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= 036757
(385 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KPJ|A Chain A, Solution Structure Of Protein Sos-Response Transcriptional
Repressor, Lexa From Eubacterium Rectale. Northeast
Structural Genomics Consortium Target Err9a
Length = 94
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 270 DTMNKVLSAHFRAYIQALEKLQLDIATSSDLIGVEARSTGLFSRGREPLKNRSAVFALGD 329
D + S + +YI EK QL+IA S IGV ++ + +G + V AL D
Sbjct: 4 DKQKAIFSENLNSYIAKSEKTQLEIAKS---IGVSPQTFNTWCKGI-AIPRMGKVQALAD 59
Query: 330 RINILK 335
NI K
Sbjct: 60 YFNINK 65
>pdb|3GCM|A Chain A, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|B Chain B, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|C Chain C, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GLL|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core
pdb|3GME|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase In
Complex With Rnase E And Manganese
Length = 549
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 95 IKESDNLVSLHDQIRDCDAILSQMETLLSGFQAEIGSISSDIKILQEKSMDMGLKLKNRK 154
+KE DN V L D + D D L M+ ++G + I ++ DIKI M + L K
Sbjct: 469 VKEGDNYVVLSDILGDEDH-LGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAK 527
Query: 155 VAESKLAKFVEDIIIPPR 172
A + +E I PR
Sbjct: 528 GARLHILGVMEQAINAPR 545
>pdb|3H1C|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|B Chain B, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|C Chain C, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|G Chain G, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|I Chain I, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|K Chain K, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|M Chain M, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|O Chain O, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|R Chain R, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|T Chain T, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|V Chain V, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|X Chain X, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
Length = 549
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 95 IKESDNLVSLHDQIRDCDAILSQMETLLSGFQAEIGSISSDIKILQEKSMDMGLKLKNRK 154
+KE DN V L D + D D L M+ ++G + I ++ DIKI M + L K
Sbjct: 469 VKEGDNYVVLSDILGDEDH-LGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAK 527
Query: 155 VAESKLAKFVEDIIIPPR 172
A + +E I PR
Sbjct: 528 GARLHILGVMEQAINAPR 545
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 95 IKESDNLVSLHDQIRDCDAILSQMETLLSGFQAEIGSISSDIKILQEKSMDMGLKLKNRK 154
+KE DN V L D + D D L M+ ++G + I ++ DIKI M + L K
Sbjct: 475 VKEGDNYVVLSDILGDEDH-LGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAK 533
Query: 155 VAESKLAKFVEDIIIPPR 172
A + +E I PR
Sbjct: 534 GARLHILGVMEQAINAPR 551
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 95 IKESDNLVSLHDQIRDCDAILSQMETLLSGFQAEIGSISSDIKILQEKSMDMGLKLKNRK 154
+KE DN V L D + D D L M+ ++G + I ++ DIKI M + L K
Sbjct: 475 VKEGDNYVVLSDILGDEDH-LGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAK 533
Query: 155 VAESKLAKFVEDIIIPPR 172
A + +E I PR
Sbjct: 534 GARLHILGVMEQAINAPR 551
>pdb|3GZU|A Chain A, Vp7 Recoated Rotavirus Dlp
pdb|3GZU|B Chain B, Vp7 Recoated Rotavirus Dlp
Length = 800
Score = 28.5 bits (62), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 53/102 (51%), Gaps = 15/102 (14%)
Query: 49 LEQELEECKNHDVVANILSKGTTLRE---YTKGVENNL----RQVELDSIQDYIKESDNL 101
L+ +L E N+D++ N + + +R Y ++ NL R + + +QD + DN
Sbjct: 177 LQHQLVEPLNNDIIFNYIPER--IRNDVNYILNMDRNLPSTARYIRPNLLQDRLNLHDNF 234
Query: 102 VSLHDQIRDCDAILSQ-----METLLSGFQAEIGSISSDIKI 138
SL D I + IL++ ++ L+S +A+I +S D+++
Sbjct: 235 ESLWDTITTSNYILARSVVPDLKELVST-EAQIQKMSQDLQL 275
>pdb|3N09|A Chain A, Atomic Model Of An Infectious Rotavirus Particle
pdb|3N09|B Chain B, Atomic Model Of An Infectious Rotavirus Particle
Length = 800
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 53/102 (51%), Gaps = 15/102 (14%)
Query: 49 LEQELEECKNHDVVANILSKGTTLRE---YTKGVENNL----RQVELDSIQDYIKESDNL 101
L+ +L E N+D++ N + + +R Y ++ NL R + + +QD + DN
Sbjct: 177 LQHQLVEPLNNDIIFNYIPER--IRNDVNYILNMDRNLPSTARYIRPNLLQDRLNLHDNF 234
Query: 102 VSLHDQIRDCDAILSQ-----METLLSGFQAEIGSISSDIKI 138
SL D I + IL++ ++ L+S +A+I +S D+++
Sbjct: 235 ESLWDTITTSNYILARSVVPDLKELVST-EAQIQKMSQDLQL 275
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 0.136 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,462,111
Number of Sequences: 62578
Number of extensions: 421192
Number of successful extensions: 1194
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1194
Number of HSP's gapped (non-prelim): 14
length of query: 385
length of database: 14,973,337
effective HSP length: 101
effective length of query: 284
effective length of database: 8,652,959
effective search space: 2457440356
effective search space used: 2457440356
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: 52 (24.6 bits)