RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 008738
(555 letters)
>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 = 439 bits (1131), Expect = e-153
Identities = 120/261 (45%), Positives = 163/261 (62%), Gaps = 7/261 (2%)
Query: 295 SALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGR 354
+ D K+ L GKL S P ++E+++VEGDSAGGSAKQGR
Sbjct: 7 HHHHHHSSGHIDDDDKHMKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGR 66
Query: 355 DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIIL 414
DR+FQAILPLRGK++N + A + KNEEI +I +G GV G DF E Y KIII+
Sbjct: 67 DRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGV-GADFSIEDANYDKIIIM 125
Query: 415 TDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGK----QVQYCYDDAEL 470
TDAD DGAHI+TLLLTFFYRY + L + G +Y+ +PPLYK+ +GK +V Y + D EL
Sbjct: 126 TDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGEL 185
Query: 471 KKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLM 530
++++ F ++QR+KGLGEM QLWETT+NPE R L ++ IED A A + LM
Sbjct: 186 EELRKQFGKG--ATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLM 243
Query: 531 GARVDTRKELIQNAANLVNLD 551
G +V+ R++ I++ +
Sbjct: 244 GDKVEPRRKWIEDNVKFTLEE 264
>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 = 426 bits (1097), Expect = e-146
Identities = 114/310 (36%), Positives = 172/310 (55%), Gaps = 11/310 (3%)
Query: 2 IVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPV 61
I LH+GGKF + Y VSGGLHGVG SVVNALSE V V+R+G + +SRG+
Sbjct: 91 IYNTLHSGGKFEQGA--YKVSGGLHGVGASVVNALSEWTVVEVFREGKHHRIAFSRGEVT 148
Query: 62 TTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 121
L V+ + + GTR+ F PD ++F ++FD + I R+RE+A+L L + +
Sbjct: 149 EPL--RVVGEAPRGKTGTRVTFKPDPEIFGN-LRFDPSKIRARLREVAYLVAGLKLVFQD 205
Query: 122 EDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAY 180
E+ + GG+ + + L + L+ R + +++ Y
Sbjct: 206 RQHGKEE----VFLDKGGVASFAKALAEGEDLLYEKPFLIRGTHGEVEVEVGFLHT-QGY 260
Query: 181 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 240
+ +L YAN I T DGGTH+ K++ +R LN KK+ K+K +G+ + EGL +
Sbjct: 261 NAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAV 320
Query: 241 ISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAA 300
+SV++PNP+FEGQTK +L NPE V Q V E L E LE +P + ++ K+L A +A
Sbjct: 321 VSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEILEENPRIAKAVYEKALRAAQAR 380
Query: 301 LAAKRARDLV 310
AA++AR+LV
Sbjct: 381 EAARKARELV 390
>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 = 416 bits (1071), Expect = e-142
Identities = 124/309 (40%), Positives = 192/309 (62%), Gaps = 12/309 (3%)
Query: 2 IVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPV 61
I+TVLHAGGKF +S Y VSGGLHGVG+SVVNALS+ LE+ + R+G + Q Y G P
Sbjct: 93 IMTVLHAGGKFDDNS--YKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQ 150
Query: 62 TTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 121
L ++ GT +RFWP + FT +F++ +A R+REL+FL+ ++I LR
Sbjct: 151 APLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLDSGVSIRLRD 206
Query: 122 EDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAY 180
+ E + + GG++ +V++LN +K P+H ++ F + DGI +++ALQW D +
Sbjct: 207 KRDGKED----HFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWN-DGF 261
Query: 181 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 240
+ + + N+I DGGTH+ G +A++TRTLN+ K K +S +G+ REGL +
Sbjct: 262 QENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAV 321
Query: 241 ISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAA 300
+SV+VP+P+F QTK +L + EV+ V+Q + E L EYL +P ++ K + A +A
Sbjct: 322 VSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAR 381
Query: 301 LAAKRARDL 309
AA+RAR++
Sbjct: 382 EAARRAREM 390
>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 = 404 bits (1040), Expect = e-140
Identities = 110/241 (45%), Positives = 155/241 (64%), Gaps = 8/241 (3%)
Query: 318 SSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEA 377
+ + D T P +SE+++VEGDSAGGSAK GRD FQAILPLRGKI+NVE+
Sbjct: 2 AHHHHHHVDDDDKTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARID 61
Query: 378 AMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 437
+ KN E+Q +I ALG G+ ++F LRYHKI+++ DADVDG HI TLLLT +R+ +
Sbjct: 62 RVLKNTEVQAIITALGTGI-HDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMR 120
Query: 438 TLFDEGCIYVGVPPLYKVERGKQ-VQYCYDDAELKKV-----KSSFPSNALYSIQRFKGL 491
L + G +++ PPLYK++ + ++ Y D E + K+ N IQR+KGL
Sbjct: 121 PLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGL 180
Query: 492 GEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANLVNL 550
GEM +LWETT++P R+L+Q+ ++DAA A+ +FS LMG VD R+ I NA ++ L
Sbjct: 181 GEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFL 240
Query: 551 D 551
D
Sbjct: 241 D 241
