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= 042541
(695 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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 63/292 (21%), Positives = 123/292 (42%), Gaps = 38/292 (13%)
Query: 179 KMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQV-QGKFKDDIFYVTVSKNPNVKAIVQ 237
K+ K ++ + G GK+ L +D + +G F + +V+V K + ++
Sbjct: 139 KLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLM 197
Query: 238 KVLHHKGYPVPEFQTDEAAIN----DLERFFKQMRIEAI------LLVLDDVWPGSESLL 287
K+ + DE+ ++E ++RI + LL+LDDVW +L
Sbjct: 198 KLQN----LCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVW--DSWVL 251
Query: 288 QKLGFQLPDYKILVTSR--SEFPQFGSVHYLKP----LTYEAARTLFLHSANLQDGNSYI 341
+ Q +IL+T+R S Y+ P L E + N++ + +
Sbjct: 252 KAFDSQC---QILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKAD--L 306
Query: 342 PDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILD--- 398
P++ I++ CKG PL + ++G +L W+ +K+ + K+ D
Sbjct: 307 PEQ--AHSIIKECKGSPLVVSLIG-ALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEA 363
Query: 399 ---CLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVF 447
+ S+++L ++K+ Y DL +D ++P L +W E V+D+
Sbjct: 364 LDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDIL 415
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 63/292 (21%), Positives = 123/292 (42%), Gaps = 38/292 (13%)
Query: 179 KMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQV-QGKFKDDIFYVTVSKNPNVKAIVQ 237
K+ K ++ + G GK+ L +D + +G F + +V+V K + ++
Sbjct: 145 KLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLM 203
Query: 238 KVLHHKGYPVPEFQTDEAAIN----DLERFFKQMRIEAI------LLVLDDVWPGSESLL 287
K+ + DE+ ++E ++RI + LL+LDDVW +L
Sbjct: 204 KLQN----LCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSW--VL 257
Query: 288 QKLGFQLPDYKILVTSR--SEFPQFGSVHYLKP----LTYEAARTLFLHSANLQDGNSYI 341
+ Q +IL+T+R S Y+ P L E + N++ + +
Sbjct: 258 KAFDSQC---QILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKAD--L 312
Query: 342 PDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILD--- 398
P++ I++ CKG PL + ++G +L W+ +K+ + K+ D
Sbjct: 313 PEQ--AHSIIKECKGSPLVVSLIG-ALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEA 369
Query: 399 ---CLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVF 447
+ S+++L ++K+ Y DL +D ++P L +W E V+D+
Sbjct: 370 LDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDIL 421
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 37.4 bits (85), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 66/308 (21%), Positives = 129/308 (41%), Gaps = 34/308 (11%)
Query: 162 PDPPVISPGLDVPLKELKMELFKDGRQ--FIVVSAPGGYGKTTLVQRLCKDDQV-QGKFK 218
P PVI + ++ +L+K + ++ + G GK+ L +D + +G F
Sbjct: 120 PQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFS 179
Query: 219 DDIFYVTVSKNPN------VKAIVQKVLHHKGYP--VPEFQTDEAAINDLERFFKQMRIE 270
+ +V++ K ++ + ++ + + +P +EA D R +
Sbjct: 180 GGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLP-LNIEEA--KDRLRVLMLRKHP 236
Query: 271 AILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQ---FGSVHYL---KPLTYEAA 324
LL+LDDVW +L+ Q +IL+T+R + G H + L E
Sbjct: 237 RSLLILDDVW--DPWVLKAFDNQC---QILLTTRDKSVTDSVMGPKHVVPVESGLGREKG 291
Query: 325 RTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSL--CGKHEVFWQRMV-- 380
+ N++ + +P E I++ CKG PL + ++G L ++ R +
Sbjct: 292 LEILSLFVNMKKED--LPAE--AHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQN 347
Query: 381 KECSRGESVFQSKNDILD-CLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMEL 439
K+ R + LD + S+++L ++K+ Y DL +D ++P L +W
Sbjct: 348 KQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE 407
Query: 440 YELVDDVF 447
E V+D+
Sbjct: 408 TEEVEDIL 415
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 65/308 (21%), Positives = 128/308 (41%), Gaps = 34/308 (11%)
Query: 162 PDPPVISPGLDVPLKELKMELFKDGRQ--FIVVSAPGGYGKTTLVQRLCKDDQV-QGKFK 218
P PVI + ++ +L+K + ++ + G GK+ L +D + +G F
Sbjct: 127 PQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFS 186
Query: 219 DDIFYVTVSKNPN------VKAIVQKVLHHKGYP--VPEFQTDEAAINDLERFFKQMRIE 270
+ +V++ K ++ + ++ + + +P +EA D R +
Sbjct: 187 GGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLP-LNIEEA--KDRLRVLMLRKHP 243
Query: 271 AILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQ---FGSVHYL---KPLTYEAA 324
LL+LDDVW +L+ Q +IL+T+ + G H + L E
Sbjct: 244 RSLLILDDVW--DPWVLKAFDNQC---QILLTTSDKSVTDSVMGPKHVVPVESGLGREKG 298
Query: 325 RTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSL--CGKHEVFWQRMV-- 380
+ N++ + +P E I++ CKG PL + ++G L ++ R +
Sbjct: 299 LEILSLFVNMKKED--LPAE--AHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQN 354
Query: 381 KECSRGESVFQSKNDILD-CLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMEL 439
K+ R + LD + S+++L ++K+ Y DL +D ++P L +W
Sbjct: 355 KQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE 414
