RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 010553
(507 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 = 435 bits (1122), Expect = e-153
Identities = 120/261 (45%), Positives = 163/261 (62%), Gaps = 7/261 (2%)
Query: 247 SALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGR 306
+ D K+ L GKL S P ++E+++VEGDSAGGSAKQGR
Sbjct: 7 HHHHHHSSGHIDDDDKHMKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGR 66
Query: 307 DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIIL 366
DR+FQAILPLRGK++N + A + KNEEI +I +G GV G DF E Y KIII+
Sbjct: 67 DRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGV-GADFSIEDANYDKIIIM 125
Query: 367 TDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGK----QVQYCYDDAEL 422
TDAD DGAHI+TLLLTFFYRY + L + G +Y+ +PPLYK+ +GK +V Y + D EL
Sbjct: 126 TDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGEL 185
Query: 423 KKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLM 482
++++ F ++QR+KGLGEM QLWETT+NPE R L ++ IED A A + LM
Sbjct: 186 EELRKQFGKG--ATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLM 243
Query: 483 GARVDTRKELIQNAANLVNLD 503
G +V+ R++ I++ +
Sbjct: 244 GDKVEPRRKWIEDNVKFTLEE 264
>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 = 401 bits (1033), Expect = e-140
Identities = 110/241 (45%), Positives = 155/241 (64%), Gaps = 8/241 (3%)
Query: 270 SSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEA 329
+ + D T P +SE+++VEGDSAGGSAK GRD FQAILPLRGKI+NVE+
Sbjct: 2 AHHHHHHVDDDDKTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARID 61
Query: 330 AMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 389
+ KN E+Q +I ALG G+ ++F LRYHKI+++ DADVDG HI TLLLT +R+ +
Sbjct: 62 RVLKNTEVQAIITALGTGI-HDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMR 120
Query: 390 TLFDEGCIYVGVPPLYKVERGKQ-VQYCYDDAELKKV-----KSSFPSNALYSIQRFKGL 443
L + G +++ PPLYK++ + ++ Y D E + K+ N IQR+KGL
Sbjct: 121 PLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGL 180
Query: 444 GEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANLVNL 502
GEM +LWETT++P R+L+Q+ ++DAA A+ +FS LMG VD R+ I NA ++ L
Sbjct: 181 GEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFL 240
Query: 503 D 503
D
Sbjct: 241 D 241
>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 = 333 bits (857), Expect = e-111
Identities = 85/262 (32%), Positives = 139/262 (53%), Gaps = 9/262 (3%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
+ +SRG+ L V+ + + GTR+ F PD ++F ++FD + I R+RE+A
Sbjct: 137 HHRIAFSRGEVTEPL--RVVGEAPRGKTGTRVTFKPDPEIFGN-LRFDPSKIRARLREVA 193
Query: 62 FLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGIT 120
+L L + + E+ + GG+ + + L + L+ R +
Sbjct: 194 YLVAGLKLVFQDRQHGKEE----VFLDKGGVASFAKALAEGEDLLYEKPFLIRGTHGEVE 249
Query: 121 IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL 180
+++ Y+ +L YAN I T DGGTH+ K++ +R LN KK+ K+K
Sbjct: 250 VEVGFLHT-QGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQP 308
Query: 181 SGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDS 240
+G+ + EGL ++SV++PNP+FEGQTK +L NPE V Q V E L E LE +P + +
Sbjct: 309 TGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEILEENPRIAKA 368
Query: 241 ILSKSLSALKAALAAKRARDLV 262
+ K+L A +A AA++AR+LV
Sbjct: 369 VYEKALRAAQAREAARKARELV 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 = 324 bits (832), Expect = e-107
Identities = 92/261 (35%), Positives = 153/261 (58%), Gaps = 10/261 (3%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
+ Q Y G P L ++ GT +RFWP + FT +F++ +A R+REL+
Sbjct: 139 IHRQIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELS 194
Query: 62 FLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGIT 120
FL+ ++I LR + E + + GG++ +V++LN +K P+H ++ F + DGI
Sbjct: 195 FLDSGVSIRLRDKRDGKED----HFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIG 250
Query: 121 IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL 180
+++ALQW D + + + + N+I DGGTH+ G +A++TRTLN+ K K +S
Sbjct: 251 VEVALQWN-DGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSA 309
Query: 181 SGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDS 240
+G+ REGL ++SV+VP+P+F QTK +L + EV+ V+Q + E L EYL +P
Sbjct: 310 TGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKI 369
Query: 241 ILSKSLSALKAALAAKRARDL 261
++ K + A +A AA+RAR++
Sbjct: 370 VVGKIIDAARAREAARRAREM 390
>3nuh_B DNA gyrase subunit B; topoisomerase, supercoiling, specialization,
