RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 000459
(1484 letters)
>3l4j_A DNA topoisomerase 2; topoisomerase, protein-DNA complex, covalently
linked comple supercoiling; HET: DNA PTR TSP; 2.48A
{Saccharomyces cerevisiae} PDB: 3l4k_A* 1bjt_A 1bgw_A
2rgr_A*
Length = 757
Score = 878 bits (2269), Expect = 0.0
Identities = 367/792 (46%), Positives = 491/792 (61%), Gaps = 59/792 (7%)
Query: 426 VRGISKLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSVVGRDRFGVFPLRGKLLNVR 485
+ KLEDAN AG + +CTL+LTEGDSA +LA+AGL+VVGRD +G +PLRGK+LNVR
Sbjct: 3 ITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVR 62
Query: 486 EASSNQVLNNSEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILI 545
EAS++Q+L N+EI IKKI+GL+ +Y + KSLRYGHLMIMTD
Sbjct: 63 EASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTD---------------- 106
Query: 546 FAWITTFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKAT--NKNGK 603
QDHDGSHIKGL+INF+ S +P LL I FL+EFITPI+K +
Sbjct: 107 ------------QDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKN 154
Query: 604 VLSFYSMPDYEAWKESLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQ 663
++FY+MPDYE W+E + +W KYYKGLGTS ++E +EYF N+ H K F
Sbjct: 155 TIAFYNMPDYEKWREEE-SHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGN 213
Query: 664 DGEAIELAFSKKKIEARKKWLLQFEPGNHLDQKEKYIKYSDFVNKELILFSMADLQRSIP 723
D + I+LAFSKKK + RK+WL Q+EPG LD K I SDF+NKELILFS+AD RSIP
Sbjct: 214 DKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIP 273
Query: 724 SMVDGLKPGQRKILFCSFKRNFIKEAKVAQFSGYVSEHSAYHHGEQSLASTILGMAQDFV 783
+++DG KPGQRK+L+ FK+N E KVAQ + YVSE +AYHHGEQSLA TI+G+AQ+FV
Sbjct: 274 NVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFV 333
Query: 784 GSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPKDDDKLLDYLNEDGQQI 843
GSNNI LL PNG FGTR GGKDAA+ARYI+T L+ +TR +F DD L Y+ ED + +
Sbjct: 334 GSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTV 393
Query: 844 EPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLNGEMMEPMHPWYRGFG 903
EP WY+PI+P +LVNG+EGIGTGWS+YIP +NP +I+ N+R L+N E +E MHPW+RG+
Sbjct: 394 EPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWT 453
Query: 904 GTIEKTASKEAGVTYTVTGIIEEVNETTLRIKELPIRRWTQDYREFLESIIDQND---SF 960
GTIE+ Y + G IE++ + L I ELP R WT +E+L + ND +
Sbjct: 454 GTIEEIEPL----RYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPW 509
Query: 961 IRGFRQYSDDTTVDFEVFLSEESMMRTKQEGLLKKFKLTTTISTSNMHLFDSKGVIKKYD 1020
I+ + DD + F + LS E M +T++ G ++FKL + IS NM FD G IKKY+
Sbjct: 510 IKDMEEQHDD-NIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYN 568
Query: 1021 TPEQILEEFFHIRLEFYEKRKKVQLENLELELLKLENKVRFILGVVNGEIVVNNRKRTDL 1080
+ +IL EF+++RLE+Y+KRK E L+ E+ K +V+FI ++ E+ V N+ R +
Sbjct: 569 SVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAI 628
Query: 1081 LLELRQKGFTPFPKNSKSIEAVVAGA-----------------TDETEESEENPEVVNGV 1123
+ EL GF F K K + + E EN
Sbjct: 629 IQELENLGFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEE 688
Query: 1124 QSIDYDYLLSMAIGTLTLEKVQGLLADRDKLNEEVDDLRKATPESLWVKDLDALDMQLDE 1183
Y+YLL M I +LT E+ Q LL + + E+++L K + + +W DL A
Sbjct: 689 LYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAF---EVG 745
Query: 1184 LDKSDARAEEER 1195
+ R E R
Sbjct: 746 YQEFLQRDAEAR 757
>3qx3_A DNA topoisomerase 2-beta; toprim domain, winged-helix domain,
coiled-coil domain, DNA and cleavage, nucleus; HET: DNA
EVP; 2.16A {Homo sapiens}
Length = 803
Score = 846 bits (2187), Expect = 0.0
Identities = 388/811 (47%), Positives = 521/811 (64%), Gaps = 55/811 (6%)
Query: 407 ANFKQSKDLKKNDGTKTEDVRGISKLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSV 466
+ + D D K ++GI KL+DAN AGG++S +CTLILTEGDSAK+LA++GL V
Sbjct: 14 DDDDKVPDPTSVDSVKYSKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGV 73
Query: 467 VGRDRFGVFPLRGKLLNVREASSNQVLNNSEIGNIKKILGLKQGVEYN---NVKSLRYGH 523
+GRDR+GVFPLRGK+LNVREAS Q++ N+EI NI KI+GL+ Y+ ++K+LRYG
Sbjct: 74 IGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGK 133
Query: 524 LMIMTDQVLLAPLSFLLWFILIFAWITTFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKI 583
+MIMTDQ D DGSHIKGLLINFIH WPSLLK
Sbjct: 134 IMIMTDQ----------------------------DQDGSHIKGLLINFIHHNWPSLLK- 164
Query: 584 PSFLVEFITPIVKATNKNGKVLSFYSMPDYEAWKESLGGNASSWSIKYYKGLGTSTSKEG 643
FL EFITPIVKA+ KN + LSFYS+P+++ WK+ + +W IKYYKGLGTST+KE
Sbjct: 165 HGFLEEFITPIVKAS-KNKQELSFYSIPEFDEWKKHIENQ-KAWKIKYYKGLGTSTAKEA 222
Query: 644 KEYFQNITLHKKDFVWEDDQDGEAIELAFSKKKIEARKKWLLQFEPGNHL---------- 693
KEYF ++ H+ F + +D AI LAFSKKKI+ RK+WL F
Sbjct: 223 KEYFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGLPEQF 282
Query: 694 --DQKEKYIKYSDFVNKELILFSMADLQRSIPSMVDGLKPGQRKILFCSFKRNFIKEAKV 751
K++ Y+DF+NKELILFS +D +RSIPS+VDG KPGQRK+LF FKRN +E KV
Sbjct: 283 LYGTATKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKV 342
Query: 752 AQFSGYVSEHSAYHHGEQSLASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASAR 811
AQ +G V+E SAYHHGEQ+L TI+ +AQ+FVGSNNINLLQP GQFGTR GGKDAAS R
Sbjct: 343 AQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPR 402
Query: 812 YIFTRLSPITRFLFPKDDDKLLDYLNEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYI 871
YIFT LS + R LFP DD LL +L +D Q++EP WY+PIIP VL+NG+EGIGTGW+ +
Sbjct: 403 YIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKL 462
Query: 872 PNYNPRDIVANVRRLLNGEMMEPMHPWYRGFGGTIEKTASKEAGVTYTVTGIIEEVNETT 931
PNY+ R+IV NVRR+L+G PM P Y+ F GTI++ Y V+G I V+ T
Sbjct: 463 PNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQN----QYAVSGEIFVVDRNT 518
Query: 932 LRIKELPIRRWTQDYREFLESIIDQN----DSFIRGFRQYSDDTTVDFEVFLSEESMMRT 987
+ I ELP+R WTQ Y+E + + + I +++Y DTTV F V ++EE + +
Sbjct: 519 VEITELPVRTWTQVYKEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQA 578
Query: 988 KQEGLLKKFKLTTTISTSNMHLFDSKGVIKKYDTPEQILEEFFHIRLEFYEKRKKVQLEN 1047
+ GL K FKL TT++ ++M LFD G +KKY+T + IL+EFF +RL +Y RK+ +
Sbjct: 579 EAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGM 638
Query: 1048 LELELLKLENKVRFILGVVNGEIVVNNRKRTDLLLELRQKGFTPFPKNSKSIEAVVAGAT 1107
L E KL N+ RFIL + G+I + NR + DL+ L Q+G+ P + A
Sbjct: 639 LGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQEKAAEE 698
Query: 1108 DETEESEENPEVVNGVQSI-DYDYLLSMAIGTLTLEKVQGLLADRDKLNEEVDDLRKATP 1166
DET+ ++ +G S D++Y+L+M++ +LT EKV+ L+ RD EV+DL++ +P
Sbjct: 699 DETQNQHDDSSSDSGTPSGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSP 758
Query: 1167 ESLWVKDLDALDMQLDELDKSDARAEEERMK 1197
LW +DL A +LD+++ +
Sbjct: 759 SDLWKEDLAAFVEELDKVESQEREDGAPGFS 789
>1pvg_A DNA topoisomerase II; GHKL ATPase domain; HET: DNA ANP; 1.80A
{Saccharomyces cerevisiae} SCOP: d.14.1.3 d.122.1.2 PDB:
1qzr_A*
Length = 418
Score = 588 bits (1519), Expect = 0.0
Identities = 199/420 (47%), Positives = 279/420 (66%), Gaps = 22/420 (5%)
Query: 16 NVVGPTAPNKTIEEMYQKKSQLEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISY 75
++V + + + YQK SQLEHIL RPDTYIGS+E Q WIY+EE+ MI + ++
Sbjct: 2 HMVTMSTEPVSASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTI 61
Query: 76 VPGLYKIFDEILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYV 135
VPGL+KIFDEILVNAADNK RDP M + V I E I V N G G+P+EIH +E +Y+
Sbjct: 62 VPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYI 121
Query: 136 PELIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYKQVFTNN 195
PE+IFGHLLTSSNYDD+ KK TGGRNGYGAKL NIFSTEFI+ETAD +KY Q + NN
Sbjct: 122 PEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENN 181
Query: 196 MGKKSEPNISKCKEGDNWTKVSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKV 255
M P I+ K+G ++TKV+FKPDL +F M L++D++ +M++RV D+ G + + + V
Sbjct: 182 MSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSV-RDINV 240
Query: 256 ELNGHRVPVKSFAEYVDMYPKSVTRF-------------------HERVNERWEICVTLS 296
LNG + +++F YV++Y KS+ + +ER+N RWE+ +S
Sbjct: 241 YLNGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWEVAFAVS 300
Query: 297 EGQFQQVSFVNGIATIKGGTHVDYVANQVANHVMAVVNKKNKNANVKAHNVKNHLWVFVN 356
+ FQQ+SFVN IAT GGTHV+Y+ +Q+ + ++ KK K +VK+ +KN++++F+N
Sbjct: 301 DISFQQISFVNSIATTMGGTHVNYITDQIVKKISEILKKKKK-KSVKSFQIKNNMFIFIN 359
Query: 357 ALIDNPAFDSQTKETLTLRQSSFGSKCELSEEFLKKVTAKSGIVETLLSWANFKQSKDLK 416
LI+NPAF SQTKE LT R FGS+CE+ E++ K+ K+ + + A+ + LK
Sbjct: 360 CLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKI-MKTDLATRMFEIADANEENALK 418
