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= psy13360
(1161 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1EI1|A Chain A, Dimerization Of E. Coli Dna Gyrase B Provides A Structural
Mechanism For Activating The Atpase Catalytic Center
pdb|1EI1|B Chain B, Dimerization Of E. Coli Dna Gyrase B Provides A Structural
Mechanism For Activating The Atpase Catalytic Center
Length = 391
Score = 369 bits (948), Expect = e-102, Method: Compositional matrix adjust.
Identities = 184/384 (47%), Positives = 249/384 (64%), Gaps = 22/384 (5%)
Query: 352 IQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYXXXXX 411
I++L+GL+AVRKRP MYIGDT DGTGLHH VFE++DNAIDE+LAG+C +I VTI+
Sbjct: 9 IKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSV 68
Query: 412 XXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNG 471
GRG SAAE++MT LHAGGKF+ NSYK+SGGLHG+G+S VN
Sbjct: 69 SVQDDGRGIPTGIHPEEGV----SAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNA 124
Query: 472 LSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDE 531
LS+ L+L I R KIH + +GV Q +P+ + G+T K GT + FW
Sbjct: 125 LSQKLELVIQREGKIHRQIYEHGVPQ------------APLAVTGETEKTGTMVRFWPSL 172
Query: 532 KIFSNI-EFHYEILKKRIRELSFLNNGVCITLIDERXXXXXXXXXXXXTSGFVSYINKSK 590
+ F+N+ EF YEIL KR+RELSFL++GV I L D+R FV Y+NK+K
Sbjct: 173 ETFTNVTEFEYEILAKRLRELSFLDSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNK 232
Query: 591 LVVHPTIFQAXXXXXXXXXXXXXXDVSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSG 650
+HP IF +V++QWN+ + ENI CFTNNI Q DGGTHL G R+
Sbjct: 233 TPIHPNIF-----YFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAA 287
Query: 651 ITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLVSSEVRKP 710
+TR +N Y+++ + KK+K+ G+D REGL V+S+K+PDPKF+SQTK+KLVSSEV+
Sbjct: 288 MTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSA 347
Query: 711 VEEIIIKTLFDFLQENPGESKLIC 734
VE+ + + L ++L ENP ++K++
Sbjct: 348 VEQQMNELLAEYLLENPTDAKIVV 371
>pdb|3NUH|B Chain B, A Domain Insertion In E. Coli Gyrb Adopts A Novel Fold That
Plays A Critical Role In Gyrase Function
Length = 420
Score = 305 bits (782), Expect = 7e-83, Method: Compositional matrix adjust.
Identities = 166/417 (39%), Positives = 238/417 (57%), Gaps = 13/417 (3%)
Query: 754 TRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVL 813
TR+K +D L KLADCQE++P L ELY+VEGDSAGGS KQGR+R+ QA+LPL+GK+L
Sbjct: 8 TRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKIL 67
Query: 814 NIEKARFEKIILSEQXXXXXXXXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLL 873
N+EKARF+K + S++ +DE+N +KLRYH III TDAD+DG+HIR LLL
Sbjct: 68 NVEKARFDKXLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIXTDADVDGSHIRTLLL 127
Query: 874 TFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISIEN 933
TFFYR+ P+++E G++YIAQPPLYK+K G E Y++DD ++Y + IA L + +
Sbjct: 128 TFFYRQXPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAXDQYQISIALDGATLHTNAS 187
Query: 934 GDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVIL---NLDTRENAEQFAK 990
+ KL+ +YN T + ++R ++ + L ++ L +L + ++
Sbjct: 188 APALAGEALEKLVSEYNATQKXINRXERRYPKAXLKELIYQPTLTEADLSDEQTVTRWVN 247
Query: 991 KIIKKLNDSNIE-IIVEFD-----QXXXXXXXXXXXXXXXXXXXXXDINFINNKDYKKLV 1044
++ +LND +FD + D FI +Y++
Sbjct: 248 ALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRR-- 305
Query: 1045 SIISTFXXXXXXXXXXXXXXXEKIKKYTANNFYKIINYLRNEAENMVIKQRYKGLGEMNP 1104
I T ++ +F + +++L E+ + QRYKGLGE NP
Sbjct: 306 --ICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEXNP 363
Query: 1105 GQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNALHAKNIDI 1161
QLWETT +P R L+V +KDAI+AD++F TL GD VE RR FIE NAL A NIDI
Sbjct: 364 EQLWETTXDPESRRXLRVTVKDAIAADQLFTTLXGDAVEPRRAFIEENALKAANIDI 420
>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 = 229 bits (583), Expect = 1e-59, Method: Compositional matrix adjust.
Identities = 128/384 (33%), Positives = 199/384 (51%), Gaps = 24/384 (6%)
Query: 346 SYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTI 405
SY AS+I++L+GLE VR RP MYIG T G HH EILDNA+DE+LAGY T+I V +
Sbjct: 2 SYDASAIRVLKGLEGVRHRPAMYIGGTGV-EGYHHLFKEILDNAVDEALAGYATEILVRL 60
Query: 406 YXXXXXXXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIG 465
GRG + A E++ LH+GGKF + +YK+SGGLHG+G
Sbjct: 61 NEDGSLTVEDNGRGIPVDLMPEEG----KPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVG 116
Query: 466 LSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDT--NKQGT 523
S VN LS + + + R K H + F G + P++++G+ K GT
Sbjct: 117 ASVVNALSEWTVVEVFREGKHHRIAFSRGEV------------TEPLRVVGEAPRGKTGT 164
Query: 524 KIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERXXXXXXXXXXXXTSGFV 583
++ F D +IF N+ F ++ R+RE+++L G+ + D + + F
Sbjct: 165 RVTFKPDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEEVFLDKGGVASFA 224
Query: 584 SYINKSKLVVHPTIFQAXXXXXXXXXXXXXXDVSMQWNNSYNENILCFTNNILQVDGGTH 643
+ + + +++ F +V YN IL + N I DGGTH
Sbjct: 225 KALAEGEDLLYEKPF-----LIRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTH 279
Query: 644 LTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLV 703
LT +S +RA+N+Y ++ K+ + G+D+ EGL V+S+K+P+P+F QTK KL+
Sbjct: 280 LTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLL 339
Query: 704 SSEVRKPVEEIIIKTLFDFLQENP 727
+ E V +++ + L + L+ENP
Sbjct: 340 NPEAGTAVGQVVYERLLEILEENP 363
>pdb|4DUH|A Chain A, Crystal Structure Of 24 Kda Domain Of E. Coli Dna Gyrase B
In Complex With Small Molecule Inhibitor
pdb|4DUH|B Chain B, Crystal Structure Of 24 Kda Domain Of E. Coli Dna Gyrase B
In Complex With Small Molecule Inhibitor
Length = 220
Score = 228 bits (581), Expect = 2e-59, Method: Composition-based stats.
Identities = 117/223 (52%), Positives = 150/223 (67%), Gaps = 17/223 (7%)
Query: 345 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVT 404
+SY +SSI++L+GL+AVRKRP MYIGDT DGTGLHH VFE++DNAIDE+LAG+C +I VT
Sbjct: 3 NSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVT 62
Query: 405 IYXXXXXXXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 464
I+ GRG SAAE++MT LHAGGKF+ NSYK+SGGLHG+
Sbjct: 63 IHADNSVSVQDDGRGIPTGIHPEEGV----SAAEVIMTVLHAGGKFDDNSYKVSGGLHGV 118
Query: 465 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTK 524
G+S VN LS+ L+L I R KIH + +GV Q +P+ + G+T K GT
Sbjct: 119 GVSVVNALSQKLELVIQREGKIHRQIYEHGVPQ------------APLAVTGETEKTGTM 166
Query: 525 IHFWVDEKIFSNI-EFHYEILKKRIRELSFLNNGVCITLIDER 566
+ FW + F+N+ EF YEIL KR+RELSFLN+GV I L D+R
Sbjct: 167 VRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKR 209
>pdb|1AJ6|A Chain A, Novobiocin-resistant Mutant (r136h) Of The N-terminal 24
Kda Fragment Of Dna Gyrase B Complexed With Novobiocin
At 2.3 Angstroms Resolution
Length = 219
Score = 226 bits (576), Expect = 6e-59, Method: Composition-based stats.
Identities = 116/223 (52%), Positives = 149/223 (66%), Gaps = 17/223 (7%)
Query: 345 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVT 404
+SY +SSI++L+GL+AVRKRP MYIGDT DGTGLHH VFE++DNAIDE+LAG+C +I VT
Sbjct: 2 NSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVT 61
Query: 405 IYXXXXXXXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 464
I+ GRG SAAE++MT LHAGGKF+ NSYK+SGGLHG+
Sbjct: 62 IHADNSVSVQDDGRGIPTGIHPEEGV----SAAEVIMTVLHAGGKFDDNSYKVSGGLHGV 117
Query: 465 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTK 524
G+S VN LS+ L+L I KIH + +GV Q +P+ + G+T K GT
Sbjct: 118 GVSVVNALSQKLELVIQHEGKIHRQIYEHGVPQ------------APLAVTGETEKTGTM 165
Query: 525 IHFWVDEKIFSNI-EFHYEILKKRIRELSFLNNGVCITLIDER 566
+ FW + F+N+ EF YEIL KR+RELSFLN+GV I L D+R
Sbjct: 166 VRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKR 208
>pdb|1KZN|A Chain A, Crystal Structure Of E. Coli 24kda Domain In Complex With
Clorobiocin
Length = 205
Score = 216 bits (551), Expect = 5e-56, Method: Composition-based stats.