>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 = 397 bits (1024), Expect = e-135
Identities = 90/313 (28%), Positives = 151/313 (48%), Gaps = 13/313 (4%)
Query: 2 IVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPV 61
I+ LHAGGKF + Y SGGLHGVG+SVVNALS+ +EV V RDG Y+ + G+ V
Sbjct: 90 ILCRLHAGGKFSNKN--YQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKV 147
Query: 62 TTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 121
L V+ K GT + FWPD+ F + +F + + ++ A L P + I +
Sbjct: 148 QDL--QVVGTCGKRNTGTSVHFWPDETFFDS-PRFSVSRLTHVLKAKAVLCPGVEITFKD 204
Query: 122 EDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAY 180
E ++ E+ + + GL +Y+ L D +D AL W +
Sbjct: 205 EINNTEQ----RWCYQDGLNDYLAEAVNGLPTLPEKPFIGNFAGDTEAVDWALLWLPEGG 260
Query: 181 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 240
Y N I T+ GGTH+ G++ L + + + + + LS E + + +
Sbjct: 261 ELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNILP-RGVKLSAEDIWDRCAYV 319
Query: 241 ISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAA 300
+SV++ +P+F GQTK RL + + V V++ +L + + + ++S+ +
Sbjct: 320 LSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFILWLNQNVQAAELLAEMAISSAQR- 378
Query: 301 LAAKRARDLVRQK 313
+ A+ +VR+K
Sbjct: 379 -RMRAAKKVVRKK 390
>3lnu_A Topoisomerase IV subunit B; PARE, ATP-binding, nucleotide-BI
topoisomerase; 2.20A {Xanthomonas oryzae PV} PDB:
3lps_A*
Length = 408
Score = 396 bits (1020), Expect = e-134
Identities = 93/313 (29%), Positives = 157/313 (50%), Gaps = 14/313 (4%)
Query: 2 IVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPV 61
I+T LHAGGKF + Y+ SGGLHGVG+SVVNALS +E+ + R+G E+ ++ G
Sbjct: 109 ILTRLHAGGKFNNRN--YTFSGGLHGVGVSVVNALSTKVELFIKREGSEHRMEFRDGNAA 166
Query: 62 TTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 121
+ L V+ K GTR+RFW D + F T +F+ + +R A L P LT+ L
Sbjct: 167 SKLE--VVGTVGKKNTGTRLRFWADPKYFDT-PKFNVRALRHLLRAKAVLCPGLTVKLHD 223
Query: 122 EDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAY 180
E + + ++F GL +Y++ + + L D+ D +D A W
Sbjct: 224 EATGEQD----SWYFENGLRDYLKGEMAEHEMLPADLFVGSLKKDTEIVDWAAGWV-PEG 278
Query: 181 SDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCI 240
Y N I T GTH+ G+++ LT L + + + L+ E V + +T +
Sbjct: 279 ELVQESYVNLIPTAQHGTHVNGLRSGLTDALREFCDFRNLLP-RGVKLAPEDVWDRVTFV 337
Query: 241 ISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAA 300
+S+++ +P+F GQTK RL + + ++ + + + YL + ++ + I ++ A
Sbjct: 338 LSLKMTDPQFSGQTKERLSSRQAAGFIEGAAHDAFSLYLNQNVEIGEKIAQIAIDRASA- 396
Query: 301 LAAKRARDLVRQK 313
K + +VR+K
Sbjct: 397 -RLKTEKQIVRKK 408
>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 = 388 bits (999), Expect = e-132
Identities = 76/300 (25%), Positives = 123/300 (41%), Gaps = 21/300 (7%)
Query: 2 IVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPV 61
+V V G G G + V ALS +V +W DG ++ G P
Sbjct: 78 LVRVATGAGFLGRP--PGDGWGWDSML--VVSLALSSRYQVDIWADGRQWRVMGEHGHPQ 133
Query: 62 TTLTCH--VLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIAL 119
+ P+ +G R+ F PD +F + FD ++ R ELA L P L ++
Sbjct: 134 GEGAAVTPMEPMPVSAERGVRVHFVPDATIFEV-LAFDRARLSRRCNELAALAPGLRVSF 192
Query: 120 RKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSD 178
+ GG+ ++ L + LH + V F DG+ + ALQWC +
Sbjct: 193 ADLQRGERT----LWHLPGGVAQWAHVLTEARPQLHPEPVVFDFTWDGLRVQCALQWC-E 247
Query: 179 AYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLT 238
T+L +AN++RT+ G H++GV +L L L + + V +GLT
Sbjct: 248 DEDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGE------TRGAFPWARVAQGLT 301
Query: 239 CIISVRVPNP--EFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSA 296
I++V P F G TK L P + + + + +Q E L HP + ++ +
Sbjct: 302 AIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELLREHPVTPALLARRTSGS 361
>3nuh_B DNA gyrase subunit B; topoisomerase, supercoiling, specialization,
isomera; HET: DNA; 3.10A {Escherichia coli}
Length = 420
Score = 317 bits (815), Expect = e-104
Identities = 98/254 (38%), Positives = 147/254 (57%), Gaps = 10/254 (3%)
Query: 303 AKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAIL 362
+ AR++ R+K L + LPGKLADC P SE+++VEGDSAGGSAKQGR+R+ QAIL
Sbjct: 1 SNAAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAIL 60
Query: 363 PLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGA 422
PL+GKILNVE+ M ++E+ LI ALG G+ +++ + LRYH III+TDADVDG+
Sbjct: 61 PLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGS 120
Query: 423 HIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNAL 482
HIRTLLLTFFYR + + G +Y+ PPLYKV++GKQ QY DD + + + S +
Sbjct: 121 HIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGA 180
Query: 483 YSIQRFKGLGEMMPVQL---------WETTLNPEQRMLKQLVIEDAAEANVVFSSLMGAR 533
++ + L + +N +R + ++++ + + +
Sbjct: 181 -TLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDE 239
Query: 534 VDTRKELIQNAANL 547