>1zxm_A TOPO IIA ATPase, DNA topoisomerase II, alpha isozyme; GHKL
nucleotide-binding fold; HET: DNA ANP; 1.87A {Homo
sapiens} PDB: 1zxn_A*
Length = 400
Score = 566 bits (1460), Expect = 0.0
Identities = 230/401 (57%), Positives = 297/401 (74%), Gaps = 13/401 (3%)
Query: 26 TIEEMYQKKSQLEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISYVPGLYKIFDE 85
++E +YQKK+QLEHILLRPDTYIGS+E TQ +W+Y+E+ + +R +++VPGLYKIFDE
Sbjct: 1 SVERIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVG-INYREVTFVPGLYKIFDE 59
Query: 86 ILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLT 145
ILVNAADNKQRDPKM ++V ID E++LIS+ N+G G+PV H+ E +YVP LIFG LLT
Sbjct: 60 ILVNAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLT 119
Query: 146 SSNYDDNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYKQVFTNNMGKKSEPNIS 205
SSNYDD+ KK TGGRNGYGAKL NIFST+F +ETA + K +KQ + +NMG+ E +
Sbjct: 120 SSNYDDDEKKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGEMELK 179
Query: 206 KCKEGDNWTKVSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVPVK 265
G+++T ++F+PDL+KF M L+ D+VALM +R D+AG K VKV LNG+++PVK
Sbjct: 180 PFN-GEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGST-KDVKVFLNGNKLPVK 237
Query: 266 SFAEYVDMY--------PKSVTRFHERVNERWEICVTLSEGQFQQVSFVNGIATIKGGTH 317
F YVDMY S+ HE+VN RWE+C+T+SE FQQ+SFVN IAT KGG H
Sbjct: 238 GFRSYVDMYLKDKLDETGNSLKVIHEQVNHRWEVCLTMSEKGFQQISFVNSIATSKGGRH 297
Query: 318 VDYVANQVANHVMAVVNKKNKN-ANVKAHNVKNHLWVFVNALIDNPAFDSQTKETLTLRQ 376
VDYVA+Q+ ++ VV KKNK VKAH VKNH+W+FVNALI+NP FDSQTKE +TL+
Sbjct: 298 VDYVADQIVTKLVDVVKKKNKGGVAVKAHQVKNHMWIFVNALIENPTFDSQTKENMTLQP 357
Query: 377 SSFGSKCELSEEFLKKVTAKSGIVETLLSWANFKQSKDLKK 417
SFGS C+LSE+F+K GIVE++L+W FK L K
Sbjct: 358 KSFGSTCQLSEKFIKAA-IGCGIVESILNWVKFKAQVQLNK 397
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 132 bits (335), Expect = 1e-31
Identities = 117/476 (24%), Positives = 200/476 (42%), Gaps = 75/476 (15%)
Query: 440 GRNSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVFPLRGKLLNVREASSNQVLNNSE 497
G+ E+ L + EGDSA G + RD+ + P+RGK+LN E SS++VL + E
Sbjct: 38 GQTREESELFIVEGDSA-----GGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQE 92
Query: 498 IGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWITTFCFMLA 557
+ +I +G+ +++ LRYG + I+ D
Sbjct: 93 VHDIAIAIGV--DPGSDDLSELRYGKICILADA--------------------------- 123
Query: 558 QDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKATNKNGKVLSFYSMPDYEAWK 617
D DG HI LL +P+L + + P + + V + E
Sbjct: 124 -DSDGLHIATLLCALFVKHFPAL--VEEGHLYVAMPPLFRIDIGKDVHYALDDEELETIL 180
Query: 618 ESLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEAIEL--AFSKK 675
+++ GN + I +KGLG + + +E + + + DD A L +KK
Sbjct: 181 KNVKGN-KNPQITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKK 239
Query: 676 KIEARKKWLLQFEPGNHLDQKEKYIKYSDFVNKELILFSMAD--------------LQRS 721
+ RK+WL Q + ++K + + + S+A+ + R+
Sbjct: 240 RAADRKQWLEQKGNLADITVEDK-LTMTSLAHHATENRSVAEFTEQAYLNYAMYVIMDRA 298
Query: 722 IPSMVDGLKPGQRKILF------CSFKRNFIKEAKVAQFSGYVSEHSAYH-HGEQSLAST 774
+P + DGLKP QR+I++ K A+ G V YH HG+ +
Sbjct: 299 LPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTV---GDVL--GKYHPHGDSACYEA 353
Query: 775 ILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPKDDDKLLD 834
++ MAQ F S L++ G +G+ + K A+ RY +LS + L + +
Sbjct: 354 MVLMAQPF--SYRYPLIEGQGNWGSPD-DPKSFAAMRYTEAKLSAYSELLLSELGQGTSE 410
Query: 835 YL-NEDGQQIEPTWYMPI-IPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLN 888
+ N DG EP +P +P +L+NG+ GI G ++ IP +N R++V L+
Sbjct: 411 WQDNFDGSLKEPIT-LPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIALIR 465
>2xcs_B DNA gyrase subunit B, DNA gyrase subunit A; isomerase, type IIA
topoisomerase; HET: DNA 5UA RXV; 2.10A {Staphylococcus
aureus} PDB: 2xct_B* 2xcr_B* 2xcq_A* 2xco_A*
Length = 692
Score = 110 bits (277), Expect = 1e-24
Identities = 120/484 (24%), Positives = 210/484 (43%), Gaps = 118/484 (24%)
Query: 441 RNSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVFPLRGKLLNVREASSNQVLNNSEI 498
++ E+C + L EGDSA G + GRD + PLRGK+LNV +A +++LNN+EI
Sbjct: 16 KSPEECEIFLVEGDSA-----GGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEI 70
Query: 499 GNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWITTFCFMLAQ 558
+ G G +++ K+ RY ++IMTD
Sbjct: 71 RQMITAFGTGIGGDFDLAKA-RYHKIVIMTDA---------------------------- 101
Query: 559 DHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKATNKNGKVLSFYSMPDYEAWKE 618
D DG+HI+ LL+ F + F+ P+++A G V + + P
Sbjct: 102 DVDGAHIRTLLLTFFY--------------RFMRPLIEA----GYV--YIAQPPTG---- 137
Query: 619 SLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEAIELAFSKKKI- 677
YKGLG + + T++ + + +AIE + + +
Sbjct: 138 -------------YKGLGEMNADQ----LWETTMNPEHRALLQVKLEDAIEADQTFEMLM 180
Query: 678 --EARKKWLLQFEPGNHLDQKEKYIKYSDFVNKEL--------ILFSMADL-QRSIPSMV 726
+ + + + + S + + + ++M+ + R++P +
Sbjct: 181 GDVVENRRQFIEDNAVYANLDFAELPQSRINERNITSEMRESFLDYAMSVIVARALPDVR 240
Query: 727 DGLKPGQRKILF------CSFKRNFIKEAKVAQFSGYVSE-HSAYH-HGEQSLASTILGM 778
DGLKP R+IL+ + +++ K A++ V + YH HG+ S+ ++ M
Sbjct: 241 DGLKPVHRRILYGLNEQGMTPDKSYKKSARI------VGDVMGKYHPHGDSSIYEAMVRM 294
Query: 779 AQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPKDDDK-LLDYL- 836
AQDF S L+ G FG+ G AA+ R+ R++ IT L +D +K +D++
Sbjct: 295 AQDF--SYRYPLVDGQGNFGSM--DGDGAAAMRFTEARMTKITLELL-RDINKDTIDFID 349
Query: 837 NEDGQQIEPTWYMPI-IPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLN------G 889
N DG + EP+ +P P +L NG+ GI G ++ IP +N +++ V L
Sbjct: 350 NYDGNEREPS-VLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIA 408
Query: 890 EMME 893
E+ME
Sbjct: 409 ELME 412
>3k9f_C DNA topoisomerase 4 subunit B; quinolone, topoisomerase,
protein-DNA cleavage complex; HET: DNA LFX; 2.90A
{Streptococcus pneumoniae} PDB: 3fof_C* 3foe_C* 3ksa_C*
3ksb_C* 3ltn_C* 3rad_C* 3rae_C* 3raf_C*
Length = 268
Score = 89.9 bits (224), Expect = 1e-19
Identities = 56/229 (24%), Positives = 91/229 (39%), Gaps = 59/229 (25%)
Query: 424 EDVRGISKLEDANLAG------GRNSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVF 475
+D +K + L+G +N + L L EGDSA G + GRDR +
Sbjct: 20 DDKHMKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSA-----GGSAKQGRDRKFQAIL 74
Query: 476 PLRGKLLNVREASSNQVLNNSEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAP 535
PLRGK++N +A +L N EI + +G G ++ +++ Y ++IMTD
Sbjct: 75 PLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADF-SIEDANYDKIIIMTD------ 127
Query: 536 LSFLLWFILIFAWITTFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKI--------PSFL 587
D DG+HI+ LL+ F + + L++ P +
Sbjct: 128 ----------------------ADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYK 165
Query: 588 VEFITPIVKATNKNGKVLSFYSMPDYEAWKESLGGNASSWSIKYYKGLG 636
+ K K Y+ D E +E +++ YKGLG
Sbjct: 166 MSK--------GKGKKEEVAYAWTDGEL-EELRKQFGKGATLQRYKGLG 205
>3m4i_A DNA gyrase subunit B; GYRB, toprim, type II topoisomerase,
tuberculosi quinolone binding site, DNA binding site,
ATP-binding; HET: DNA; 1.95A {Mycobacterium
tuberculosis} PDB: 3ig0_A* 2zjt_A*
Length = 242
Score = 83.3 bits (207), Expect = 9e-18
Identities = 54/208 (25%), Positives = 82/208 (39%), Gaps = 53/208 (25%)
Query: 441 RNSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVFPLRGKLLNVREASSNQVLNNSEI 498
+ + L + EGDSA G + GRD + PLRGK++NV +A ++VL N+E+
Sbjct: 15 TDPRKSELYVVEGDSA-----GGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEV 69
Query: 499 GNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWITTFCFMLAQ 558
I LG E+ ++ LRY +++M D A
Sbjct: 70 QAIITALGTGIHDEF-DIGKLRYHKIVLMAD----A------------------------ 100
Query: 559 DHDGSHIKGLLINFIHSFWPSLLKIPSFLVE----FIT--PIVKATNKNGKVLSFYSMPD 612
D DG HI LL+ + F L+E F+ P+ K + YS +
Sbjct: 101 DVDGQHISTLLLTLLFRFMRP-------LIENGHVFLAQPPLYKLKWQRSDPEFAYSDRE 153
Query: 613 YEAWKESLGGNA----SSWSIKYYKGLG 636
+ E+ I+ YKGLG
Sbjct: 154 RDGLLEAGLKAGKKINKEDGIQRYKGLG 181
>3nuh_B DNA gyrase subunit B; topoisomerase, supercoiling, specialization,
isomera; HET: DNA; 3.10A {Escherichia coli}
Length = 420
Score = 83.4 bits (206), Expect = 1e-16
Identities = 49/167 (29%), Positives = 73/167 (43%), Gaps = 41/167 (24%)
Query: 424 EDVRGISKLEDANLAGG------RNSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVF 475