Identities = 111/211 (52%), Positives = 139/211 (65%), Gaps = 17/211 (8%)
Query: 357 GLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYXXXXXXXXXX 416
GL+AVRKRP MYIGDT DGTGLHH VFE++DNAIDE+LAG+C +I VTI+
Sbjct: 1 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD 60
Query: 417 GRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFL 476
GRG SAAE++MT LHAGGKF+ NSYK+SGGLHG+G+S VN LS+ L
Sbjct: 61 GRGIPTGIHPEEGV----SAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKL 116
Query: 477 QLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSN 536
+L I R KIH + +GV Q +P+ + G+T K GT + FW + F+N
Sbjct: 117 ELVIQREGKIHRQIYEHGVPQ------------APLAVTGETEKTGTMVRFWPSLETFTN 164
Query: 537 I-EFHYEILKKRIRELSFLNNGVCITLIDER 566
+ EF YEIL KR+RELSFLN+GV I L D+R
Sbjct: 165 VTEFEYEILAKRLRELSFLNSGVSIRLRDKR 195
>pdb|4HYP|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HYP|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HYP|C Chain C, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HYP|D Chain D, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
Length = 215
Score = 216 bits (551), Expect = 5e-56, Method: Composition-based stats.
Identities = 111/211 (52%), Positives = 139/211 (65%), Gaps = 17/211 (8%)
Query: 357 GLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYXXXXXXXXXX 416
GL+AVRKRP MYIGDT DGTGLHH VFE++DNAIDE+LAG+C +I VTI+
Sbjct: 2 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD 61
Query: 417 GRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFL 476
GRG SAAE++MT LHAGGKF+ NSYK+SGGLHG+G+S VN LS+ L
Sbjct: 62 GRGIPTGIHPEEGV----SAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKL 117
Query: 477 QLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSN 536
+L I R KIH + +GV Q +P+ + G+T K GT + FW + F+N
Sbjct: 118 ELVIQREGKIHRQIYEHGVPQ------------APLAVTGETEKTGTMVRFWPSLETFTN 165
Query: 537 I-EFHYEILKKRIRELSFLNNGVCITLIDER 566
+ EF YEIL KR+RELSFLN+GV I L D+R
Sbjct: 166 VTEFEYEILAKRLRELSFLNSGVSIRLRDKR 196
>pdb|3G7E|A Chain A, Crystal Structure Of E. Coli Gyrase B Co-Complexed With
Inhibitor
Length = 203
Score = 216 bits (551), Expect = 5e-56, Method: Composition-based stats.
Identities = 111/211 (52%), Positives = 139/211 (65%), Gaps = 17/211 (8%)
Query: 357 GLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYXXXXXXXXXX 416
GL+AVRKRP MYIGDT DGTGLHH VFE++DNAIDE+LAG+C +I VTI+
Sbjct: 1 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD 60
Query: 417 GRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFL 476
GRG SAAE++MT LHAGGKF+ NSYK+SGGLHG+G+S VN LS+ L
Sbjct: 61 GRGIPTGIHPEEGV----SAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKL 116
Query: 477 QLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSN 536
+L I R KIH + +GV Q +P+ + G+T K GT + FW + F+N
Sbjct: 117 ELVIQREGKIHRQIYEHGVPQ------------APLAVTGETEKTGTMVRFWPSLETFTN 164
Query: 537 I-EFHYEILKKRIRELSFLNNGVCITLIDER 566
+ EF YEIL KR+RELSFLN+GV I L D+R
Sbjct: 165 VTEFEYEILAKRLRELSFLNSGVSIRLRDKR 195
>pdb|3QSB|B Chain B, Structure Of E. Coli Poliiibeta With
(Z)-5-(1-((4'-Fluorobiphenyl-4-
Yl)methoxyimino)butyl)-2,2-Dimethyl-4,
6-Dioxocyclohexanecarbonitrile
Length = 366
Score = 204 bits (518), Expect = 3e-52, Method: Composition-based stats.
Identities = 114/356 (32%), Positives = 196/356 (55%), Gaps = 18/356 (5%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 6 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 66 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 124
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL + I
Sbjct: 125 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 184
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 185 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 243
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKAS 307
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 244 YRRVLPKNPDKHLEAGXDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAE 303
Query: 308 EELEINYNGKDKNF---IKFL-----------IKIMLLKNKNSYDIQD--TQESSY 347
E L++ Y+G + + ++ +++ML + +S I+D +Q ++Y
Sbjct: 304 EILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAY 359
>pdb|3Q4L|A Chain A, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4L|B Chain B, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
Length = 368
Score = 203 bits (516), Expect = 6e-52, Method: Composition-based stats.
Identities = 114/356 (32%), Positives = 196/356 (55%), Gaps = 18/356 (5%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 8 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 67
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 68 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 126
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL + I
Sbjct: 127 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 186
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 187 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 245
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKAS 307
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 246 YRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAE 305
Query: 308 EELEINYNGKDKNF---IKFL-----------IKIMLLKNKNSYDIQD--TQESSY 347
E L++ Y+G + + ++ +++ML + +S I+D +Q ++Y
Sbjct: 306 EILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAY 361
>pdb|2POL|A Chain A, Three-Dimensional Structure Of The Beta Subunit Of
Escherichia Coli Dna Polymerase Iii Holoenzyme: A
Sliding Dna Clamp
pdb|2POL|B Chain B, Three-Dimensional Structure Of The Beta Subunit Of
Escherichia Coli Dna Polymerase Iii Holoenzyme: A
Sliding Dna Clamp
pdb|1MMI|A Chain A, E. Coli Dna Polymerase Beta Subunit
pdb|1MMI|B Chain B, E. Coli Dna Polymerase Beta Subunit
pdb|1UNN|A Chain A, Complex Of Beta-Clamp Processivity Factor And Little
Finger Domain Of Poliv
pdb|1UNN|B Chain B, Complex Of Beta-Clamp Processivity Factor And Little
Finger Domain Of Poliv
pdb|1OK7|A Chain A, A Conserved Protein Binding-site On Bacterial Sliding
Clamps
pdb|1OK7|B Chain B, A Conserved Protein Binding-site On Bacterial Sliding
Clamps
pdb|3BEP|A Chain A, Structure Of A Sliding Clamp On Dna
pdb|3BEP|B Chain B, Structure Of A Sliding Clamp On Dna
pdb|3D1E|A Chain A, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound To
A Polymerase Ii Peptide
pdb|3D1E|B Chain B, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound To
A Polymerase Ii Peptide
pdb|3D1F|A Chain A, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound To
A Polymerase Iii Peptide
pdb|3D1F|B Chain B, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound To
A Polymerase Iii Peptide
pdb|3D1G|A Chain A, Structure Of A Small Molecule Inhibitor Bound To A Dna
Sliding Clamp
pdb|3D1G|B Chain B, Structure Of A Small Molecule Inhibitor Bound To A Dna
Sliding Clamp
pdb|3QSB|A Chain A, Structure Of E. Coli Poliiibeta With
(Z)-5-(1-((4'-Fluorobiphenyl-4-
Yl)methoxyimino)butyl)-2,2-Dimethyl-4,
6-Dioxocyclohexanecarbonitrile
pdb|3Q4J|A Chain A, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|B Chain B, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|C Chain C, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|D Chain D, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|E Chain E, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|F Chain F, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4K|A Chain A, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4K|B Chain B, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
Length = 366
Score = 203 bits (516), Expect = 6e-52, Method: Composition-based stats.
Identities = 114/356 (32%), Positives = 196/356 (55%), Gaps = 18/356 (5%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 6 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 66 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 124
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL + I
Sbjct: 125 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 184
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 185 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 243
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKAS 307
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 244 YRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAE 303
Query: 308 EELEINYNGKDKNF---IKFL-----------IKIMLLKNKNSYDIQD--TQESSY 347
E L++ Y+G + + ++ +++ML + +S I+D +Q ++Y
Sbjct: 304 EILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAY 359
>pdb|3PWE|A Chain A, Crystal Structure Of The E. Coli Beta Clamp Mutant R103c,
I305c, C260s, C333s At 2.2a Resolution
pdb|3PWE|B Chain B, Crystal Structure Of The E. Coli Beta Clamp Mutant R103c,
I305c, C260s, C333s At 2.2a Resolution
Length = 366
Score = 201 bits (512), Expect = 1e-51, Method: Composition-based stats.
Identities = 114/356 (32%), Positives = 195/356 (54%), Gaps = 18/356 (5%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 6 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG S+F+L TL A ++P + + +
Sbjct: 66 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGCSRFSLSTLPAADFPNLD-DWQS 124
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL + I
Sbjct: 125 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 184
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 185 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 243
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKAS 307
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 244 YRRVLPKNPDKHLEAGSDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAE 303
Query: 308 EELEINYNGKDKNF---IKFL-----------IKIMLLKNKNSYDIQD--TQESSY 347
E L++ Y+G + + ++ +++ML + +S I+D +Q ++Y
Sbjct: 304 ECLDVTYSGAEMEIGFNVSYVLDVLNALKSENVRMMLTDSVSSVQIEDAASQSAAY 359
>pdb|2XUR|A Chain A, The G157c Mutation In The Escherichia Coli Sliding Clamp
Specifically Affects Initiation Of Replication
pdb|2XUR|B Chain B, The G157c Mutation In The Escherichia Coli Sliding Clamp
Specifically Affects Initiation Of Replication
Length = 373
Score = 199 bits (507), Expect = 6e-51, Method: Composition-based stats.
