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= psy11240
(363 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FM9|A Chain A, Human Topoisomerase Ii Alpha Bound To Dna
Length = 763
Score = 292 bits (748), Expect = 2e-79, Method: Compositional matrix adjust.
Identities = 138/180 (76%), Positives = 157/180 (87%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRR 70
GLGTSTSKEAKEYF++M+RHRI FKYSG DDA I +AFSKK +D+RK WLT +ME+ R+
Sbjct: 185 GLGTSTSKEAKEYFADMKRHRIQFKYSGPEDDAAISLAFSKKQIDDRKEWLTNFMEDRRQ 244
Query: 71 RKEMGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCL 130
RK +G+ EDYLY +TT +TY +F+NKELILFSN DNERSIPS+ DGLKPG RKVLFTC
Sbjct: 245 RKLLGLPEDYLYGQTTTYLTYNDFINKELILFSNSDNERSIPSMVDGLKPGQRKVLFTCF 304
Query: 131 KRNDRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGTFL 190
KRND+REVKVAQLAGSVAE S+YHHGE SLM TIINLAQNFVGSNN+NLLQPIGQFGT L
Sbjct: 305 KRNDKREVKVAQLAGSVAEMSSYHHGEMSLMMTIINLAQNFVGSNNLNLLQPIGQFGTRL 364
Score = 179 bits (455), Expect = 2e-45, Method: Compositional matrix adjust.
Identities = 87/141 (61%), Positives = 109/141 (77%)
Query: 219 DYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278
DY+EYHTDTTVKFVV M+ +KL +AE GLHKVFKLQT+L +SM FD G L K+DT
Sbjct: 526 DYREYHTDTTVKFVVKMTEEKLAEAERVGLHKVFKLQTSLTCNSMVLFDHVGCLKKYDTV 585
Query: 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIA 338
IL++F+ +RL+YY RK++L G+LGAE+ KL NQARFI+EK DG + IEN+ KKE+I
Sbjct: 586 LDILRDFFELRLKYYGLRKEWLLGMLGAESAKLNNQARFILEKIDGKIIIENKPKKELIK 645
Query: 339 ELIKRKYDSDPVKSWKMKQNK 359
LI+R YDSDPVK+WK Q K
Sbjct: 646 VLIQRGYDSDPVKAWKEAQQK 666
>pdb|3QX3|A Chain A, Human Topoisomerase Iibeta In Complex With Dna And
Etoposide
pdb|3QX3|B Chain B, Human Topoisomerase Iibeta In Complex With Dna And
Etoposide
Length = 803
Score = 289 bits (739), Expect = 2e-78, Method: Compositional matrix adjust.
Identities = 135/180 (75%), Positives = 155/180 (86%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRR 70
GLGTST+KEAKEYF++MERHRILF+Y+G DDA I +AFSKK +D+RK WLT +ME+ R+
Sbjct: 213 GLGTSTAKEAKEYFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQ 272
Query: 71 RKEMGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCL 130
R+ G+ E +LY TK +TY +F+NKELILFSN DNERSIPSL DG KPG RKVLFTC
Sbjct: 273 RRLHGLPEQFLYGTATKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCF 332
Query: 131 KRNDRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGTFL 190
KRND+REVKVAQLAGSVAE SAYHHGEQ+LM TI+NLAQNFVGSNNINLLQPIGQFGT L
Sbjct: 333 KRNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRL 392
Score = 180 bits (456), Expect = 1e-45, Method: Compositional matrix adjust.
