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= 039361
(253 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1R05|A Chain A, Solution Structure Of Max B-Hlh-Lz
pdb|1R05|B Chain B, Solution Structure Of Max B-Hlh-Lz
Length = 87
Score = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 90 IERQRRQHLSMLHASLRSLLPLQSITGKRSISDHI-NEARNYINYLNKNIQELGLKRDKL 148
+ER+RR H+ SLR +P S+ G+++ I ++A YI Y+ + + L D L
Sbjct: 11 LERKRRDHIKDSFHSLRDSVP--SLQGEKASRAQILDKATEYIQYMRRKVHTLQQDIDDL 68
Query: 149 KNLSEL 154
K + L
Sbjct: 69 KRQNAL 74
>pdb|3DRF|A Chain A, Lactococcal Oppa Complexed With An Endogenous Peptide In
The Closed Conformation
pdb|3DRG|A Chain A, Lactococcal Oppa Complexed With Bradykinin In The Closed
Conformation
pdb|3DRH|A Chain A, Crystal Structure Of Lactococcal Oppa Co-Crystallized With
Leu- Enkephalin In An Open Conformation
pdb|3DRI|A Chain A, Crystal Structure Of Lactococcal Oppa Co-Crystallized With
An Octamer Peptide In An Open Conformation
pdb|3DRJ|A Chain A, Crystal Structure Of Lactococcal Oppa Co-Crystallized With
Pth-Related Peptide In An Open Conformation
pdb|3DRK|A Chain A, Crystal Structure Of Lactococcal Oppa Co-Crystallized With
Neuropeptide S In An Open Conformation
pdb|3RYA|A Chain A, Lactococcal Oppa Complexed With Slsqlssqs
pdb|3RYB|A Chain A, Lactococcal Oppa Complexed With Slsqslsqs
Length = 590
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 159 HGSSNWDNCLQNCVTIHPYSGGVEIVINSV--HKEENLKLSKVMEAVLEEGLDVIRCAST 216
+GS W + L N V + Y G I+ + EN K+ KV ++ G+ T
Sbjct: 131 YGSDRWTDSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKEMKPGM-------T 183
Query: 217 QTDEGFFHTIQAEESQVGDLTCVDL 241
Q+ G+F A + D+ DL
Sbjct: 184 QSGNGYFLETVAPYQYLKDVAPKDL 208
>pdb|3E7H|A Chain A, The Crystal Structure Of The Beta Subunit Of The Dna-
Directed Rna Polymerase From Vibrio Cholerae O1 Biovar
Eltor
pdb|3E7H|B Chain B, The Crystal Structure Of The Beta Subunit Of The Dna-
Directed Rna Polymerase From Vibrio Cholerae O1 Biovar
Eltor
Length = 103
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 109 LPLQSITGKRSISDHINEARNYINYLNKNIQELGLKRDKLKNLSELG 155
+P++ I GK S D++NEA + + N QE+ L + L NLS+ G
Sbjct: 61 VPVEYIVGKVSAKDYVNEATGEL-IITAN-QEISL--EALANLSQAG 103
>pdb|3Q22|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Gtp And
Magnesium: Substrate Complex I
pdb|3Q22|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Gtp And
Magnesium: Substrate Complex I
pdb|3Q23|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Gmpcpp And
Manganese: Sustrate Complex Ii
pdb|3Q23|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Gmpcpp And
Manganese: Sustrate Complex Ii
pdb|3Q0A|A Chain A, X-Ray Crystal Structure Of The Transcription Initiation
Complex Of The N4 Mini-Vrnap With P2 Promoter: Mismatch
Complex
pdb|3Q0A|B Chain B, X-Ray Crystal Structure Of The Transcription Initiation
Complex Of The N4 Mini-Vrnap With P2 Promoter: Mismatch
Complex
pdb|4FF1|A Chain A, N4 Mini-vrnap Transcription Initiation Complex, 1 Min After
Soaking Gtp, Atp And Mn
pdb|4FF1|B Chain B, N4 Mini-vrnap Transcription Initiation Complex, 1 Min After
Soaking Gtp, Atp And Mn
pdb|4FF2|A Chain A, N4 Mini-vrnap Transcription Initiation Complex, 2 Min After
Soaking Gtp, Atp And Mn
pdb|4FF2|B Chain B, N4 Mini-vrnap Transcription Initiation Complex, 2 Min After
Soaking Gtp, Atp And Mn
pdb|4FF3|A Chain A, N4 Mini-vrnap Transcription Initiation Complex, 3 Min After
Soaking Gtp, Atp And Mn
pdb|4FF3|B Chain B, N4 Mini-vrnap Transcription Initiation Complex, 3 Min After
Soaking Gtp, Atp And Mn
pdb|4FF4|A Chain A, N4 Mini-vrnap Transcription Initiation Complex, 4 Min After
Soaking Gtp, Atp And Mn
pdb|4FF4|B Chain B, N4 Mini-vrnap Transcription Initiation Complex, 4 Min After
Soaking Gtp, Atp And Mn
Length = 1118
Score = 27.7 bits (60), Expect = 6.4, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 28 YQEHSNIQQDQILQGQALLERNINSSKMGKGQQHKLL 64
Y + N D I +L+ERN+ + +G +HK+L
Sbjct: 1026 YDQRENATVDDIANAASLIERNLRNIALGVDIRHKVL 1062
>pdb|3C2P|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap P1 Promoter
Complex
pdb|3C2P|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap P1 Promoter
Complex
pdb|3C3L|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap P2 Promoter
Complex
pdb|3C3L|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap P2 Promoter
Complex
pdb|3C46|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap P2_7a Promoter
Complex Soaked With Mgcl2
pdb|3C46|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap P2_7a Promoter
Complex Soaked With Mgcl2
pdb|3Q24|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Pppgpg And
Pyrophosphate: Product Complex
pdb|3Q24|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Pppgpg And
Pyrophosphate: Product Complex
Length = 1117
Score = 27.7 bits (60), Expect = 6.4, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 28 YQEHSNIQQDQILQGQALLERNINSSKMGKGQQHKLL 64
Y + N D I +L+ERN+ + +G +HK+L
Sbjct: 1026 YDQRENATVDDIANAASLIERNLRNIALGVDIRHKVL 1062
>pdb|2PO4|A Chain A, X-Ray Crystal Structure Of Polymerase Domain Of The
Bacteriophage N4 Virion Rna Polymerase
Length = 1104
Score = 27.7 bits (60), Expect = 6.5, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 28 YQEHSNIQQDQILQGQALLERNINSSKMGKGQQHKLL 64
Y + N D I +L+ERN+ + +G +HK+L
Sbjct: 1014 YDQRENATVDDIANAASLIERNLRNIALGVDIRHKVL 1050
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 0.133 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,707,035
Number of Sequences: 62578
Number of extensions: 239763
Number of successful extensions: 650
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 647
Number of HSP's gapped (non-prelim): 12
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
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: 50 (23.9 bits)