+ + + L
Sbjct: 240 QTVTRWVNALVSEL 253
Score = 119 bits (299), Expect = 2e-29
Identities = 47/183 (25%), Positives = 78/183 (42%), Gaps = 6/183 (3%)
Query: 372 ERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHI--RTLLL 429
+ E+ + + E + I+ + VD + +
Sbjct: 240 QTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFIT 299
Query: 430 TFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFK 489
YR TL ++ + ERG++ Q + SIQR+K
Sbjct: 300 GGEYRRICTLGEKLRGLLEEDAFI--ERGERRQPVASFEQALDWLVKESRRG-LSIQRYK 356
Query: 490 GLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANLV 548
GLGEM P QLWETT++PE R + ++ ++DA A+ +F++LMG V+ R+ I+ NA
Sbjct: 357 GLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAA 416
Query: 549 NLD 551
N+D
Sbjct: 417 NID 419
>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 = 274 bits (703), Expect = 5e-87
Identities = 54/307 (17%), Positives = 107/307 (34%), Gaps = 39/307 (12%)
Query: 1 MIVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTV--WRDGMEYHQKYSRG 58
MI L + V+GG +G G + N S + G +Y QK+
Sbjct: 124 MIFGHLLTSSNYDDDE--KKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENN 181
Query: 59 KPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIA 118
+ + K T++ F PD F + D++ + R + +N +
Sbjct: 182 MSICHP--PKITSYKKGPSYTKVTFKPDLTRFGM-KELDNDILGVMRRRVYDINGSVRDI 238
Query: 119 LRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH--------DVVGFRKDVDGITID 170
+ K F +E Y++ L ++ + D+ + +
Sbjct: 239 NVYLNGKSLK----IRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWE 294
Query: 171 LALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSG 230
+A SD + + NSI T GGTH+ + + + ++ + KK K S+
Sbjct: 295 VAFAV-SDISFQ-QISFVNSIATTMGGTHVNYITDQIVKKISEILKK-----KKKKSVKS 347
Query: 231 EHVREGLTCIISVRVPNPEFEGQTKTRLGNPE-------------VRKVVDQSVQEYLTE 277
++ + I+ + NP F QTK +L + K++ + + E
Sbjct: 348 FQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFE 407
Query: 278 YLELHPD 284
+ + +
Sbjct: 408 IADANEE 414
>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 = 254 bits (651), Expect = 1e-79
Identities = 53/311 (17%), Positives = 97/311 (31%), Gaps = 31/311 (9%)
Query: 1 MIVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVW--RDGMEYHQKYSRG 58
+I L + V+GG +G G + N S V + Q +
Sbjct: 112 LIFGQLLTSSNYDDDE--KKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDN 169
Query: 59 KPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAG---RIRELAFLNPKL 115
+ T I F PD F D + +A R ++A +
Sbjct: 170 MGRAGE---MELKPFNGEDYTCITFQPDLSKFKM-QSLDKDIVALMVRRAYDIAGSTKDV 225
Query: 116 TIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQ 174
+ L G YV DK + + + ++ L
Sbjct: 226 KVFLN-----------GNKLPVKGFRSYVDMYLKDKLDETGNSLKVIHEQVNHRWEVCLT 274
Query: 175 WCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVR 234
S+ + + NSI T GG H++ V + L + KK +++ V+
Sbjct: 275 M-SEKGF-QQISFVNSIATSKGGRHVDYVADQIVTKLVDVVKKKN---KGGVAVKAHQVK 329
Query: 235 EGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSL 294
+ ++ + NP F+ QTK + + E + +++SIL +
Sbjct: 330 NHMWIFVNALIENPTFDSQTKENMTLQPKSFGSTCQLSEKFIKAAIGCG-IVESIL--NW 386
Query: 295 SALKAALAAKR 305
KA + +
Sbjct: 387 VKFKAQVQLNK 397
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 254 bits (652), Expect = 5e-76
Identities = 115/267 (43%), Positives = 161/267 (60%), Gaps = 10/267 (3%)
Query: 286 LDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDS 345
++ +SK+ LKAA +R K ++ +LPGKLADC T EESE+FIVEGDS
Sbjct: 1 MEMAISKAGRRLKAAKKVER-------KKIVSGPALPGKLADCVGQTREESELFIVEGDS 53
Query: 346 AGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA 405
AGGSAKQ RD+ FQAI+P+RGKILN + ++E+ ++ A+G+ +D +
Sbjct: 54 AGGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSDDLSE-- 111
Query: 406 LRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCY 465
LRY KI IL DAD DG HI TLL F ++ L +EG +YV +PPL++++ GK V Y
Sbjct: 112 LRYGKICILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYAL 171
Query: 466 DDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAE-ANV 524
DD EL+ + + N I RFKGLGEM +QL ETT++P R L QL ++DA A +
Sbjct: 172 DDEELETILKNVKGNKNPQITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGL 231
Query: 525 VFSSLMGARVDTRKELIQNAANLVNLD 551
+ L R RK+ ++ NL ++
Sbjct: 232 LDKLLAKKRAADRKQWLEQKGNLADIT 258
>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 = 250 bits (640), Expect = 3e-74
Identities = 64/259 (24%), Positives = 103/259 (39%), Gaps = 9/259 (3%)
Query: 299 AALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGR---D 355
+ S ++ D E + + EGDSA A G
Sbjct: 16 DDKVPDPTSVDSVKYSKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIG 75
Query: 356 RRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA----LRYHKI 411
R + PLRGKILNV + +N EI N+I+ +GL + + LRY KI