Identities = 87/142 (61%), Positives = 108/142 (76%)
Query: 218 NDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDT 277
+DYKEYHTDTTVKFVV M+ +KL +AE GLHKVFKLQTTL +SM FD G L K++T
Sbjct: 553 SDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYET 612
Query: 278 TNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMI 337
ILKEF+ +RL YY RK++L G+LGAE+ KL NQARFI+EK G + IENR KK++I
Sbjct: 613 VQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLI 672
Query: 338 AELIKRKYDSDPVKSWKMKQNK 359
L++R Y+SDPVK+WK Q K
Sbjct: 673 QMLVQRGYESDPVKAWKEAQEK 694
>pdb|2RGR|A Chain A, Topoisomerase Iia Bound To G-segment Dna
Length = 759
Score = 189 bits (479), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 100/178 (56%), Positives = 121/178 (67%), Gaps = 12/178 (6%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRR 70
GLGTS ++E +EYFSN++RH +F ND +I +AFSKK D+RK WL R
Sbjct: 186 GLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWL--------R 237
Query: 71 RKEMGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCL 130
+ E G D T K I ++F+NKELILFS DN RSIP++ DG KPG RKVL+ C
Sbjct: 238 QYEPGTVLD----PTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCF 293
Query: 131 KRNDRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGT 188
K+N + E+KVAQLA V+E +AYHHGEQSL TII LAQNFVGSNNI LL P G FGT
Sbjct: 294 KKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGT 351
Score = 95.1 bits (235), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 47/122 (38%), Positives = 78/122 (63%), Gaps = 1/122 (0%)
Query: 219 DYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278
D +E H D +KF++T+SP+++ K G ++ FKL + +++ +M AFD +G + K+++
Sbjct: 514 DMEEQHDDN-IKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSV 572
Query: 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIA 338
N+IL EFY VRLEYY KRKD++ L E K + Q +FI + +L + N+ + +I
Sbjct: 573 NEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQ 632
Query: 339 EL 340
EL
Sbjct: 633 EL 634
>pdb|3L4J|A Chain A, Topoisomerase Ii-Dna Cleavage Complex, Apo
pdb|3L4K|A Chain A, Topoisomerase Ii-Dna Cleavage Complex, Metal-Bound
Length = 722
Score = 189 bits (479), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 100/178 (56%), Positives = 121/178 (67%), Gaps = 12/178 (6%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRR 70
GLGTS ++E +EYFSN++RH +F ND +I +AFSKK D+RK WL R
Sbjct: 184 GLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWL--------R 235
Query: 71 RKEMGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCL 130
+ E G D T K I ++F+NKELILFS DN RSIP++ DG KPG RKVL+ C
Sbjct: 236 QYEPGTVLD----PTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCF 291
Query: 131 KRNDRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGT 188
K+N + E+KVAQLA V+E +AYHHGEQSL TII LAQNFVGSNNI LL P G FGT
Sbjct: 292 KKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGT 349
Score = 95.1 bits (235), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 47/122 (38%), Positives = 78/122 (63%), Gaps = 1/122 (0%)
Query: 219 DYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278
D +E H D +KF++T+SP+++ K G ++ FKL + +++ +M AFD +G + K+++
Sbjct: 513 DMEEQHDDN-IKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSV 571
Query: 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIA 338
N+IL EFY VRLEYY KRKD++ L E K + Q +FI + +L + N+ + +I
Sbjct: 572 NEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQ 631
Query: 339 EL 340
EL
Sbjct: 632 EL 633
>pdb|1BGW|A Chain A, Topoisomerase Residues 410-1202
pdb|1BJT|A Chain A, Topoisomerase Ii Residues 409-1201
Length = 793
Score = 188 bits (478), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 100/178 (56%), Positives = 121/178 (67%), Gaps = 12/178 (6%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRR 70
