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= 037694
(355 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 122 bits (305), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 101/373 (27%), Positives = 176/373 (47%), Gaps = 37/373 (9%)
Query: 10 INFLKILNSPDPAISDLPLINRKSSNSRVSQGLLTDVSWIFLSHSFCTRSLTKSNAAKAF 69
+N ++ L +P + ++P+ R SN+ + + R+ N AK F
Sbjct: 26 LNLVEQLKKGEPLVMEIPM--RTLSNAIYDEKRKLLLL----GEKKLRRNFLDLNEAKRF 79
Query: 70 VRVWKVMETCFQILSQEKRVTQRELFYK----LLCDSPE---------YFTSQLQVNRTI 116
++ + + L ++ T R+L+Y+ LL S E + Q + + I
Sbjct: 80 MQTVLMASIIYDALVSDEYPTIRDLYYRGKHSLLLKSIEGNKIVSEENTWDEQKESDSVI 139
Query: 117 QDVIALLHCSRFSLGIVASSRGLVAGRLMLQEPNQEVIDCSACGSSGYSISGDLSLLEKL 176
D+ R + I++ +G V G L ++ N +VID S G Y+I L++ +
Sbjct: 140 VDIEVFTSLLREEMLILSKEKGKVVGNLRIRSGN-DVIDLSKTGHGAYAIEPTPDLIDFI 198
Query: 177 DLKTDARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLP 236
D+ DA +++VVEK A+FQ+L + Q SILIT+ G PD ATR + RLN LP
Sbjct: 199 DV--DAEFVLVVEKDAVFQQLHRAGFWKQYKSILITSAGQPDRATRRFVRRLNEELK-LP 255
Query: 237 ILALVDWNPAGLAILCTFKFGSIGMGMEAYRYAC-NVKWLGLRGDDV-----------QL 284
+ L D +P G I F+ GSI + E+ R A + K+LG+ D+ +
Sbjct: 256 VYILTDADPYGWYIFSVFRIGSISLSYESERLATPDAKFLGVSMGDIFGNSRKKPYLSEA 315
Query: 285 IPEQSLLPLKPRDLQIARSLMSSEILQ-ENYKEELSLMVHNGQRAEVEALYFHGYDYLG- 342
+ ++ K D++ A + + E + + ++EE++ + + E+EA+ G +L
Sbjct: 316 ERKNYIIKAKDADIKRAEEIKNYEWFKTKAWQEEINTFLQRKAKLEIEAMASKGLKFLAF 375
Query: 343 KYIAKKIVQADYI 355
+YI +KI DYI
Sbjct: 376 QYIPEKITNKDYI 388
>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 = 107 bits (266), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 90/296 (30%), Positives = 147/296 (49%), Gaps = 15/296 (5%)
Query: 64 NAAKAFVRVWKVMETCFQILSQEKRVTQRELFYKLLCDSPEYFTSQLQVNRTIQDVIALL 123
N AK F + K++E Q+L + T RE +Y F Q N I+D+ A L
Sbjct: 3 NQAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAAL 62
Query: 124 HCSRFSLGIVASSRGL-VAGRLMLQEPNQE---VIDCSACGSSGYSISGDLSLLEKLDLK 179
R LG + G V G L + E E V+DC+ G+ Y+I D++ KL+L+
Sbjct: 63 GVLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYNIPNDVT---KLNLE 119
Query: 180 TDARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNRAFPDLPILA 239
TDA +I+ +E +F RL + +++ IL++ KG P ATR + RL+ DLP+L
Sbjct: 120 TDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEH-DLPVLV 178
Query: 240 LVDWNPAG-LAILCTFKFGSIGMGMEAYRYAC-NVKWLGLRGDDVQLIPEQSLLPLKPRD 297
D +P G L I T K GS A + + + +G+ D+ + + PLK +D
Sbjct: 179 FTDGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDI-IDYDLPTHPLKEQD 237
Query: 298 LQ-IARSLMSSEILQE--NYKEELSLMVHNGQRAEVEALYFHGYDY-LGKYIAKKI 349
++ I L + + ++ +++ L M+ G RAE ++L +G Y + Y+ +KI
Sbjct: 238 IKRIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKI 293
>pdb|2Q2E|A Chain A, Crystal Structure Of The Topoisomerase Vi Holoenzyme From
Methanosarcina Mazei
Length = 369
Score = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 73/293 (24%), Positives = 134/293 (45%), Gaps = 22/293 (7%)
Query: 65 AAKAFVRVWKVMETCF-------QILSQEKRVTQRELFYKLLCDSPEY--FTSQLQVNRT 115
+AK +++++T + + L++ + T REL+Y + + +Y F Q + +R
Sbjct: 68 SAKTVKGAFQLLKTTYATDFLINEHLARNRGSTLRELYY--ISEGWDYAKFKEQGESDRL 125
Query: 116 IQDVIALLHCSRFSLGIVASSRGLVA-GRLMLQEP---NQEVIDCSA-CGSSGYSISGDL 170
I+D+ L R + G G + + E + I C G GY I ++
Sbjct: 126 IEDLEILTSLQREYFHMRPEEDGATMFGPIEITEQTKRGERNIHCQKDVGEGGYQIPFNV 185
Query: 171 SLLEKLDLKTDARYIIVVEKHAIFQRLTEDFVFNQIPSILITAKGYPDIATRFLLHRLNR 230
+E K DA II +E ++ RL E+ +IL+ KG P +TR ++ R+N
Sbjct: 186 ENIEFQ--KHDASMIIAIETGGMYARLMENGFDEAYNAILVHLKGQPARSTRRIIKRMNE 243
Query: 231 AFPDLPILALVDWNPAGLAILCTFKFGSIGMG-MEAYRYACNVKWLGLRGDDVQLIPEQS 289
+P+ D +P I + +G+I + + K+LGL+ D+ + E S
Sbjct: 244 EL-GIPVAVFTDGDPWSYRIYASVAYGAIKSAHLSEFMATPAAKFLGLQPSDI-VEYELS 301
Query: 290 LLPLKPRDLQIARSLMSSEILQENY-KEELSLMVHNGQRAEVEALYFHGYDYL 341
L +D+ RS +S + +Y KE++ L + G++AE +A G D++
Sbjct: 302 TDKLTEQDVSALRSELSDPRFESDYWKEQIQLQLDIGKKAEQQAFAGKGLDFV 354
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
0.324 0.138 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,768,377
Number of Sequences: 62578
Number of extensions: 370792
Number of successful extensions: 724
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 716
Number of HSP's gapped (non-prelim): 3
length of query: 355
length of database: 14,973,337
effective HSP length: 100
effective length of query: 255
effective length of database: 8,715,537
effective search space: 2222461935
effective search space used: 2222461935
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)