RPS-BLAST 2.2.22 [Sep-27-2009]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= gi|254780353|ref|YP_003064766.1| DNA topoisomerase IV subunit A
[Candidatus Liberibacter asiaticus str. psy62]
(753 letters)
>d1ab4a_ e.11.1.1 (A:) DNA Gyrase A {Escherichia coli [TaxId: 562]}
Length = 493
Score = 450 bits (1158), Expect = e-127
Identities = 210/496 (42%), Positives = 297/496 (59%), Gaps = 45/496 (9%)
Query: 40 ERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLV 99
RA+PD+RDG KPVHRR+++AM+ +G D+ A+KKSAR+VG+VIGK HPHGD +VYD++V
Sbjct: 2 GRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIV 61
Query: 100 RLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYN 159
R+AQPF RY L+ GQGNFG+IDGDSAAA RYTE R+ ++A ++ ++++ VDF D Y+
Sbjct: 62 RMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYD 121
Query: 160 EEDSEPVVFPSKFPNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLE 219
+ P V P+K PNLL NG+SGIAVGMAT+IP HN+ E+ LA ID+ +ISIE L+E
Sbjct: 122 GTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLME 181
Query: 220 YIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWCVEEVGR-GSWCIVVTEIPYQVQ 278
+I GPDFPT II R I E+YR GRG +RAR VE + G I+V EIPYQV
Sbjct: 182 HIPGPDFPTAAIIN-GRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRETIIVHEIPYQVN 240
Query: 279 KSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETR 338
K+RLIEKIAEL+ KR+ + +RDES +D ++ R ++++ +++ + ++
Sbjct: 241 KARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVS 300
Query: 339 FPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYL 398
F +NM L G+ P++M L I+ ++ HRREV+ RR+ F ++ R IL+ L +A
Sbjct: 301 FGINMVALHHGQ-PKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALA 359
Query: 399 NIDEIIAIIRNEDKPKPVMV-------------------------------------SRF 421
NID II +IR+ P +
Sbjct: 360 NIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLY 419
Query: 422 SLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIRE 481
LTE Q AIL+LRL+ L LE ++ E LL + ++ +L S + I E+
Sbjct: 420 YLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELEL 479
Query: 482 VKEIFSKSTDLGRRRT 497
V+E F +RRT
Sbjct: 480 VREQFGD-----KRRT 490
>d1bjta_ e.11.1.1 (A:) DNA topoisomerase II, C-terminal fragment
(residues 410-1202) {Baker's yeast (Saccharomyces
cerevisiae) [TaxId: 4932]}
Length = 760
Score = 225 bits (573), Expect = 1e-59
Identities = 93/539 (17%), Positives = 194/539 (35%), Gaps = 90/539 (16%)
Query: 10 NTLVEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFG 69
T+++ +K + + + + + ++L+ R+IP++ DGFKP R++++ + L
Sbjct: 242 GTVLDPTLKEIPISDFINKELILFSLADN-IRSIPNVLDGFKPGQRKVLYGCFKKNLKSE 300
Query: 70 AAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQR----YPLISGQGNFGNIDGDS 125
+ A V E + HG+QS+ +++ LAQ FV L +G G
Sbjct: 301 LKVAQLAPYVSECTA--YHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKD 358
Query: 126 AAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANGTSGIAV 185
AAA RY + ++ I D+ + + EP + P +L NG GI
Sbjct: 359 AAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKT-VEPEWYLPILPMILVNGAEGIGT 417
Query: 186 GMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRL 245
G +T IP N EI + L+++ E +E++ + G I
Sbjct: 418 GWSTYIPPFNPLEIIKNIRHLMNDEE--LEQMHPWFRGWTGTIEEI-------------- 461
Query: 246 GRGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKR--IPLLEDIRD 303
+R+ R G + +TE+P + S + E + + P ++D+ +