Identities = 113/356 (31%), Positives = 195/356 (54%), Gaps = 18/356 (5%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 13 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 72
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 73 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 131
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLN +L + + + V++DGHRL + I
Sbjct: 132 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNCMLFETEGEELRTVATDGHRLAVCSMPI 191
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 192 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 250
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKAS 307
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 251 YRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAE 310
Query: 308 EELEINYNGKDKNF---IKFL-----------IKIMLLKNKNSYDIQD--TQESSY 347
E L++ Y+G + + ++ +++ML + +S I+D +Q ++Y
Sbjct: 311 EILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAY 366
>pdb|1JQL|A Chain A, Mechanism Of Processivity Clamp Opening By The Delta
Subunit Wrench Of The Clamp Loader Complex Of E. Coli
Dna Polymerase Iii: Structure Of Beta-Delta (1-140)
pdb|1JQJ|A Chain A, Mechanism Of Processivity Clamp Opening By The Delta
Subunit Wrench Of The Clamp Loader Complex Of E. Coli
Dna Polymerase Iii: Structure Of The Beta-Delta Complex
pdb|1JQJ|B Chain B, Mechanism Of Processivity Clamp Opening By The Delta
Subunit Wrench Of The Clamp Loader Complex Of E. Coli
Dna Polymerase Iii: Structure Of The Beta-Delta Complex
Length = 366
Score = 195 bits (495), Expect = 1e-49, Method: Composition-based stats.
Identities = 113/356 (31%), Positives = 194/356 (54%), Gaps = 18/356 (5%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 6 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 66 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 124
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL + I
Sbjct: 125 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 184
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 185 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 243
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKAS 307
Y+ V+ +K + L ++ R + SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 244 YRRVLPKNPDKHLEAGCDLLKQAFARAAAASNEKFRGVRLYVSENQLKITANNPEQEEAE 303
Query: 308 EELEINYNGKDKNF---IKFL-----------IKIMLLKNKNSYDIQD--TQESSY 347
E L++ Y+G + + ++ +++ML + +S I+D +Q ++Y
Sbjct: 304 EILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAY 359
>pdb|3F1V|A Chain A, E. Coli Beta Sliding Clamp, 148-153 Ala Mutant
pdb|3F1V|B Chain B, E. Coli Beta Sliding Clamp, 148-153 Ala Mutant
Length = 366
Score = 191 bits (485), Expect = 2e-48, Method: Composition-based stats.
Identities = 111/356 (31%), Positives = 192/356 (53%), Gaps = 18/356 (5%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 6 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 66 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 124
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A YYLNG+L + + + V++DGHRL + I
Sbjct: 125 EVEFTLPQATMKRLIEATQFSMAAAAAAYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 184
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 185 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 243
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKAS 307
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 244 YRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAE 303
Query: 308 EELEINYNGKDKNF---IKFL-----------IKIMLLKNKNSYDIQD--TQESSY 347
E L++ Y+G + + ++ +++ML + +S I+D +Q ++Y
Sbjct: 304 EILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAY 359
>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 = 185 bits (470), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 88/154 (57%), Positives = 110/154 (71%), Gaps = 1/154 (0%)
Query: 760 IDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKAR 819
+D L KLADC K+PE CE+++VEGDSAGGS K GRD R QA+LPLRGK+LN+EKAR
Sbjct: 1 MDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKAR 60
Query: 820 FEKIILSEQXXXXXXXXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRK 879
++I+ + + D F+L K RYH+I+IMTDAD+DGAHIR LLLTFFYR
Sbjct: 61 LDRILNNNEIRQMITAFGTGIGGD-FDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRF 119
Query: 880 MPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIE 913
M LIE GY+YIAQPPLYK+ G + Y+ +D E
Sbjct: 120 MRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRE 153
Score = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 45/66 (68%), Positives = 53/66 (80%), Gaps = 1/66 (1%)
Query: 1095 RYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNAL 1154
RYKGLGEMN QLWETTMNP R LL+VK++DAI AD+ F LMGD VE RR+FIE NA+
Sbjct: 171 RYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAV 230
Query: 1155 HAKNID 1160
+A N+D
Sbjct: 231 YA-NLD 235
>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 = 185 bits (470), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 88/154 (57%), Positives = 110/154 (71%), Gaps = 1/154 (0%)
Query: 760 IDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKAR 819
+D L KLADC K+PE CE+++VEGDSAGGS K GRD R QA+LPLRGK+LN+EKAR
Sbjct: 1 MDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKAR 60
Query: 820 FEKIILSEQXXXXXXXXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRK 879
++I+ + + D F+L K RYH+I+IMTDAD+DGAHIR LLLTFFYR
Sbjct: 61 LDRILNNNEIRQMITAFGTGIGGD-FDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRF 119
Query: 880 MPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIE 913
M LIE GY+YIAQPPLYK+ G + Y+ +D E
Sbjct: 120 MRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRE 153
Score = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 45/66 (68%), Positives = 53/66 (80%), Gaps = 1/66 (1%)
Query: 1095 RYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNAL 1154
RYKGLGEMN QLWETTMNP R LL+VK++DAI AD+ F LMGD VE RR+FIE NA+
Sbjct: 171 RYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAV 230
Query: 1155 HAKNID 1160
+A N+D
Sbjct: 231 YA-NLD 235
>pdb|3LNU|A Chain A, Crystal Structure Of Pare Subunit
pdb|3LPS|A Chain A, Crystal Structure Of Pare
Length = 408
Score = 183 bits (465), Expect = 4e-46, Method: Compositional matrix adjust.
Identities = 116/389 (29%), Positives = 189/389 (48%), Gaps = 28/389 (7%)
Query: 340 QDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCT 399
+ + + Y+A+ I++L GL+ V++RP MY +D +H E++DN++DE+LAG+
Sbjct: 17 RGSHNTRYNAADIEVLSGLDPVKRRPGMY----TDTARPNHLAQEVIDNSVDEALAGHAK 72
Query: 400 KINVTIYXXXXXXXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISG 459
+I VT+Y GRG E+++T LHAGGKFN +Y SG
Sbjct: 73 QIEVTLYKDGSCEVSDDGRGMPVDIHPEEKI----PGVELILTRLHAGGKFNNRNYTFSG 128
Query: 460 GLHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTN 519
GLHG+G+S VN LS ++L I R H MEFR +G + S ++++G
Sbjct: 129 GLHGVGVSVVNALSTKVELFIKREGSEHRMEFR------------DGNAASKLEVVGTVG 176
Query: 520 KQ--GTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERXXXXXXXXXXX 577
K+ GT++ FW D K F +F+ L+ +R + L G+ + L DE
Sbjct: 177 KKNTGTRLRFWADPKYFDTPKFNVRALRHLLRAKAVLCPGLTVKLHDE---ATGEQDSWY 233
Query: 578 XTSGFVSYINKSKLVVHPTIFQAXXXXXXXXXXXXXXDVSMQWNNSYNENILCFTNNILQ 637
+G Y+ K ++ H + A D + W + N I
Sbjct: 234 FENGLRDYL-KGEMAEH-EMLPADLFVGSLKKDTEIVDWAAGWVPEGELVQESYVNLIPT 291
Query: 638 VDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQ 697
GTH+ GLRSG+T A+ ++ + L + +++ ED+ + +T VLS+K+ DP+F+ Q
Sbjct: 292 AQHGTHVNGLRSGLTDALREFCDFRNLLPRG-VKLAPEDVWDRVTFVLSLKMTDPQFSGQ 350
Query: 698 TKNKLVSSEVRKPVEEIIIKTLFDFLQEN 726
TK +L S + +E +L +N
Sbjct: 351 TKERLSSRQAAGFIEGAAHDAFSLYLNQN 379
>pdb|4HXZ|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HXZ|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HY1|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HY1|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HYM|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HYM|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
Length = 390
Score = 179 bits (455), Expect = 6e-45, Method: Compositional matrix adjust.
Identities = 124/393 (31%), Positives = 195/393 (49%), Gaps = 31/393 (7%)
Query: 346 SYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTI 405
+Y+A SI++L GL+ V+KRP MY ++ +H + EI+DN++DE LAG+ +KIN+T+
Sbjct: 3 NYNAKSIEVLTGLDPVKKRPGMY----TNIENPNHLIQEIIDNSVDEVLAGFASKINITL 58
Query: 406 YXXXXXXXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIG 465
Y GRG S E++MT+LH+GGKF+ +Y SGGLHG+G
Sbjct: 59 YEDNSIEVADDGRGMPVDIHPEHKM----SGIELIMTKLHSGGKFSNKNYTHSGGLHGVG 114
Query: 466 LSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ--GT 523
+S VN LS L+ I R+ ++++ F +G ++II + K+ GT
Sbjct: 115 VSVVNALSTRLEAEIKRDGNVYHIVFE------------DGFKTKDLEIIDNVGKKNTGT 162
Query: 524 KIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERXXXXXXXXXXXXTSGFV 583
KI FW ++K F +I+ +++ LK + + L + I +E G++
Sbjct: 163 KIRFWPNKKYFDDIKVNFKALKNLLEAKAILCKALTIKYSNEIKKEKLTWHFETGLKGYL 222
Query: 584 SY-INKSKLVVHPTIFQAXXXXXXXXXXXXXXDVSMQWNNSYNENIL-CFTNNILQVDGG 641
+ + L P I D W +E+I + N I G
Sbjct: 223 DHKLEAETLPAEPFIID------NFSNGDSYLDAVFCWCEDPSESIKNSYVNLIPTPQDG 276
Query: 642 THLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNK 701
TH+TGL++GI AI YIE+N K+ I+I D L V+S+KI +P+F QTK K
Sbjct: 277 THVTGLKNGIYDAIKAYIEKNSLSVKN-IKITANDSFAQLNYVISVKITNPQFAGQTKEK 335
Query: 702 LVSSEVRKPVEEIIIKTLFDFLQENPGESKLIC 734
L + +V V + L +L +NP E++ I
Sbjct: 336 LSNKDVTNFVATAVKDLLTIWLNQNPDEARQIV 368
>pdb|1S16|A Chain A, Crystal Structure Of E. Coli Topoisomerase Iv Pare 43kda
Subunit Complexed With Adpnp
pdb|1S16|B Chain B, Crystal Structure Of E. Coli Topoisomerase Iv Pare 43kda
Subunit Complexed With Adpnp
Length = 390
Score = 174 bits (441), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 113/392 (28%), Positives = 193/392 (49%), Gaps = 29/392 (7%)
Query: 346 SYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTI 405
+Y+A +I++L GLE VR+RP MY +D T +H E++DN++DE+LAG+ +++V +
Sbjct: 4 TYNADAIEVLTGLEPVRRRPGMY----TDTTRPNHLGQEVIDNSVDEALAGHAKRVDVIL 59
Query: 406 YXXXXXXXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIG 465
+ GRG A E+++ LHAGGKF+ +Y+ SGGLHG+G
Sbjct: 60 HADQSLEVIDDGRGMPVDIHPEEGV----PAVELILCRLHAGGKFSNKNYQFSGGLHGVG 115
Query: 466 LSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ--GT 523
+S VN LS+ +++ + R+ +++ + F NG V ++++G K+ GT
Sbjct: 116 ISVVNALSKRVEVNVRRDGQVYNIAFE------------NGEKVQDLQVVGTCGKRNTGT 163
Query: 524 KIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERXXXXXXXXXXXXTSGFV 583
+HFW DE F + F L ++ + L GV IT DE G
Sbjct: 164 SVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDE---INNTEQRWCYQDGLN 220
Query: 584 SYINKSKLVVHPTIFQAXXXXXXXXXXXXXXDVSMQWNNSYNENIL-CFTNNILQVDGGT 642
Y+ ++ + PT+ + D ++ W E + + N I + GGT
Sbjct: 221 DYLAEAVNGL-PTLPE-KPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGT 278
Query: 643 HLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKL 702
H+ GLR G+ A+ ++ E L + +++ EDI + VLS+K+ DP+F QTK +L
Sbjct: 279 HVNGLRQGLLDAMREFCEYRNILPRG-VKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERL 337
Query: 703 VSSEVRKPVEEIIIKTLFDFLQENPGESKLIC 734
S + V ++ +L +N ++L+
Sbjct: 338 SSRQCAAFVSGVVKDAFILWLNQNVQAAELLA 369
>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 = 172 bits (437), Expect = 7e-43, Method: Compositional matrix adjust.