Sbjct: 76 RDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQY-KKSYDDAESLKTLRYGKI 134
Query: 412 IILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELK 471
+I+TD D DG+HI+ LL+ F + +L G + + P+ K + KQ Y E
Sbjct: 135 MIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPIVKASKNKQELSFYSIPEFD 194
Query: 472 KVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMG 531
+ K + + I+ +KGLG + E + E+ + + + +
Sbjct: 195 EWKKHIENQKAWKIKYYKGLGTSTAKEAKEYFADMERHRILF-RYAGPEDDAAITLAFSK 253
Query: 532 ARVDTRKELIQNAANLVNL 550
++D RKE + N
Sbjct: 254 KKIDDRKEWLTNFMEDRRQ 272
>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 = 202 bits (516), Expect = 2e-57
Identities = 120/237 (50%), Positives = 147/237 (62%), Gaps = 35/237 (14%)
Query: 319 SSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAA 378
+SLPGKLADCSS +PEE EIF+VEGDSAGGS K GRD R QAILPLRGKILNVE+
Sbjct: 4 ASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDR 63
Query: 379 MYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKT 438
+ N EI+ +I A G G+ G DF RYHKI+I+TDADVDGAHIRTLLLTFFYR+ +
Sbjct: 64 ILNNNEIRQMITAFGTGIGG-DFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 439 LFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQ 498
L + G +Y+ PP +KGLGEM Q
Sbjct: 123 LIEAGYVYIAQPP----------------------------------TGYKGLGEMNADQ 148
Query: 499 LWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 555
LWETT+NPE R L Q+ +EDA EA+ F LMG V+ R++ I++ A NLD ++
Sbjct: 149 LWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAEL 205
>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 = 181 bits (461), Expect = 6e-54
Identities = 63/136 (46%), Positives = 83/136 (61%), Gaps = 10/136 (7%)
Query: 2 IVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSR-GKP 60
I T+LHAGGKFG GY SGGLHGVG SVVNALS LEV + RDG Y Q++ GKP
Sbjct: 98 IFTILHAGGKFGQG--GYKTSGGLHGVGSSVVNALSSWLEVEITRDGAVYKQRFENGGKP 155
Query: 61 VTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALR 120
VTTL + K + GT++ F PD +F+T F +NTI+ R+ E AFL +T++L
Sbjct: 156 VTTLK--KIGTALKSKTGTKVTFMPDATIFST-TDFKYNTISERLNESAFLLKNVTLSLT 212
Query: 121 KEDSDPEKNQYNEYFF 136
+ +D E+ +
Sbjct: 213 DKRTDEAI----EFHY 224
>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 = 181 bits (461), Expect = 7e-54
Identities = 59/137 (43%), Positives = 82/137 (59%), Gaps = 10/137 (7%)
Query: 2 IVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPV 61
I+TVLHAGGKF +S Y VSGGLHGVG+SVVNALS+ LE+ + R+G + Q Y G P
Sbjct: 94 IMTVLHAGGKFDDNS--YKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQ 151
Query: 62 TTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 121
L ++ GT +RFWP + FT +F++ +A R+REL+FLN ++I LR
Sbjct: 152 APLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRD 207
Query: 122 EDSDPEKNQYNEYFFAG 138
+ E + + G
Sbjct: 208 KRDGKED----HFHYEG 220
>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 = 179 bits (456), Expect = 2e-53
Identities = 50/127 (39%), Positives = 72/127 (56%), Gaps = 5/127 (3%)
Query: 2 IVTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPV 61
I+ LHAGGKF + Y SGGLHGVG+SVVNALS+ +EV V RDG Y+ + G+ V
Sbjct: 76 ILCRLHAGGKFSNKN--YQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKV 133
Query: 62 TTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 121
L V+ K GT + FWPD+ F + +F + + ++ A L P + I +
Sbjct: 134 QDLQ--VVGTCGKRNTGTSVHFWPDETFFDS-PRFSVSRLTHVLKAKAVLCPGVEITFKD 190
Query: 122 EDSDPEK 128
E ++ E+
Sbjct: 191 EINNTEQ 197
>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 = 152 bits (386), Expect = 1e-39
Identities = 63/239 (26%), Positives = 108/239 (45%), Gaps = 11/239 (4%)
Query: 324 KLADCS---STTPEESEIFIVEGDSAGGSAKQGR---DRRFQAILPLRGKILNVERKDEA 377
KL D + + + + + EGDSA A G R + PLRGK+LNV
Sbjct: 8 KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASAD 67
Query: 378 AMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 437
+ KN EIQ + + +GL + + ++LRY ++I+TD D DG+HI+ L++ F
Sbjct: 68 QILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFP 127
Query: 438 TLFD-EGCIYVGVPPLYKVERGKQVQYC---YDDAELKKVKSSFPSNALYSIQRFKGLGE 493
L D +G + + P+ KV K + Y+ + +K + + + +KGLG
Sbjct: 128 GLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGT 187
Query: 494 MMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDH 552
+ ++ E N + R LK + + + + + D RKE ++ LD
Sbjct: 188 SLAQEVREYFSNLD-RHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDP 245
>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 = 137 bits (348), Expect = 5e-38
Identities = 46/110 (41%), Positives = 63/110 (57%), Gaps = 5/110 (4%)
Query: 31 SVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVF 90
SVVNALS+ LEV V R+ YHQ Y +G P L V + D+ GT IRF D ++F
Sbjct: 94 SVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKE----VGTTDKTGTVIRFKADGEIF 149