GLGTS ++E +EYFSN++RH +F ND +I +AFSKK D+RK WL R
Sbjct: 196 GLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWL--------R 247
Query: 71 RKEMGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCL 130
+ E G D T K I ++F+NKELILFS DN RSIP++ DG KPG RKVL+ C
Sbjct: 248 QYEPGTVLD----PTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCF 303
Query: 131 KRNDRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGT 188
K+N + E+KVAQLA V+E +AYHHGEQSL TII LAQNFVGSNNI LL P G FGT
Sbjct: 304 KKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGT 361
Score = 95.1 bits (235), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 47/122 (38%), Positives = 78/122 (63%), Gaps = 1/122 (0%)
Query: 219 DYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278
D +E H D +KF++T+SP+++ K G ++ FKL + +++ +M AFD +G + K+++
Sbjct: 524 DMEEQHDDN-IKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSV 582
Query: 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIA 338
N+IL EFY VRLEYY KRKD++ L E K + Q +FI + +L + N+ + +I
Sbjct: 583 NEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQ 642
Query: 339 EL 340
EL
Sbjct: 643 EL 644
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 182 bits (461), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 97/175 (55%), Positives = 118/175 (67%), Gaps = 12/175 (6%)
Query: 14 TSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRRRKE 73
TS ++E +EYFSN++RH +F ND +I +AFSKK D+RK WL R+ E
Sbjct: 564 TSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWL--------RQYE 615
Query: 74 MGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCLKRN 133
G D T K I ++F+NKELILFS DN RSIP++ DG KPG RKVL+ C K+N
Sbjct: 616 PGTVLD----PTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKN 671
Query: 134 DRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGT 188
+ E+KVAQLA V+E +AYHHGEQSL TII LAQNFVGSNNI LL P G FGT
Sbjct: 672 LKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGT 726
Score = 95.1 bits (235), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 47/122 (38%), Positives = 78/122 (63%), Gaps = 1/122 (0%)
Query: 219 DYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278
D +E H D +KF++T+SP+++ K G ++ FKL + +++ +M AFD +G + K+++
Sbjct: 890 DMEEQHDDN-IKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSV 948
Query: 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIA 338
N+IL EFY VRLEYY KRKD++ L E K + Q +FI + +L + N+ + +I
Sbjct: 949 NEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQ 1008
Query: 339 EL 340
EL
Sbjct: 1009 EL 1010
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 182 bits (461), Expect = 4e-46, Method: Compositional matrix adjust.
Identities = 97/175 (55%), Positives = 118/175 (67%), Gaps = 12/175 (6%)
Query: 14 TSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRRRKE 73
TS ++E +EYFSN++RH +F ND +I +AFSKK D+RK WL R+ E
Sbjct: 568 TSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWL--------RQYE 619
Query: 74 MGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCLKRN 133
G D T K I ++F+NKELILFS DN RSIP++ DG KPG RKVL+ C K+N
Sbjct: 620 PGTVLD----PTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKN 675
Query: 134 DRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGT 188
+ E+KVAQLA V+E +AYHHGEQSL TII LAQNFVGSNNI LL P G FGT
Sbjct: 676 LKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGT 730
Score = 95.1 bits (235), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 47/122 (38%), Positives = 78/122 (63%), Gaps = 1/122 (0%)
Query: 219 DYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278
D +E H D +KF++T+SP+++ K G ++ FKL + +++ +M AFD +G + K+++
Sbjct: 894 DMEEQHDDN-IKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSV 952
