPETEHMINDETLKLF 274
>pdb|1SJJ|A Chain A, Cryo-Em Structure Of Chicken Gizzard Smooth Muscle Alpha-
Actinin
pdb|1SJJ|B Chain B, Cryo-Em Structure Of Chicken Gizzard Smooth Muscle Alpha-
Actinin
Length = 863
Score = 31.6 bits (70), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 31/108 (28%), Positives = 47/108 (43%), Gaps = 11/108 (10%)
Query: 9 MDYLVCPLCGVISKHCGYVCGLTDSLNSLREARRD-LENITRDVEARVDLAVE--QRSRP 65
+DY P ++ C +C D+L +L + RR+ LE + +E L +E +R+ P
Sbjct: 440 LDYYDSP---SVNARCQKICDQWDNLGALTQKRREALERTEKLLETIDQLYLEYAKRAAP 496
Query: 66 RHEVNGWLESAQFMLREVDGILQRGDEEIQKTCLRKTCFPGTWCSRDK 113
N W+E A L+ D + EEIQ F T DK
Sbjct: 497 ---FNNWMEGAMEDLQ--DTFIVHTIEEIQGLTTAHEQFKATLPDADK 539
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 30.8 bits (68), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 13/98 (13%)
Query: 510 DGWHEAVR----LSLWGSSIDFLALVEAPSCPQVRTLLA---RLTMLHTLPIPSRFFDSM 562
DG ++++ L L G+ I LAL ++ L+A L L PI +
Sbjct: 69 DGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPI-----GHL 123
Query: 563 DALEVLDLSYNLDLN-QLPEEIGRLKNLHHLNLSNTSI 599
L+ L++++NL + +LPE L NL HL+LS+ I
Sbjct: 124 KTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 161
Score = 30.0 bits (66), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 32/117 (27%), Positives = 50/117 (42%), Gaps = 27/117 (23%)
Query: 550 HTLPIPSRFFDSMDALEVLDLSYN-LDLNQLPEEIGRLKNLHHLNLSNTSIGCLPTAXXX 608
HT + F+ + +LEVL ++ N N LP+ L+NL L+LS
Sbjct: 432 HTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLS------------- 478
Query: 609 XXXXXXXXXXXXQCHL-SIPEGVISSLSSLQVFSCFSTELVELIDPLFNETAILDEL 664
QC L + +SLSSLQV + S +L + D +F+ L ++
Sbjct: 479 ------------QCQLEQLSPTAFNSLSSLQVLNMASNQLKSVPDGIFDRLTSLQKI 523
>pdb|3RG1|A Chain A, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|E Chain E, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|I Chain I, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|M Chain M, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|B Chain B, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|F Chain F, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|J Chain J, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|N Chain N, Crystal Structure Of The Rp105MD-1 Complex
Length = 612
Score = 30.8 bits (68), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 536 CPQVRTLLARLTMLHTLPIPSRFFDSMDALEVLDLSYNLDLNQLPEEIGRLKNLHHLNLS 595
CPQ+ L T LH + P F ++ L VL+LS+ L + L++L HLNL
Sbjct: 398 CPQLELLDVAFTHLH-VKAPHSPFQNLHLLRVLNLSHCLLDTSNQHLLAGLQDLRHLNLQ 456
Query: 596 NTSI 599
S
Sbjct: 457 GNSF 460
>pdb|3FXI|A Chain A, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
pdb|3FXI|B Chain B, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
Length = 605
Score = 30.8 bits (68), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 13/98 (13%)
Query: 510 DGWHEAVR----LSLWGSSIDFLALVEAPSCPQVRTLLA---RLTMLHTLPIPSRFFDSM 562
DG ++++ L L G+ I LAL ++ L+A L L PI +
Sbjct: 69 DGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPI-----GHL 123
Query: 563 DALEVLDLSYNLDLN-QLPEEIGRLKNLHHLNLSNTSI 599
L+ L++++NL + +LPE L NL HL+LS+ I
Sbjct: 124 KTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 161
>pdb|4G8A|A Chain A, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
pdb|4G8A|B Chain B, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
Length = 635
Score = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 13/98 (13%)
Query: 510 DGWHEAVR----LSLWGSSIDFLALVEAPSCPQVRTLLA---RLTMLHTLPIPSRFFDSM 562
DG ++++ L L G+ I LAL ++ L+A L L PI +
Sbjct: 93 DGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPI-----GHL 147
Query: 563 DALEVLDLSYNLDLN-QLPEEIGRLKNLHHLNLSNTSI 599
L+ L++++NL + +LPE L NL HL+LS+ I
Sbjct: 148 KTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 185
>pdb|3UL9|A Chain A, Structure Of The Tv3 Mutant M41e
Length = 278
Score = 30.0 bits (66), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 13/98 (13%)