Identities = 81/136 (59%), Positives = 99/136 (72%), Gaps = 1/136 (0%)
Query: 760 IDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKAR 819
+D L KLADC K+PE CE+++VEGDSAGGS K GRD R QA+LPLRGK+LN+EKAR
Sbjct: 1 MDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKAR 60
Query: 820 FEKIILSEQXXXXXXXXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRK 879
++I+ + + D F+L K RYH+I+IMTDAD+DGAHIR LLLTFFYR
Sbjct: 61 LDRILNNNEIRQMITAFGTGIGGD-FDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRF 119
Query: 880 MPKLIEYGYIYIAQPP 895
M LIE GY+YIAQPP
Sbjct: 120 MRPLIEAGYVYIAQPP 135
Score = 90.1 bits (222), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 51/88 (57%), Positives = 62/88 (70%), Gaps = 5/88 (5%)
Query: 1076 FYKIINYLRNEAENMVIKQR---YKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADK 1132
FY+ + L EA + I Q YKGLGEMN QLWETTMNP R LL+VK++DAI AD+
Sbjct: 116 FYRFMRPL-IEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQ 174
Query: 1133 IFMTLMGDNVELRRKFIELNALHAKNID 1160
F LMGD VE RR+FIE NA++A N+D
Sbjct: 175 TFEMLMGDVVENRRQFIEDNAVYA-NLD 201
>pdb|4HZ5|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|C Chain C, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|D Chain D, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|E Chain E, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|F Chain F, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|G Chain G, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|H Chain H, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|J Chain J, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
Length = 216
Score = 170 bits (431), Expect = 3e-42, Method: Composition-based stats.
Identities = 101/212 (47%), Positives = 124/212 (58%), Gaps = 20/212 (9%)
Query: 357 GLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYXXXXXXXXXX 416
GLEAVRKRP MYIG T D GLHH V+EI+DNA+DE+L+GY +INVTI
Sbjct: 2 GLEAVRKRPGMYIGST-DSRGLHHLVYEIVDNAVDEALSGYGNEINVTIQKDNSICVADS 60
Query: 417 GRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFL 476
GRG E++ T LHAGGKF + YK SGGLHG+G S VN LS++L
Sbjct: 61 GRGMPTGMHASGI-----PTVEVIFTVLHAGGKFGQGGYKTSGGLHGVGASVVNALSKWL 115
Query: 477 QLTINRNKKIHYME-FRYGVLQNRIIKTINGISVSPIKIIGDTNKQ-GTKIHFWVDEKIF 534
++ I R+ + YME F G G V +K IG T K+ GT + F D+ IF
Sbjct: 116 EVHIVRD-GVEYMERFEDG-----------GKPVGTLKKIGKTKKRNGTSVTFLPDDTIF 163
Query: 535 SNIEFHYEILKKRIRELSFLNNGVCITLIDER 566
S F YEIL +R+RE +FL GV ITL DER
Sbjct: 164 STTNFSYEILAERLRESAFLLKGVKITLTDER 195
>pdb|4EM7|A Chain A, Crystal Structure Of A Topoisomerase Atp Inhibitor
pdb|4EMV|A Chain A, Crystal Structure Of A Topoisomerase Atp Inhibitor
Length = 226
Score = 165 bits (417), Expect = 2e-40, Method: Composition-based stats.
Identities = 93/224 (41%), Positives = 129/224 (57%), Gaps = 19/224 (8%)
Query: 345 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVT 404
++Y+ +IQ+LEGL+AVRKRP MYIG T DG GLHH V+EI+DNA+DE+L+G+ +I+VT
Sbjct: 9 NNYNDDAIQVLEGLDAVRKRPGMYIGST-DGAGLHHLVWEIVDNAVDEALSGFGDRIDVT 67
Query: 405 IYXXXXXXXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 464
I GRG E++ T LHAGGKF + YK SGGLHG+
Sbjct: 68 INKDGSLTVQDHGRGMPTGMHAMGI-----PTVEVIFTILHAGGKFGQGGYKTSGGLHGV 122
Query: 465 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDT--NKQG 522
G S VN LS +L++ I R+ ++ F G G V+ +K IG +K G
Sbjct: 123 GSSVVNALSSWLEVEITRDGAVYKQRFENG-----------GKPVTTLKKIGTALKSKTG 171
Query: 523 TKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDER 566
TK+ F D IFS +F Y + +R+ E +FL V ++L D+R
Sbjct: 172 TKVTFMPDATIFSTTDFKYNTISERLNESAFLLKNVTLSLTDKR 215
>pdb|3FOE|C Chain C, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOE|D Chain D, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOF|C Chain C, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOF|D Chain D, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3K9F|C Chain C, Detailed Structural Insight Into The Quinolone-Dna
Cleavage Complex Of Type Iia Topoisomerases
pdb|3K9F|D Chain D, Detailed Structural Insight Into The Quinolone-Dna
Cleavage Complex Of Type Iia Topoisomerases
pdb|3KSA|C Chain C, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Cleaved Form)
pdb|3KSA|D Chain D, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Cleaved Form)
pdb|3KSB|C Chain C, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Re-Sealed Form)
pdb|3KSB|D Chain D, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Re-Sealed Form)
pdb|3LTN|C Chain C, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
(S. Pneumoniae)
pdb|3LTN|D Chain D, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
(S. Pneumoniae)
pdb|3RAF|C Chain C, Quinazolinedione-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAF|D Chain D, Quinazolinedione-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAD|C Chain C, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAD|D Chain D, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAE|C Chain C, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAE|D Chain D, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
Length = 268
Score = 155 bits (392), Expect = 1e-37, Method: Composition-based stats.
Identities = 82/149 (55%), Positives = 99/149 (66%), Gaps = 1/149 (0%)
Query: 757 KNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIE 816
KN D LS KL Q KNP ELY+VEGDSAGGS KQGRDR+FQA+LPLRGKV+N
Sbjct: 25 KNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTA 84
Query: 817 KARFEKIILSEQXXXXXXXXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFF 876
KA+ I+ +E+ D F++E Y +IIIMTDAD DGAHI+ LLLTFF
Sbjct: 85 KAKMADILKNEEINTMIYTIGAGVGAD-FSIEDANYDKIIIMTDADTDGAHIQTLLLTFF 143
Query: 877 YRKMPKLIEYGYIYIAQPPLYKIKYGNNE 905
YR M L+E G++YIA PPLYK+ G +
Sbjct: 144 YRYMRPLVEAGHVYIALPPLYKMSKGKGK 172
Score = 76.6 bits (187), Expect = 7e-14, Method: Composition-based stats.
Identities = 39/70 (55%), Positives = 46/70 (65%)
Query: 1083 LRNEAENMVIKQRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNV 1142
LR + QRYKGLGEMN QLWETTMNP R L++V I+D A++ LMGD V
Sbjct: 188 LRKQFGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKV 247
Query: 1143 ELRRKFIELN 1152
E RRK+IE N
Sbjct: 248 EPRRKWIEDN 257
>pdb|2ZJT|A Chain A, Crystal Structure Of Dna Gyrase B' Domain Sheds Lights On
The Mechanism For T-Segment Navigation
pdb|2ZJT|B Chain B, Crystal Structure Of Dna Gyrase B' Domain Sheds Lights On
The Mechanism For T-Segment Navigation
Length = 247
Score = 141 bits (355), Expect = 2e-33, Method: Composition-based stats.
Identities = 73/159 (45%), Positives = 104/159 (65%), Gaps = 1/159 (0%)
Query: 776 NPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQXXXXXXX 835
+P ELY+VEGDSAGGS K GRD FQA+LPLRGK++N+EKAR ++++ + +
Sbjct: 8 DPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITA 67
Query: 836 XXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPP 895
DEF++ KLRYH+I++M DAD+DG HI LLLT +R M LIE G++++AQPP
Sbjct: 68 LGTGI-HDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPP 126
Query: 896 LYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISIENG 934
LYK+K+ ++ E +L+ K K I+ E+G
Sbjct: 127 LYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDG 165
Score = 80.1 bits (196), Expect = 6e-15, Method: Composition-based stats.
