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= 029346
(194 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1D3Y|A Chain A, Structure Of The Dna Topoisomerase Vi A Subunit
pdb|1D3Y|B Chain B, Structure Of The Dna Topoisomerase Vi A Subunit
Length = 301
Score = 69.7 bits (169), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 43/126 (34%), Positives = 67/126 (53%), Gaps = 8/126 (6%)
Query: 71 DCNPYG-IHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDD 129
D +PYG ++I GS +L++P + +G+ P D+ Y++P L + D
Sbjct: 181 DGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPT---HPLKEQD 237
Query: 130 ISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFR 189
I ++K L+ D FVRS W+K L++M G +AE ++L Y KY+ N YLP K +
Sbjct: 238 IKRIKDGLKNDD---FVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIK 294
Query: 190 AED-WL 194
E WL
Sbjct: 295 DESTWL 300
>pdb|2ZBK|A Chain A, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|C Chain C, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|E Chain E, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|G Chain G, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
Length = 389
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/149 (28%), Positives = 77/149 (51%), Gaps = 12/149 (8%)
Query: 54 LLREIRCKLKKSVLGSFDCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLG-----LF 108
+R + +LK V D +PYG +I +V+ GS +++ + RLA P+ K+LG +F
Sbjct: 244 FVRRLNEELKLPVYILTDADPYGWYIFSVFRIGSISLSYESERLATPDAKFLGVSMGDIF 303
Query: 109 PSDLEKYNIPKLCRQ---ILSKDDISKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEK 165
+ +K + + R+ I +KD + +K E + F +W++E+ + K
Sbjct: 304 GNSRKKPYLSEAERKNYIIKAKD--ADIKRAEEIKNYEWF--KTKAWQEEINTFLQRKAK 359
Query: 166 AEIEALDMYEYKYLANKYLPSKFRAEDWL 194
EIEA+ K+LA +Y+P K +D++
Sbjct: 360 LEIEAMASKGLKFLAFQYIPEKITNKDYI 388
>pdb|2Q2E|A Chain A, Crystal Structure Of The Topoisomerase Vi Holoenzyme From
Methanosarcina Mazei
Length = 369
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 31/119 (26%), Positives = 58/119 (48%), Gaps = 8/119 (6%)
Query: 71 DCNPYGIHILTVYMFGSKNMAGRNLRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDI 130
D +P+ I +G+ A + +A P K+LGL PSD+ +Y +L L++ D+
Sbjct: 254 DGDPWSYRIYASVAYGAIKSAHLSEFMATPAAKFLGLQPSDIVEY---ELSTDKLTEQDV 310
Query: 131 SKLKTFLEKGDLVAFVRSNASWEKELQKMSKEGEKAEIEALDMYEYKYLANKYLPSKFR 189
S L++ L + W++++Q G+KAE +A ++ YLP++ +
Sbjct: 311 SALRSELSDPRF-----ESDYWKEQIQLQLDIGKKAEQQAFAGKGLDFVTEVYLPNRLK 364
>pdb|1UM9|A Chain A, Branched-chain 2-oxo Acid Dehydrogenase (e1) From Thermus
Thermophilus Hb8 In Apo-form
pdb|1UM9|C Chain C, Branched-chain 2-oxo Acid Dehydrogenase (e1) From Thermus
Thermophilus Hb8 In Apo-form
pdb|1UMB|A Chain A, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 In Holo-Form
pdb|1UMB|C Chain C, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 In Holo-Form
pdb|1UMC|A Chain A, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 With 4-Methylpentanoate
pdb|1UMC|C Chain C, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 With 4-Methylpentanoate
pdb|1UMD|A Chain A, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 With 4-Methyl-2-Oxopentanoate As An
Intermediate
pdb|1UMD|C Chain C, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 With 4-Methyl-2-Oxopentanoate As An
Intermediate
Length = 367
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%)
Query: 95 LRLAVPNIKWLGLFPSDLEKYNIPKLCRQILSKDDISKLKTFLEKGDLVAFVRSNASWE 153
+RL +WLG FP DLE + +L R +L+ + + T L + +F+ A E
Sbjct: 16 IRLIGEEGEWLGDFPLDLEGEKLRRLYRDMLAARMLDERYTILIRTGKTSFIAPAAGHE 74
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
0.323 0.138 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,399,832
Number of Sequences: 62578
Number of extensions: 210127
Number of successful extensions: 531
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 518
Number of HSP's gapped (non-prelim): 13
length of query: 194
length of database: 14,973,337
effective HSP length: 94
effective length of query: 100
effective length of database: 9,091,005
effective search space: 909100500
effective search space used: 909100500
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)