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= 002520
(913 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1B8P|A Chain A, Malate Dehydrogenase From Aquaspirillum Arcticum
pdb|1B8U|A Chain A, Malate Dehydrogenase From Aquaspirillum Arcticum
pdb|1B8V|A Chain A, Malate Dehydrogenase From Aquaspirillum Arcticum
Length = 329
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 615 GIERSDRCET--QTSTPEGSTVDASESRNIGVEVVKQP 650
G+ER D E Q T +G +DA SRNI V VV P
Sbjct: 98 GMERKDLLEANAQIFTVQGKAIDAVASRNIKVLVVGNP 135
>pdb|3AQB|B Chain B, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium
pdb|3AQB|D Chain D, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium
pdb|3AQC|B Chain B, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium And Fpp Analogue
pdb|3AQC|D Chain D, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium And Fpp Analogue
Length = 325
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 226 GHCQYGVSETVVDDLVDPSQETAELDKPSG 255
GHC G+S ++DD++D + + A L KP G
Sbjct: 200 GHC-IGMSYQIIDDILDYTSDEATLGKPVG 228
>pdb|3IXQ|A Chain A, Structure Of Ribose 5-Phosphate Isomerase A From
Methanocaldococcus Jannaschii
pdb|3IXQ|B Chain B, Structure Of Ribose 5-Phosphate Isomerase A From
Methanocaldococcus Jannaschii
pdb|3IXQ|C Chain C, Structure Of Ribose 5-Phosphate Isomerase A From
Methanocaldococcus Jannaschii
pdb|3IXQ|D Chain D, Structure Of Ribose 5-Phosphate Isomerase A From
Methanocaldococcus Jannaschii
Length = 226
Score = 29.6 bits (65), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 33/115 (28%), Positives = 53/115 (46%), Gaps = 7/115 (6%)
Query: 748 IRNMEHRIAHETLPLKEEKQIIREIKQLKQRREQISSSIGEHDEVQLAFDQKDQIEEKMK 807
IR + +RI E L + E K L + E ++ E+D V +AFD D++EE
Sbjct: 36 IRELGNRIREEELTVFGIPTSF-EAKMLAMQYEIPLVTLDEYD-VDIAFDGADEVEETTL 93
Query: 808 FLRKEADSL--RENVIKAEAATQAVKKLHREESEKLKRLLGQFKAADEIRQEAYK 860
FL K +E ++ A V +ES+ +K+L +F E+ AY+
Sbjct: 94 FLIKGGGGCHTQEKIVDYNANEFVV---LVDESKLVKKLGEKFPIPVEVIPSAYR 145
>pdb|1ARO|P Chain P, T7 Rna Polymerase Complexed With T7 Lysozyme
Length = 883
Score = 29.6 bits (65), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 185 DQNTDEASRPVAV---AVAGVDLQLGMQIVRGSVTVESERGLDAGHCQYGVSETVVDDLV 241
D+NT E S V + A+AG L G V SVT S L G ++G + V++D +
Sbjct: 599 DENTGEISEKVKLGTKALAGQWLAYG---VTRSVTKRSVMTLAYGSKEFGFRQQVLEDTI 655
Query: 242 DPS 244
P+
Sbjct: 656 QPA 658
>pdb|3E2E|A Chain A, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 7nt Of Rna
pdb|3E3J|C Chain C, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 8nt Of Rna
pdb|3E3J|B Chain B, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 8nt Of Rna
Length = 889
Score = 29.3 bits (64), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 185 DQNTDEASRPVAV---AVAGVDLQLGMQIVRGSVTVESERGLDAGHCQYGVSETVVDDLV 241
D+NT E S V + A+AG L G V SVT S L G ++G + V++D +
Sbjct: 605 DENTGEISEKVKLGTKALAGQWLAYG---VTRSVTKRSVMTLAYGSKEFGFRQQVLEDTI 661
Query: 242 DPS 244
P+
Sbjct: 662 QPA 664
>pdb|4RNP|A Chain A, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|4RNP|B Chain B, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|4RNP|C Chain C, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|1CEZ|A Chain A, Crystal Structure Of A T7 Rna Polymerase-T7 Promoter
Complex
pdb|1QLN|A Chain A, Structure Of A Transcribing T7 Rna Polymerase Initiation
Complex
pdb|1H38|A Chain A, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|B Chain B, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|C Chain C, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|D Chain D, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1MSW|D Chain D, Structural Basis For The Transition From Initiation To
Elongation Transcription In T7 Rna Polymerase
pdb|1S0V|A Chain A, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|B Chain B, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|C Chain C, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|D Chain D, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S76|D Chain D, T7 Rna Polymerase Alpha Beta Methylene Atp Elongation
Complex
pdb|1S77|D Chain D, T7 Rnap Product Pyrophosphate Elongation Complex
Length = 883
Score = 29.3 bits (64), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 185 DQNTDEASRPVAV---AVAGVDLQLGMQIVRGSVTVESERGLDAGHCQYGVSETVVDDLV 241
D+NT E S V + A+AG L G V SVT S L G ++G + V++D +
Sbjct: 599 DENTGEISEKVKLGTKALAGQWLAYG---VTRSVTKRSVMTLAYGSKEFGFRQQVLEDTI 655
Query: 242 DPS 244
P+
Sbjct: 656 QPA 658
>pdb|2PI4|A Chain A, T7rnap Complexed With A Phi10 Protein And Initiating Gtps.
pdb|2PI5|A Chain A, T7 Rna Polymerase Complexed With A Phi10 Promoter
Length = 878
Score = 29.3 bits (64), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 185 DQNTDEASRPVAV---AVAGVDLQLGMQIVRGSVTVESERGLDAGHCQYGVSETVVDDLV 241
D+NT E S V + A+AG L G V SVT S L G ++G + V++D +
Sbjct: 594 DENTGEISEKVKLGTKALAGQWLAYG---VTRSVTKRSVMTLAYGSKEFGFRQQVLEDTI 650
Query: 242 DPS 244
P+
Sbjct: 651 QPA 653
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
0.308 0.127 0.346
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,483,449
Number of Sequences: 62578
Number of extensions: 991459
Number of successful extensions: 2340
Number of sequences better than 100.0: 47
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 36
Number of HSP's that attempted gapping in prelim test: 2303
Number of HSP's gapped (non-prelim): 61
length of query: 913
length of database: 14,973,337
effective HSP length: 108
effective length of query: 805
effective length of database: 8,214,913
effective search space: 6613004965
effective search space used: 6613004965
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 56 (26.2 bits)