Identities = 35/68 (51%), Positives = 50/68 (73%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 1153
QRYKGLGEM+ +LWETTM+P +R L +V + DA +AD++F LMG++V+ RR FI NA
Sbjct: 167 QRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNA 226
Query: 1154 LHAKNIDI 1161
+ +D+
Sbjct: 227 KDVRFLDV 234
>pdb|3IG0|A Chain A, Crystal Structure Of The Second Part Of The Mycobacterium
Tuberculosis Dna Gyrase Reaction Core: The Toprim Domain
At 2.1 A Resolution
pdb|3M4I|A Chain A, Crystal Structure Of The Second Part Of The Mycobacterium
Tuberculosis Dna Gyrase Reaction Core: The Toprim Domain
At 1.95 A Resolution
Length = 242
Score = 140 bits (353), Expect = 4e-33, Method: Composition-based stats.
Identities = 73/161 (45%), Positives = 105/161 (65%), Gaps = 1/161 (0%)
Query: 774 EKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQXXXXX 833
+ +P ELY+VEGDSAGGS K GRD FQA+LPLRGK++N+EKAR ++++ + +
Sbjct: 14 KTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAII 73
Query: 834 XXXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQ 893
DEF++ KLRYH+I++M DAD+DG HI LLLT +R M LIE G++++AQ
Sbjct: 74 TALGTGI-HDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQ 132
Query: 894 PPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISIENG 934
PPLYK+K+ ++ E +L+ K K I+ E+G
Sbjct: 133 PPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDG 173
Score = 79.7 bits (195), Expect = 8e-15, Method: Composition-based stats.
Identities = 35/68 (51%), Positives = 50/68 (73%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 1153
QRYKGLGEM+ +LWETTM+P +R L +V + DA +AD++F LMG++V+ RR FI NA
Sbjct: 175 QRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNA 234
Query: 1154 LHAKNIDI 1161
+ +D+
Sbjct: 235 KDVRFLDV 242
>pdb|4GEE|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4GFN|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic
pdb|4GGL|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HXW|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
Length = 215
Score = 139 bits (349), Expect = 1e-32, Method: Composition-based stats.
Identities = 92/211 (43%), Positives = 123/211 (58%), Gaps = 18/211 (8%)
Query: 357 GLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYXXXXXXXXXX 416
GLEAVRKRP MYIG TS G GLHH V+EI+DN+IDE+LAG+ I V I
Sbjct: 1 GLEAVRKRPGMYIGSTS-GEGLHHLVWEIVDNSIDEALAGFAKSIQVIIEPDDSITVIDD 59
Query: 417 GRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFL 476
GRG R A E V T LHAGGKF YK+SGGLHG+G S VN LS L
Sbjct: 60 GRGIPVGIQAKTG----RPAVETVFTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSTSL 115
Query: 477 QLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSN 536
+ + ++ K++Y E+R G + V +K+I +T++ GT +HF D +IF+
Sbjct: 116 DVRVYKDGKVYYQEYRRGAV------------VDDLKVIEETDRHGTTVHFIPDPEIFTE 163
Query: 537 IE-FHYEILKKRIRELSFLNNGVCITLIDER 566
+ ++ L R+REL+FLN G+ I++ D R
Sbjct: 164 TTVYDFDKLATRVRELAFLNRGLHISIEDRR 194
>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 = 138 bits (347), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 71/172 (41%), Positives = 101/172 (58%), Gaps = 7/172 (4%)
Query: 756 KKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNI 815
+K ++ L KLADC + E EL+IVEGDSAGGS KQ RD+ FQA++P+RGK+LN
Sbjct: 20 RKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQARDKNFQAIMPIRGKILNT 79
Query: 816 EKARFEKIILSEQXXXXXXXXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTF 875
+ ++++ S++ D +L +LRY +I I+ DAD DG HI LL
Sbjct: 80 WEVSSDEVLASQEVHDIAIAIGVDPGSD--DLSELRYGKICILADADSDGLHIATLLCAL 137
Query: 876 FYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVK 927
F + P L+E G++Y+A PPL++I G + Y DD E L+ KNVK
Sbjct: 138 FVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEE-----LETILKNVK 184
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/33 (57%), Positives = 25/33 (75%)
Query: 1095 RYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDA 1127
R+KGLGEMN QL ETTM+P R L+++ + DA
Sbjct: 193 RFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDA 225
>pdb|2XKJ|E Chain E, Crystal Structure Of Catalytic Core Of A. Baumannii Topo
Iv (Pare-Parc Fusion Truncate)
Length = 767
Score = 137 bits (346), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 71/172 (41%), Positives = 101/172 (58%), Gaps = 7/172 (4%)
Query: 756 KKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNI 815
+K ++ L KLADC + E EL+IVEGDSAGGS KQ RD+ FQA++P+RGK+LN
Sbjct: 20 RKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQARDKNFQAIMPIRGKILNT 79
Query: 816 EKARFEKIILSEQXXXXXXXXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTF 875
+ ++++ S++ D +L +LRY +I I+ DAD DG HI LL
Sbjct: 80 WEVSSDEVLASQEVHDIAIAIGVDPGSD--DLSELRYGKICILADADSDGLHIATLLCAL 137
Query: 876 FYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVK 927
F + P L+E G++Y+A PPL++I G + Y DD E L+ KNVK
Sbjct: 138 FVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEE-----LETILKNVK 184
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/33 (57%), Positives = 25/33 (75%)
Query: 1095 RYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDA 1127
R+KGLGEMN QL ETTM+P R L+++ + DA
Sbjct: 193 RFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDA 225
>pdb|3TTZ|A Chain A, Crystal Structure Of A Topoisomerase Atpase Inhibitor
pdb|3TTZ|B Chain B, Crystal Structure Of A Topoisomerase Atpase Inhibitor
pdb|3U2D|A Chain A, S. Aureus Gyrb Atpase Domain In Complex With Small
Molecule Inhibitor
pdb|3U2D|B Chain B, S. Aureus Gyrb Atpase Domain In Complex With Small
Molecule Inhibitor
pdb|3U2K|A Chain A, S. Aureus Gyrb Atpase Domain In Complex With A Small
Molecule Inhibitor
pdb|3U2K|B Chain B, S. Aureus Gyrb Atpase Domain In Complex With A Small
Molecule Inhibitor
Length = 198
Score = 134 bits (337), Expect = 3e-31, Method: Composition-based stats.
Identities = 88/221 (39%), Positives = 119/221 (53%), Gaps = 41/221 (18%)
Query: 347 YSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIY 406
Y A IQ+LEGLEAVRKRP MYIG TS+ GLHH V+EI+DN+IDE+LAGY +I V I
Sbjct: 2 YGAGQIQVLEGLEAVRKRPGMYIGSTSE-RGLHHLVWEIVDNSIDEALAGYANQIEVVIE 60
Query: 407 XXXXXXXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGL 466
GRG R A E+++T
Sbjct: 61 KDNWIKVTDNGRG----IPVDIQEKMGRPAVEVILTS----------------------- 93
Query: 467 SCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIH 526
S VN LS+ L++ ++RN+ I++ ++ GV Q +K +G T+K GT I
Sbjct: 94 SVVNALSQDLEVYVHRNETIYHQAYKKGVPQ------------FDLKEVGTTDKTGTVIR 141
Query: 527 FWVDEKIFSNIE-FHYEILKKRIRELSFLNNGVCITLIDER 566
F D +IF+ ++YE L++RIREL+FLN G+ ITL DER
Sbjct: 142 FKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDER 182
>pdb|4B6C|A Chain A, Structure Of The M. Smegmatis Gyrb Atpase Domain In
Complex With An Aminopyrazinamide
pdb|4B6C|B Chain B, Structure Of The M. Smegmatis Gyrb Atpase Domain In
Complex With An Aminopyrazinamide
Length = 196
Score = 134 bits (337), Expect = 3e-31, Method: Composition-based stats.
Identities = 80/220 (36%), Positives = 120/220 (54%), Gaps = 39/220 (17%)
Query: 347 YSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIY 406
Y A SI ILEGLEAVRKRP MYIG T + GLHH ++E++DNA+DE++AG+ T+++V I+
Sbjct: 5 YGADSITILEGLEAVRKRPGMYIGSTGE-RGLHHLIWEVVDNAVDEAMAGFATRVDVKIH 63
Query: 407 XXXXXXXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGL 466
GRG + E+HA G I + +G+
Sbjct: 64 ADGSVEVRDDGRG--------------------IPVEMHATGM-----PTIDVVMTQVGV 98
Query: 467 SCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIH 526
S VN LS L+ T+ R+ Y F+Y +++ G +K G+T + GT I
Sbjct: 99 SVVNALSTRLEATVLRDG---YEWFQY------YDRSVPG----KLKQGGETKETGTTIR 145
Query: 527 FWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDER 566
FW D +IF ++++E + +R++E++FLN G+ I L DER
Sbjct: 146 FWADPEIFETTDYNFETVARRLQEMAFLNKGLTIELTDER 185
>pdb|3G75|A Chain A, Crystal Structure Of Staphylococcus Aureus Gyrase B Co-
Complexed With Inhibitor
pdb|3G75|B Chain B, Crystal Structure Of Staphylococcus Aureus Gyrase B Co-
Complexed With Inhibitor
pdb|3G7B|A Chain A, Staphylococcus Aureus Gyrase B Co-Complex With Inhibitor
pdb|3G7B|B Chain B, Staphylococcus Aureus Gyrase B Co-Complex With Inhibitor
Length = 184
Score = 128 bits (322), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 82/211 (38%), Positives = 112/211 (53%), Gaps = 41/211 (19%)
Query: 357 GLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYXXXXXXXXXX 416
GLEAVRKRP MYIG TS+ GLHH V+EI+DN+IDE+LAGY +I V I
Sbjct: 1 GLEAVRKRPGMYIGSTSE-RGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDN 59
Query: 417 GRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFL 476
GRG R A E+++T S VN LS+ L
Sbjct: 60 GRG----IPVDIQEKMGRPAVEVILTS-----------------------SVVNALSQDL 92
Query: 477 QLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSN 536
++ ++RN+ I++ ++ GV Q +K +G T+K GT I F D +IF+
Sbjct: 93 EVYVHRNETIYHQAYKKGVPQ------------FDLKEVGTTDKTGTVIRFKADGEIFTE 140
Query: 537 IE-FHYEILKKRIRELSFLNNGVCITLIDER 566
++YE L++RIREL+FLN G+ ITL DER
Sbjct: 141 TTVYNYETLQQRIRELAFLNKGIQITLRDER 171
>pdb|4HZ0|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HZ0|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
Length = 213
Score = 128 bits (321), Expect = 2e-29, Method: Composition-based stats.
