RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy8714
(562 letters)
>d1mw9x_ e.10.1.1 (X:) DNA topoisomerase I, 67K N-terminal domain
{Escherichia coli [TaxId: 562]}
Length = 591
Score = 275 bits (704), Expect = 1e-85
Identities = 116/507 (22%), Positives = 190/507 (37%), Gaps = 26/507 (5%)
Query: 58 GHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCD 117
D N VDP + E K K+ + L A+ + + L D D
Sbjct: 55 AKKPKKDERGALVNRMGVDPWHNWEAHYEVLPG--KEKVVSELKQLAEKADHIYLATDLD 112
Query: 118 KEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDAR 177
+EGE I + + E + R F+ IT I+ A + NI + AR
Sbjct: 113 REGEAIAWHLREVIG-----GDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQAR 167
Query: 178 QELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYW 237
+ +D +G + K +S G Q+ + VER +I+ F PE +W
Sbjct: 168 RFMDRVVGYMVSPLLWKKIARG--------LSAGRVQSVAVRLVVEREREIKAFVPEEFW 219
Query: 238 LLDLTLNLNG---VAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSK--TK 292
+D + +A+ VT F AV + ++ K
Sbjct: 220 EVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKP 279
Query: 293 PQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQ 352
T L + AS+ LG G M +A+RLY GY++Y RT++T + D V ++R
Sbjct: 280 GAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQ--DAVNMVRGY 337
Query: 353 ESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATR-TQLDGDAWRLYDYIVRHF 411
S ++ E + SK + P +A ++ DA +LY I R F
Sbjct: 338 ISDNFGKKYLPESPNQYASKENSQEAREAIRPSDVNVMAESLKDMEADAQKLYQLIWRQF 397
Query: 412 IGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSA--MKNESIPDFKPGDL 469
+ Y D + L G+T VM ++ +P GD
Sbjct: 398 VACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDA 457
Query: 470 IPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRL 529
+ + + + T PP +E+ L+ +EK GIG ++ I+ I R YV V RR
Sbjct: 458 LTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRV-ENRRF 516
Query: 530 VPTSLGIVLVHGYQKIDRELVEPTMRS 556
+G ++ ++ REL+ +
Sbjct: 517 YAEKMGEIVTDRLEENFRELMNYDFTA 543
>d1i7da_ e.10.1.1 (A:) DNA topoisomerase III {Escherichia coli
[TaxId: 562]}
Length = 620
Score = 241 bits (614), Expect = 2e-72
Identities = 104/547 (19%), Positives = 200/547 (36%), Gaps = 51/547 (9%)
Query: 51 FKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATP---KLKLPAFLANEAKDC 107
+T GH++ Y++ L EK + P K + +
Sbjct: 36 QVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEA 95
Query: 108 EFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPN 167
+V D D+EG+ + EV++ ++ + + V R + + + ++ A+ L +
Sbjct: 96 SEIVHAGDPDREGQLLVDEVLDYLQ--LAPEKRQQVQRCLINDLNPQAVERAIDRLRSNS 153
Query: 168 IFEARSVDA--RQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERH 225
F V A R D G TR T + ++S G QTP LG V R
Sbjct: 154 EFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQ---GVLSVGRVQTPVLGLVVRRD 210
Query: 226 DKIRTFKPEPYWLLDLTLNLNGVA------------VSVTWSRGHIFDKSTCNVFFKAVE 273
++I F + ++ + + G + + +
Sbjct: 211 EEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRIS 270
Query: 274 KEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQ-GYVSYP 332
+ + V +S++ P + L A+ G+ + + I ++LY +++P
Sbjct: 271 GQPAI-VTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITFP 329
Query: 333 RTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPR--KGKDVGDHPPITPTKL 390
R++ PE S D + + + + + R K V H I PT
Sbjct: 330 RSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTAR 389
Query: 391 ATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTG- 449
++ L + ++Y+ I R ++ C D V+ + V + +A F +A++L G+
Sbjct: 390 SSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTL 449
