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= 038110
(667 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 33.5 bits (75), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 33/123 (26%), Positives = 51/123 (41%), Gaps = 23/123 (18%)
Query: 240 LKKNKTILMILDNIWENLDLLAIGIPHGNDHKGCKILLTARSEDTLSRKMDSKQNFSV-- 297
L+K+ L+ILD++W+ L A C+ILLT R + M K V
Sbjct: 232 LRKHPRSLLILDDVWDPWVLKAFD-------NQCQILLTTRDKSVTDSVMGPKHVVPVES 284
Query: 298 GILKE-------------EEAWSGEFKWVAKECAGLPVSIVTVSRALRNKSLFEWKDALQ 344
G+ +E +E E + KEC G P+ + + LR+ W L+
Sbjct: 285 GLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLR 343
Query: 345 QLR 347
QL+
Sbjct: 344 QLQ 346
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 32.7 bits (73), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 32/106 (30%), Positives = 46/106 (43%), Gaps = 11/106 (10%)
Query: 484 NSFFAIPHNLFRSMLQVRVLDLTDMNLLSLPSSI-GLLTNLHTL--CLYGGVGVVDGVKN 540
N A+P +F S+ Q+ VLDL L LPS++ L +L L C + G+
Sbjct: 74 NQLGALPVGVFDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFMCCNKLTELPRGI-- 131
Query: 541 ASLEELKHFPNLTSLELEVNDANTLPRGGLFFEKPERYKILTGHRW 586
E L H LT L L+ N ++P G + L G+ W
Sbjct: 132 ---ERLTH---LTHLALDQNQLKSIPHGAFDRLSSLTHAYLFGNPW 171
>pdb|3OJA|B Chain B, Crystal Structure Of Lrim1APL1C COMPLEX
Length = 597
Score = 32.3 bits (72), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 8/96 (8%)
Query: 483 KNSFF-AIPHNLFRSMLQVRVLDLTDMNLLSLPSSIGLLTNLHTLC-LYGGVGVVDGVKN 540
KNS +P L S QV +L+L D+ + + + HT+ LY G + ++
Sbjct: 59 KNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYA--FAYAHTIQKLYMGF---NAIRY 113
Query: 541 ASLEELKHFPNLTSLELEVNDANTLPRGGLFFEKPE 576
++ P LT L LE ND ++LPR G+F P+
Sbjct: 114 LPPHVFQNVPLLTVLVLERNDLSSLPR-GIFHNTPK 148
>pdb|3T6Q|A Chain A, Crystal Structure Of Mouse Rp105MD-1 Complex
pdb|3T6Q|B Chain B, Crystal Structure Of Mouse Rp105MD-1 Complex
Length = 606
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 30/97 (30%), Positives = 47/97 (48%), Gaps = 8/97 (8%)
Query: 466 PEVME--CPQLKLFSMPAEKNSFFAIPHNLFRSMLQVRVLDLTDMNLLSLPSSIGLLTNL 523
P V E C ++ + S+ +K+ FF I N F ++ LDLT +L LPS + L+ L
Sbjct: 245 PAVFEGLC-EMSVESINLQKHYFFNISSNTFHCFSGLQELDLTATHLSELPSGLVGLSTL 303
Query: 524 HTLCLYGGVGVVDGVKNASLEELKHFPNLTSLELEVN 560
L L + +N +FP+LT L ++ N
Sbjct: 304 KKLVLSA-----NKFENLCQISASNFPSLTHLSIKGN 335
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 49/100 (49%), Gaps = 8/100 (8%)
Query: 484 NSFFAIPHNLFRSMLQVRVLDLTDMNLLSLPSSI-GLLTNLHTLCLYGGVGVVDGVKNAS 542
N ++P+ +F + ++ L L + L SLP + LTNL L LY + +
Sbjct: 95 NQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLYLYHNQ--LQSLPKGV 152
Query: 543 LEELKHFPNLTSLELEVNDANTLPRGGLFFEKPERYKILT 582
++L NLT L+L+ N +LP G F+K + K L+
Sbjct: 153 FDKLT---NLTRLDLDNNQLQSLPEG--VFDKLTQLKQLS 187
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 32/123 (26%), Positives = 50/123 (40%), Gaps = 23/123 (18%)
Query: 240 LKKNKTILMILDNIWENLDLLAIGIPHGNDHKGCKILLTARSEDTLSRKMDSKQNFSV-- 297
L+K+ L+ILD++W+ L A C+ILLT + M K V
Sbjct: 239 LRKHPRSLLILDDVWDPWVLKAFD-------NQCQILLTTSDKSVTDSVMGPKHVVPVES 291
Query: 298 GILKE-------------EEAWSGEFKWVAKECAGLPVSIVTVSRALRNKSLFEWKDALQ 344
G+ +E +E E + KEC G P+ + + LR+ W L+
Sbjct: 292 GLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLR 350
Query: 345 QLR 347
QL+
Sbjct: 351 QLQ 353
>pdb|3O6N|A Chain A, Crystal Structure Of Apl1 Leucine-Rich Repeat Domain
Length = 390
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 7/89 (7%)
Query: 489 IPHNLFRSMLQVRVLDLTDMNLLSLPSSIGLLTNLHTLC-LYGGVGVVDGVKNASLEELK 547
+P L S QV +L+L D+ + + + HT+ LY G + ++ +
Sbjct: 60 LPAALLDSFRQVELLNLNDLQIEEIDTYA--FAYAHTIQKLYMGF---NAIRYLPPHVFQ 114
Query: 548 HFPNLTSLELEVNDANTLPRGGLFFEKPE 576
+ P LT L LE ND ++LPR G+F P+
Sbjct: 115 NVPLLTVLVLERNDLSSLPR-GIFHNTPK 142
>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 = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 33/123 (26%), Positives = 52/123 (42%), Gaps = 23/123 (18%)
Query: 240 LKKNKTILMILDNIWENLDLLAIGIPHGNDHKGCKILLTARSEDTLSRKMDSKQ----NF 295
L+K+ L+ILD++W++ L A C+ILLT R + M K
Sbjct: 232 LRKHPRSLLILDDVWDSWVLKAFD-------SQCQILLTTRDKSVTDSVMGPKYVVPVES 284
Query: 296 SVGILKEEEAWS-----------GEFKWVAKECAGLPVSIVTVSRALRNKSLFEWKDALQ 344
S+G K E S + + KEC G P+ + + LR+ W+ L+