isomera; HET: DNA; 3.10A {Escherichia coli}
Length = 420
Score = 314 bits (807), Expect = e-103
Identities = 98/254 (38%), Positives = 147/254 (57%), Gaps = 10/254 (3%)
Query: 255 AKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAIL 314
+ AR++ R+K L + LPGKLADC P SE+++VEGDSAGGSAKQGR+R+ QAIL
Sbjct: 1 SNAAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAIL 60
Query: 315 PLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGA 374
PL+GKILNVE+ M ++E+ LI ALG G+ +++ + LRYH III+TDADVDG+
Sbjct: 61 PLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGS 120
Query: 375 HIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNAL 434
HIRTLLLTFFYR + + G +Y+ PPLYKV++GKQ QY DD + + + S +
Sbjct: 121 HIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGA 180
Query: 435 YSIQRFKGLGEMMPVQL---------WETTLNPEQRMLKQLVIEDAAEANVVFSSLMGAR 485
++ + L + +N +R + ++++ + + +
Sbjct: 181 -TLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDE 239
Query: 486 VDTRKELIQNAANL 499
+ + + L
Sbjct: 240 QTVTRWVNALVSEL 253
Score = 118 bits (296), Expect = 4e-29
Identities = 47/183 (25%), Positives = 78/183 (42%), Gaps = 6/183 (3%)
Query: 324 ERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHI--RTLLL 381
+ E+ + + E + I+ + VD + +
Sbjct: 240 QTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFIT 299
Query: 382 TFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFK 441
YR TL ++ + ERG++ Q + SIQR+K
Sbjct: 300 GGEYRRICTLGEKLRGLLEEDAFI--ERGERRQPVASFEQALDWLVKESRRG-LSIQRYK 356
Query: 442 GLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ-NAANLV 500
GLGEM P QLWETT++PE R + ++ ++DA A+ +F++LMG V+ R+ I+ NA
Sbjct: 357 GLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAA 416
Query: 501 NLD 503
N+D
Sbjct: 417 NID 419
>3lnu_A Topoisomerase IV subunit B; PARE, ATP-binding, nucleotide-BI
topoisomerase; 2.20A {Xanthomonas oryzae PV} PDB:
3lps_A*
Length = 408
Score = 304 bits (781), Expect = 3e-99
Identities = 65/265 (24%), Positives = 121/265 (45%), Gaps = 12/265 (4%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
E+ ++ G + L V+ K GTR+RFW D + F T +F+ + +R A
Sbjct: 155 EHRMEFRDGNAASKLE--VVGTVGKKNTGTRLRFWADPKYFDT-PKFNVRALRHLLRAKA 211
Query: 62 FLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGIT 120
L P LT+ L E + + ++F GL +Y++ + + L D+ D
Sbjct: 212 VLCPGLTVKLHDEATGEQD----SWYFENGLRDYLKGEMAEHEMLPADLFVGSLKKDTEI 267
Query: 121 IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL 180
+D A W Y N I T GTH+ G+++ LT L + + + L
Sbjct: 268 VDWAAGWV-PEGELVQESYVNLIPTAQHGTHVNGLRSGLTDALREFCDFRNLLP-RGVKL 325
Query: 181 SGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDS 240
+ E V + +T ++S+++ +P+F GQTK RL + + ++ + + + YL + ++ +
Sbjct: 326 APEDVWDRVTFVLSLKMTDPQFSGQTKERLSSRQAAGFIEGAAHDAFSLYLNQNVEIGEK 385
Query: 241 ILSKSLSALKAALAAKRARDLVRQK 265
I ++ A K + +VR+K
Sbjct: 386 IAQIAIDRASA--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 = 302 bits (775), Expect = 6e-99
Identities = 63/252 (25%), Positives = 106/252 (42%), Gaps = 17/252 (6%)
Query: 2 EYHQKYSRGKPVTTLTCH--VLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRE 59
++ G P + P+ +G R+ F PD +F + FD ++ R E
Sbjct: 122 QWRVMGEHGHPQGEGAAVTPMEPMPVSAERGVRVHFVPDATIFEV-LAFDRARLSRRCNE 180
Query: 60 LAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDG 118
LA L P L ++ + GG+ ++ L + LH + V F DG
Sbjct: 181 LAALAPGLRVSFADLQRGERT----LWHLPGGVAQWAHVLTEARPQLHPEPVVFDFTWDG 236
Query: 119 ITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDI 178
+ + ALQWC + T+L +AN++RT+ G H++GV +L L L +
Sbjct: 237 LRVQCALQWC-EDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGE------TRG 289
Query: 179 SLSGEHVREGLTCIISVRVPNP--EFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPD 236
+ V +GLT I++V P F G TK L P + + + + +Q E L HP
Sbjct: 290 AFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELLREHPV 349
Query: 237 VLDSILSKSLSA 248
+ ++ +
Sbjct: 350 TPALLARRTSGS 361
>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 = 302 bits (775), Expect = 9e-99
Identities = 60/265 (22%), Positives = 116/265 (43%), Gaps = 11/265 (4%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
Y+ + G+ V L V+ K GT + FWPD+ F + +F + + ++ A
Sbjct: 136 VYNIAFENGEKVQDL--QVVGTCGKRNTGTSVHFWPDETFFDS-PRFSVSRLTHVLKAKA 192
Query: 62 FLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGIT 120
L P + I + E ++ E+ + + GL +Y+ L D
Sbjct: 193 VLCPGVEITFKDEINNTEQ----RWCYQDGLNDYLAEAVNGLPTLPEKPFIGNFAGDTEA 248