Query: 91 TTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGL 140
T +++ T+ RIRELAFLN + I LR E + + + Y + GG+
Sbjct: 150 TETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVRE-DSYHYEGGI 198
>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 = 66.8 bits (162), Expect = 1e-11
Identities = 86/557 (15%), Positives = 168/557 (30%), Gaps = 162/557 (29%)
Query: 71 VDSKDR-QGTRIRFW-----PDKQV---FTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 121
+ SKD GT FW ++ V ++ ++ + I+ P + +
Sbjct: 55 IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT-EQRQPSMMTRMYI 113
Query: 122 EDSDPEKNQYNEYF---FAGGLEEYVQ---WLNTDKKP----LHDVVGFRKDVDGITIDL 171
E D N N+ F L+ Y++ L + + V+G K +
Sbjct: 114 EQRDRLYND-NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW------V 166
Query: 172 ALQWCSDAYSDTM---------LGYANSIRTI-------------------DGGT----H 199
AL C L NS T+ D +
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR 226
Query: 200 IEGVKASLTRTL------NSL---------------GKKSKTV---KDKDIS-------- 227
I ++A L R L N L K + + K ++
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT 286
Query: 228 --LSGEHVREGLTC---------IISVRVPN-PEFEGQTKTRLGNPEVRKVVDQSVQEYL 275
+S +H LT + R + P + T NP ++ +S+++ L
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR---EVLT--TNPRRLSIIAESIRDGL 341
Query: 276 T---EYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSS-LPGKL-----A 326
+ ++ D L +I+ SL+ L+ A K L SV S+ +P L
Sbjct: 342 ATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL----SVFPPSAHIPTILLSLIWF 397
Query: 327 DCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAI----LPLRGKILN--------VERK 374
D + +V ++ +I L L+ K+ N V+
Sbjct: 398 DVIKSDVMV----VVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHY 453
Query: 375 DEAAMYKNEEIQNL-------------IRALGLGVKGEDFKKEALRYH----KIIILTDA 417
+ + ++++ ++ + + F+ L + KI + A
Sbjct: 454 NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTA 513
Query: 418 DVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYK--VERGKQVQYCYDDAELKKVKS 475
I L + Y+ + D Y + + + ++ C +L ++
Sbjct: 514 WNASGSILNTLQQLKF-YKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIAL 572
Query: 476 SFPSNALYS-----IQR 487
A++ +QR
Sbjct: 573 MAEDEAIFEEAHKQVQR 589
>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 = 51.6 bits (123), Expect = 7e-07
Identities = 70/427 (16%), Positives = 137/427 (32%), Gaps = 167/427 (39%)
Query: 77 QGTRIRFWPD-KQVFTTAIQFDHNTIAGRIRELAF--LNPKLTIALRKEDSDPEKNQYNE 133
QG ++ + + ++ T ++ + G + + + L+ L + D EK
Sbjct: 163 QGNTDDYFEELRDLYQT-----YHVLVGDLIKFSAETLSE-----LIRTTLDAEK----- 207
Query: 134 YFFAGGLEEYVQWL-NTDKKPLHD-------------------------VVG-----FRK 162
F GL ++WL N P D ++G R
Sbjct: 208 -VFTQGLN-ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRS 265
Query: 163 DVDGIT-----------IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTL 211
+ G T I W +++ + + + I I GV+
Sbjct: 266 YLKGATGHSQGLVTAVAIAETDSW--ESF------FVSVRKAITVLFFI-GVRCYEAYPN 316
Query: 212 NSLGKKSKTVKDKDISLSGEHVREGL-TCIISVR-VPNPEFE---GQTKTRL-------- 258
SL ++D S E+ EG+ + ++S+ + + + +T + L
Sbjct: 317 TSL--PPSILED-----SLEN-NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 259 ------------GNPE--------VRKV-----VDQS-----------VQEYL------- 275
G P+ +RK +DQS +L
Sbjct: 369 SLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFH 428
Query: 276 TEYLE-----LHPDVLDSILSKSLSALKAAL-AAKRARDLVRQKSVLRSSSLPGKLADCS 329
+ L ++ D++ + +S + ++ + DL R S S+ ++ DC
Sbjct: 429 SHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDL-RVLS----GSISERIVDCI 483
Query: 330 STTP---EESEIF----IVE---GDSAG-GS----AKQGRDRRFQAILPLRGKILNVERK 374
P E + F I++ G ++G G K G R I+ G L++
Sbjct: 484 IRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRV--IVA--GT-LDINPD 538
Query: 375 DEAAMYK 381
D+ +K
Sbjct: 539 DDYG-FK 544
Score = 48.9 bits (116), Expect = 4e-06
Identities = 45/245 (18%), Positives = 79/245 (32%), Gaps = 69/245 (28%)
Query: 10 GKFGGSSSGYSVSGGLHGVGLSVVNALSES-----------LEVTVWRDGMEYHQKYSRG 58
G+ G +G G+ +V A ++S + V + G+ ++ Y
Sbjct: 261 GELRSYLKG--ATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFI-GVRCYEAY--- 314
Query: 59 KPVTTLTCHVLPVDSKDR-QGT-----RIRFWPDKQVFTTAIQFD-------------HN 99
P T+L +L DS + +G I +QV + + N
Sbjct: 315 -PNTSLPPSIL-EDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVN 372
Query: 100 T-----IAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPL 154
++G + L LN + LRK + +Q F L+ ++L P
Sbjct: 373 GAKNLVVSGPPQSLYGLN----LTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVA-SPF 427
Query: 155 H-----DVVGFRKDVDGITIDLALQWCSDAYSDTMLG---YANSIRTIDGGTHIEGVKAS 206
H D I DL S D + Y T D G+ + + S
Sbjct: 428 HSHLLVPA------SDLINKDLVKNNVSFNAKD--IQIPVYD----TFD-GSDLRVLSGS 474
Query: 207 LTRTL 211