Identities = 71/214 (33%), Positives = 114/214 (53%), Gaps = 22/214 (10%)
Query: 354 ILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYXXXXXXX 413
+L GLE VR+RP MY +D T +H E++DN++DE+LAG+ +++V ++
Sbjct: 1 VLTGLEPVRRRPGMY----TDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEV 56
Query: 414 XXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLS 473
GRG A E+++ LHAGGKF+ +Y+ SGGLHG+G+S VN LS
Sbjct: 57 IDDGRGMPVDIHPEEGV----PAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALS 112
Query: 474 RFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ--GTKIHFWVDE 531
+ +++ + R+ +++ + F NG V ++++G K+ GT +HFW DE
Sbjct: 113 KRVEVNVRRDGQVYNIAFE------------NGEKVQDLQVVGTCGKRNTGTSVHFWPDE 160
Query: 532 KIFSNIEFHYEILKKRIRELSFLNNGVCITLIDE 565
F + F L ++ + L GV IT DE
Sbjct: 161 TFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDE 194
>pdb|3FV5|A Chain A, Crystal Structure Of E. Coli Topoisomerase Iv Co-Complexed
With Inhibitor
pdb|3FV5|B Chain B, Crystal Structure Of E. Coli Topoisomerase Iv Co-Complexed
With Inhibitor
Length = 201
Score = 125 bits (315), Expect = 1e-28, Method: Composition-based stats.
Identities = 70/211 (33%), Positives = 112/211 (53%), Gaps = 22/211 (10%)
Query: 357 GLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYXXXXXXXXXX 416
GLE VR+RP MY +D T +H E++DN++DE+LAG+ +++V ++
Sbjct: 1 GLEPVRRRPGMY----TDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDD 56
Query: 417 GRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFL 476
GRG A E+++ LHAGGKF+ +Y+ SGGLHG+G+S VN LS+ +
Sbjct: 57 GRGMPVDIHPEEGV----PAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRV 112
Query: 477 QLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ--GTKIHFWVDEKIF 534
++ + R+ +++ + F NG V ++++G K+ GT +HFW DE F
Sbjct: 113 EVNVRRDGQVYNIAFE------------NGEKVQDLQVVGTCGKRNTGTSVHFWPDETFF 160
Query: 535 SNIEFHYEILKKRIRELSFLNNGVCITLIDE 565
+ F L ++ + L GV IT DE
Sbjct: 161 DSPRFSVSRLTHVLKAKAVLCPGVEITFKDE 191
>pdb|2AWA|A Chain A, Crystal Structure Of Dna Polymerase Iii, Beta Chain (Ec
2.7.7.7) (Np_344555.1) From Streptococcus Pneumoniae
Tigr4 At 2.50 A Resolution
pdb|2AWA|B Chain B, Crystal Structure Of Dna Polymerase Iii, Beta Chain (Ec
2.7.7.7) (Np_344555.1) From Streptococcus Pneumoniae
Tigr4 At 2.50 A Resolution
pdb|2AWA|C Chain C, Crystal Structure Of Dna Polymerase Iii, Beta Chain (Ec
2.7.7.7) (Np_344555.1) From Streptococcus Pneumoniae
Tigr4 At 2.50 A Resolution
pdb|2AWA|D Chain D, Crystal Structure Of Dna Polymerase Iii, Beta Chain (Ec
2.7.7.7) (Np_344555.1) From Streptococcus Pneumoniae
Tigr4 At 2.50 A Resolution
Length = 390
Score = 92.0 bits (227), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 82/321 (25%), Positives = 155/321 (48%), Gaps = 15/321 (4%)
Query: 9 KNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSI 68
KN L L + KN +PILS + + +E I+ + ++ ++ I + + ++ +
Sbjct: 20 KNLFLQALNTTKRAISSKNAIPILSTVKIDVTNEGITLIGSNGQISIENFISQKNEDAGL 79
Query: 69 ------NIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYP-IM 121
+I++ A FI+++ SLP+ IE + + SGKS+ TL+ D+++YP I
Sbjct: 80 LITSLGSILLEASFFINVVSSLPDVTLDFKEIEQNQIVLTSGKSEITLKGKDSEQYPRIQ 139
Query: 122 TLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGL--LLSFQKKNIIAVSSDGHR 179
+++ L K LK I+N F+ + Q+ R L G+ +LS Q K + V++D HR
Sbjct: 140 EISAST--PLILETKLLKKIINETAFAASTQESRPILTGVHFVLS-QHKELKTVATDSHR 196
Query: 180 LTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXX 239
L+ ++ ++K S D++IP +++ + + VE+ +NNQ
Sbjct: 197 LSQKKLTLEKN-SDDFDVVIPSRSLREFSAVFTDDIETVEIFFANNQILFRSENISFYTR 255
Query: 240 XXDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKG-VRLVIKPNYLKITV 298
+G + D +I + + N L +S +R ++S+ G V+L IK + V
Sbjct: 256 LLEGNYPDTDRLIPTDFNTTITFNVVNLRQSXERARLLSSATQNGTVKLEIKDGVVSAHV 315
Query: 299 SSSNREKASEELEIN-YNGKD 318
S K +EE++ + G+D
Sbjct: 316 HSPEVGKVNEEIDTDQVTGED 336
>pdb|2AVT|A Chain A, Crystal Structure Of The Beta Subunit From Dna Polymerase
Of Streptococcus Pyogenes
pdb|2AVT|B Chain B, Crystal Structure Of The Beta Subunit From Dna Polymerase
Of Streptococcus Pyogenes
Length = 378
Score = 89.0 bits (219), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 81/327 (24%), Positives = 152/327 (46%), Gaps = 13/327 (3%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
+Q +N + +H L + KN +PILS+I + S ++ ++ ++ I
Sbjct: 2 IQFSIN--RTLFIHALNTTKRAISTKNAIPILSSIKIEVTSTGVTLTGSNGQISIENTIP 59
Query: 61 VGYGNSSI------NIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLD 114
V N+ + I++ A FI+I+ SLP+ IE + + SGKS+ TL+ D
Sbjct: 60 VSNENAGLLITSPGAILLEASFFINIISSLPDISINVKEIEQHQVVLTSGKSEITLKGKD 119
Query: 115 AKEYPIMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQ-KKNIIAV 173
+YP + S + L K LK I+ F+ + Q+ R L G+ + K+ AV
Sbjct: 120 VDQYPRLQEVSTEN-PLILKTKLLKSIIAETAFAASLQESRPILTGVHIVLSNHKDFKAV 178
Query: 174 SSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXX 233
++D HR++ + +D S+ +++P K++ + + VE+ S +Q
Sbjct: 179 ATDSHRMSQRLITLDNT-SADFMVVLPSKSLREFSAVFTDDIETVEVFFSPSQILFRSEH 237
Query: 234 XXXXXXXXDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKG-VRLVIKPN 292
+G + D ++ ++E + N L +++R +ISN G V+L I N
Sbjct: 238 ISFYTRLLEGNYPDTDRLLMTEFETEVVFNTQSLRHAMERAFLISNATQNGTVKLEITQN 297
Query: 293 YLKITVSSSNREKASEELEI-NYNGKD 318
++ V+S K +E+L+I + +G D
Sbjct: 298 HISAHVNSPEVGKVNEDLDIVSQSGSD 324
>pdb|1S14|A Chain A, Crystal Structure Of Escherichia Coli Topoisomerase Iv
Pare 24kda Subunit
pdb|1S14|B Chain B, Crystal Structure Of Escherichia Coli Topoisomerase Iv
Pare 24kda Subunit
Length = 194
Score = 87.0 bits (214), Expect = 5e-17, Method: Composition-based stats.
Identities = 59/222 (26%), Positives = 102/222 (45%), Gaps = 45/222 (20%)
Query: 346 SYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTI 405
+Y+A +I++L GLE VR+RP MY +D T +H E++DN++DE+LAG+ +++V +
Sbjct: 4 TYNADAIEVLTGLEPVRRRPGMY----TDTTRPNHLGQEVIDNSVDEALAGHAKRVDVIL 59
Query: 406 YXXXXXXXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTELHAGGKFNKNSYKISGGLHGIG 465
+ GRG A E+++
Sbjct: 60 HADQSLEVIDDGRGMPVDIHPEEGV----PAVELILC----------------------- 92
Query: 466 LSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ--GT 523
+S VN LS+ +++ + R+ +++ + F NG V ++++G K+ GT
Sbjct: 93 ISVVNALSKRVEVNVRRDGQVYNIAFE------------NGEKVQDLQVVGTCGKRNTGT 140
Query: 524 KIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDE 565
+HFW DE F + F L ++ + L GV IT DE
Sbjct: 141 SVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDE 182
>pdb|1VPK|A Chain A, Crystal Structure Of Dna Polymerase Iii, Beta Subunit
(Tm0262) From Thermotoga Maritima At 2.00 A Resolution
Length = 378
Score = 84.7 bits (208), Expect = 3e-16, Method: Composition-based stats.