Query: 440 YELVDDVF 447
E V+D+
Sbjct: 415 TEEVEDIL 422
>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 = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 34/127 (26%), Positives = 63/127 (49%), Gaps = 8/127 (6%)
Query: 570 LQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVS 629
L+++ L LI+T F L+ L +L + + SLP+ + ++ +L ++
Sbjct: 81 LKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFD-KLTNLTYLN 139
Query: 630 LVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCD-IVSMEKLRITNCHRL 688
L N Q F D NL E+D+ Y N L LP+G+ D + ++ LR+ ++L
Sbjct: 140 LAH-NQLQSLPKGVF---DKLTNLTELDLSY-NQLQSLPEGVFDKLTQLKDLRLYQ-NQL 193
Query: 689 SALPEGI 695
++P+G+
Sbjct: 194 KSVPDGV 200
>pdb|2Q8Y|A Chain A, Structural Insight Into The Enzymatic Mechanism Of The
Phophothreonine Lyase
pdb|2Z8P|A Chain A, Structural Basis For The Catalytic Mechanism Of
Phosphothreonine Lyase
Length = 241
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 198 YGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN--PNVKAIVQKVLHHKGYPVPEFQTDEA 255
+G + + Q QGKF D F+++V ++ P + +L + PV D+
Sbjct: 81 HGYDVFIHARRESPQSQGKFAGDKFHISVLRDMVPQAFQALSGLLFSEDSPV-----DKW 135
Query: 256 AINDLERFFKQMRI 269
A+ D+E+ +Q R+
Sbjct: 136 AVTDMEKVVQQARV 149
>pdb|3V44|A Chain A, Crystal Structure Of The N-Terminal Fragment Of Zebrafish
Tlr5
Length = 407
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 5/90 (5%)
Query: 606 IRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLI 665
+ L ++ N + R+ LQ + + G V RN+TFR +L+ + +DY N +
Sbjct: 37 LSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFR---GLSSLIILKLDY-NQFL 92
Query: 666 ELPDGLCD-IVSMEKLRITNCHRLSALPEG 694
+L G + + ++E L +T C+ A+ G
Sbjct: 93 QLETGAFNGLANLEVLTLTQCNLDGAVLSG 122
>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 = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 5/90 (5%)
Query: 606 IRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLI 665
+ L ++ N + R+ LQ + + G V RN+TFR +L+ + +DY N +
Sbjct: 37 LSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFR---GLSSLIILKLDY-NQFL 92
Query: 666 ELPDGLCD-IVSMEKLRITNCHRLSALPEG 694
+L G + + ++E L +T C+ A+ G
Sbjct: 93 QLETGAFNGLANLEVLTLTQCNLDGAVLSG 122
>pdb|4GOU|A Chain A, Crystal Structure Of An Rgs-rhogef From Entamoeba
Histolytica
Length = 518
Score = 29.6 bits (65), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 24/49 (48%)
Query: 641 NSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLS 689
N RISDA L L E +G+C I S+++ T+ ++LS
Sbjct: 377 NKIERISDALKLLFPFSFTSIXPLFEGKNGICGIASLDRFDKTDINQLS 425
>pdb|1ULT|A Chain A, Crystal Structure Of Tt0168 From Thermus Thermophilus Hb8
pdb|1ULT|B Chain B, Crystal Structure Of Tt0168 From Thermus Thermophilus Hb8
pdb|1V25|A Chain A, Crystal Structure Of Tt0168 From Thermus Thermophilus Hb8
pdb|1V25|B Chain B, Crystal Structure Of Tt0168 From Thermus Thermophilus Hb8
pdb|1V26|A Chain A, Crystal Structure Of Tt0168 From Thermus Thermophilus Hb8
pdb|1V26|B Chain B, Crystal Structure Of Tt0168 From Thermus Thermophilus Hb8
Length = 541
Score = 29.6 bits (65), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 25/117 (21%), Positives = 50/117 (42%), Gaps = 26/117 (22%)
Query: 25 EKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRM----------- 73
+++ V KDRL+ L +++ WI ++ N ++ PK + +V +
Sbjct: 423 DEEGYVEIKDRLKDL---IKSGGEWISSVDLENALMGHPKVKEAAVVAIPHPKWQERPLA 479
Query: 74 ----------MEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQH 120
E++ + + K KW YV+A++I + TS F + +L Q+
Sbjct: 480 VVVPRGEKPTPEELNEHLLKAGFAKWQLPDAYVFAEEIPR--TSAGKFLKRALREQY 534
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 29.3 bits (64), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 6/126 (4%)
Query: 570 LQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVS 629
L+++ L LI+T F L+ L +L + + SLP+ + ++ +L +
Sbjct: 81 LKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFD-KLTNLTYLY 139
Query: 630 LVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLS 689
L N Q F D NL +D+D N L LP+G+ D ++ K N ++L
Sbjct: 140 LYH-NQLQSLPKGVF---DKLTNLTRLDLDN-NQLQSLPEGVFDKLTQLKQLSLNDNQLK 194
Query: 690 ALPEGI 695
++P+G+
Sbjct: 195 SVPDGV 200
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 0.137 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,026,657
Number of Sequences: 62578
Number of extensions: 837587
Number of successful extensions: 2421
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 2391
Number of HSP's gapped (non-prelim): 46
length of query: 695
length of database: 14,973,337
effective HSP length: 106
effective length of query: 589
effective length of database: 8,340,069
effective search space: 4912300641
effective search space used: 4912300641
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: 55 (25.8 bits)