++ +
Sbjct: 475 ISERI 479
Score = 47.0 bits (111), Expect = 2e-05
Identities = 69/386 (17%), Positives = 122/386 (31%), Gaps = 118/386 (30%)
Query: 242 SVRVPNP----------EFEGQTKTRLGNPEVRKVVDQ---SVQEYLTEYL-----ELHP 283
+ VP +F K L P D + E + ++L + P
Sbjct: 19 VLLVPTASFFIASQLQEQF---NKI-LPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEP 74
Query: 284 DV---LDSILSKSLS-------------ALKAALAAKRARDLVRQKSVLRSSSLPGKLAD 327
D +L+ L+ AL A L + LV+ K ++++ +A
Sbjct: 75 SKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAK 134
Query: 328 CSSTTPEESEIF--IVEGDSA-----GGSAKQG-RDRRFQAILPLRGKILNVERKDE-AA 378
S +F + EG++ GG QG D F +E
Sbjct: 135 RPFDKKSNSALFRAVGEGNAQLVAIFGG---QGNTDDYF----------------EELRD 175
Query: 379 MYK--NEEIQNLIRALG-----LGVKGEDFKKEALRYHKIII---LTDADV--DGAHIRT 426
+Y+ + + +LI+ L D +K + + I L + D ++ +
Sbjct: 176 LYQTYHVLVGDLIKFSAETLSELIRTTLDAEK--VFTQGLNILEWLENPSNTPDKDYLLS 233
Query: 427 -------LLLTFFYRYQKTLFDEGCIYVGVPP--LYKVERGKQVQYCYDD----AELKKV 473
+ + Y T +G P L +G + +
Sbjct: 234 IPISCPLIGVIQLAHYVVT-----AKLLGFTPGELRSYLKG--ATGHSQGLVTAVAIAET 286
Query: 474 KS--SFPSNALYSIQRFKGLG----EMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFS 527
S SF + +I +G E P T+L P ++ED+ E N
Sbjct: 287 DSWESFFVSVRKAITVLFFIGVRCYEAYPN----TSLPPS-------ILEDSLENNEGVP 335
Query: 528 SLMGARVDTRKELIQNAANLVNLDHL 553
S M + + +E +Q+ N N HL
Sbjct: 336 SPMLSISNLTQEQVQDYVNKTN-SHL 360
Score = 42.7 bits (100), Expect = 3e-04
Identities = 48/282 (17%), Positives = 76/282 (26%), Gaps = 119/282 (42%)
Query: 44 VWRDGMEYH--QKYS-------RGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAI 94
VW + + H Y P LT H +G RIR +F T +
Sbjct: 1645 VW-NRADNHFKDTYGFSILDIVINNP-VNLTIHFGG-----EKGKRIRENYSAMIFETIV 1697
Query: 95 QFDHNTIAGRI--------RELAFLNPK----LT-----------IA----LRKEDSDPE 127
D +I F + K T A L+ + P
Sbjct: 1698 --DGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPA 1755
Query: 128 KNQYNEYFFAG---GLEEY--------VQWLNTDKKPLHD---VVGFRKDVDGITIDLAL 173
+ FAG G EY V + + VV +R G+T+ +A+
Sbjct: 1756 -----DATFAGHSLG--EYAALASLADV--M-----SIESLVEVVFYR----GMTMQVAV 1797
Query: 174 ------------------------------QWCSDAYSDTMLGY----AN----SIRTID 195
T G+ N + + +
Sbjct: 1798 PRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRT--GWLVEIVNYNVENQQYVA 1855
Query: 196 GGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGL 237
G + + +T LN + + + + SLS E V L
Sbjct: 1856 AG-DLRALDT-VTNVLNFIKLQKIDIIELQKSLSLEEVEGHL 1895
Score = 42.3 bits (99), Expect = 4e-04
Identities = 42/293 (14%), Positives = 82/293 (27%), Gaps = 128/293 (43%)
Query: 139 GLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGT 198
G++ Y +DV + A D + G+ SI I
Sbjct: 1632 GMDLYKT---------SKAA---QDV----WNRA-----DNHFKDTYGF--SILDI---- 1664
Query: 199 HIEGVKASLTR-TLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTR 257
V + T++ G+K K +++ ++ E + +G
Sbjct: 1665 ----VINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDG--------------------- 1699
Query: 258 LGNPEVRKVVDQSVQEYLTEYLELHP-DVLDS-------ILSKSLSALK----------- 298
+ + + + E+ T Y +L + + +A +
Sbjct: 1700 ---KLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPAD 1756
Query: 299 -----------AALAA-------KRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFI 340
AALA+ + ++V R G +
Sbjct: 1757 ATFAGHSLGEYAALASLADVMSIESLVEVVFY----R-----GMTMQVA----------- 1796
Query: 341 VEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALG 393
V D G S + AI P G++ AA + E +Q ++ +G
Sbjct: 1797 VPRDELGRS-----NYGMIAINP--GRV--------AASFSQEALQYVVERVG 1834
>1jmo_A HC-II, heparin cofactor II, HLS2, serin; serpin, thrombin,
protease, inhibition, inhibitor, blood CLO; HET: TYS NDG
NAG; 2.20A {Homo sapiens} SCOP: e.1.1.1 PDB: 1jmj_A*
Length = 480
Score = 31.6 bits (72), Expect = 0.76
Identities = 4/44 (9%), Positives = 16/44 (36%), Gaps = 10/44 (22%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
+ + L + N+ + + +G + +T +++
Sbjct: 117 NLYRVLKDQVNTFDNIFIAPVGISTAMGMISLGLKGETHEQVHS 160
>2oay_A C1-inhibitor, plasma protease C1 inhibitor, C1 INH, C1INH; latent
serpin, RCL insertion, immune system,hydrolase inhibi;
HET: NAG; 2.35A {Homo sapiens}
Length = 390
Score = 31.1 bits (71), Expect = 1.0
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 10/44 (22%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
++ E N+ FS +GA +T+ L
Sbjct: 42 KLYHAFSAMKKVETNMAFSPFSIASLLTQVLLGAGENTKTNLES 85
>3kcg_I Antithrombin-III, ATIII; michaelis complex, blood coagulation,
calcium, disulfide bond, EGF-like domain, glycoprotein,
hemophilia, hydrolase; HET: NAG FUC MAN NTP; 1.70A {Homo
sapiens} PDB: 1e04_I* 1ath_A 1ant_L* 1br8_L 1azx_I*
1dzh_L* 1e03_L* 1dzg_L* 1e05_L* 1jvq_L* 1lk6_L* 1nq9_I*
1oyh_L* 1r1l_L* 1sr5_A* 2ant_L* 2beh_L* 2hij_L* 2znh_A*
3evj_I* ...