Identities = 65/295 (22%), Positives = 132/295 (44%), Gaps = 5/295 (1%)
Query: 25 KKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFIDILRSL 84
KK++ PIL+ L +TD E + + +V +++ L
Sbjct: 35 KKSVKPILAGFLFEVKDGNFYICATDLETGVKATVNAAEISGEARFVVPGDVIQKMVKVL 94
Query: 85 PETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCILNM 144
P+ E + +E + I SG + F + T+ A E+P +T ++ F + L+ ++
Sbjct: 95 PD-EITELSLEGDALVISSGSTVFRITTMPADEFPEIT-PAESGITFEVDTSLLEEMVEK 152
Query: 145 VYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTV 204
V F+ A+ + LNG+ K + V+SDG RL + + ++ K++
Sbjct: 153 VIFAAAKDEFMRNLNGVFWELHKNLLRLVASDGFRLAL--AEEQIENEEEASFLLSLKSM 210
Query: 205 FTLQRLLENKENP-VELKISNNQXXXXXXXXXXXXXXXDGKFLDYKYVISNKYEKSFLVN 263
+Q +L+N P + ++ + D +F DYK VI ++ +V+
Sbjct: 211 KEVQNVLDNTTEPTITVRYDGRRVSLSTNDVETVMRVVDAEFPDYKRVIPETFKTKVVVS 270
Query: 264 RNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKASEELEINYNGKD 318
R +L SL+R+ +I++ + V+ I+ N +++ S + + +E+E+ G+D
Sbjct: 271 RKELRESLKRVMVIASKGSESVKFEIEENVMRLVSKSPDYGEVVDEVEVQKEGED 325
>pdb|4FM9|A Chain A, Human Topoisomerase Ii Alpha Bound To Dna
Length = 763
Score = 75.1 bits (183), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 51/158 (32%), Positives = 78/158 (49%), Gaps = 10/158 (6%)
Query: 756 KKNLIDDIELSTKLADCQEKNPELCELYIVEGDSA-----GGSVKQGRDRRFQAVLPLRG 810
K N I I D +N C L + EGDSA G GRD+ V PLRG
Sbjct: 1 KHNRIKGIPKLDDANDAGGRNSTECTLILTEGDSAKTLAVSGLGVVGRDK--YGVFPLRG 58
Query: 811 KVLNIEKARFEKIILSEQXXXXXXXXXXXXE---QDEFNLEKLRYHRIIIMTDADIDGAH 867
K+LN+ +A ++I+ + + + +DE +L+ LRY +I+IMTD D DG+H
Sbjct: 59 KILNVREASHKQIMENAEINNIIKIVGLQYKKNYEDEDSLKTLRYGKIMIMTDQDQDGSH 118
Query: 868 IRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNE 905
I+ LL+ F + P L+ + ++ P+ K+ E
Sbjct: 119 IKGLLINFIHHNWPSLLRHRFLEEFITPIVKVSKNKQE 156
>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 = 75.1 bits (183), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 45/127 (35%), Positives = 70/127 (55%), Gaps = 10/127 (7%)
Query: 771 DCQEKNPELCELYIVEGDSA-----GGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIIL 825
D K+ C L + EGDSA G GRDR V PLRGK+LN+ +A ++I+
Sbjct: 44 DAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDR--YGVFPLRGKILNVREASHKQIME 101
Query: 826 SEQXXXXXXXXXXXXEQ---DEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPK 882
+ + ++ D +L+ LRY +I+IMTD D DG+HI+ LL+ F + P
Sbjct: 102 NAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPS 161
Query: 883 LIEYGYI 889
L+++G++
Sbjct: 162 LLKHGFL 168
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 66.6 bits (161), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 135/585 (23%), Positives = 214/585 (36%), Gaps = 117/585 (20%)
Query: 348 SASSIQILEGLEAVRKRPEMYIGDTSDG----------------------TGLHHFVFEI 385
++ Q + LE + KRP+ YIG GL EI
Sbjct: 2 ASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEI 61
Query: 386 LDNAIDESLAGYCTK-INVTIYXXXXX-XXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTE 443
L NA D + K I+V I+ G+G E++
Sbjct: 62 LVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYI----PEMIFGH 117
Query: 444 LHAGGKFNKNSYKISGGLHGIGLSCVNGLS-RFLQLTINRNKKIHYMEFRYGVLQNRIIK 502
L ++ + K++GG +G G N S F+ T + N V Q + K
Sbjct: 118 LLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLN-----------VGQKYVQK 166
Query: 503 TINGISVS-PIKIIGDTNKQG---TKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGV 558
N +S+ P KI + K+G TK+ F D F E +IL R + +N V
Sbjct: 167 WENNMSICHPPKIT--SYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSV 224
Query: 559 CITLIDERXXXXXXXXXXXXTSGFVSYINKSKLVVHPTIFQAXXXXXXXXXXXXXXDVSM 618
R F +Y+ + PTI D+S
Sbjct: 225 -------RDINVYLNGKSLKIRNFKNYVELYLKSLIPTILYERINNRWEVAFAVS-DISF 276
Query: 619 QWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIR 678
Q + F N+I GGTH+ + I + I++ +++ + +I +
Sbjct: 277 Q--------QISFVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSFQI-----K 323
Query: 679 EGLTCVLSIKIPDPKFNSQTKNKLVS------SEVRKPVEEI--IIKT-----LFDFLQE 725
+ ++ I +P F SQTK +L + S P+E I I+KT +F+
Sbjct: 324 NNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIADA 383
Query: 726 NPGESKLICXXXXXXXXXXXXXXXXXXLTRKKNLIDDIELSTKLADCQEKNPELCELYIV 785
N ES++ T L D + TK C L +
Sbjct: 384 N--ESRI---------------------TNYPKLEDANKAGTKEG-------YKCTLVLT 413
Query: 786 EGDSA-----GGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQXXXXXXXXXXXX 840
EGDSA G GRD + PLRGK+LN+ +A ++I+ + +
Sbjct: 414 EGDSALSLAVAGLAVVGRD--YYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQH 471
Query: 841 EQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIE 885
+ + + LRY ++IMTD D DG+HI+ L++ F P L++
Sbjct: 472 RKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLD 516
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 66.2 bits (160), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 133/583 (22%), Positives = 209/583 (35%), Gaps = 117/583 (20%)
Query: 348 SASSIQILEGLEAVRKRPEMYIGDTSDG----------------------TGLHHFVFEI 385
++ Q + LE + KRP+ YIG GL EI
Sbjct: 2 ASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEI 61
Query: 386 LDNAIDESLAGYCTK-INVTIYXXXXX-XXXXXGRGXXXXXXXXXXXXXXRSAAEIVMTE 443
L NA D + K I+V I+ G+G E++
Sbjct: 62 LVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYI----PEMIFGH 117
Query: 444 LHAGGKFNKNSYKISGGLHGIGLSCVNGLS-RFLQLTINRNKKIHYMEFRYGVLQNRIIK 502
L ++ + K++GG +G G N S F+ T + N V Q + K
Sbjct: 118 LLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLN-----------VGQKYVQK 166
Query: 503 TINGISVS-PIKIIGDTNKQG---TKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGV 558
N +S+ P KI + K+G TK+ F D F E +IL R + +N V
Sbjct: 167 WENNMSICHPPKIT--SYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSV 224
Query: 559 CITLIDERXXXXXXXXXXXXTSGFVSYINKSKLVVHPTIFQAXXXXXXXXXXXXXXDVSM 618
R F +Y+ + PTI D+S
Sbjct: 225 -------RDINVYLNGKSLKIRNFKNYVELYLKSLIPTILYERINNRWEVAFAVS-DISF 276
Query: 619 QWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIR 678
Q + F N+I GGTH+ + I + I++ +++ + +I +
Sbjct: 277 Q--------QISFVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSFQI-----K 323
Query: 679 EGLTCVLSIKIPDPKFNSQTKNKLVS------SEVRKPVEEI--IIKTLFDFLQENPGES 730
+ ++ I +P F SQTK +L + S P+E I I+KT
Sbjct: 324 NNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKT------------ 371
Query: 731 KLICXXXXXXXXXXXXXXXXXXLTRKKNLIDDIELSTKLADCQE---KNPELCELYIVEG 787
TR + I KL D + K C L + EG
Sbjct: 372 --------------------DLATRMFEIASRITNYPKLEDANKAGTKEGYKCTLVLTEG 411
Query: 788 DSA-----GGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQXXXXXXXXXXXXEQ 842
DSA G GRD + PLRGK+LN+ +A ++I+ + + +
Sbjct: 412 DSALSLAVAGLAVVGRD--YYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRK 469
Query: 843 DEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIE 885
+ + LRY ++IMTD D DG+HI+ L++ F P L++
Sbjct: 470 KYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLD 512
>pdb|3T0P|A Chain A, Crystal Structure Of A Putative Dna Polymerase Iii Beta
Subunit (Eubrec_0002; Ere_29750) From Eubacterium
Rectale Atcc 33656 At 2.26 A Resolution
pdb|3T0P|B Chain B, Crystal Structure Of A Putative Dna Polymerase Iii Beta
Subunit (Eubrec_0002; Ere_29750) From Eubacterium
Rectale Atcc 33656 At 2.26 A Resolution
Length = 371
Score = 65.1 bits (157), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 62/273 (22%), Positives = 120/273 (43%), Gaps = 10/273 (3%)
Query: 9 KNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSI 68
K +L + +V V + IL IL+ ++ +I + D E+ I T I
Sbjct: 8 KANLLKGVNIVSKAVPTRTTXAILECILIDASANEIKLXANDXELGIETIIDGTIEERGI 67
Query: 69 NIIVAARKFIDILRSLPETEKVTIYIENKHMF---IKSGKSKFTLQTLDAKEYPIMTLNS 125
I + A+ F +I+R LP+ + + IE F I K+KF + ++ +
Sbjct: 68 -IALDAKIFSEIVRKLPDND---VTIETDASFKTVISCEKAKFNIIGKSGDDFSYIPYVE 123
Query: 126 KYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQV 185
+ + LSQ TLK ++ FSIA D G L ++ + VS DGHR++ +
Sbjct: 124 RNE-SIVLSQFTLKEVIRQTIFSIADNDNNKLXTGELFEIEENKLRVVSLDGHRISIRYI 182
Query: 186 NIDKKFSSCSDIIIPRKTVFTLQRLLE-NKENPVELKISNNQXXXXXXXXXXXXXXXDGK 244
