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= 008183
(575 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 271 WNAMMAGYAQQGDQSTVLELFHLLEMRGFAPDEYSFLAVLTALCNAGL-AGESEKWIERM 329
+NA+M G+A+QG ++ + +++ G PD S+ A L + AG E+ +E+M
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227
>pdb|2PGG|A Chain A, Crystal Structure Of A Birnavirus (Ibdv) Rna-Dependent Rna
Polymerase Vp1
Length = 774
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 10/70 (14%)
Query: 332 RYKLEPGLEHYTCLISAMGRAGRLEDA-------ERIAMAMPFEPDAAVWRALLSFSAIH 384
RY+ E GL L +A R L+DA E++ + P +PDA + + S +
Sbjct: 694 RYRNEAGLSGLVLLATARSR---LQDAVKAKAEAEKLHKSKPDDPDADWFERSETLSDLL 750
Query: 385 GKADMASKMG 394
KAD+ASK+
Sbjct: 751 EKADIASKVA 760
>pdb|2PUS|A Chain A, Unprecedented Activation Mechanism Of A Non-Canonical
Rna-Dependent Rna Polymerase
pdb|2QJ1|A Chain A, Crystal Structure Of Infectious Bursal Disease Virus Vp1
Polymerase Incubated With An Oligopeptide Mimicking The
Vp3 C-Terminus
pdb|2R70|A Chain A, Crystal Structure Of Infectious Bursal Disease Virus Vp1
Polymerase, Cocrystallized With An Oligopeptide
Mimicking The Vp3 C-Terminus.
pdb|2R72|A Chain A, Crystal Structure Of Infectious Bursal Disease Virus Vp1
Polymerase, Incubated With Mg2+ Ion
Length = 852
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 10/70 (14%)
Query: 332 RYKLEPGLEHYTCLISAMGRAGRLEDA-------ERIAMAMPFEPDAAVWRALLSFSAIH 384
RY+ E GL L +A R L+DA E++ + P +PDA + + S +
Sbjct: 731 RYRNEAGLSGLVLLATARSR---LQDAVKAKAEAEKLHKSKPDDPDADWFERSETLSDLL 787
Query: 385 GKADMASKMG 394
KAD+ASK+
Sbjct: 788 EKADIASKVA 797
>pdb|1XI4|A Chain A, Clathrin D6 Coat
pdb|1XI4|B Chain B, Clathrin D6 Coat
pdb|1XI4|C Chain C, Clathrin D6 Coat
pdb|1XI4|D Chain D, Clathrin D6 Coat
pdb|1XI4|E Chain E, Clathrin D6 Coat
pdb|1XI4|F Chain F, Clathrin D6 Coat
pdb|1XI4|G Chain G, Clathrin D6 Coat
pdb|1XI4|H Chain H, Clathrin D6 Coat
pdb|1XI4|I Chain I, Clathrin D6 Coat
pdb|1XI5|A Chain A, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|B Chain B, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|C Chain C, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|D Chain D, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|E Chain E, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|F Chain F, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|G Chain G, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|H Chain H, Clathrin D6 Coat With Auxilin J-Domain
pdb|1XI5|I Chain I, Clathrin D6 Coat With Auxilin J-Domain
pdb|3IYV|A Chain A, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|B Chain B, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|C Chain C, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|D Chain D, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|E Chain E, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|F Chain F, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|G Chain G, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|H Chain H, Clathrin D6 Coat As Full-Length Triskelions
pdb|3IYV|I Chain I, Clathrin D6 Coat As Full-Length Triskelions
Length = 1630
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 69/172 (40%), Gaps = 36/172 (20%)
Query: 258 VFDENLSVLNSIAWNAMMAGYAQQGDQSTVLELFHLLEMRGFAPDEYSFLAVLTALCNAG 317
VF E+ ++ N + A+ A D++ V+E + L+ APD A
Sbjct: 1017 VFSEHRNLQNLLILTAIKA------DRTRVMEYINRLDNYD-APD------------IAN 1057
Query: 318 LAGESEKWIERMKVRYKLEPGLEHYTCLISAMGRAGR-LEDAERIAMAMPFEPDAAVWRA 376
+A +E + E + K + LI +G R E AER EP AVW
Sbjct: 1058 IAISNELFEEAFAIFRKFDVNTSAVQVLIEHIGNLDRAYEFAERCN-----EP--AVWSQ 1110
Query: 377 LLSFSAIHGKADMASKMGKRLID--INPYDDSAYVIVANVLSGVGRWDEVAE 426
L KA + M K ID I D S+Y+ V + G W+E+ +
Sbjct: 1111 L-------AKAQLQKGMVKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVK 1155
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
0.322 0.136 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,841,076
Number of Sequences: 62578
Number of extensions: 534466
Number of successful extensions: 1200
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1199
Number of HSP's gapped (non-prelim): 5
length of query: 575
length of database: 14,973,337
effective HSP length: 104
effective length of query: 471
effective length of database: 8,465,225
effective search space: 3987120975
effective search space used: 3987120975
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: 54 (25.4 bits)