E R L+ A L G R+ L L EGDSA G + GR+R +
Sbjct: 6 EMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSA-----GGSAKQGRNRKNQAIL 60
Query: 476 PLRGKLLNVREASSNQVLNNSEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAP 535
PL+GK+LNV +A +++L++ E+ + LG G + N LRY ++IMTD
Sbjct: 61 PLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDA----- 115
Query: 536 LSFLLWFILIFAWITTFCFMLAQDHDGSHIKGLLINFIHSFWPSLLK 582
D DGSHI+ LL+ F + P +++
Sbjct: 116 -----------------------DVDGSHIRTLLLTFFYRQMPEIVE 139
>3lnu_A Topoisomerase IV subunit B; PARE, ATP-binding, nucleotide-BI
topoisomerase; 2.20A {Xanthomonas oryzae PV} PDB:
3lps_A*
Length = 408
Score = 79.5 bits (197), Expect = 2e-15
Identities = 54/303 (17%), Positives = 112/303 (36%), Gaps = 50/303 (16%)
Query: 101 DAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGR 160
++V + ++ V + G G+PV+IH EE + ELI L +++ +GG
Sbjct: 72 KQIEVTLYKDGS-CEVSDDGRGMPVDIHPEEKIPGVELILTRLHAGGKFNNRNYTFSGGL 130
Query: 161 NGYGAKLTNIFSTEFIIETA-DGKRLKKYKQVFTNNMGKKSEP--NISKCKEGDNWTKVS 217
+G G + N ST+ + +G +++ F + G + + + + T++
Sbjct: 131 HGVGVSVVNALSTKVELFIKREG---SEHRMEFRD--GNAASKLEVVGTVGKKNTGTRLR 185
Query: 218 FKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVP----------VKSF 267
F D F+ + + A L + V+L+ ++ +
Sbjct: 186 FWADPKYFDTPKFNVRALR---HLLRAKA-VLCPGLTVKLHDEATGEQDSWYFENGLRDY 241
Query: 268 AEYVD-----MYPKSVTRFHERVNERWEICVT-LSEGQFQQVSFVNGIATIKGGTHV--- 318
+ + ++ E + + EG+ Q S+VN I T + GTHV
Sbjct: 242 LKGEMAEHEMLPADLFVGSLKKDTEIVDWAAGWVPEGELVQESYVNLIPTAQHGTHVNGL 301
Query: 319 ---------DYVANQVANHVMAVVNKKNKNANVKAHNVKNHLWVFVNALIDNPAFDSQTK 369
++ + N + + +V + + ++ + +P F QTK
Sbjct: 302 RSGLTDALREFCDFR---------NLLPRGVKLAPEDVWDRVTFVLSLKMTDPQFSGQTK 352
Query: 370 ETL 372
E L
Sbjct: 353 ERL 355
>1kij_A DNA gyrase subunit B; topoisomerase, gyrase B-coumarin complex,
isomerase; HET: DNA NOV; 2.30A {Thermus thermophilus}
SCOP: d.14.1.3 d.122.1.2
Length = 390
Score = 79.4 bits (197), Expect = 2e-15
Identities = 53/243 (21%), Positives = 103/243 (42%), Gaps = 41/243 (16%)
Query: 101 DAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGR 160
+ V ++++ ++V ++G G+PV++ EEG E+I+ L + ++ K +GG
Sbjct: 54 TEILVRLNED-GSLTVEDNGRGIPVDLMPEEGKPAVEVIYNTLHSGGKFEQGAYKVSGGL 112
Query: 161 NGYGAKLTNIFSTEFIIETA-DGKRLKKYKQVFTNNMGKKSEP--NISKCKEGDNWTKVS 217
+G GA + N S ++E +GK ++ F+ G+ +EP + + G T+V+
Sbjct: 113 HGVGASVVNALSEWTVVEVFREGKH---HRIAFSR--GEVTEPLRVVGEAPRGKTGTRVT 167
Query: 218 FKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVP----------VKSF 267
FKPD F + + R+ ++A L +K+ + V SF
Sbjct: 168 FKPDPEIFGNLRFDPSKIR---ARLREVA-YLVAGLKLVFQDRQHGKEEVFLDKGGVASF 223
Query: 268 AEYVDMYPKSVTRFHERV----NERWEICV--------TLSEGQFQQVSFVNGIATIKGG 315
A+ + + +E+ E+ V + ++ N I T GG
Sbjct: 224 AKALA---EGEDLLYEKPFLIRGTHGEVEVEVGFLHTQGYNAEIL---TYANMIPTRDGG 277
Query: 316 THV 318
TH+
Sbjct: 278 THL 280
>1s16_A Topoisomerase IV subunit B; two-domain protein complexed with
ADPNP; HET: ANP; 2.10A {Escherichia coli} SCOP: d.14.1.3
d.122.1.2
Length = 390
Score = 77.5 bits (192), Expect = 7e-15
Identities = 61/304 (20%), Positives = 108/304 (35%), Gaps = 51/304 (16%)
Query: 101 DAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGR 160
V V++ + + V + G G+PV+IH EEGV ELI L + + + +GG
Sbjct: 53 KRVDVILHADQS-LEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGL 111
Query: 161 NGYGAKLTNIFSTEFIIETA-DGKRLKKYKQVFTNNMGKKSEP--NISKCKEGDNWTKVS 217
+G G + N S + DG + Y F N G+K + + C + + T V
Sbjct: 112 HGVGISVVNALSKRVEVNVRRDG---QVYNIAFEN--GEKVQDLQVVGTCGKRNTGTSVH 166
Query: 218 FKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVP----------VKSF 267
F PD F+ + + A L V++ + +
Sbjct: 167 FWPDETFFDSPRFSVSRLT---HVLKAKA-VLCPGVEITFKDEINNTEQRWCYQDGLNDY 222
Query: 268 AEYVD-----MYPKSVTRFHERVNERWEICVTLSEGQFQQV--SFVNGIATIKGGTHV-- 318
+ K E + + + + S+VN I T++GGTHV
Sbjct: 223 LAEAVNGLPTLPEKPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNG 282
Query: 319 ----------DYVANQVANHVMAVVNKKNKNANVKAHNVKNHLWVFVNALIDNPAFDSQT 368
++ + N + + A ++ + ++ + +P F QT
Sbjct: 283 LRQGLLDAMREFCEYR---------NILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQT 333
Query: 369 KETL 372
KE L
Sbjct: 334 KERL 337
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 77.6 bits (190), Expect = 2e-14
Identities = 94/658 (14%), Positives = 196/658 (29%), Gaps = 215/658 (32%)
Query: 218 FKPDLAK-FNMTHLEDDVVALMKKRVVD--------------LAGCL---GKSV------ 253
F+ F+ ++D +++ K +D L L + +
Sbjct: 25 FEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVE 84
Query: 254 --------------KVELNGHRVPVKSFAEYVD-MY--PKSVTRFH-ERVNERWEICVTL 295
K E + + + E D +Y + +++ R+ ++ L
Sbjct: 85 EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQAL 144
Query: 296 SEGQFQQVSFVNGIATIKG-GTHVDYVANQVAN------------------------HVM 330
E + + ++G+ G G VA V V+
Sbjct: 145 LELRPAKNVLIDGVL---GSGKTW--VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL 199
Query: 331 AVVNK------KN--------KNANVKAHNVKNHL------WVFVNALI--DN------- 361
++ K N N ++ H+++ L + N L+ N
Sbjct: 200 EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW 259
Query: 362 PAFDSQTKETLTLRQSS------FGSKCELSEEFLKKVTAKSGIVETLLSWANFKQSKDL 415
AF+ K LT R + +S + + LL + + + +DL
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR-PQDL 318
Query: 416 KKNDGTKTEDVRGISKLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSV-VGRDRFGV 474
+V + L++ S+ G +
Sbjct: 319 P-------REVLTTNPR-------------------------RLSIIAESIRDGLATWDN 346
Query: 475 FPLRG--KLLNVREASSNQVLNNSEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVL 532
+ KL + E+S N VL +E ++ + L +
Sbjct: 347 WKHVNCDKLTTIIESSLN-VLEPAE---------YRK----------MFDRLSVFPPSAH 386
Query: 533 LAPLSFL--LWFILIFAWITTFCFMLAQDHDGSHIKGLLINFIHSFWP--SLLKIPSFLV 588
+ P L +WF + I + ++ H L+ P S + IPS +
Sbjct: 387 I-PTILLSLIWFDV----IKSDVMVVVNK---LHKYSLVEK-----QPKESTISIPSIYL 433
Query: 589 EFITPIVKATNKNGKVLSFYSMPD-YEAWKESLGGNASSWSIKY---YKG--LGTSTSKE 642
E + + ++ Y++P +++ + +Y + G L E
Sbjct: 434 ELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP-----PYLDQYFYSHIGHHLKNIEHPE 488
Query: 643 GKEYFQNITLHKKDFVWEDDQDGEAIELAFSKKKIEARKKWLLQFEPGNHLDQKEKYIKY 702
F+ + L DF F ++KI R G+ L+ ++ Y
Sbjct: 489 RMTLFRMVFL---DF-------------RFLEQKI--RHDSTAWNASGSILNTLQQLKFY 530
Query: 703 SDFVNKELILFSMADLQRSIPSMVDGLKPGQRKILFCSFKRNFIKEAKVAQFSGYVSE 760
++ + +R + +++D L P + L CS + ++ A +A+ E
Sbjct: 531 KPYICD-----NDPKYERLVNAILDFL-PKIEENLICSKYTDLLRIALMAEDEAIFEE 582
Score = 69.9 bits (170), Expect = 6e-12
Identities = 101/736 (13%), Positives = 209/736 (28%), Gaps = 214/736 (29%)
Query: 166 KLTNIFSTEFIIETADGKRLKKY-KQVFTNNMGKKSEPNISKCKEGDNWTKVSF-----K 219
+ ++F F+ + D K ++ K + + K+ +I K+ + T F K
Sbjct: 20 DILSVFEDAFV-DNFDCKDVQDMPKSILS----KEEIDHIIMSKDAVSGTLRLFWTLLSK 74
Query: 220 PD--LAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVPVKSFAEYVD-MY-- 274
+ + KF L + LM +K E + + + E D +Y
Sbjct: 75 QEEMVQKFVEEVLRINYKFLMSP------------IKTEQRQPSMMTRMYIEQRDRLYND 122
Query: 275 PKSVTRFH-ERVNERWEICVTLSEGQFQQVSFVNGIATIKG-GTHVDYVANQVANHVMAV 332
+ +++ R+ ++ L E + + ++G+ G G VA V
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL---GSGKTW--VALDVCL----- 172
Query: 333 VNKKNKNANVKAHNVKNHLWVFVNALIDNPAFDSQTKETLTLRQSSFGSKCELSEEFLKK 392
+ V+ W+ + C E L+
Sbjct: 173 ------SYKVQCKMDFKIFWL------------------------NLK-NCNSPETVLE- 200
Query: 393 VTAKSGIVETLLSWA--NFKQSKDLKKNDGTKTEDVRGISKLEDANLAGGRNSEQCTLIL 450
+++ LL N+ D N + + + E L + E C L+L
Sbjct: 201 ------MLQKLLYQIDPNWTSRSDHSSNIKLRIHSI----QAELRRLLKSKPYENCLLVL 250
Query: 451 TEGDSAKALAMAGLSVVGRDRFGVFPLRGK-LLNVREASSNQVLNNSEIGNIKKILGLKQ 509
+AKA F L K LL R L+ + +I +
Sbjct: 251 LNVQNAKAWN-------------AFNLSCKILLTTRFKQVTDFLSAATTTHIS-LDHHSM 296
Query: 510 GVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFA-WITTFCFML-AQDHDGSHIKG 567
+ + VKSL ++ L + +
Sbjct: 297 TLTPDEVKSL--------------------------LLKYLDCRPQDLPREVLTTN---- 326
Query: 568 LLINFIHSFWPSLLK-IPSFLVEFITPIVKATNKNGKVLSFYSMPDYEAWKESLGGNASS 626
P L I + + + AT N + + + + SS
Sbjct: 327 ----------PRRLSIIAESIRDGL-----ATWDN------WKHVNCDKLTTII---ESS 362
Query: 627 WSIKYYKGLGTSTSKEGKEYFQNITLHKKD---------FVWEDDQDGEAIELAFSKKKI 677
L E ++ F +++ +W D + + +
Sbjct: 363 -----LNVL---EPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV-----N 409