+ S +++P KT+ + +++ + + V + I+NN +G+
Sbjct: 183 EXKNHYDS-KKVVVPGKTLQEISKIIPGSADEDVVIYITNNHIVFEFENTTVVSRLIEGE 241
Query: 245 FLDYKYVISNKYEKSFLVNRNKLLRSLQRISII 277
+ +S+ Y+ +N+ +LL + R +++
Sbjct: 242 YFKIDQXLSSDYDTKVRINKRELLDCIDRATLL 274
>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 = 64.7 bits (156), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 36/111 (32%), Positives = 57/111 (51%), Gaps = 7/111 (6%)
Query: 780 CELYIVEGDSA-----GGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQXXXXXX 834
C L + EGDSA G GRD + PLRGK+LN+ +A ++I+ + +
Sbjct: 23 CTLVLTEGDSALSLAVAGLAVVGRD--YYGCYPLRGKMLNVREASADQILKNAEIQAIKK 80
Query: 835 XXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIE 885
+ + + LRY ++IMTD D DG+HI+ L++ F P L++
Sbjct: 81 IMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLD 131
>pdb|3RB9|A Chain A, Crystal Structure Of The M. Tuberculosis Beta Clamp
pdb|3RB9|B Chain B, Crystal Structure Of The M. Tuberculosis Beta Clamp
Length = 395
Score = 61.6 bits (148), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 52/307 (16%), Positives = 135/307 (43%), Gaps = 22/307 (7%)
Query: 23 VEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFIDILR 82
+ + +P+LS +L+ + ++ D EV S +++V+ R DI R
Sbjct: 26 LPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEI-VSPGSVLVSGRLLSDITR 84
Query: 83 SLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCIL 142
+LP + V +++E + + G ++F+L T+ ++YP TL + + L + +
Sbjct: 85 ALPN-KPVDVHVEGNRVALTCGNARFSLPTMPVEDYP--TLPTLPEETGLLPAELFAEAI 141
Query: 143 NMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSD-----I 197
+ V + + D L G+ + + ++ ++D RL ++ K+S+ S +
Sbjct: 142 SQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVREL----KWSASSPDIEAAV 197
Query: 198 IIPRKTVFTLQRLLENKENPVELKISNNQXXX-------XXXXXXXXXXXXDGKFLDYKY 250
++P KT+ + + V L + D +F ++
Sbjct: 198 LVPAKTLAEAAKAGIGGSD-VRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFPKFRQ 256
Query: 251 VISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKASEEL 310
++ ++ ++ +L+ +++ +++++ D+ VR+ ++++ + + +A E+L
Sbjct: 257 LLPTEHTAVATMDVAELIEAIKLVALVA-DRGAQVRMEFADGSVRLSAGADDVGRAEEDL 315
Query: 311 EINYNGK 317
++Y G+
Sbjct: 316 VVDYAGE 322
>pdb|3P16|A Chain A, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|B Chain B, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|C Chain C, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|D Chain D, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|E Chain E, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|F Chain F, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
Length = 408
Score = 61.6 bits (148), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 52/307 (16%), Positives = 135/307 (43%), Gaps = 22/307 (7%)
Query: 23 VEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFIDILR 82
+ + +P+LS +L+ + ++ D EV S +++V+ R DI R
Sbjct: 39 LPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEI-VSPGSVLVSGRLLSDITR 97
Query: 83 SLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCIL 142
+LP + V +++E + + G ++F+L T+ ++YP TL + + L + +
Sbjct: 98 ALPN-KPVDVHVEGNRVALTCGNARFSLPTMPVEDYP--TLPTLPEETGLLPAELFAEAI 154
Query: 143 NMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSD-----I 197
+ V + + D L G+ + + ++ ++D RL ++ K+S+ S +
Sbjct: 155 SQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVREL----KWSASSPDIEAAV 210
Query: 198 IIPRKTVFTLQRLLENKENPVELKISNNQXXX-------XXXXXXXXXXXXDGKFLDYKY 250
++P KT+ + + V L + D +F ++
Sbjct: 211 LVPAKTLAEAAKAGIGGSD-VRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFPKFRQ 269
Query: 251 VISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKASEEL 310
++ ++ ++ +L+ +++ +++++ D+ VR+ ++++ + + +A E+L
Sbjct: 270 LLPTEHTAVATMDVAELIEAIKLVALVA-DRGAQVRMEFADGSVRLSAGADDVGRAEEDL 328
Query: 311 EINYNGK 317
++Y G+
Sbjct: 329 VVDYAGE 335
>pdb|1BGW|A Chain A, Topoisomerase Residues 410-1202
pdb|1BJT|A Chain A, Topoisomerase Ii Residues 409-1201
Length = 793
Score = 60.8 bits (146), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 34/102 (33%), Positives = 53/102 (51%), Gaps = 7/102 (6%)
Query: 780 CELYIVEGDSA-----GGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQXXXXXX 834
C L + EGDSA G GRD + PLRGK+LN+ +A ++I+ + +
Sbjct: 35 CTLVLTEGDSALSLAVAGLAVVGRD--YYGCYPLRGKMLNVREASADQILKNAEIQAIKK 92
Query: 835 XXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFF 876
+ + + LRY ++IMTD D DG+HI+ L++ F
Sbjct: 93 IMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFL 134
>pdb|2RGR|A Chain A, Topoisomerase Iia Bound To G-segment Dna
Length = 759
Score = 60.8 bits (146), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 34/102 (33%), Positives = 53/102 (51%), Gaps = 7/102 (6%)
Query: 780 CELYIVEGDSA-----GGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQXXXXXX 834
C L + EGDSA G GRD + PLRGK+LN+ +A ++I+ + +
Sbjct: 25 CTLVLTEGDSALSLAVAGLAVVGRD--YYGCYPLRGKMLNVREASADQILKNAEIQAIKK 82
Query: 835 XXXXXXEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFF 876
+ + + LRY ++IMTD D DG+HI+ L++ F
Sbjct: 83 IMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFL 124
>pdb|3CWV|A Chain A, Crystal Structure Of B-Subunit Of The Dna Gyrase From
Myxococcus Xanthus
pdb|3CWV|B Chain B, Crystal Structure Of B-Subunit Of The Dna Gyrase From
Myxococcus Xanthus
Length = 369
Score = 48.9 bits (115), Expect = 2e-05, Method: Composition-based stats.
Identities = 43/226 (19%), Positives = 94/226 (41%), Gaps = 17/226 (7%)
Query: 506 GISVSPIKIIGDTNKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDE 565
G +V+P++ + + ++G ++HF D IF + F L +R EL+ L G+ ++ D
Sbjct: 136 GAAVTPMEPMPVSAERGVRVHFVPDATIFEVLAFDRARLSRRCNELAALAPGLRVSFADL 195
Query: 566 RXXXXXXXXXXXXTSGFVSYINKSKLVVH--PTIFQAXXXXXXXXXXXXXXDVSMQWNNS 623
+ + + + +++ +H P +F ++QW
Sbjct: 196 QRGERTLWHLPGGVAQWAHVLTEARPQLHPEPVVFD-------FTWDGLRVQCALQWCED 248
Query: 624 YNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTC 683
+ +L F N + V G H+ G+ + A+ K E ++ + +GLT
Sbjct: 249 EDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGE------TRGAFPWARVAQGLTA 302
Query: 684 VLSIKIPDPK--FNSQTKNKLVSSEVRKPVEEIIIKTLFDFLQENP 727
++++ P + F TK L + + + + + + L+E+P
Sbjct: 303 IVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELLREHP 348
Score = 44.7 bits (104), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/44 (47%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 358 LEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKI 401
+E VRKRP MY GD + GLHH V+ +LD A +E+ G C +
Sbjct: 12 VENVRKRPGMYCGDVGE-YGLHHLVYFLLDVAYEEARRGECRDV 54
>pdb|2Y69|D Chain D, Bovine Heart Cytochrome C Oxidase Re-Refined With
Molecular Oxygen
pdb|2Y69|Q Chain Q, Bovine Heart Cytochrome C Oxidase Re-Refined With
Molecular Oxygen
Length = 169
Score = 29.6 bits (65), Expect = 9.5, Method: Composition-based stats.
Identities = 28/101 (27%), Positives = 44/101 (43%), Gaps = 9/101 (8%)
Query: 39 KNSEKISFLSTDTEVQITTY-----TAVGYGNSSIN----IIVAARKFIDILRSLPETEK 89
K EK S+ S + ++ Y + N S N ++ AA FI L EK
Sbjct: 63 KEKEKASWSSLSIDEKVELYRLKFKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEK 122
Query: 90 VTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFE 130
+Y H F + +K T + LD K PI ++K+D++
Sbjct: 123 HYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYD 163
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 0.138 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,709,474
Number of Sequences: 62578
Number of extensions: 1091177
Number of successful extensions: 3326
Number of sequences better than 100.0: 54
Number of HSP's better than 100.0 without gapping: 49
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 3145
Number of HSP's gapped (non-prelim): 76
length of query: 1161
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1052
effective length of database: 8,152,335
effective search space: 8576256420
effective search space used: 8576256420
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: 57 (26.6 bits)