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= psy8717
(69 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1MW8|X Chain X, Crystal Structure Of A Complex Between H365r Mutant Of 67
Kda N-Terminal Fragment Of E. Coli Dna Topoisomerase I
And 5'-Acttcgggatg-3'
pdb|1MW9|X Chain X, Crystal Structure Of H365r Mutant Of 67 Kda N-Terminal
Fragment Of E. Coli Dna Topoisomerase I
Length = 592
Score = 30.0 bits (66), Expect = 0.39, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD 58
+S G Q+ + VER +I+ F PE +W +D
Sbjct: 191 LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVD 223
>pdb|3PX7|A Chain A, Crystal Structure Of Covalent Complex Of Topoisomerase 1a
With Substrate
Length = 595
Score = 30.0 bits (66), Expect = 0.39, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD 58
+S G Q+ + VER +I+ F PE +W +D
Sbjct: 191 LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVD 223
>pdb|3PWT|A Chain A, Crystal Structure Of Mutant E.Coli Topoisomerase Ia
Length = 596
Score = 30.0 bits (66), Expect = 0.39, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD 58
+S G Q+ + VER +I+ F PE +W +D
Sbjct: 191 LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVD 223
>pdb|1ECL|A Chain A, Amino Terminal 67kda Domain Of Escherichia Coli Dna
Topoisomerase I (Residues 2-590 Of Mature Protein)
Cloning Artifact Adds Two Residues To The Amino-Terminus
Which Were Not Observed In The Experimental Electron
Density (Gly-2, Ser-1)
Length = 597
Score = 30.0 bits (66), Expect = 0.39, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD 58
+S G Q+ + VER +I+ F PE +W +D
Sbjct: 191 LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVD 223
>pdb|1CY1|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptpt
pdb|1CY2|A Chain A, Complex Of E.Coli Dna Topoisomerase I With Tptptp3'
pdb|1CY6|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3' Thymidine
Monophosphate
pdb|1CY7|A Chain A, Complex Of E.coli Dna Topoisomerase I With 5'-thymidine
Monophosphate
pdb|1CY8|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'-Thymidine
Monophosphate And 3'-Thymidine Monophosphate
pdb|1CY0|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3'-5'-Adenosine
Diphosphate
pdb|1CY4|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptptp3'
Length = 599
Score = 30.0 bits (66), Expect = 0.39, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD 58
+S G Q+ + VER +I+ F PE +W +D
Sbjct: 193 LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVD 225
>pdb|1QP2|A Chain A, Solution Structure Of Photosystem I Accessory Protein E
From The Cyanobacterium Nostoc Sp. Strain Pcc 8009
pdb|1QP3|A Chain A, Solution Structure Of Photosystem I Accessory Protein E
From The Cyanobacterium Nostoc Sp. Strain Pcc 8009
Length = 70
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 40 VERHDKIRTFKPEPYWLLDL 59
V+R K+R +PE YW D+
Sbjct: 2 VQRGSKVRILRPESYWFQDV 21
>pdb|3U4F|A Chain A, Crystal Structure Of A Mandelate Racemase (Muconate
Lactonizing Enzyme Family Protein) From Roseovarius
Nubinhibens
pdb|3U4F|B Chain B, Crystal Structure Of A Mandelate Racemase (Muconate
Lactonizing Enzyme Family Protein) From Roseovarius
Nubinhibens
pdb|3U4F|C Chain C, Crystal Structure Of A Mandelate Racemase (Muconate
Lactonizing Enzyme Family Protein) From Roseovarius
Nubinhibens
pdb|3U4F|D Chain D, Crystal Structure Of A Mandelate Racemase (Muconate
Lactonizing Enzyme Family Protein) From Roseovarius
Nubinhibens
Length = 388
Score = 26.6 bits (57), Expect = 4.3, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 19 GDLDASLIS----YGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLT 60
GD A LI Y P Q LG ++ H +P PYW L+ T
Sbjct: 197 GDSAALLIDANSCYAPAQAIELGKLLQDHGFSHFEEPCPYWELEQT 242
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
0.320 0.142 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,434,721
Number of Sequences: 62578
Number of extensions: 83241
Number of successful extensions: 177
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 170
Number of HSP's gapped (non-prelim): 7
length of query: 69
length of database: 14,973,337
effective HSP length: 39
effective length of query: 30
effective length of database: 12,532,795
effective search space: 375983850
effective search space used: 375983850
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)