Query: 450 ---VMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLME-------- 498
+P GD + + ++VER+T PP + T++ L+S M
Sbjct: 450 LGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQD 509
Query: 499 ---------KHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDREL 549
G+GT+A+ I + +R ++T GR + T G L H +
Sbjct: 510 KDLKKILRATDGLGTEATRAGIIELLFKRGFLTK-KGRYIHSTDAGKALFHSLPE---MA 565
Query: 550 VEPTMRS 556
P M +
Sbjct: 566 TRPDMTA 572
>d1gkub3 e.10.1.1 (B:499-1054) Topoisomerase "domain" of reverse
gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}
Length = 556
Score = 199 bits (506), Expect = 2e-57
Identities = 101/536 (18%), Positives = 181/536 (33%), Gaps = 69/536 (12%)
Query: 41 VGPLFGDLVLFKMTSVCGHIMGL-------------DFTSKYNNWDKVDPLELF------ 81
V + + +T+ GH++ L F Y + +
Sbjct: 39 VYEIPMQKYVLMVTASIGHVVDLITNRGFHGVLVNGRFVPVYASIKRCRDCGYQFTEDRE 98
Query: 82 SCPTEKREATP-KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP 140
SCP E L A D EF+++ D D EGE I +++ ++
Sbjct: 99 SCPKCGSENVDNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNL------LSGC 152
Query: 141 KTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKY 200
V RA F +T + I A+ +L + ++ R+ D IG ++ + F +
Sbjct: 153 GAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFNNRN 212
Query: 201 GDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIF 260
+S G QT LG+ ++R + R + F
Sbjct: 213 -------LSAGRAQTLVLGWIIDRFQESRERRKIAIV--------------------RDF 245
Query: 261 DKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIA 320
D + E+E +T+ V+ + +T T ++ A+ L MQIA
Sbjct: 246 DL-----VLEHDEEEFDLTIKLVEEREELRTPLPPYTTETMLSDANRILKFSVKQTMQIA 300
Query: 321 ERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVG 380
+ L+ G ++Y RT++T+ + +A + I R
Sbjct: 301 QELFENGLITYHRTDSTRVSDVGQRIAKEYLGDDFVGREWGESG-AHECIRPTRPLTRDD 359
Query: 381 DHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAK 440
I L L + + LYD I R F+ + C K + E
Sbjct: 360 VQRLIQEGVLVV-EGLRWEHFALYDLIFRRFMASQCRPFKVVVKKYSIEFDGKTAEEE-- 416
Query: 441 YLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKH 500
++ + A+ + + G VK T+SE+I +M++
Sbjct: 417 RIVRAEGRAYELYRAVWVK--NELPTGTFRVKAEVK----SVPKVLPFTQSEIIQMMKER 470
Query: 501 GIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
GIG ++ ++ + RNYV R++PT LGI + + + V
Sbjct: 471 GIGRPSTYATIVDRLFMRNYVVE-KYGRMIPTKLGIDVFRFLVRRYAKFVSEDRTR 525
>d1cy9a_ e.10.1.1 (A:) DNA topoisomerase I, 67K N-terminal domain
{Escherichia coli [TaxId: 562]}
Length = 260
Score = 112 bits (280), Expect = 1e-28
Identities = 56/266 (21%), Positives = 99/266 (37%), Gaps = 18/266 (6%)
Query: 231 FKPEPYWLLDLTLNLNG---VAVSVTWSRGH---IFDKSTCNVFFKAVEKEKHVTVVDVQ 284
F PE +W +D + +A+ VT +K +EK ++ +V++ +
Sbjct: 1 FVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARY-SVLERE 59
Query: 285 SSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFD 344
+ T L + AS+ LG G M +A+RLY GY++Y RT++T ++
Sbjct: 60 DKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAV 119
Query: 345 LVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATR----TQLDGDA 400
+ + S ++G + K H I P+ + ++ DA
Sbjct: 120 NMV---RGYISDNFGKKYLPE--SPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADA 174
Query: 401 WRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNES 460
+LY I R F+ Y D + L G+T VM +E
Sbjct: 175 QKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDED 234
Query: 461 --IPDFKPGDLIPIQSVKMVERKTTP 484
+P GD + + + + T P
Sbjct: 235 RILPAVNKGDALTLVELTPAQHFTKP 260
>d1nkua_ a.96.1.4 (A:) 3-Methyladenine DNA glycosylase I (Tag)