Sbjct: 462 EPLRYRMYGRI----EQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEE 517
Query: 304 ESAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSM-GRVPQVMPLDGILK 362
+ ++++ ++ + + + +NM G++ + ++ IL
Sbjct: 518 QHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILS 577
Query: 363 EWLAHRREVLFRRSSFRMQAIDRRVEILKG------------LLIAYLNIDEIIAIIRNE 410
E+ R E +R + + VE L + + II + N
Sbjct: 578 EFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENL 637
Query: 411 DKPK----------------------------------------PVMVSRFSLTENQVDA 430
P+ +++ +
Sbjct: 638 GFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTYEY 697
Query: 431 ILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLN-SGKQQWNQIACEIREVKEIFSK 488
+L +R+ SL K ++ + E +++LL S K WN +++ + + +
Sbjct: 698 LLGMRIWSLTKERYQKLLKQKQEKETE---LENLLKLSAKDIWNT---DLKAFEVGYQE 750
>d1x75a1 e.11.1.1 (A:363-494) DNA Gyrase A {Escherichia coli [TaxId:
562]}
Length = 132
Score = 75.9 bits (186), Expect = 1e-14
Identities = 34/131 (25%), Positives = 50/131 (38%), Gaps = 37/131 (28%)
Query: 374 RRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDKPKPVMVSRF------------ 421
RR+ F ++ R IL+ L +A NID II +IR+ P +
Sbjct: 2 RRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAM 61
Query: 422 -------------------------SLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLA 456
LTE Q AIL+LRL+ L LE ++ E LL
Sbjct: 62 LERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLD 121
Query: 457 EKEKIDSLLNS 467
+ ++ +L S
Sbjct: 122 QIAELLRILGS 132
>d1wp5a_ b.68.10.1 (A:) Topoisomerase IV subunit A, ParC, C-terminal
domain {Bacillus stearothermophilus [TaxId: 1422]}
Length = 323
Score = 71.5 bits (174), Expect = 2e-13
Identities = 31/180 (17%), Positives = 59/180 (32%), Gaps = 8/180 (4%)
Query: 514 MIEKEPITVVISNRGWIRSLKSHSV---DLSALHFKEGDSLKIALHAHTTDRILLLSTDG 570
M+ E + V ++ G+++ S + K+ D L L +T D +LL + G
Sbjct: 1 MVASEDVIVTVTKDGYVKRTSLRSYAASNGQDFAMKDTDRLLAMLEMNTKDVLLLFTNKG 60
Query: 571 KAYTLPAGNLLSGRGH--GEAIQLLIDLNHNQDIVTAF---VYDSTCKLLVVSSKGNAFI 625
P L R G+ I +I ++ +++I+ A ++ L V+ G
Sbjct: 61 NYLYCPVHELPDIRWKDLGQHIANIIPIDRDEEIIKAIPINDFELNGYFLFVTRNGMVKK 120
Query: 626 VEESEIIANTRKGKTFLKVSSEEKMKLVVKVTGDHVAVVGENRKLLIFSIDQIPEMSRGK 685
E A + + V +T + D+ G
Sbjct: 121 TELKHYKAQRYSKPLTGINLKNDDQVVDVHLTDGMNELFLVTHNGYALWFDESEVSIVGV 180
Score = 29.2 bits (64), Expect = 1.4
Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 1/45 (2%)
Query: 653 VVKVTGDHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGG 696
VV D + + E + + I R G + ++ G
Sbjct: 253 VVAQDSDTIYLQTEKSFIETIKVGDIRFSDRYSNGSFVLDEEENG 297
>d1suua_ b.68.10.1 (A:) DNA gyrase A C-terminal domain {Lyme disease
spirochete (Borrelia burgdorferi) [TaxId: 139]}
Length = 304
Score = 41.8 bits (97), Expect = 2e-04
Identities = 35/181 (19%), Positives = 73/181 (40%), Gaps = 14/181 (7%)
Query: 518 EPITVVISNRGWI--------RSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLSTD 569
E I V+++ +G++ + + LS+ +GD + IAL +T D + ++S +
Sbjct: 1 ENIVVMLTKKGFLKRLSQNEYKLQGTGGKGLSSFDLNDGDEIVIALCVNTHDYLFMISNE 60
Query: 570 GKAYTLPAGNLLSGRGHGEAIQL-----LIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAF 624
GK Y + A + + + L D I + LL+ ++ G
Sbjct: 61 GKLYLINAYEIKDSSRASKGQNISELINLGDQEEILTIKNSKDLTDDAYLLLTTASGKIA 120
Query: 625 IVEESEIIANTRKGKTFLKVSSEEKMKLVVKVTGD-HVAVVGENRKLLIFSIDQIPEMSR 683
E ++ A +G +K++ ++ + V D V + + IF+ + +R