Query: 678 EARKKWLLQFEPGNHLDQKEKYIKYSDFVNKELILFSMADLQRSIPSMVDGLKPGQRKIL 737
+ K L++ KE I S+ + + ++ R I+
Sbjct: 410 KLHKYSLVE------KQPKESTI-------------SIPSIYLELKVKLENEYALHRSIV 450
Query: 738 FC-SFKRNFIKEAKVAQF-SGYVSEHSAYHHGEQSLASTILGMAQDFVGSNNINLLQPNG 795
+ + F + + + Y H +H + F+ + L+
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL---DFRFLEQK- 506
Query: 796 QFGTRNQGGKDAASARYI--FTRLSPITRFLFPKDD------DKLLDYLNEDGQQIEPTW 847
R+ AS + +L ++ D + +LD+L + + + +
Sbjct: 507 ---IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSK 563
Query: 848 YMPIIPTVLVNGSEGI 863
Y ++ L+ E I
Sbjct: 564 YTDLLRIALMAEDEAI 579
Score = 68.0 bits (165), Expect = 2e-11
Identities = 75/539 (13%), Positives = 153/539 (28%), Gaps = 161/539 (29%)
Query: 923 IIEEVN--ETTLRIKELPIRRWTQDYREFLESIIDQNDSFI---------------RGFR 965
II + TLR+ + + + ++F+E ++ N F+ R +
Sbjct: 54 IIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI 113
Query: 966 QYSDDTTVDFEVF----LSEESMMRTKQEGLLK----KF----------KLTTTISTSNM 1007
+ D D +VF +S ++ LL+ K K +
Sbjct: 114 EQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLS 173
Query: 1008 HLFDSK---GV----IKKYDTPEQILEE----FFHIRLEFYE-----KRKKVQLENLELE 1051
+ K + +K ++PE +LE + I + K+++ +++ E
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 1052 LLKLENKVRF-----IL-GVVNGEIV---------------------VNNRKRTDLLLEL 1084
L +L + +L V N + ++ T + L+
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293
Query: 1085 RQKGFTPFPKNSKSIEAVVAGATDETEESEE----NPEVVNGV--------------QSI 1126
T P KS+ + E NP ++ + + +
Sbjct: 294 HSMTLT--PDEVKSLLLKYLD-CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV 350
Query: 1127 DYDYL---LSMAIGTLTLEKVQGLLADRDKLNEEVDDLRKATPESLWVKDLDALDMQ-LD 1182
+ D L + ++ L + + + + +W + + M ++
Sbjct: 351 NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA-HIPTILLSLIWFDVIKSDVMVVVN 409
Query: 1183 EL-DKS--DARAEEER---------MKIKGNGNGDAGPKIVAK-RAPKNARKNDKKSN-- 1227
+L S + + +E +K+K IV PK +D
Sbjct: 410 KLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL 469
Query: 1228 -------------NARATEAMGEMDNV--------TKVVKPKGRAGLKKAPAEKL----- 1261
N E M V K ++ A
Sbjct: 470 DQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK-IRHDSTAWNASGSILNTLQQLK 528
Query: 1262 -------DDDEEDE--VPDLKQRLAKLNEQLASTK------LEPSPDQSGVMETEKVQV 1305
D+D + E V + L K+ E L +K + + + E QV
Sbjct: 529 FYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587
Score = 43.3 bits (101), Expect = 7e-04
Identities = 40/253 (15%), Positives = 80/253 (31%), Gaps = 70/253 (27%)
Query: 27 IEEMYQKKSQLEHILLRPDTYIGSIEKHTQALW---IYEEE--------SKTMIHRTISY 75
+M+ + S + P +I +W I + +++ +
Sbjct: 371 YRKMFDRLS-----VFPPSAHIP--TILLSLIWFDVIKSDVMVVVNKLHKYSLVEK--QP 421
Query: 76 VPGLYKIFDEILVNAADNKQRDPKMDAV-KVVIDQEHDLISVHNSGDGVPVEIHQEEGVY 134
I L + K + A+ + ++D +++ +S D +P + Q Y
Sbjct: 422 KESTISIPSIYL----ELKVKLENEYALHRSIVDH-YNIPKTFDSDDLIPPYLDQ----Y 472
Query: 135 VPELIFGHLLTSSNYDDNVKKTTGGRNGY------GAKL----TNIFSTEFIIETADGKR 184
I HL + + + T R + K+ T ++ I+ T ++
Sbjct: 473 FYSHIGHHLKNIEHPE----RMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTL--QQ 526
Query: 185 LKKYKQVFTNNMGK-------------KSEPNISKCKEGDNWTKVSFKPDLAKFNMTHLE 231
LK YK +N K K E N+ K DL + + E
Sbjct: 527 LKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKY----------TDLLRIALMA-E 575
Query: 232 DDVVALMKKRVVD 244
D+ + + V
Sbjct: 576 DEAIFEEAHKQVQ 588
>3ilw_A DNA gyrase subunit A; DNA topology, topoisomerase, antibiotic
resistance, breakage-reunion domain, struct genomics;
HET: DNA; 1.60A {Mycobacterium tuberculosis} PDB:
3ifz_A*
Length = 470
Score = 72.9 bits (180), Expect = 3e-13
Identities = 57/180 (31%), Positives = 92/180 (51%), Gaps = 23/180 (12%)
Query: 720 RSIPSMVDGLKPGQRKILF------CSFKRNFIKEAKVAQFSGYVSEHSA-YH-HGEQSL 771
R++P + DGLKP R++L+ R+ K A+ V+E YH HG+ S+
Sbjct: 9 RALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARS------VAETMGNYHPHGDASI 62
Query: 772 ASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPKDDDK 831
+++ MAQ + S L+ G FG+ G A+ RY RL+P+ + ++ D+
Sbjct: 63 YDSLVRMAQPW--SLRYPLVDGQGNFGSP--GNDPPAAMRYTEARLTPLAMEML-REIDE 117
Query: 832 -LLDYL-NEDGQQIEPTWYMPI-IPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLN 888
+D++ N DG+ EPT +P P +L NGS GI G ++ IP +N R++ V L
Sbjct: 118 ETVDFIPNYDGRVQEPT-VLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALE 176
>3lpx_A GYRA, DNA gyrase, A subunit; topoisomraseii, ATP-binding,
isomerase, nucleo binding; HET: DNA; 2.60A {Colwellia
psychrerythraea} PDB: 2wl2_A* 2y3p_A* 3nuh_A* 1ab4_A
Length = 500
Score = 73.0 bits (180), Expect = 3e-13
Identities = 59/171 (34%), Positives = 90/171 (52%), Gaps = 21/171 (12%)
Query: 720 RSIPSMVDGLKPGQRKILFC------SFKRNFIKEAKVAQFSGYVSEHSAYH-HGEQSLA 772
R++P + DGLKP R++LF + + + K A+V G V YH HG+ ++
Sbjct: 2 RALPDVRDGLKPVHRRVLFAMDVLGNDWNKAYKKSARVV---GDVI--GKYHPHGDTAVY 56
Query: 773 STILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPKDDDK- 831
TI+ MAQ F S L+ G FG+ + G AA+ RY R+S I + D DK
Sbjct: 57 DTIVRMAQPF--SLRYMLVDGQGNFGSVD--GDSAAAMRYTEIRMSKIAHSIL-ADLDKE 111
Query: 832 LLDY-LNEDGQQIEPTWYMPI-IPTVLVNGSEGIGTGWSSYIPNYNPRDIV 880
+D+ N DG + P MP +P +LVNG+ GI G ++ IP +N +++
Sbjct: 112 TVDFVPNYDGTEHIPA-VMPTRVPNLLVNGTSGIAVGMATNIPPHNLTEVI 161
>2nov_A DNA topoisomerase 4 subunit A; protein, PARC, TOPO IV,
GRAM-positive bacteria, quinolone target, DNA binding,
DNA cleavage; HET: DNA; 2.67A {Streptococcus pneumoniae}
PDB: 3foe_A* 3fof_A* 3k9f_A* 3ksa_A* 3ksb_A* 3ltn_A*
3rad_A* 3rae_A* 3raf_A*
Length = 496
Score = 71.0 bits (175), Expect = 2e-12
Identities = 55/171 (32%), Positives = 93/171 (54%), Gaps = 21/171 (12%)
Query: 720 RSIPSMVDGLKPGQRKILF------CSFKRNFIKEAKVAQFSGYVSEHSAYH-HGEQSLA 772
R++P + DGLKP QR+IL+ +F +++ K AK G + +H HG+ S+
Sbjct: 28 RALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSV---GNIM--GNFHPHGDSSIY 82
Query: 773 STILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPKDDDK- 831
++ M+Q++ N L++ +G G + G A+ RY RLS I +L +D +K
Sbjct: 83 DAMVRMSQNW--KNREILVEMHGNNG--SMDGDPPAAMRYTEARLSEIAGYLL-QDIEKK 137
Query: 832 LLDY-LNEDGQQIEPTWYMPI-IPTVLVNGSEGIGTGWSSYIPNYNPRDIV 880
+ + N D + EPT +P P +LVNGS GI G+++ IP +N +++
Sbjct: 138 TVPFAWNFDDTEKEPT-VLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVI 187
>2inr_A DNA topoisomerase 4 subunit A; topoisomerase II fold; HET: DNA;
2.80A {Staphylococcus aureus}
Length = 514
Score = 70.6 bits (174), Expect = 2e-12
Identities = 53/171 (30%), Positives = 88/171 (51%), Gaps = 21/171 (12%)
Query: 720 RSIPSMVDGLKPGQRKILF------CSFKRNFIKEAKVAQFSGYVSEHSAYH-HGEQSLA 772
R++P + DGLKP QR+IL+ + +NF K AK G V YH HG+ S+
Sbjct: 52 RALPDVRDGLKPVQRRILYAMYSSGNTHDKNFRKSAKTV---GDVI--GQYHPHGDSSVY 106
Query: 773 STILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPKDDDK- 831
++ ++QD+ L++ +G G + A+ RY +LS + L +D +K
Sbjct: 107 EAMVRLSQDW--KLRHVLIEMHGNNG--SIDNDPPAAMRYTEAKLSLLAEELL-RDINKE 161
Query: 832 LLDY-LNEDGQQIEPTWYMPI-IPTVLVNGSEGIGTGWSSYIPNYNPRDIV 880
+ + N D +EP +P P +LVNGS GI G+++ IP +N +++
Sbjct: 162 TVSFIPNYDDTTLEPM-VLPSRFPNLLVNGSTGISAGYATDIPPHNLAEVI 211
>3fv5_A DNA topoisomerase 4 subunit B; topoisomerase IV B subunit complex,
antibiotic resistance, ATP-binding, nucleotide-binding;
HET: DNA 1EU; 1.80A {Escherichia coli} PDB: 1s14_A*
Length = 201
Score = 66.0 bits (162), Expect = 3e-12
Identities = 42/166 (25%), Positives = 66/166 (39%), Gaps = 17/166 (10%)
Query: 101 DAVKVVI--DQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTG 158
V V++ DQ + V + G G+PV+IH EEGV ELI L + + + +G
Sbjct: 39 KRVDVILHADQS---LEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSG 95
Query: 159 GRNGYGAKLTNIFSTEFIIETA-DGKRLKKYKQVFTNNMGKKSEP--NISKCKEGDNWTK 215
G +G G + N S + DG + Y F N G+K + + C + + T
Sbjct: 96 GLHGVGISVVNALSKRVEVNVRRDG---QVYNIAFEN--GEKVQDLQVVGTCGKRNTGTS 150
Query: 216 VSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHR 261
V F PD F+ + + A L V++
Sbjct: 151 VHFWPDETFFDSPRFSVSR---LTHVLKAKA-VLCPGVEITFKDEI 192
>1ei1_A DNA gyrase B, GYRB; ATPase domain, dimer, isomerase; HET: DNA ANP;
2.30A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2
Length = 391
Score = 67.5 bits (166), Expect = 1e-11
Identities = 67/245 (27%), Positives = 106/245 (43%), Gaps = 46/245 (18%)
