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= 005258
(705 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 413 DPLQSISGLKFSPPGVTSVLSQNFLLSKRKKSEF---DPMKQFIRELHSDLEVVYVGQLC 469
D + ++ + P V + Q L + +EF PM QF L D + +G
Sbjct: 319 DDIPPVANTQLRNPAVRNTPEQKAALKAEQATEFYVHTPMVQFYETLGKDRILELMGAGT 378
Query: 470 LSWEILHWQYEKSLE 484
L+ E+L+ + KSLE
Sbjct: 379 LNKELLNDNHAKSLE 393
>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 = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 413 DPLQSISGLKFSPPGVTSVLSQNFLLSKRKKSEF---DPMKQFIRELHSDLEVVYVGQLC 469
D + ++ + P V + Q L + +EF PM QF L D + +G
Sbjct: 319 DDIPPVANTQLRNPAVRNTPEQKAALKAEQATEFYVHTPMVQFYETLGKDRILELMGAGT 378
Query: 470 LSWEILHWQYEKSLE 484
L+ E+L+ + KSLE
Sbjct: 379 LNKELLNDNHAKSLE 393
>pdb|2PO4|A Chain A, X-Ray Crystal Structure Of Polymerase Domain Of The
Bacteriophage N4 Virion Rna Polymerase
Length = 1104
Score = 30.4 bits (67), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 413 DPLQSISGLKFSPPGVTSVLSQNFLLSKRKKSEF---DPMKQFIRELHSDLEVVYVGQLC 469
D + ++ + P V + Q L + +EF PM QF L D + +G
Sbjct: 307 DDIPPVANTQLRNPAVRNTPEQKAALKAEQATEFYVHTPMVQFYETLGKDRILELMGAGT 366
Query: 470 LSWEILHWQYEKSLE 484
L+ E+L+ + KSLE
Sbjct: 367 LNKELLNDNHAKSLE 381
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
0.316 0.132 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,729,552
Number of Sequences: 62578
Number of extensions: 670726
Number of successful extensions: 1422
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1420
Number of HSP's gapped (non-prelim): 8
length of query: 705
length of database: 14,973,337
effective HSP length: 106
effective length of query: 599
effective length of database: 8,340,069
effective search space: 4995701331
effective search space used: 4995701331
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)