Sbjct: 285 SLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRWEYYLK 343
Query: 345 QLR 347
QL+
Sbjct: 344 QLQ 346
>pdb|2R9U|A Chain A, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|B Chain B, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|C Chain C, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|D Chain D, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
Length = 174
Score = 30.4 bits (67), Expect = 3.3, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 484 NSFFAIPHNLFRSMLQVRVLDLTDMNLLSLPSSIGLLTNLHTL 526
N AIP +F + Q+ LDL D +L S+P G NL +L
Sbjct: 67 NKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPR--GAFDNLKSL 107
>pdb|2A0Z|A Chain A, The Molecular Structure Of Toll-like Receptor 3 Ligand
Binding Domain
Length = 705
Score = 29.6 bits (65), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 482 EKNSFFAIPHNLFRSMLQVRVLDLTDMNLLSLPSSI 517
E N F IP +F+ + +++++DL NL +LP+S+
Sbjct: 549 ESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASV 584
>pdb|3ULU|A Chain A, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form1)
pdb|3ULV|A Chain A, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form2)
Length = 694
Score = 29.6 bits (65), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 482 EKNSFFAIPHNLFRSMLQVRVLDLTDMNLLSLPSSI 517
E N F IP +F+ + +++++DL NL +LP+S+
Sbjct: 554 ESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASV 589
>pdb|1ZIW|A Chain A, Human Toll-Like Receptor 3 Extracellular Domain Structure
Length = 680
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 482 EKNSFFAIPHNLFRSMLQVRVLDLTDMNLLSLPSSI 517
E N F IP +F+ + +++++DL NL +LP+S+
Sbjct: 544 ESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASV 579
>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 = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 33/123 (26%), Positives = 52/123 (42%), Gaps = 23/123 (18%)
Query: 240 LKKNKTILMILDNIWENLDLLAIGIPHGNDHKGCKILLTARSEDTLSRKMDSKQ----NF 295
L+K+ L+ILD++W++ L A C+ILLT R + M K
Sbjct: 238 LRKHPRSLLILDDVWDSWVLKAFD-------SQCQILLTTRDKSVTDSVMGPKYVVPVES 290
Query: 296 SVGILKEEEAWS-----------GEFKWVAKECAGLPVSIVTVSRALRNKSLFEWKDALQ 344
S+G K E S + + KEC G P+ + + LR+ W+ L+
Sbjct: 291 SLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRWEYYLK 349
Query: 345 QLR 347
QL+
Sbjct: 350 QLQ 352
>pdb|2O6R|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B61
Length = 177
Score = 29.6 bits (65), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 6/88 (6%)
Query: 482 EKNSFFAIPHNLFRSMLQVRVLDLTDMNLLSLPSSI-GLLTNLHTLCLYGGVGVVDGVKN 540
E N ++PH +F + Q+ L L+ + SLP + LT L L L+ + + N
Sbjct: 36 ESNKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHE--NKLQSLPN 93
Query: 541 ASLEELKHFPNLTSLELEVNDANTLPRG 568
++L L L L+ N ++P G
Sbjct: 94 GVFDKLTQ---LKELALDTNQLKSVPDG 118
>pdb|3S6J|A Chain A, The Crystal Structure Of A Hydrolase From Pseudomonas
Syringae
pdb|3S6J|B Chain B, The Crystal Structure Of A Hydrolase From Pseudomonas
Syringae
pdb|3S6J|C Chain C, The Crystal Structure Of A Hydrolase From Pseudomonas
Syringae
pdb|3S6J|D Chain D, The Crystal Structure Of A Hydrolase From Pseudomonas
Syringae
pdb|3S6J|E Chain E, The Crystal Structure Of A Hydrolase From Pseudomonas
Syringae
pdb|3S6J|F Chain F, The Crystal Structure Of A Hydrolase From Pseudomonas
Syringae
Length = 233
Score = 29.3 bits (64), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 509 NLLSLPSSIGLLTNLHTLCLYGGVGVVDGVKNASLEELKHFPNLTSLELEVNDANTLPRG 568
+++LP ++ LL L L + G+ A++ NL +L+L++N N + R
Sbjct: 89 QIIALPGAVELLETLDKENLKWCIATSGGIDTATI-------NLKALKLDINKINIVTRD 141
Query: 569 GLFFEKPE 576
+ + KP+
Sbjct: 142 DVSYGKPD 149
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
0.318 0.135 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,058,830
Number of Sequences: 62578
Number of extensions: 777417
Number of successful extensions: 2617
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 2591
Number of HSP's gapped (non-prelim): 52
length of query: 667
length of database: 14,973,337
effective HSP length: 105
effective length of query: 562
effective length of database: 8,402,647
effective search space: 4722287614
effective search space used: 4722287614
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)