Query: 101 DAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGR 160
+ V I ++ +SV + G G+P IH EEGV E+I L +DDN K +GG
Sbjct: 56 KEIIVTIHADNS-VSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGL 114
Query: 161 NGYGAKLTNIFSTEFIIETA-DGKRLKKYKQVFTNNMGKKSEP--NISKCKE-GDNWTKV 216
+G G + N S + + +G K ++Q++ + G P + ++ G T V
Sbjct: 115 HGVGVSVVNALSQKLELVIQREG---KIHRQIYEH--GVPQAPLAVTGETEKTG---TMV 166
Query: 217 SFKPDLAKF-NMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVP----------VK 265
F P L F N+T E +++A KR+ +L+ L V + L R +K
Sbjct: 167 RFWPSLETFTNVTEFEYEILA---KRLRELS-FLDSGVSIRLRDKRDGKEDHFHYEGGIK 222
Query: 266 SFAEYVDMYPKSVTRFHERV----NERWEICV--------TLSEGQFQQVSFVNGIATIK 313
+F EY++ K+ T H + E+ I V E + F N I
Sbjct: 223 AFVEYLN---KNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIY---CFTNNIPQRD 276
Query: 314 GGTHV 318
GGTH+
Sbjct: 277 GGTHL 281
>1zvu_A Topoisomerase IV subunit A; beta-pinwheel, ATPase, supercoiling,
decatenation, DNA bindi topology; 3.00A {Escherichia
coli}
Length = 716
Score = 66.1 bits (162), Expect = 7e-11
Identities = 54/180 (30%), Positives = 87/180 (48%), Gaps = 18/180 (10%)
Query: 718 LQRSIPSMVDGLKPGQRKILF------CSFKRNFIKEAKVAQFSGYVSEHSAYH-HGEQS 770
+ R++P + DGLKP QR+I++ + F K A+ G V YH HG+ +
Sbjct: 1 MDRALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSART---VGDVL--GKYHPHGDSA 55
Query: 771 LASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPKDDD 830
++ MAQ F S L+ G +G + K A+ RY +RLS + L +
Sbjct: 56 CYEAMVLMAQPF--SYRYPLVDGQGNWGAPD-DPKSFAAMRYTESRLSKYSELLLSELGQ 112
Query: 831 KLLDY-LNEDGQQIEPTWYMPI-IPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLN 888
D+ N DG EP +P +P +L+NG+ GI G ++ IP +N R++ L++
Sbjct: 113 GTADWVPNFDGTLQEPKM-LPARLPNILLNGTTGIAVGMATDIPPHNLREVAQAAIALID 171
>4emv_A DNA topoisomerase IV, B subunit; protein-inhibitor complex, ATP
binding, structure-based drug antimicrobial, virtual
screen; HET: DNA 0R9; 1.70A {Streptococcus pneumoniae
GA47373} PDB: 4em7_A*
Length = 226
Score = 60.2 bits (147), Expect = 5e-10
Identities = 47/164 (28%), Positives = 75/164 (45%), Gaps = 13/164 (7%)
Query: 101 DAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGR 160
D + V I + ++V + G G+P +H G+ E+IF L + KT+GG
Sbjct: 62 DRIDVTI-NKDGSLTVQDHGRGMPTGMH-AMGIPTVEVIFTILHAGGKFGQGGYKTSGGL 119
Query: 161 NGYGAKLTNIFSTEFIIETA-DGKRLKKYKQVFTNNMGKKSEP--NISKCKEGDNWTKVS 217
+G G+ + N S+ +E DG YKQ F N GK I + TKV+
Sbjct: 120 HGVGSSVVNALSSWLEVEITRDGAV---YKQRFEN-GGKPVTTLKKIGTALKSKTGTKVT 175
Query: 218 FKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHR 261
F PD F+ T + + ++ +R+ + A L K+V + L R
Sbjct: 176 FMPDATIFSTTDFKYNTIS---ERLNESA-FLLKNVTLSLTDKR 215
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 62.0 bits (150), Expect = 1e-09
Identities = 110/664 (16%), Positives = 198/664 (29%), Gaps = 224/664 (33%)
Query: 350 HLWV----FVNALIDNPAFDSQTKETLTLRQSSFGSK-----------CELSEEFLKKVT 394
L +V++L++ P+ Q + L L + F + +L +E +
Sbjct: 59 ELVGKFLGYVSSLVE-PSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLV 117
Query: 395 AKSGIVETLLSWANFKQSKDLKKNDGTKTEDVRGISKL------EDANLA---GGR-NSE 444
+++ N+ ++ + K K + S L +A L GG+ N++
Sbjct: 118 KTKELIK------NYITARIMAKRPFDKKSN----SALFRAVGEGNAQLVAIFGGQGNTD 167
Query: 445 QCTLILTEGDSAKALAMAGLSVVGRDRFGVF-PLRGKLLNVREASSNQVLNN--SEIGNI 501
E L RD + + L G L+ S + L+ +
Sbjct: 168 DY---FEE-----------L----RDLYQTYHVLVGDLIK----FSAETLSELIRTTLDA 205
Query: 502 KKILGLKQGVEYNNVKS-LRYGHLMIMTDQVLLAPLSFLLWFILIFAWITTFCFMLAQDH 560
+K+ QG+ N+ L D +L P+S L ++ A +L
Sbjct: 206 EKVFT--QGL---NILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTP 260
Query: 561 D--GSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKATNKNGKVLSFYSMPDYEAWKE 618
S++KG HS +V A + D +W E
Sbjct: 261 GELRSYLKGAT---GHS----------------QGLVTAV--------AIAETD--SW-E 290
Query: 619 SLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEAIE---LAFSKK 675
S + +I +G E + N +L + + ++ E + L+ S
Sbjct: 291 SFFVSVRK-AITVLFFIGV----RCYEAYPNTSLPPS-ILEDSLENNEGVPSPMLSIS-- 342
Query: 676 KIEARKKWLLQFEPGNHLDQKEKYIKYSDFVNKELILFSMADLQRSIPSMVDGLKPGQRK 735
+Q + Y+ N L P ++
Sbjct: 343 --------------NLTQEQVQDYVNK---TNSHL--------------------PAGKQ 365
Query: 736 I---LFCSFKRNFIKEAKVAQFSGYVSEHSAYHHGEQSLASTILGMAQDFVGSNNINLLQ 792
+ L +N + V SG QSL L + + S L Q
Sbjct: 366 VEISLVNG-AKNLV----V---SGPP----------QSLYGLNLTLRKAKAPS---GLDQ 404
Query: 793 PNGQFGTRNQGGKDAASARYIFTRLSPIT-----RFLFPKDDDKLLDYLNEDGQQIEPT- 846
F R K S R+ L P+ L P D D L ++
Sbjct: 405 SRIPFSER----KLKFSNRF----L-PVASPFHSHLLVPASDLINKD-LVKNNVSFNAKD 454
Query: 847 WYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLNGEMM-EPMHPWYRGFGGT 905
+P+ T +GS + R + ++ + ++ P+ W
Sbjct: 455 IQIPVYDT--FDGS--------------DLRVLSGSISERIVDCIIRLPVK-W------- 490
Query: 906 IEKTASKEAGVTYTVT---GIIEEVNETTLRIKELPIRRWTQDYREFLESIIDQNDSFIR 962
E T +A T+ + G + T R K+ R + +D N
Sbjct: 491 -ETTTQFKA--THILDFGPGGASGLGVLTHRNKD---GTGV---RVIVAGTLDINPDDDY 541
Query: 963 GFRQ 966
GF+Q
Sbjct: 542 GFKQ 545
Score = 52.4 bits (125), Expect = 1e-06
Identities = 114/711 (16%), Positives = 197/711 (27%), Gaps = 279/711 (39%)
Query: 644 KEYFQNITLHKKDFVWEDDQDGEAIELAFSKKKIEARKKWLLQFEPGNHLDQKEKYIKYS 703
+E F I + DD+ EL + L + + L + K ++
Sbjct: 34 QEQFNKILPEPTEGFAADDEPTTPAELV-------GK---FLGYV--SSLVEPSKVGQFD 81
Query: 704 DFVNKELILFSMADLQ--------RSIPSMVDGLKPGQRKILFCSF------KRNFIK-- 747
+N L F L+ + D ++++ KR F K
Sbjct: 82 QVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKS 141
Query: 748 -----------EAKV-AQFSG------YVSE----HSAYHHGEQSLASTILGMAQDFVGS 785
A++ A F G Y E + YH + D +
Sbjct: 142 NSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHV-----------LVGDLI-K 189
Query: 786 NNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPKDDDKLLDYLNEDGQQIEP 845
+ L + A +FT+ I +L + DYL
Sbjct: 190 FSAETLSEL---------IRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLL-------- 232
Query: 846 TWYMPI-IPTVLVNGSEGIG-TGWSSYIPNYNPRDIVANVRRLLNGEMMEPMHPWYRGFG 903
+PI P IG + Y+ + A + GE+ +
Sbjct: 233 --SIPISCP--------LIGVIQLAHYV-------VTAKLLGFTPGELRSYLK------- 268
Query: 904 GTIEKTASKEAGVTYTVTGIIEEVNETTLRIKELPIRRWTQDYREFLESIIDQND-SFIR 962
G T G++ T + I E T + F S+ F
Sbjct: 269 -----------GATGHSQGLV-----TAVAIAE------TDSWESFFVSVRKAITVLFFI 306
Query: 963 GFR--QYSDDTTVDFEVFLSEESMMRTKQEGL---------LKKFKLTTTISTSNMHLFD 1011
G R + +T++ + E+S+ EG+ L + ++ ++ +N HL
Sbjct: 307 GVRCYEAYPNTSLPPSI--LEDSL--ENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPA 362
Query: 1012 SKGV-IKKYDTPEQILEEFFHIRLEFYEKRKKV------QLENLELELLKLE-------N 1057
K V I + + + V L L L L K + +
Sbjct: 363 GKQVEISLVNGAKNL-----------------VVSGPPQSLYGLNLTLRKAKAPSGLDQS 405
Query: 1058 KVRFILGVVNGEIVVNNRKRTDLLLELRQKGF----TPFPKNSKSIEAVVAGATDETEES 1113
++ F + RK L R F +PF +S
Sbjct: 406 RIPF-----------SERK---LKFSNR---FLPVASPF--HSH---------------- 430
Query: 1114 EENPEVVNGVQSIDYDYLLSMAIGTLTLEKVQGLLADRDKLNEEVD--DLRKATPESLWV 1171
LL A + D K N + D++ P V
Sbjct: 431 -----------------LLVPA--------SDLINKDLVKNNVSFNAKDIQ--IP----V 459
Query: 1172 KD-LDALDMQLDELDKSDARAEEERMKIKGNGNGDAGPKIVAKRAPKNARKND-KKSNNA 1229
D D D++ L S + ER+ D I+ + +
Sbjct: 460 YDTFDGSDLR--VLSGSIS----ERIV-------DC---IIRLPV-------KWETTTQF 496
Query: 1230 RATEAM----GEMDNVTKVVKP--KGRAGLKKAPAEKLDDDEEDEVPDLKQ 1274
+AT + G + + G G++ A LD + +D+ KQ
Sbjct: 497 KATHILDFGPGGASGLGVLTHRNKDGT-GVRVIVAGTLDINPDDDY-GFKQ 545
Score = 46.6 bits (110), Expect = 8e-05
Identities = 46/297 (15%), Positives = 100/297 (33%), Gaps = 100/297 (33%)
Query: 918 YTVTGIIEEVNETTLRI-----KELPIRRWTQDYREFL-ESIIDQNDSFIRGFRQYSDDT 971
+++ I+ N L I K IR ++Y + E+I+D + F++ ++ +
Sbjct: 1659 FSILDIVIN-NPVNLTIHFGGEKGKRIR---ENYSAMIFETIVDGKLKTEKIFKEINEHS 1714
Query: 972 T-VDFEVFLSEESMMRTK--QEGLLKKFKLTTTISTSNMHLFDSKGVIKKYDTPEQILEE 1028
T F + + T+ Q L + + SKG+I
Sbjct: 1715 TSYTFRS--EKGLLSATQFTQPALT-------LMEKAAFEDLKSKGLIPADA-------- 1757
Query: 1029 FF--HIRLEFYEKRKKVQLENL-E---L----ELLKLENKVRFILGVVNGEIVVNNRKRT 1078
F H +L E L +++ +E+ V +V R
Sbjct: 1758 TFAGH---------------SLGEYAALASLADVMSIESLVE---------VV---FYRG 1790
Query: 1079 DLLLELRQKGFTPFPKNSKSIEAV-----VAGATDET---------EESEENPEVVN--- 1121
+ + +++ + A+ A + E + + E+VN
Sbjct: 1791 MTMQVAVPRD--ELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNV 1848
