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= 004612
(742 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z59|A Chain A, Topoisomerase Vi-B, Adp-Bound Monomer Form
pdb|1Z5C|A Chain A, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
pdb|1Z5C|B Chain B, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
Length = 469
Score = 39.3 bits (90), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 159 ELLDNSLDEVCNGATYSNIDMLINRKDGSRMLL---IEDNGGGMNPDKMRHCMS-LGYSA 214
EL++NSLD NI + I+ D +R + + DNG G+ P ++ + + YS+
Sbjct: 37 ELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSS 96
Query: 215 KSKAANTIGQYGNGFKTSTM 234
K T G YG G K + +
Sbjct: 97 KYVNRQTRGXYGLGVKAAVL 116
>pdb|1MX0|A Chain A, Structure Of Topoisomerase Subunit
pdb|1MX0|B Chain B, Structure Of Topoisomerase Subunit
pdb|1MX0|C Chain C, Structure Of Topoisomerase Subunit
pdb|1MX0|D Chain D, Structure Of Topoisomerase Subunit
pdb|1MX0|E Chain E, Structure Of Topoisomerase Subunit
pdb|1MX0|F Chain F, Structure Of Topoisomerase Subunit
Length = 472
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 159 ELLDNSLDEVCNGATYSNIDMLINRKDGSRMLL---IEDNGGGMNPDKMRHCMS-LGYSA 214
EL++NSLD NI + I+ D +R + + DNG G+ P ++ + + YS+
Sbjct: 40 ELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSS 99
Query: 215 KSKAANTIGQYGNGFKTSTM 234
K T G YG G K + +
Sbjct: 100 KYVNRQTRGXYGLGVKAAVL 119
>pdb|1Z5A|A Chain A, Topoisomerase Vi-B, Adp-Bound Dimer Form
pdb|1Z5A|B Chain B, Topoisomerase Vi-B, Adp-Bound Dimer Form
pdb|1Z5B|A Chain A, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
pdb|1Z5B|B Chain B, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
pdb|2HKJ|A Chain A, Topoisomerase Vi-B Bound To Radicicol
Length = 469
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 159 ELLDNSLDEVCNGATYSNIDMLINRKDGSRMLL---IEDNGGGMNPDKMRHCMS-LGYSA 214
EL++NSLD NI + I+ D +R + + DNG G+ P ++ + + YS+
Sbjct: 37 ELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSS 96
Query: 215 KSKAANTIGQYGNGFKTSTM 234
K T G YG G K + +
Sbjct: 97 KYVNRQTRGMYGLGVKAAVL 116
>pdb|1MU5|A Chain A, Structure Of Topoisomerase Subunit
Length = 471
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 159 ELLDNSLDEVCNGATYSNIDMLINRKDGSRMLL---IEDNGGGMNPDKMRHCMS-LGYSA 214
EL++NSLD NI + I+ D +R + + DNG G+ P ++ + + YS+
Sbjct: 39 ELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSS 98
Query: 215 KSKAANTIGQYGNGFKTSTM 234
K T G YG G K + +
Sbjct: 99 KYVNRQTRGMYGLGVKAAVL 118
>pdb|2ZBK|B Chain B, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|D Chain D, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|F Chain F, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|H Chain H, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
Length = 530
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 159 ELLDNSLDEVCNGATYSNIDMLINRKDGSRMLL---IEDNGGGMNPDKMRHCMS-LGYSA 214
EL++NSLD NI + I+ D +R + + DNG G+ P ++ + + YS+
Sbjct: 38 ELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSS 97
Query: 215 KSKAANTIGQYGNGFKTSTM 234
K T G YG G K + +
Sbjct: 98 KYVNRQTRGMYGLGVKAAVL 117
>pdb|1KIJ|A Chain A, Crystal Structure Of The 43k Atpase Domain Of Thermus
Thermophilus Gyrase B In Complex With Novobiocin
pdb|1KIJ|B Chain B, Crystal Structure Of The 43k Atpase Domain Of Thermus
Thermophilus Gyrase B In Complex With Novobiocin
Length = 390
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 132 GMDHVRVHPKFLHSNATSHKWALGAFAELLDNSLDEVCNGATYSNIDMLINRKDGSRMLL 191
G++ VR P ++ T + F E+LDN++DE G Y+ ++ +DGS L
Sbjct: 13 GLEGVRHRPA-MYIGGTGVEGYHHLFKEILDNAVDEALAG--YATEILVRLNEDGS--LT 67
Query: 192 IEDNGGGMNPDKM 204
+EDNG G+ D M
Sbjct: 68 VEDNGRGIPVDLM 80
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 0.133 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,248,086
Number of Sequences: 62578
Number of extensions: 998516
Number of successful extensions: 1897
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1893
Number of HSP's gapped (non-prelim): 10
length of query: 742
length of database: 14,973,337
effective HSP length: 106
effective length of query: 636
effective length of database: 8,340,069
effective search space: 5304283884
effective search space used: 5304283884
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)