Length = 432
Score = 31.1 bits (71), Expect = 1.0
Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 10/44 (22%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
+ L N+ S L +GA DT ++L++
Sbjct: 61 TFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLME 104
>2wxy_C Angiotensinogen, serpin A8; glycoprotein, hypertension,
vasoconstrictor, renin, serpins, vasoactive, hormone;
2.10A {Mus musculus} PDB: 2wxx_A 2wy0_C 2wxz_A 2wxz_C
2wy1_A
Length = 453
Score = 30.8 bits (70), Expect = 1.2
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 10/44 (22%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
RM K L + + + S +G+ T +L
Sbjct: 83 RMYKMLNEAGSGASGAILSPPALFGTLVSFYLGSLDPTASQLQT 126
>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 = 29.9 bits (66), Expect = 1.2
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 11/26 (42%)
Query: 459 KQVQYCYDDAELKKVKSSFPSNALYS 484
KQ LKK+++S LY+
Sbjct: 19 KQ--------ALKKLQASL---KLYA 33
>1vr5_A Oligopeptide ABC transporter, periplasmic oligope binding protein;
TM1223, periplasmic oligopepti binding, structural
genomics; HET: EPE; 1.73A {Thermotoga maritima} SCOP:
c.94.1.1
Length = 547
Score = 30.8 bits (70), Expect = 1.3
Identities = 10/64 (15%), Positives = 23/64 (35%), Gaps = 9/64 (14%)
Query: 117 IALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRK------DVDGITID 170
+ + K+ N + + ++N +K PL FR+ + + I +
Sbjct: 243 VPVLKKAYGIVTWYENAPYMLPANTAGI-YINVNKYPLSIPE-FRRAMAYAINPEKI-VT 299
Query: 171 LALQ 174
A +
Sbjct: 300 RAYE 303
>3k7d_A Glutamate-ammonia-ligase adenylyltransferase; nucleotidyl
transferase domain, ATP-binding, nucleotide-BIND
nucleotidyltransferase; 2.40A {Escherichia coli}
Length = 498
Score = 30.7 bits (69), Expect = 1.6
Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 11/56 (19%)
Query: 273 EYLTEYLELHPDVLDSILS-------KSLSALKAALAAKRAR----DLVRQKSVLR 317
+ L +P +LD +L + A + L R D +Q LR
Sbjct: 115 PMIASQLARYPLLLDELLDPNTLYQPTATDAYRDELRQYLLRVPEDDEEQQLEALR 170
>2fcj_A Small toprim domain protein; structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; HET: MES; 1.30A {Geobacillus
stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A*
Length = 119
Score = 29.0 bits (65), Expect = 1.7
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 403 KEALRYHKIIILTDADVDGAHIRTLLLTFF 432
+ L + + +L DAD G +R F
Sbjct: 45 ADELEGYDVYLLADADEAGEKLRRQFRRMF 74
>1v4a_A Glutamate-ammonia-ligase adenylyltransferase; main alpha helix, DNA
polymerase beta motif; 2.00A {Escherichia coli} SCOP:
a.24.16.4 d.218.1.9
Length = 440
Score = 29.4 bits (66), Expect = 3.5
Identities = 9/52 (17%), Positives = 16/52 (30%), Gaps = 7/52 (13%)
Query: 273 EYLTEYLELHPDVLDSILS-----KSLSALKAALAAKRAR--DLVRQKSVLR 317
+++ + + HP+ L + S A L D LR
Sbjct: 40 DFVQDSVIAHPEWLTELESQPPQADEWQHYAAWLQEALCNVSDEAGLMRELR 91
>1as4_A Antichymotrypsin, ACT; serpin, serine protease inhibitor; 2.10A
{Homo sapiens} SCOP: e.1.1.1 PDB: 2ach_A* 4caa_A 3caa_A
Length = 341
Score = 29.1 bits (66), Expect = 3.6
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 11/44 (25%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
+ KQLV++ + NV+FS L +GA T E+++
Sbjct: 17 SLYKQLVLKAPDK-NVIFSPLSISTALAFLSLGAHNTTLTEILK 59
>3ndd_A Alpha-1-antitrypsin; serpin, hydrolase inhibitor; 1.50A {Homo
sapiens} PDB: 3ndf_A 7api_A* 8api_A* 9api_A* 1d5s_A
1ezx_A 3t1p_A 2d26_A 1qmb_A
Length = 343
Score = 29.1 bits (66), Expect = 3.7
Identities = 9/44 (20%), Positives = 20/44 (45%), Gaps = 11/44 (25%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
+ +QL + + N+ FS + +G + DT E+++
Sbjct: 21 SLYRQLAHQSNST-NIFFSPVSIATAFAMLSLGTKADTHDEILE 63
>1yxa_A Serine (OR cysteine) proteinase inhibitor, clade 3N; serpin,
antichymotrypsin, protease inhibitor, reactive centr
plasma, hydrolase inhibitor; 2.10A {Mus musculus}
Length = 398
Score = 29.1 bits (66), Expect = 4.1
Identities = 12/44 (27%), Positives = 25/44 (56%), Gaps = 11/44 (25%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
+ K+LV+++ N+VFS L +GA+ +T +E+++
Sbjct: 37 SLYKELVLKNPDT-NIVFSPLSISAALALVSLGAKGNTLEEILE 79
>2vdx_A Corticosteroid-binding globulin; transport protein, cortisol
binding globulin, glycoprotein, lipid-binding, disease
mutation, CBG, SERP cleaved; 1.84A {Homo sapiens} PDB:
2vdy_A*
Length = 373
Score = 28.7 bits (65), Expect = 4.6
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 11/44 (25%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
+ K LV + N+ S + +G TR +L+Q
Sbjct: 17 SLYKHLVALSPKK-NIFISPVSISMALAMLSLGTCGHTRAQLLQ 59
>1qhu_A Protein (hemopexin); beta propeller, HAEM binding and transport,
iron metabolism, binding protein; HET: HEM; 2.30A
{Oryctolagus cuniculus} SCOP: b.66.1.1 b.66.1.1 PDB:
1qjs_A*
Length = 460
Score = 29.0 bits (64), Expect = 4.6