Query: 510 DGWHEAVR----LSLWGSSIDFLALVEAPSCPQVRTLLA---RLTMLHTLPIPSRFFDSM 562
DG ++++ L L G+ I LAL ++ L+A L L PI +
Sbjct: 70 DGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPI-----GHL 124
Query: 563 DALEVLDLSYNLDLN-QLPEEIGRLKNLHHLNLSNTSI 599
L+ L++++NL + +LPE L NL HL+LS+ I
Sbjct: 125 KTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 162
>pdb|2Z62|A Chain A, Crystal Structure Of The Tv3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z65|A Chain A, Crystal Structure Of The Human Tlr4 Tv3
Hybrid-Md-2-Eritoran Complex
pdb|2Z65|B Chain B, Crystal Structure Of The Human Tlr4 Tv3
Hybrid-Md-2-Eritoran Complex
Length = 276
Score = 30.0 bits (66), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 13/98 (13%)
Query: 510 DGWHEAVR----LSLWGSSIDFLALVEAPSCPQVRTLLA---RLTMLHTLPIPSRFFDSM 562
DG ++++ L L G+ I LAL ++ L+A L L PI +
Sbjct: 69 DGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPI-----GHL 123
Query: 563 DALEVLDLSYNLDLN-QLPEEIGRLKNLHHLNLSNTSI 599
L+ L++++NL + +LPE L NL HL+LS+ I
Sbjct: 124 KTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 161
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 30.0 bits (66), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 13/98 (13%)
Query: 510 DGWHEAVR----LSLWGSSIDFLALVEAPSCPQVRTLLA---RLTMLHTLPIPSRFFDSM 562
DG ++++ L L G+ I LAL ++ L+A L L PI +
Sbjct: 71 DGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVALETNLASLENFPI-----GHL 125
Query: 563 DALEVLDLSYNLDLN-QLPEEIGRLKNLHHLNLSNTSI 599
L+ L++++NL + +LPE L NL HL+LS+ I
Sbjct: 126 KTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 163
>pdb|3ULA|A Chain A, Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran
Complex
pdb|3ULA|C Chain C, Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran
Complex
Length = 279
Score = 29.6 bits (65), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 13/98 (13%)
Query: 510 DGWHEAVR----LSLWGSSIDFLALVEAPSCPQVRTLLA---RLTMLHTLPIPSRFFDSM 562
DG ++++ L L G+ I LAL ++ L+A L L PI +
Sbjct: 71 DGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPI-----GHL 125
Query: 563 DALEVLDLSYNLDLN-QLPEEIGRLKNLHHLNLSNTSI 599
L+ L++++NL + +LPE L NL HL+LS+ I
Sbjct: 126 KTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 163
>pdb|3UL7|A Chain A, Crystal Structure Of The Tv3 Mutant F63w
Length = 278
Score = 29.6 bits (65), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 13/98 (13%)
Query: 510 DGWHEAVR----LSLWGSSIDFLALVEAPSCPQVRTLLA---RLTMLHTLPIPSRFFDSM 562
DG ++++ L L G+ I LAL ++ L+A L L PI +
Sbjct: 70 DGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPI-----GHL 124
Query: 563 DALEVLDLSYNLDLN-QLPEEIGRLKNLHHLNLSNTSI 599
L+ L++++NL + +LPE L NL HL+LS+ I
Sbjct: 125 KTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI 162
>pdb|3J0A|A Chain A, Homology Model Of Human Toll-Like Receptor 5 Fitted Into
An Electron Microscopy Single Particle Reconstruction
pdb|3J0A|B Chain B, Homology Model Of Human Toll-Like Receptor 5 Fitted Into
An Electron Microscopy Single Particle Reconstruction
Length = 844
Score = 29.6 bits (65), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 33/51 (64%), Gaps = 2/51 (3%)
Query: 556 SRFFDSMDALEVLDLSYNLDLNQLPEE-IGRLKNLHHLNLSNTSIGCLPTA 605
SR F+++ L+VL+L+YN +N++ +E L NL LNLS +G L ++
Sbjct: 283 SRVFETLKDLKVLNLAYN-KINKIADEAFYGLDNLQVLNLSYNLLGELYSS 332
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
0.321 0.137 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,356,281
Number of Sequences: 62578
Number of extensions: 892007
Number of successful extensions: 1900
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 1836
Number of HSP's gapped (non-prelim): 83
length of query: 885
length of database: 14,973,337
effective HSP length: 107
effective length of query: 778
effective length of database: 8,277,491
effective search space: 6439887998
effective search space used: 6439887998
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)