{Escherichia coli [TaxId: 562]}
Length = 187
Score = 28.0 bits (62), Expect = 2.1
Identities = 29/143 (20%), Positives = 46/143 (32%), Gaps = 25/143 (17%)
Query: 38 HEWVGPLFGDLVLFKMTSVCGHIMGLDFT---SKYNNWDKV----DPLELFSCPTEKREA 90
+EW P LF+M + G GL + K N+ DP+++ + E E
Sbjct: 19 NEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQFDPVKVAAMQEEDVER 78
Query: 91 T--------PKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKT 142
+ K+ A + N +L ++ GE V V HQ + T
Sbjct: 79 LVQDAGIIRHRGKIQAIIGN-------ARAYLQMEQNGEPFADFVWSFVNHQPQMTQATT 131
Query: 143 VWRARFSAITDKDIKAAMWNLVK 165
+ A L K
Sbjct: 132 ---LSEIPTSTPASDALSKALKK 151
>d1jb0e_ b.34.4.2 (E:) Photosystem I accessory protein E (PsaE)
{Synechococcus elongatus [TaxId: 32046]}
Length = 69
Score = 25.5 bits (56), Expect = 3.7
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 222 VERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRG 257
V+R K++ +PE YW ++ G SV + G
Sbjct: 1 VQRGSKVKILRPESYWYNEV-----GTVASVDQTPG 31
>d1mtyb_ a.25.1.2 (B:) Methane monooxygenase hydrolase beta subunit
{Methylococcus capsulatus [TaxId: 414]}
Length = 384
Score = 27.9 bits (62), Expect = 3.7
Identities = 9/70 (12%), Positives = 15/70 (21%)
Query: 205 ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKST 264
+ + DKI + L + G S + +
Sbjct: 159 SQGAREALSDVTRVSLAFWGFDKIDIAQMIQLERGFLAKIVPGFDESTAVPKAEWTNGEV 218
Query: 265 CNVFFKAVEK 274
AVE
Sbjct: 219 YKSARLAVEG 228
>d1f61a_ c.1.12.7 (A:) Isocitrate lyase {Mycobacterium tuberculosis
[TaxId: 1773]}
Length = 418
Score = 27.7 bits (61), Expect = 3.8
Identities = 11/78 (14%), Positives = 21/78 (26%), Gaps = 19/78 (24%)
Query: 295 ALNTVELMRVASSGLGMGPHHAMQIAERLY-TQGYVSYPRTETTQYPENFDLVAVLRQQE 353
+ +L + M + +Q E +GY A Q+E
Sbjct: 355 NYSMFDLAY-GYAQNQMSAYVELQEREFAAEERGYT-----------------ATKHQRE 396
Query: 354 SSPDWGDHVREVLSNGIS 371
+ D + + S
Sbjct: 397 VGAGYFDRIATTVDPNSS 414
>d1gxie_ b.34.4.2 (E:) Photosystem I accessory protein E (PsaE)
{Cyanobacterium (Synechocystis sp.), pcc 6803 [TaxId:
1143]}
Length = 73
Score = 25.6 bits (56), Expect = 4.9
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 222 VERHDKIRTFKPEPYWLLDLTLNLNGVAVSV 252
+ R DK+R + E YW D+ G SV
Sbjct: 2 LNRGDKVRIKRTESYWYGDV-----GTVASV 27
>d1xm5a_ d.92.1.15 (A:) Hypothetical protein YbeY {Escherichia coli
[TaxId: 562]}
Length = 152
Score = 26.5 bits (58), Expect = 6.2
Identities = 9/50 (18%), Positives = 18/50 (36%)
Query: 432 DEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERK 481
E ++ Y T V+++ + GDL+ + V E +
Sbjct: 49 AESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQ 98
>d1vf8a1 c.1.8.5 (A:1-245,A:316-372) Chitinase-like lectin ym1,
saccharide binding domain {Mouse (Mus musculus) [TaxId:
10090]}
Length = 302
Score = 26.7 bits (58), Expect = 8.7
Identities = 5/20 (25%), Positives = 10/20 (50%)
Query: 435 FTMEAKYLLHPGFTGVMTWS 454
F ++A++L G + W
Sbjct: 251 FKLKAQWLKDNNLGGAVVWP 270
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
0.320 0.136 0.416
Gapped
Lambda K H
0.267 0.0500 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 2,133,022
Number of extensions: 100491
Number of successful extensions: 248
Number of sequences better than 10.0: 1
Number of HSP's gapped: 229
Number of HSP's successfully gapped: 12
Length of query: 562
Length of database: 2,407,596
Length adjustment: 90
Effective length of query: 472
Effective length of database: 1,171,896
Effective search space: 553134912
Effective search space used: 553134912
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: 55 (25.5 bits)