Identities = 7/50 (14%), Positives = 12/50 (24%), Gaps = 10/50 (20%)
Query: 134 YFFAGGLEEYVQWLNTDK--------KPLHDVVGFRKDVDGITIDLALQW 175
Y + +L K L +G + +D A
Sbjct: 317 YLIQD--TKVYVFLTKGGYTLVNGYPKRLEKELGSPPVISLEAVDAAFVC 364
>3ne4_A Alpha-1-antitrypsin; serpin, LUNG disease, liver disease,
polymerisation, hydrolase inhibitor; 1.81A {Homo
sapiens} PDB: 1qlp_A 2qug_A 3cwl_A 3cwm_A* 1psi_A 3drm_A
1kct_A 3dru_A 1hp7_A 1iz2_A* 1oph_A 1oo8_A 1atu_A 1d5s_B
1qmb_B
Length = 424
Score = 28.8 bits (65), Expect = 4.8
Identities = 9/44 (20%), Positives = 20/44 (45%), Gaps = 11/44 (25%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
+ +QL + + N+ FS + +G + DT E+++
Sbjct: 66 SLYRQLAHQSNST-NIFFSPVSIATAFAMLSLGTKADTHDEILE 108
>3juy_B 3B3 single chain variant HIV-1 antibody; envelope protein GP120,
broadly neutralizing antibody, 3B3 single chain variable
fragment, immune system; 2.50A {Homo sapiens}
Length = 256
Score = 28.5 bits (64), Expect = 5.0
Identities = 14/43 (32%), Positives = 14/43 (32%), Gaps = 3/43 (6%)
Query: 3 VTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVW 45
V V GG GS G S GG V LS S
Sbjct: 129 VIVSSGGG---GSGGGGSGGGGSEIVLTQAPGTLSLSPGERAT 168
>3dy0_A N-terminus plasma serine protease inhibitor; serpin, blood
clotting, hydrolase inhibitor; HET: IDS SGN; 1.55A {Homo
sapiens} PDB: 1lq8_A* 2hi9_A*
Length = 336
Score = 28.7 bits (65), Expect = 5.0
Identities = 7/44 (15%), Positives = 19/44 (43%), Gaps = 11/44 (25%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
+ + L ++ N+ FS + +GA T+ ++++
Sbjct: 15 DLYRALASAAPSQ-NIFFSPVSISMSLAMLSLGAGSSTKMQILE 57
>3le2_A Serpin-ZX; apoplast, glycoprotein, protease inhibitor, secreted,
serine protease inhibitor, hydrolase; 2.20A {Arabidopsis
thaliana}
Length = 393
Score = 28.5 bits (64), Expect = 5.7
Identities = 7/44 (15%), Positives = 18/44 (40%), Gaps = 10/44 (22%)
Query: 509 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 542
+ K ++ + +NV+FS G+ T+ +++
Sbjct: 18 NLAKHVITTVSQNSNVIFSPASINVVLSIIAAGSAGATKDQILS 61
>3bjc_A CGMP-specific 3',5'-cyclic phosphodiesterase; PDE5, erectIle
dysfunction, inhibitor design, allosteric enzyme,
alternative splicing, CGMP binding; HET: WAN; 2.00A
{Homo sapiens} SCOP: a.211.1.2 PDB: 3mf0_A 3lfv_A 2xss_A
2k31_A*
Length = 878
Score = 28.6 bits (63), Expect = 6.1
Identities = 24/179 (13%), Positives = 48/179 (26%), Gaps = 14/179 (7%)
Query: 252 GQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILS-KSLSALKAALAAKRARDLV 310
+ R ++ Q Q+ + +L+ H D S K+ + A A+R +
Sbjct: 10 SFGQQRQQQQPQQQKQQQRDQDSVEAWLDDHWDFTFSYFVRKATREMVNAWFAERVHTIP 69
Query: 311 RQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGG-----------SAKQGRDRRFQ 359
K +R + S + S + +G
Sbjct: 70 VCKEGIRGHTESCSCPLQQSPRADNSVPGTPTRKISASEFDRPLRPIVVKDSEGTVSFLS 129
Query: 360 AILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDAD 418
L R D + + L++ + + + + I L AD
Sbjct: 130 DSEKKEQMPLTPPRFDHDEGDQCSRLLELVKDISSHLDVTALCHKIFLH--IHGLISAD 186
>2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein,
decatenation, ATPase, drug design, DNA-binding,
magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus
shibatae}
Length = 530
Score = 28.2 bits (62), Expect = 8.5
Identities = 12/126 (9%), Positives = 32/126 (25%), Gaps = 18/126 (14%)
Query: 12 FGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPV 71
S + G++G+G+ S+ + + + + L +
Sbjct: 94 LYSSKYVNRQTRGMYGLGVKAAVLYSQM-------HQDKPIEIETSPVNSKRIYTFKLKI 146
Query: 72 D--------SKDRQGTRIRFWPDKQVFTTA---IQFDHNTIAGRIRELAFLNPKLTIALR 120
D + R + V + + I I+ + P +
Sbjct: 147 DINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFK 206
Query: 121 KEDSDP 126
+ +
Sbjct: 207 DPEGNV 212
>1t6t_1 Putative protein; structural genomics, PSI, protein structur
initiative, midwest center for structural genomics,
MCSG, U function; 1.80A {Aquifex aeolicus} SCOP:
c.136.1.1
Length = 118
Score = 26.9 bits (59), Expect = 9.5
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 3/72 (4%)
Query: 365 RGKILNVE-RKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAH 423
R ++ VE + D+ A+ I+N+I G + ++ K+I+L D D G
Sbjct: 20 REAVILVEGKNDKKAL-SKFSIKNVIDLSGKRYA-DVVDMLEGKWEKVILLFDLDTHGER 77
Query: 424 IRTLLLTFFYRY 435
I +
Sbjct: 78 INQKMKELLSSQ 89
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
0.317 0.135 0.387
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: 8,584,537
Number of extensions: 543437
Number of successful extensions: 1336
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1254
Number of HSP's successfully gapped: 54
Length of query: 555
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 457
Effective length of database: 3,965,535
Effective search space: 1812249495
Effective search space used: 1812249495
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.7 bits)