Sbjct: 121 RFESTDFKAVKSRGVIVIKLNDKDFVTSAEIVFKDEKVICLSKKGSAFIFNSRDVRLTNR 180
Query: 684 G 684
G
Sbjct: 181 G 181
Score = 39.1 bits (90), Expect = 0.001
Identities = 28/168 (16%), Positives = 58/168 (34%), Gaps = 7/168 (4%)
Query: 540 LSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPAGNLLSGRGHGEAIQLLIDLNHN 599
+ + + D + A ++++ LS G A+ + ++ G + L
Sbjct: 135 VIVIKLNDKDFVTSAEIVFKDEKVICLSKKGSAFIFNSRDVRL-TNRGTQGVCGMKLKEG 193
Query: 600 QDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRKG-KTFLKVSSEEKMKLVVKV-- 656
V LL+VS G + S+I R S++K VV
Sbjct: 194 DLFVKVLSVKENPYLLIVSENGYGKRLNMSKISELKRGATGYTSYKKSDKKAGSVVDAIA 253
Query: 657 --TGDHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGGISDVI 701
D + +V + K L ++ E + +G+++ + + V
Sbjct: 254 VSEDDEILLVSKRSKALRTVAGKVSEQGKDARGIQVLFLDNDSLVSVS 301
Score = 34.1 bits (77), Expect = 0.036
Identities = 21/116 (18%), Positives = 39/116 (33%), Gaps = 4/116 (3%)
Query: 544 HFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPAGNLL-SGRGHGEAIQLLIDLNHNQDI 602
KEGD L +L++S +G L + RG +
Sbjct: 189 KLKEGDLFVKVLSVKENPYLLIVSENGYGKRLNMSKISELKRGATGYTSYKKSDKKAGSV 248
Query: 603 VTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTR--KGKTFLKVSSEEKMKLVVKV 656
V A ++L+VS + A ++ + +G L + ++ + V K
Sbjct: 249 VDAIAVSEDDEILLVSKRSKALRTVAGKVSEQGKDARGIQVLFLDNDSLVS-VSKF 303
Score = 28.7 bits (63), Expect = 1.8
Identities = 24/141 (17%), Positives = 48/141 (34%), Gaps = 13/141 (9%)
Query: 457 EKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLGRRRTT--FCEVSRADKATLQQAM 514
+K+ + S K + + S+ L R T + ++
Sbjct: 142 DKDFVTSAEIVFKDEKVICLSKKGSAFIFNSRDVRLTNRGTQGVCGMKLKEGDLFVKVLS 201
Query: 515 IEKEPITVVISNRGWIRSLKSHSVDLSA----------LHFKEGDSLKIALHAHTTDRIL 564
+++ P +++S G+ + L + K+ S+ A+ D IL
Sbjct: 202 VKENPYLLIVSENGYGKRLNMSKISELKRGATGYTSYKKSDKKAGSVVDAIAVSEDDEIL 261
Query: 565 LLSTDGKAYTLPAGNL-LSGR 584
L+S KA AG + G+
Sbjct: 262 LVSKRSKALRTVAGKVSEQGK 282
>d1sxja1 a.80.1.1 (A:548-693) Replication factor C1 {Baker's yeast
(Saccharomyces cerevisiae) [TaxId: 4932]}
Length = 146
Score = 26.7 bits (59), Expect = 6.5
Identities = 9/49 (18%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 425 ENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWN 473
EN + ++ LE +E N ++ + ++ + S +Q W+
Sbjct: 47 ENYLSTRPSVLKPGQSHLEAV---AEAANCISLGDIVEKKIRSSEQLWS 92
>d1cjaa_ d.144.1.3 (A:) Actin-fragmin kinase, catalytic domain
{Physarum polycephalum [TaxId: 5791]}
Length = 342
Score = 26.8 bits (59), Expect = 6.9
Identities = 9/50 (18%), Positives = 16/50 (32%), Gaps = 2/50 (4%)
Query: 350 RVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLN 399
P+V + +E + SFR+ I LL+ +
Sbjct: 118 HAPKVRVVSSNSEEGTNMLECLAAIDKSFRV--ITTLANQANILLMELVR 165
Database: scop70_1_75
Posted date: Mar 27, 2010 6:21 PM
Number of letters in database: 2,407,596
Number of sequences in database: 13,730
Lambda K H
0.319 0.137 0.389
Gapped
Lambda K H
0.267 0.0576 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 2,793,414
Number of extensions: 137618
Number of successful extensions: 372
Number of sequences better than 10.0: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 17
Length of query: 753
Length of database: 2,407,596
Length adjustment: 92
Effective length of query: 661
Effective length of database: 1,144,436
Effective search space: 756472196
Effective search space used: 756472196
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.7 bits)