Query: 1122 -GVQSIDYDYLLSMAIGTLT-LEKVQGLLADRDKLNEEVDDLRKATPESLWVKDLDA 1176
Q Y+ + G L L+ V +L + + + D+ + +SL +++++
Sbjct: 1849 ENQQ-----YVAA---GDLRALDTVTNVL---NFIKLQKIDIIEL-QKSLSLEEVEG 1893
Score = 41.2 bits (96), Expect = 0.003
Identities = 44/253 (17%), Positives = 72/253 (28%), Gaps = 83/253 (32%)
Query: 643 GKEYFQNITLHKKDFVWE--DDQDGEAIELAFSKKKI--EARKKWLLQF--EPGNHLDQK 696
G + ++ + VW D+ + FS I + F E G + +
Sbjct: 1632 GMDLYKTSKAAQD--VWNRADNHFKDT--YGFSILDIVINNPVNLTIHFGGEKGKRI--R 1685
Query: 697 EKYIK-----YSDFVNKELILFSMADLQRSIPSMVDGLKPG---------QRKIL----- 737
E Y D K +F + + S Q +
Sbjct: 1686 ENYSAMIFETIVDGKLKTEKIFKEIN-EHSTSYTFRS--EKGLLSATQFTQPALTLMEKA 1742
Query: 738 -FCSFKRNFIKEAKVAQFSGYVSEHSAYHHGEQS-LAST--ILGMAQDFV------GSNN 787
F K + A F+G HS GE + LAS ++ + V G
Sbjct: 1743 AFEDLKSKGLIPADAT-FAG----HSL---GEYAALASLADVMSIE-SLVEVVFYRG--- 1790
Query: 788 INLLQ---PNGQFGTRNQG-----------GKDAASARYIFTRLSPITRFLFPKDDDKLL 833
+Q P + G N G + +Y+ R+ K L+
Sbjct: 1791 -MTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVG--------KRTGWLV 1841
Query: 834 D---YLNEDGQQI 843
+ Y N + QQ
Sbjct: 1842 EIVNY-NVENQQY 1853
Score = 40.8 bits (95), Expect = 0.004
Identities = 72/497 (14%), Positives = 136/497 (27%), Gaps = 200/497 (40%)
Query: 929 ETTLRIKELPIRRW---TQDYREFLESIIDQNDSFIRGFRQYSDDTTVDFEV---FLS-- 980
E L + P + +Q +F + + + + F D+ T E+ FL
Sbjct: 17 EHVLLV---PTASFFIASQLQEQFNKILPEPTEGFAA-----DDEPTTPAELVGKFLGYV 68
Query: 981 ----EESMMRTKQEGL---LKKFKLTTTISTSNMHLF-------DSKGVIKKYDTPEQIL 1026
E S + + L L +F+ + +++H + ++K + ++
Sbjct: 69 SSLVEPSKVGQFDQVLNLCLTEFE-NCYLEGNDIHALAAKLLQENDTTLVKTKE----LI 123
Query: 1027 EEFFHIRLEFYEKRKKVQLENLELELLK--LENKVRFIL-----GVVNGEIVVNNRKRTD 1079
+ + R+ K L + E + + G N + D
Sbjct: 124 KNYITARIMAKRPFDKKS----NSALFRAVGEGNAQLVAIFGGQG--NTD---------D 168
Query: 1080 LLLELRQ--KGFTPFPKNSKSIEAVVAGATDETEESEENPEVVNGV--QSIDY------- 1128
ELR + + + ++ + + E V Q ++
Sbjct: 169 YFEELRDLYQTYHVL------VGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENP 222
Query: 1129 ------DYLLSMA-----IGTLTLE------KVQGLLADRDKLNEEVDDLRKATPESLWV 1171
DYLLS+ IG + L K+ G TP L
Sbjct: 223 SNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGF-----------------TPGEL-- 263
Query: 1172 KDLDALDMQLDELDKSDARAEEERMKIKG-NGNGDAGPKIVAKRAPKNARKNDKKS--NN 1228
R +KG G+ +V A A + +S +
Sbjct: 264 -----------------------RSYLKGATGHSQG---LVTAVAI--AETDSWESFFVS 295
Query: 1229 A------------RATEAMGEMDNVTKVVKPKGRAGLKKAPAEKLDDDEEDE--VP---- 1270
R EA P L+D E+ VP
Sbjct: 296 VRKAITVLFFIGVRCYEAYPNTS----------------LPPSILEDSLENNEGVPSPML 339
Query: 1271 --------DLKQRLAKLNEQLASTK-----LEPSPDQ---SG--------VMETEKVQVP 1306
++ + K N L + K L SG + K + P
Sbjct: 340 SISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAP 399
Query: 1307 AKKKEPSKRTAAQKKVV 1323
+ + S+ +++K+
Sbjct: 400 SGLDQ-SRIPFSERKLK 415
Score = 37.0 bits (85), Expect = 0.060
Identities = 57/369 (15%), Positives = 102/369 (27%), Gaps = 140/369 (37%)
Query: 195 NMGK---KSEPNISKC--KEGDNWTKVSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCL 249
MG K+ ++ DN K ++ F++ + V+ + G
Sbjct: 1630 GMGMDLYKTSK-AAQDVWNRADNHFKDTYG-----FSILDI---VINNPVNLTIHFGGEK 1680
Query: 250 GKSVKVELNGHRVPVKSFAEYVDMYPKSVTRFHERVNERWEICV------TLSEGQFQQV 303
GK ++ F VD K+ F E +NE LS QF Q
Sbjct: 1681 GKRIR-----ENYSAMIFETIVDGKLKTEKIFKE-INEHSTSYTFRSEKGLLSATQFTQP 1734
Query: 304 S-FVNGIATI-----KGGTHVDYVANQVANH-------------VMAVVNKKNKNANVKA 344
+ + A KG D A H VM++ ++ V+
Sbjct: 1735 ALTLMEKAAFEDLKSKGLIPADAT---FAGHSLGEYAALASLADVMSI-----ESL-VEV 1785
Query: 345 HNVKNHLWVFV--NALIDNPAFDSQTKET---LTLRQSSFGSKC--ELSEEFLKKVTAKS 397
VF + D + + + + E + +++V ++
Sbjct: 1786 --------VFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRT 1837
Query: 398 G-IVETLLSWANFKQSKDLKKNDGTKTEDVRGISKLEDANLAGGRNSEQCTLILTEGDSA 456
G +VE N+ N+ +Q
Sbjct: 1838 GWLVEI----VNY--------------------------NVEN----QQY---------- 1853
Query: 457 KALAMAGLSVVGRDRFGVFPLRGKLLNVREASSNQVLNNSEIGNIKKILGLKQGVEYNNV 516
V G L + + VLN ++ I I+ L++ + V
Sbjct: 1854 ---------VAA----------GDLRALDTVT--NVLNFIKLQKI-DIIELQKSLSLEEV 1891
Query: 517 KSLRYGHLM 525
+ GHL
Sbjct: 1892 E----GHLF 1896
Score = 37.0 bits (85), Expect = 0.068
Identities = 51/326 (15%), Positives = 94/326 (28%), Gaps = 129/326 (39%)
Query: 1008 HLFDSKG-----VIKKYDTPEQILEEFF-----HIRLEFYEKRKKVQLENLELELLKL-- 1055
H D+ G ++ + P + F IR E Y + + +L+ K+
Sbjct: 1652 HFKDTYGFSILDIVI--NNPVNLTIHFGGEKGKRIR-ENYSAMIFETIVDGKLKTEKIFK 1708
Query: 1056 ---ENKVRFILGVVNGEIVVNNRKRTD-----LLL-------ELRQKGFTPFPKNSKSIE 1100
E+ + G + T L L +L+ KG P
Sbjct: 1709 EINEHSTSYTFRSEKGLL-----SATQFTQPALTLMEKAAFEDLKSKGLIPAD------- 1756
Query: 1101 AVVAGATDETEES--EENPEVVNGVQSIDYDY--LLSMAIGTLTLEKVQGLLADRDKLNE 1156
A AG S E Y L S+A +++E + ++ R
Sbjct: 1757 ATFAG------HSLGE---------------YAALASLA-DVMSIESLVEVVFYRGMT-- 1792
Query: 1157 EVDDLRKATPESLWVKDLDALDMQLDELDKSD---ARAEEERMKIKGNGNGDAGPKIVAK 1213
++ A P DEL +S+ R+ + +A +V +
Sbjct: 1793 ----MQVAVPR--------------DELGRSNYGMIAINPGRVAASFSQ--EALQYVVER 1832
Query: 1214 RAPKNARK----NDKKSNNAR------ATEAMGEMDNVTKVVKPKGRAGLKKAPAEKLDD 1263
+ N N A G++ + V L +K+D
Sbjct: 1833 VGKRTGWLVEIVNY----NVENQQYVAA----GDLRALDTVTNV-----LNFIKLQKID- 1878
Query: 1264 DEEDEVPDLKQRLAKLNEQLASTKLE 1289
+ +L + L+ ++E
Sbjct: 1879 ------------IIELQKSLSLEEVE 1892
>4duh_A DNA gyrase subunit B; structure-based drug design, antibacterial,
DNA gyrase B, GY isomerase-isomerase inhibitor complex;
HET: DNA RLI; 1.50A {Escherichia coli} PDB: 1aj6_A*
1kzn_A* 3g7e_A*
Length = 220
Score = 56.8 bits (138), Expect = 6e-09
Identities = 49/166 (29%), Positives = 79/166 (47%), Gaps = 18/166 (10%)
Query: 101 DAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGR 160
+ V I ++ +SV + G G+P IH EEGV E+I L +DDN K +GG
Sbjct: 57 KEIIVTIHADNS-VSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGL 115
Query: 161 NGYGAKLTNIFSTEFIIETA-DGKRLKKYKQVFTNNMGKKSEP--NISKCKE-GDNWTKV 216
+G G + N S + + +G K ++Q++ + G P + ++ G T V
Sbjct: 116 HGVGVSVVNALSQKLELVIQREG---KIHRQIYEH--GVPQAPLAVTGETEKTG---TMV 167
Query: 217 SFKPDLAKF-NMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHR 261
F P L F N+T E +++A KR+ +L+ L V + L R
Sbjct: 168 RFWPSLETFTNVTEFEYEILA---KRLRELS-FLNSGVSIRLRDKR 209
>3cwv_A DNA gyrase, B subunit, truncated; structural genomics, unknown
function, B-subunit binding, isomerase,
nucleotide-binding, topoisomerase; HET: DNA; 1.95A
{Myxococcus xanthus}
Length = 369
Score = 52.9 bits (128), Expect = 4e-07
Identities = 30/245 (12%), Positives = 74/245 (30%), Gaps = 54/245 (22%)
Query: 101 DAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGR 160
V + + I++ + V E + + G
Sbjct: 52 RDVVLEV-GGDGSIALFCTSRTVTAEN-----------LVRVATGAGFLGRPPGDGWGWD 99
Query: 161 NGYGAKLTNIFSTEFIIE-TADGKRLKKYKQVFTNNMGKKSEPNISKCKEG----DNWTK 215
+ ++ S+ + ++ ADG++ ++ + + + ++ + + +
Sbjct: 100 SMLV--VSLALSSRYQVDIWADGRQ---WRVMGEHGHPQGEGAAVTPMEPMPVSAERGVR 154
Query: 216 VSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVP----------VK 265
V F PD F + + ++ +R +LA L ++V + V
Sbjct: 155 VHFVPDATIFEVLAFDRARLS---RRCNELA-ALAPGLRVSFADLQRGERTLWHLPGGVA 210
Query: 266 SFAEYVDMYPKSVTRFHERV----NERWEICV--------TLSEGQFQQVSFVNGIATIK 313
+A + ++ + H + V SF N + T++
Sbjct: 211 QWAHVLT---EARPQLHPEPVVFDFTWDGLRVQCALQWCEDEDSTLL---SFANAVRTVR 264
Query: 314 GGTHV 318
G HV
Sbjct: 265 HGAHV 269
>3ttz_A DNA gyrase subunit B; protein-inhibitor complex, ATP-binding,
structure-based drug antimicrobial, isomerase-isomerase
inhibitor complex; HET: DNA 07N; 1.63A {Staphylococcus
aureus} PDB: 3u2d_A* 3u2k_A* 3g75_A* 3g7b_A*
Length = 198
Score = 40.9 bits (97), Expect = 0.001
Identities = 36/166 (21%), Positives = 65/166 (39%), Gaps = 41/166 (24%)
Query: 101 DAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGR 160
+ ++VVI ++ + I V ++G G+PV+I ++ G E+I LTSS
Sbjct: 53 NQIEVVI-EKDNWIKVTDNGRGIPVDIQEKMGRPAVEVI----LTSS------------- 94
Query: 161 NGYGAKLTNIFSTEFIIETA-DGKRLKKYKQVFTNNMGKKSEP--NISKCKE-GDNWTKV 216
+ N S + + + Y Q + G + + G T +
Sbjct: 95 ------VVNALSQDLEVYVHRNETI---YHQAYKK--GVPQFDLKEVGTTDKTG---TVI 140
Query: 217 SFKPDLAKF-NMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHR 261
FK D F T + + +R+ +LA L K +++ L R
Sbjct: 141 RFKADGEIFTETTVYNYETLQ---QRIRELA-FLNKGIQITLRDER 182