Query: 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIA 338
N+IL EFY VRLEYY KRKD++ L E K + Q +FI + +L + N+ + +I
Sbjct: 953 NEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQ 1012
Query: 339 EL 340
EL
Sbjct: 1013 EL 1014
>pdb|3IFZ|A Chain A, Crystal Structure Of The First Part Of The Mycobacterium
Tuberculosis Dna Gyrase Reaction Core: The Breakage And
Reunion Domain At 2.7 A Resolution
pdb|3IFZ|B Chain B, Crystal Structure Of The First Part Of The Mycobacterium
Tuberculosis Dna Gyrase Reaction Core: The Breakage And
Reunion Domain At 2.7 A Resolution
Length = 508
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 4/82 (4%)
Query: 109 RSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSA-YH-HGEQSLMSTIIN 166
R++P + DGLKP R+VL+ R + A+ A SVAE YH HG+ S+ +++
Sbjct: 39 RALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVR 98
Query: 167 LAQNFVGSNNINLLQPIGQFGT 188
+AQ + S L+ G FG+
Sbjct: 99 MAQPW--SLRYPLVDGQGNFGS 118
>pdb|3ILW|A Chain A, Structure Of Dna Gyrase Subunit A N-Terminal Domain
pdb|3ILW|B Chain B, Structure Of Dna Gyrase Subunit A N-Terminal Domain
Length = 470
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 4/82 (4%)
Query: 109 RSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSA-YH-HGEQSLMSTIIN 166
R++P + DGLKP R+VL+ R + A+ A SVAE YH HG+ S+ +++
Sbjct: 9 RALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVR 68
Query: 167 LAQNFVGSNNINLLQPIGQFGT 188
+AQ + S L+ G FG+
Sbjct: 69 MAQPW--SLRYPLVDGQGNFGS 88
>pdb|2XCO|A Chain A, The 3.1a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase
pdb|2XCQ|A Chain A, The 2.98a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase
Length = 726
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 109 RSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVAEHSAYH-HGEQSLMSTI 164
R++P + DGLKP R++L+ ++ D+ K A++ G V YH HG+ S+ +
Sbjct: 268 RALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVM--GKYHPHGDSSIYEAM 325
Query: 165 INLAQNFVGSNNINLLQPIGQFGTF 189
+ +AQ+F S L+ G FG+
Sbjct: 326 VRMAQDF--SYRYPLVDGQGNFGSM 348
>pdb|2XCR|B Chain B, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
pdb|2XCR|D Chain D, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
pdb|2XCR|S Chain S, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
pdb|2XCR|U Chain U, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
Length = 726
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 109 RSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVAEHSAYH-HGEQSLMSTI 164
R++P + DGLKP R++L+ ++ D+ K A++ G V YH HG+ S+ +
Sbjct: 268 RALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVM--GKYHPHGDSSIYEAM 325
Query: 165 INLAQNFVGSNNINLLQPIGQFGTF 189
+ +AQ+F S L+ G FG+
Sbjct: 326 VRMAQDF--SYRYPLVDGQGNFGSM 348
>pdb|2XCS|B Chain B, The 2.1a Crystal Structure Of S. Aureus Gyrase Complex
With Gsk299423 And Dna
pdb|2XCS|D Chain D, The 2.1a Crystal Structure Of S. Aureus Gyrase Complex
With Gsk299423 And Dna
pdb|2XCT|B Chain B, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
pdb|2XCT|D Chain D, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
pdb|2XCT|S Chain S, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
pdb|2XCT|U Chain U, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
Length = 692
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 109 RSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVAEHSAYH-HGEQSLMSTI 164
R++P + DGLKP R++L+ ++ D+ K A++ G V YH HG+ S+ +
Sbjct: 234 RALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVM--GKYHPHGDSSIYEAM 291
Query: 165 INLAQNFVGSNNINLLQPIGQFGTF 189
+ +AQ+F S L+ G FG+
Sbjct: 292 VRMAQDF--SYRYPLVDGQGNFGSM 314
>pdb|3LPX|A Chain A, Crystal Structure Of Gyra
pdb|3LPX|B Chain B, Crystal Structure Of Gyra
Length = 500