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 36.7 bits (84), Expect = 0.029
Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 15/92 (16%)
Query: 1148 LADRDKLNEEVDDLRKATPESLWVKDLDALDMQLDELDKSDARAEEERMKIKGNGNGDAG 1207
+A D+L +E + +RK W ++ +L ELD + E+E + K + +
Sbjct: 74 IAQADRLTQEPESIRK------WREEQRK---RLQELDAASKVMEQE-WREKAKKDLEEW 123
Query: 1208 PKIVAKRAPKNARKNDKKSNNARATEAMGEMD 1239
+R + KN K +N + D
Sbjct: 124 ----NQRQSEQVEKN-KINNRIADKAFYQQPD 150
Score = 29.7 bits (66), Expect = 5.5
Identities = 11/59 (18%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 1142 EKVQGLLADRDKLNEEVDDLRKATPESLW---VKDLDALDMQLDE-LDKS--DARAEEE 1194
E ++ ++ K +E+D K + KDL+ + + E ++K+ + R ++
Sbjct: 85 ESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADK 143
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 34.5 bits (78), Expect = 0.086
Identities = 12/52 (23%), Positives = 17/52 (32%), Gaps = 28/52 (53%)
Query: 410 KQSKDLKKNDGTKTEDVRGISKLEDANLAGGRNSEQCTLILTEGDSAKALAM 461
KQ+ + KL+ +L L DSA ALA+
Sbjct: 19 KQA----------------LKKLQA------------SLKLYADDSAPALAI 42
Score = 34.2 bits (77), Expect = 0.14
Identities = 12/35 (34%), Positives = 14/35 (40%), Gaps = 14/35 (40%)
Query: 1273 KQRLAKLNEQLASTKLEPSPDQSGVMETEKVQVPA 1307
KQ L KL AS KL + D + PA
Sbjct: 19 KQALKKLQ---ASLKLY-ADDSA----------PA 39
Score = 32.6 bits (73), Expect = 0.47
Identities = 9/30 (30%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 1402 EKK-VRKMRAS--PFNKKSGSMLGRAGTIE 1428
EK+ ++K++AS + S L T+E
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATME 47
>2btz_A Pyruvate dehydrogenase kinase isoenzyme 2; GHKL motif regulation,
transferase; 2.2A {Homo sapiens} PDB: 2bu2_A* 2bu5_A*
2bu6_A* 2bu7_A* 2bu8_A* 3crk_A* 1jm6_A* 3crl_A*
Length = 394
Score = 35.2 bits (80), Expect = 0.15
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 72 TISYVPG-LYKIFDEILVNA----ADNKQRDPKMDAVKVVI--DQEHDLISVHNSGDGVP 124
+ YVP LY + E+ NA ++ + + +KV++ +E I + + G GVP
Sbjct: 224 HMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVP 283
Query: 125 VEIHQ 129
+ +
Sbjct: 284 LRKIE 288
>2q8g_A [pyruvate dehydrogenase [lipoamide]] kinase isozy; GHKL
ATPase/kinase family, pyruvate dehydrogenase complex,
mitochondrial kinase; HET: AZX; 1.90A {Homo sapiens}
PDB: 2q8f_A* 2q8h_A
Length = 407
Score = 34.0 bits (77), Expect = 0.36
Identities = 18/104 (17%), Positives = 38/104 (36%), Gaps = 15/104 (14%)
Query: 72 TISYVPG-LYKIFDEILVNA----ADNKQRDPKMDAVKVVI--DQEHDLISVHNSGDGVP 124
+ YVP LY + E+ NA ++ ++V + E + + + G GVP
Sbjct: 236 QVVYVPSHLYHMVFELFKNAMRATMEHHANRGVYPPIQVHVTLGNEDLTVKMSDRGGGVP 295
Query: 125 VEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGRNGYGAKLT 168
+ + +F ++ +++ G+G L
Sbjct: 296 LRKI--------DRLFNYMYSTAPRPRVETSRAVPLAGFGYGLP 331
>1y8q_B Anthracycline-, ubiquitin-like 2 activating enzyme E1B; SUMO,
heterodimer, UBL, ligase; HET: ATP; 2.25A {Homo sapiens}
PDB: 1y8r_B* 3kyc_B* 3kyd_B* 2px9_A
Length = 640
Score = 33.9 bits (77), Expect = 0.43
Identities = 21/129 (16%), Positives = 43/129 (33%), Gaps = 12/129 (9%)
Query: 1260 KLDDDEEDEVPDLKQRLAKLNEQLASTKLEPSPDQSGVMETEKVQVPAKKKEPSKRTAA- 1318
+ + + D Q L L S L + V + + P + ++ +K
Sbjct: 510 GIRNGSRLQADDFLQDYTLLINILHSEDLGKDVEFEVVGDAPEKVGPKQAEDAAKSITNG 569
Query: 1319 ---QKKVVTVETSDSEDEIIIDDDEAFEIAAPEEGKKGGRKAAGNSKAAKPAAETKKRGP 1375
+ T + +D +I+D D EE + ++ K + K+
Sbjct: 570 SDDGAQPSTSTAQEQDDVLIVDSD--------EEDSSNNADVSEEERSRKRKLDEKENLS 621
Query: 1376 AKKQQPEAS 1384
AK+ + E
Sbjct: 622 AKRSRIEQK 630
Score = 29.7 bits (66), Expect = 8.3
Identities = 14/102 (13%), Positives = 30/102 (29%), Gaps = 1/102 (0%)
Query: 1237 EMDNVTKVVKPKGRAGLKKAPAEKLDDDEEDEVPDLKQRLAKLNEQLASTKLEPSPDQSG 1296
D +VV K + + + EQ ++ + S
Sbjct: 539 GKDVEFEVVGDAPEKVGPKQAEDAAKSITNGSDDGAQPSTSTAQEQDDVLIVDSDEEDSS 598
Query: 1297 VMETEKVQVPAKK-KEPSKRTAAQKKVVTVETSDSEDEIIID 1337
+ ++K K K + K+ + + +D I +D
Sbjct: 599 NNADVSEEERSRKRKLDEKENLSAKRSRIEQKEELDDVIALD 640
>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC
repeat; 2.70A {Saccharomyces cerevisiae}
Length = 963
Score = 34.0 bits (77), Expect = 0.53
Identities = 21/156 (13%), Positives = 42/156 (26%), Gaps = 16/156 (10%)
Query: 1241 VTKVVKPKGRAGLKKAPAEKLDDDEEDEVPDLKQRLAKLNEQLASTKLEPSPDQSGVMET 1300
T V+ RA + +K E+E + K E E + +
Sbjct: 811 ATAVLSTTARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKGIKETKENDEEFYKN 870
Query: 1301 EKVQVPAKKKEPSKRTAAQKKVVT---------VETSDSEDEIIIDDDEAFEIAAPEEGK 1351
+ P K ++ Q + ++ V + +++ D P+E
Sbjct: 871 KYSSKPYKVDNMTRILPQQSRYISFIKDDRFVPVRKFKGNNGVVVLRDR-----EPKEPV 925
Query: 1352 K--GGRKAAGNSKAAKPAAETKKRGPAKKQQPEASL 1385
+ + A P + SL
Sbjct: 926 ALIETVRQMKDVNAPLPTPFKVDDNVDFPSALQPSL 961
>2obx_A DMRL synthase 1, 6,7-dimethyl-8-ribityllumazine synthase 1,
riboflavin S; alpha-beta, transferase; HET: INI; 2.53A
{Mesorhizobium loti}
Length = 157
Score = 31.8 bits (73), Expect = 0.79
Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
+ GG ++VA+ V + +M V
Sbjct: 79 FVVNGGIYRHEFVASAVIDGMMNV 102
>1kz1_A 6,7-dimethyl-8-ribityllumazine synthase; riboflavin biosynthesis,
ligand binding, transferase; 2.00A {Schizosaccharomyces
pombe} SCOP: c.16.1.1 PDB: 2a59_A* 2a58_A* 2a57_A*
1kyv_A* 1kyx_A* 1kyy_A* 1kz9_A 1kz4_A 1kz6_A
Length = 159
Score = 31.8 bits (73), Expect = 0.90
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
IKG T H +Y++ V + +M V
Sbjct: 86 VLIKGSTMHFEYISEAVVHGLMRV 109
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment
2, heavy meromyosin, essential light chain, motor
protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1
PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 32.9 bits (75), Expect = 0.93
Identities = 33/274 (12%), Positives = 102/274 (37%), Gaps = 27/274 (9%)
Query: 1140 TLEKVQGLLADRDKLNEEVDDLRKATPESLWVKDLDALDMQLDELDKSDARAEEERMKIK 1199
L+ L A+ +++ + +K E + + ++ + + + A ++ + ++
Sbjct: 900 KLQAETELYAEAEEMRVRLA-AKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQML 958
Query: 1200 GNGNGDAGPKIVAKRAPKNARKNDKKSNNARATEAMGEMDNVTKVVK--PKGRAGLKKAP 1257
D ++ + A + + +K + + + + ++ + K R L++
Sbjct: 959 -----DLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERV 1013
Query: 1258 AEKLDD--DEEDEVPDLKQRLAKLNEQLASTKLEPSPDQSGVMETEKVQVPAKKKEPSKR 1315
++ + +EE++ +L + K ++ ++ ++ E EK K+K +
Sbjct: 1014 SDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEK----IKRKLEGES 1069
Query: 1316 TAAQKKVVTVETSDSEDEIIIDDDEAFEIAAPEEGKKGGRKAAGNSKAAKPAAETKKRGP 1375
+ +++ ++ +E + + E EE + + + A + +
Sbjct: 1070 SDLHEQIAELQAQIAELKAQLAKKE-------EELQAALARLEDETSQKNNALKKIRELE 1122
Query: 1376 AKKQQPEASLGQRLLTEMLKPAESSPEKKVRKMR 1409
+ + L E K A + EK+ R +
Sbjct: 1123 SHISDLQEDL------ESEKAARNKAEKQKRDLS 1150
Score = 30.2 bits (68), Expect = 6.2
Identities = 24/156 (15%), Positives = 51/156 (32%), Gaps = 23/156 (14%)
Query: 1142 EKVQGLLADRDKLNEEVDDLRKATPE------------SLWVKDLDALDMQLDELDKSDA 1189
EK + L ++K + +L + + L Q+ EL A
Sbjct: 1025 EKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIA 1084
Query: 1190 RAEEERMKIKGNGNGDAGPKIVAKRAPKNARKNDKKSNNARATEAMGEMDNVTKVVKPKG 1249
+ + K K A ++ + + KN + + ++ ++++
Sbjct: 1085 ELKAQLAK-KEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLESEKA------ 1137
Query: 1250 RAGLKKAPAEKLDDDEEDEVPDLKQRLAKLNEQLAS 1285
+ AEK D +E+ LK L + A+
Sbjct: 1138 ----ARNKAEKQKRDLSEELEALKTELEDTLDTTAT 1169
>1rqg_A Methionyl-tRNA synthetase; translation, dimerization, ligase; 2.90A
{Pyrococcus abyssi} SCOP: a.27.1.1 c.26.1.1 g.41.1.1
Length = 722
Score = 32.8 bits (75), Expect = 0.93
Identities = 9/80 (11%), Positives = 21/80 (26%), Gaps = 3/80 (3%)
Query: 1259 EKLDDDEEDEVPDLKQRLAKLNEQLASTKLEPSPDQSGVMETEKVQVPAKKKEPSKRTAA 1318
+K+ DD+ + L + + + + E R
Sbjct: 546 KKVTDDQIIY---FILNYMAKGNPEGARILLDKYYKREDVIRVAKEKFGDEAEVVLRRVY 602
Query: 1319 QKKVVTVETSDSEDEIIIDD 1338
+ + + E + DD
Sbjct: 603 KDIKLKEKKEGKEMYVKFDD 622
>1di0_A Lumazine synthase; transferase; 2.70A {Brucella abortus} SCOP:
c.16.1.1 PDB: 1t13_A* 1xn1_A
Length = 158
Score = 31.4 bits (72), Expect = 0.98
Identities = 10/24 (41%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
I GG D+VA V N +M V
Sbjct: 78 FVIDGGIYDHDFVATAVINGMMQV 101
>1ejb_A Lumazine synthase; analysis, inhibitor complex, vitamin
biosynthesis transferase; HET: INJ; 1.85A {Saccharomyces