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 31/85 (36%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 109 RSIPSLCDGLKPGSRKVLFTC-LKRNDRREV--KVAQLAGSVAEHSAYH-HGEQSLMSTI 164
R++P + DGLKP R+VLF + ND + K A++ G V YH HG+ ++ TI
Sbjct: 2 RALPDVRDGLKPVHRRVLFAMDVLGNDWNKAYKKSARVVGDVI--GKYHPHGDTAVYDTI 59
Query: 165 INLAQNFVGSNNINLLQPIGQFGTF 189
+ +AQ F S L+ G FG+
Sbjct: 60 VRMAQPF--SLRYMLVDGQGNFGSV 82
>pdb|2Y3P|A Chain A, Crystal Structure Of N-Terminal Domain Of Gyra With The
Antibiotic Simocyclinone D8
pdb|2Y3P|B Chain B, Crystal Structure Of N-Terminal Domain Of Gyra With The
Antibiotic Simocyclinone D8
Length = 522
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 109 RSIPSLCDGLKPGSRKVLFTC-LKRNDRREV--KVAQLAGSVAEHSAYH-HGEQSLMSTI 164
R++P + DGLKP R+VL+ + ND + K A++ G V YH HG+ ++ TI
Sbjct: 31 RALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVI--GKYHPHGDSAVYDTI 88
Query: 165 INLAQNFVGSNNINLLQPIGQFGTF 189
+ +AQ F S L+ G FG+
Sbjct: 89 VRMAQPF--SLRYMLVDGQGNFGSI 111
>pdb|1AB4|A Chain A, 59kda Fragment Of Gyrase A From E. Coli
Length = 493
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 109 RSIPSLCDGLKPGSRKVLFTC-LKRNDRREV--KVAQLAGSVAEHSAYH-HGEQSLMSTI 164
R++P + DGLKP R+VL+ + ND + K A++ G V YH HG+ ++ TI
Sbjct: 3 RALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVI--GKYHPHGDSAVYDTI 60
Query: 165 INLAQNFVGSNNINLLQPIGQFGTF 189
+ +AQ F S L+ G FG+
Sbjct: 61 VRMAQPF--SLRYMLVDGQGNFGSI 83
>pdb|2XKK|A Chain A, Crystal Structure Of Moxifloxacin, Dna, And A. Baumannii
Topo Iv (Pare-Parc Fusion Truncate)
pdb|2XKK|C Chain C, Crystal Structure Of Moxifloxacin, Dna, And A. Baumannii
Topo Iv (Pare-Parc Fusion Truncate)
Length = 767
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 46/190 (24%), Positives = 83/190 (43%), Gaps = 21/190 (11%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAF-----SKKLVDERKTWLTTWM 65
GLG + + +E + R++ D DDAH+ +KK +RK WL
Sbjct: 196 GLGEMNAIQLRETTMDPNTRRLV---QLDLDDAHLTAGLLDKLLAKKRAADRKQWLEQKG 252
Query: 66 EECRRRKEMGIGEDYLYTKTTKAITYTEFVNKELI---LFSNMDNERSIPSLCDGLKPGS 122
E + L T+ + EF + + ++ MD R++P + DGLKP
Sbjct: 253 NLADITVEDKLTMTSLAHHATENRSVAEFTEQAYLNYAMYVIMD--RALPHISDGLKPVQ 310
Query: 123 RKVLFTCLK---RNDRREVKVAQLAGSVAEHSAYH-HGEQSLMSTIINLAQNFVGSNNIN 178
R++++ + ++ + K A+ G V YH HG+ + ++ +AQ F S
Sbjct: 311 RRIVYAMSELGLKSSGKPKKSARTVGDVL--GKYHPHGDSACYEAMVLMAQPF--SYRYP 366
Query: 179 LLQPIGQFGT 188
L++ G +G+
Sbjct: 367 LIEGQGNWGS 376
>pdb|2XKJ|E Chain E, Crystal Structure Of Catalytic Core Of A. Baumannii Topo
Iv (Pare-Parc Fusion Truncate)
Length = 767
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 46/190 (24%), Positives = 83/190 (43%), Gaps = 21/190 (11%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAF-----SKKLVDERKTWLTTWM 65
GLG + + +E + R++ D DDAH+ +KK +RK WL
Sbjct: 196 GLGEMNAIQLRETTMDPNTRRLV---QLDLDDAHLTAGLLDKLLAKKRAADRKQWLEQKG 252
Query: 66 EECRRRKEMGIGEDYLYTKTTKAITYTEFVNKELI---LFSNMDNERSIPSLCDGLKPGS 122
E + L T+ + EF + + ++ MD R++P + DGLKP
Sbjct: 253 NLADITVEDKLTMTSLAHHATENRSVAEFTEQAYLNYAMYVIMD--RALPHISDGLKPVQ 310
Query: 123 RKVLFTCLK---RNDRREVKVAQLAGSVAEHSAYH-HGEQSLMSTIINLAQNFVGSNNIN 178
R++++ + ++ + K A+ G V YH HG+ + ++ +AQ F S
Sbjct: 311 RRIVYAMSELGLKSSGKPKKSARTVGDVL--GKYHPHGDSACYEAMVLMAQPF--SYRYP 366
Query: 179 LLQPIGQFGT 188
L++ G +G+
Sbjct: 367 LIEGQGNWGS 376
>pdb|3NUH|A Chain A, A Domain Insertion In E. Coli Gyrb Adopts A Novel Fold
That Plays A Critical Role In Gyrase Function
Length = 525
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 45/85 (52%), Gaps = 8/85 (9%)
Query: 109 RSIPSLCDGLKPGSRKVLFTC-LKRNDRREV--KVAQLAGSVAEHSAYH-HGEQSLMSTI 164
R++P + DGLKP R+VL+ + ND + K A++ G V YH HG+ ++ TI
Sbjct: 32 RALPDVRDGLKPVHRRVLYAXNVLGNDWNKAYKKSARVVGDVI--GKYHPHGDSAVYDTI 89
Query: 165 INLAQNFVGSNNINLLQPIGQFGTF 189
+ AQ F S L+ G FG+
Sbjct: 90 VRXAQPF--SLRYXLVDGQGNFGSI 112
>pdb|2INR|A Chain A, Crystal Structure Of A 59 Kda Fragment Of Topoisomerase Iv
Subunit A (Grla) From Staphylococcus Aureus
Length = 514
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 6/68 (8%)
Query: 108 ERSIPSLCDGLKPGSRKVLFTCLKR---NDRREVKVAQLAGSVAEHSAYH-HGEQSLMST 163
ER++P + DGLKP R++L+ +D+ K A+ G V YH HG+ S+
Sbjct: 51 ERALPDVRDGLKPVQRRILYAMYSSGNTHDKNFRKSAKTVGDVI--GQYHPHGDSSVYEA 108
Query: 164 IINLAQNF 171
++ L+Q++
Sbjct: 109 MVRLSQDW 116
>pdb|2JKB|A Chain A, Crystal Structure Of Streptococcus Pneumoniae Nanb In
Complex With 2,7-Anhydro-Neu5ac
Length = 686
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 4 IHDVMIAGLGTSTSKEAKEYFSNMERHRIL-FKYSGDND 41
+ DVM AG+G + + +A F + H L K +GDND
Sbjct: 331 LADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDND 369
>pdb|2VW0|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae
pdb|2VW1|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae
pdb|2VW2|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae
pdb|4FOQ|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With 2-Aminoethanesulfonic Acid
pdb|4FOV|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With 3-Cyclohexyl-1-Propylsulfonic
Acid
pdb|4FOW|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With 3-Ammoniopropane-1-Sulfonate
pdb|4FOY|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-(Benzylammonio)ethanesulfonate
pdb|4FP2|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2[(Cyclohexylmethyl)ammonio]sulfonate
pdb|4FP3|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(Furan-2-Ylmethyl)ammonio]sulfonate
pdb|4FPC|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(4-Chlorobenzyl)ammonio]ethanesulfonate
pdb|4FPE|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(4-Methoxybenzyl)ammonio]ethanesulfonate
pdb|4FPF|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(3-Chlorobenzyl)ammonio]ethanesulfonate
pdb|4FPG|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(3-Hydroxybenzyl)ammonio]ethanesulfonate
pdb|4FPH|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(3-Fluorobenzyl)ammonio]ethanesulfonate
pdb|4FPJ|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(3-Methoxybenzyl)ammonio]ethanesulfonate
pdb|4FPK|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(3-Methylbenzyl)ammonio]ethanesulfonate
pdb|4FPL|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(3,4-Dichlorobenzyl)ammonio]ethanesulfonate
pdb|4FPO|B Chain B, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(3-Chloro-4-Methoxybenzyl)ammonio]ethanesulfonate
pdb|4FPY|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(3-Bromobenzyl)ammonio]ethanesulfonate
pdb|4FQ4|A Chain A, Crystal Structure Of The Nanb Sialidase From Streptococcus
Pneumoniae In Complex With
2-[(4-Fluoro-3-Methylbenzyl)ammonio]ethanesulfonate
Length = 697
Score = 28.5 bits (62), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 4 IHDVMIAGLGTSTSKEAKEYFSNMERHRIL-FKYSGDND 41
+ DVM AG+G + + +A F + H L K +GDND
Sbjct: 342 LADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDND 380
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
0.319 0.133 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,531,252
Number of Sequences: 62578
Number of extensions: 421494
Number of successful extensions: 1005
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 967
Number of HSP's gapped (non-prelim): 41
length of query: 363
length of database: 14,973,337
effective HSP length: 100
effective length of query: 263
effective length of database: 8,715,537
effective search space: 2292186231
effective search space used: 2292186231
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)