cerevisiae} SCOP: c.16.1.1 PDB: 2jfb_A
Length = 168
Score = 31.4 bits (72), Expect = 1.2
Identities = 7/24 (29%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
IKG T H +Y+++ + +M +
Sbjct: 89 VLIKGSTMHFEYISDSTTHALMNL 112
>1c41_A Lumazine synthase; riboflavin biosynthesis, transferase; HET: LMZ;
3.10A {Magnaporthe grisea} SCOP: c.16.1.1
Length = 200
Score = 31.4 bits (71), Expect = 1.4
Identities = 10/24 (41%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
IKG T H +Y+A+ V++ +M V
Sbjct: 119 VLIKGETMHFEYIADSVSHGLMRV 142
>2i0f_A 6,7-dimethyl-8-ribityllumazine synthase 1; lumazine synthase RIBH1,
transferase; 2.22A {Brucella abortus} PDB: 2f59_A
2o6h_A*
Length = 157
Score = 31.0 bits (71), Expect = 1.4
Identities = 7/24 (29%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
I+G T H D V+N+ + +
Sbjct: 82 TVIRGETYHFDIVSNESCRALTDL 105
>2c92_A 6,7-dimethyl-8-ribityllumazine synthase; transferase, riboflavin
biosynthesis, inhibitor binding; HET: TP6; 1.6A
{Mycobacterium tuberculosis} PDB: 1w29_A* 1w19_A*
2c94_A* 2c97_A* 2c9b_A* 2c9d_A* 2vi5_A*
Length = 160
Score = 31.0 bits (71), Expect = 1.5
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
I+G T H DYV + V + V
Sbjct: 81 VVIRGQTPHFDYVCDAVTQGLTRV 104
>1hqk_A 6,7-dimethyl-8-ribityllumazine synthase; analysi stability, vitamin
biosynthesis, transferase; 1.60A {Aquifex aeolicus}
SCOP: c.16.1.1 PDB: 1nqu_A* 1nqv_A* 1nqw_A* 1nqx_A*
Length = 154
Score = 31.0 bits (71), Expect = 1.6
Identities = 8/24 (33%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
I+G T H DY+A++V+ + +
Sbjct: 80 VLIRGATPHFDYIASEVSKGLANL 103
>2jjz_A Ionized calcium-binding adapter molecule 2; EF-hand, actin
crosslinking, ionized calciu binding adapter molecule 2,
metal-binding protein; 2.15A {Homo sapiens} PDB: 2jjz_B
2vtg_A
Length = 150
Score = 30.6 bits (69), Expect = 1.7
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 970 DTTVDFEVFLSEESMMRTKQEGLLKKFKL 998
T+ + F++ MM K+ +LK +
Sbjct: 100 SDTISYRDFVN---MMLGKRSAVLKLVMM 125
>3nq4_A 6,7-dimethyl-8-ribityllumazine synthase; 30MER, icosahedral,
flavodoxin like fold, transferase, DMRL riboflavin
biosynthesis, drug targe; 3.50A {Salmonella typhimurium}
PDB: 3mk3_A
Length = 156
Score = 30.6 bits (70), Expect = 2.0
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
I+GGT H +YVA +N + +V
Sbjct: 81 TVIRGGTAHFEYVAGGASNGLASV 104
>1rvv_A Riboflavin synthase; transferase, flavoprotein; HET: INI; 2.40A
{Bacillus subtilis} SCOP: c.16.1.1 PDB: 1zis_A* 1vsw_A
1vsx_A 3jv8_A
Length = 154
Score = 30.6 bits (70), Expect = 2.0
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
I+G T H DYV N+ A +
Sbjct: 80 TVIRGATTHYDYVCNEAAKGIAQA 103
>1c2y_A Protein (lumazine synthase); riboflavin biosynthesis, transferase;
HET: LMZ; 3.30A {Spinacia oleracea} SCOP: c.16.1.1
Length = 156
Score = 30.6 bits (70), Expect = 2.1
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 310 ATIKGGT-HVDYVANQVANHVMAV 332
A +KG T H D V N ++ V++
Sbjct: 80 AVVKGDTSHYDAVVNSASSGVLSA 103
>3gdb_A Endo-D, putative uncharacterized protein SPR0440; alpha-beta-barrels,
cell WALL, peptidoglycan-anchor, secreted, hydrolase;
HET: PGE; 1.87A {Streptococcus pneumoniae} PDB: 2xqx_A
Length = 937
Score = 31.1 bits (69), Expect = 3.2
Identities = 21/188 (11%), Positives = 52/188 (27%), Gaps = 16/188 (8%)
Query: 1294 QSGVMETEKVQVPAKKKEPSKRTAAQKKVVTVETSDSEDEIIIDDDEAFEIAAPEEGKKG 1353
++ + E+ VP ++ + + + T E + + EG
Sbjct: 15 ENLYFQGEETAVPENSGANTELVSGESEHSTNEADKQNEG----EHARENKLEKAEGVAT 70
Query: 1354 GRKAAGNSKAAKPAAETKKRGPAKKQQPEASLGQRLLTEMLKPAESSPEKKVRKMRASPF 1413
+ A + ET + A +PE + + A+ +K+ +
Sbjct: 71 ASETASPASNEAATTETAE--AASAAKPEEKASEVVAETPSAEAKPKSDKETEAKPEAT- 127
Query: 1414 NKKSGSMLGRAGTIEEPSGSSPSTSEEVAEVLPPKARPQRANRRQARYVLSDSESEKATD 1473
G +P+ + T +EV +P + + +
Sbjct: 128 ---------NQGDESKPAAEANKTEKEVQPDVPKNTEKTLKPKEIKFNSWEELLKWEPGA 178
Query: 1474 DSEFDEDE 1481
+ +
Sbjct: 179 REDDAINR 186
>1q16_A Respiratory nitrate reductase 1 alpha chain; membrane protein,
electron-transfer, oxidoreductase; HET: FME MD1 HEM AGA
3PH; 1.90A {Escherichia coli} SCOP: b.52.2.2 c.81.1.1
PDB: 3ir7_A* 1y5i_A* 1siw_A* 1y4z_A* 1r27_A* 1y5l_A*
1y5n_A* 3ir6_A* 3ir5_A* 3egw_A*
Length = 1247
Score = 30.8 bits (69), Expect = 5.1
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 853 PTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLNGEMMEP 894
PT ++ G + G++ Y + RD VR++ N + ++
Sbjct: 1195 PTHMIGGYAHLAYGFNYYGTVGSNRDEFVVVRKMKNIDWLDG 1236
>1e5k_A Molybdopterin-guanine dinucleotide biosynthesis protein A;
molybdopterin nucleotidyl-transferase,; HET: CIT; 1.35A
{Escherichia coli} SCOP: c.68.1.8 PDB: 1h4e_A* 1hjl_A*
1hjj_A* 1h4c_A* 1h4d_A* 1fr9_A 1frw_A*
Length = 201
Score = 29.6 bits (67), Expect = 5.7
Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 4/47 (8%)
Query: 66 KTMIHRTISYVPGLYKIFDEILVNAADNKQRDPKMDAVKVVIDQEHD 112
K + L ++VNA +++ + +KV+ D D
Sbjct: 33 KPLWQHVAD---ALMTQLSHVVVNANRHQEI-YQASGLKVIEDSLAD 75
>2wol_A ORF15, clavulanic acid biosynthesis oligopeptide binding protein 2;
solute-binding protein; 1.45A {Streptomyces
clavuligerus} PDB: 2wok_A 2wop_A*
Length = 562
Score = 30.1 bits (68), Expect = 6.7
Identities = 6/61 (9%), Positives = 19/61 (31%), Gaps = 1/61 (1%)
Query: 875 NPRDIVANVRRLLNGEMMEPMHPWYRGFGGTIEKTASKEAGVTYTVTGIIEEVNETTLRI 934
D+ V+R+ +++ + E+ + + +E T+
Sbjct: 116 TSDDVRHAVQRVFAQDVLPGGPTYLIPLLDDPERPYPGPYRTDEPLRS-VLTPDEHTIVF 174
Query: 935 K 935
+
Sbjct: 175 R 175
>2l4b_A Acyl carrier protein; infectious disease, human granulocytic
anaplasmosis, ssgcid, structural genomics; NMR {Anaplasma
phagocytophilum}
Length = 88
Score = 27.4 bits (61), Expect = 8.8
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 12/63 (19%)
Query: 1141 LEKVQGLLADRDKLNEEVDDLRKATPESLWVKDL--DALD-----MQLDE---LDKSDAR 1190
+V + KLN+ + + + + KD D+LD M L+E L+ SD
Sbjct: 10 KAQVMESVIGCLKLND--EQKQILSGTTNLAKDFNLDSLDFVDLIMSLEERFSLEISDED 67
Query: 1191 AEE 1193
A++
Sbjct: 68 AQK 70
>3it4_A Arginine biosynthesis bifunctional protein ARGJ alpha chain;
ornithine acetyltransferase, structural genomics; 1.70A
{Mycobacterium tuberculosis} PDB: 3it6_A
Length = 199
Score = 29.1 bits (66), Expect = 9.2
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 905 TIEKTASKEAGVTYTVTGI 923
+ K + +TV G+
Sbjct: 169 NVPKQVALHHHDNWTVGGM 187
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 29.7 bits (67), Expect = 9.5
Identities = 25/175 (14%), Positives = 56/175 (32%), Gaps = 11/175 (6%)
Query: 1142 EKVQGLLADRDKLNEEVDDLRKATPESLWVKDLDALDMQLDELDKSDARAEEERMKIKGN 1201
V+ L ++ L++ E K+ +L +++ L+ + E E+++
Sbjct: 914 RSVERYKKLHIGLENKIMQLQRKIDEQ--NKEYKSLLEKMNNLEIT-YSTETEKLR---- 966
Query: 1202 GNGDAGPKIVAKRAPKNARKNDKKSNNARATEAMGEMDNVTKVVKPKGRAGLK-KAPAEK 1260
++ N S + E+ K K K E+
Sbjct: 967 ---SDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQ 1023
Query: 1261 LDDDEEDEVPDLKQRLAKLNEQLASTKLEPSPDQSGVMETEKVQVPAKKKEPSKR 1315
L + +++ LK +LN ++ E + + E Q+ + R
Sbjct: 1024 LVSELKEQNTLLKTEKEELNRRIHDQAKEITETMEKKLVEETKQLELDLNDERLR 1078
>1g62_A Ribosome anti-association factor EIF6; alpha-beta barrel, velcro
closure, subdomain, structural genomics, PSI; 2.50A
{Saccharomyces cerevisiae} SCOP: d.126.1.1 PDB: 2x7n_B
Length = 224
Score = 29.2 bits (65), Expect = 9.6
Identities = 16/75 (21%), Positives = 34/75 (45%)
Query: 1101 AVVAGATDETEESEENPEVVNGVQSIDYDYLLSMAIGTLTLEKVQGLLADRDKLNEEVDD 1160
+VA E S E+ + + + + IG +T +GLL ++E+
Sbjct: 24 CLVAVGGSENFYSAFEAELGDAIPIVHTTIAGTRIIGRMTAGNRRGLLVPTQTTDQELQH 83
Query: 1161 LRKATPESLWVKDLD 1175
LR + P+S+ ++ ++
Sbjct: 84 LRNSLPDSVKIQRVE 98
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.313 0.132 0.373
Gapped
Lambda K H
0.267 0.0814 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 22,471,331
Number of extensions: 1423598
Number of successful extensions: 2711
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2616
Number of HSP's successfully gapped: 95
Length of query: 1484
Length of database: 6,701,793
Length adjustment: 106
Effective length of query: 1378
Effective length of database: 3,742,167
Effective search space: 5156706126
Effective search space used: 5156706126
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 64 (28.3 bits)