Query: 121 IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL 180
+D AL W + Y N I T+ GGTH+ G++ L + + + + + L
Sbjct: 249 VDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNILP-RGVKL 307
Query: 181 SGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDS 240
S E + + ++SV++ +P+F GQTK RL + + V V++ +L + +
Sbjct: 308 SAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFILWLNQNVQAAEL 367
Query: 241 ILSKSLSALKAALAAKRARDLVRQK 265
+ ++S+ + + A+ +VR+K
Sbjct: 368 LAEMAISSAQR--RMRAAKKVVRKK 390
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 253 bits (647), Expect = 6e-76
Identities = 115/267 (43%), Positives = 161/267 (60%), Gaps = 10/267 (3%)
Query: 238 LDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDS 297
++ +SK+ LKAA +R K ++ +LPGKLADC T EESE+FIVEGDS
Sbjct: 1 MEMAISKAGRRLKAAKKVER-------KKIVSGPALPGKLADCVGQTREESELFIVEGDS 53
Query: 298 AGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA 357
AGGSAKQ RD+ FQAI+P+RGKILN + ++E+ ++ A+G+ +D +
Sbjct: 54 AGGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSDDLSE-- 111
Query: 358 LRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCY 417
LRY KI IL DAD DG HI TLL F ++ L +EG +YV +PPL++++ GK V Y
Sbjct: 112 LRYGKICILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYAL 171
Query: 418 DDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAE-ANV 476
DD EL+ + + N I RFKGLGEM +QL ETT++P R L QL ++DA A +
Sbjct: 172 DDEELETILKNVKGNKNPQITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGL 231
Query: 477 VFSSLMGARVDTRKELIQNAANLVNLD 503
+ 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 = 246 bits (630), Expect = 2e-73
Identities = 64/259 (24%), Positives = 103/259 (39%), Gaps = 9/259 (3%)
Query: 251 AALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGR---D 307
+ S ++ D E + + EGDSA A G
Sbjct: 16 DDKVPDPTSVDSVKYSKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIG 75
Query: 308 RRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA----LRYHKI 363
R + PLRGKILNV + +N EI N+I+ +GL + + LRY KI
Sbjct: 76 RDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQY-KKSYDDAESLKTLRYGKI 134
Query: 364 IILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELK 423
+I+TD D DG+HI+ LL+ F + +L G + + P+ K + KQ Y E
Sbjct: 135 MIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPIVKASKNKQELSFYSIPEFD 194
Query: 424 KVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMG 483
+ K + + I+ +KGLG + E + E+ + + + +
Sbjct: 195 EWKKHIENQKAWKIKYYKGLGTSTAKEAKEYFADMERHRILF-RYAGPEDDAAITLAFSK 253
Query: 484 ARVDTRKELIQNAANLVNL 502
++D RKE + N
Sbjct: 254 KKIDDRKEWLTNFMEDRRQ 272
>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 = 200 bits (511), Expect = 3e-59
Identities = 43/256 (16%), Positives = 91/256 (35%), Gaps = 35/256 (13%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
+Y QK+ + + K T++ F PD F + D++ + R +
Sbjct: 173 KYVQKWENNMSICHP--PKITSYKKGPSYTKVTFKPDLTRFGM-KELDNDILGVMRRRVY 229
Query: 62 FLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH--------DVVGFR 113
+N + + K F +E Y++ L ++ + D+
Sbjct: 230 DINGSVRDINVYLNGKSLK----IRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTIL 285
Query: 114 KDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTV 173
+ ++A SD + + NSI T GGTH+ + + + ++ + KK
Sbjct: 286 YERINNRWEVAFAV-SDISFQ-QISFVNSIATTMGGTHVNYITDQIVKKISEILKK---- 339
Query: 174 KDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPE-------------VRKVVD 220
K S+ ++ + I+ + NP F QTK +L + K++
Sbjct: 340 -KKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMK 398
Query: 221 QSVQEYLTEYLELHPD 236
+ + E + + +
Sbjct: 399 TDLATRMFEIADANEE 414
>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 = 201 bits (513), Expect = 2e-57
Identities = 120/237 (50%), Positives = 147/237 (62%), Gaps = 35/237 (14%)
Query: 271 SSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAA 330
+SLPGKLADCSS +PEE EIF+VEGDSAGGS K GRD R QAILPLRGKILNVE+
Sbjct: 4 ASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDR 63
Query: 331 MYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKT 390
+ N EI+ +I A G G+ G DF RYHKI+I+TDADVDGAHIRTLLLTFFYR+ +
Sbjct: 64 ILNNNEIRQMITAFGTGIGG-DFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 391 LFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQ 450
L + G +Y+ PP +KGLGEM Q
Sbjct: 123 LIEAGYVYIAQPP----------------------------------TGYKGLGEMNADQ 148
Query: 451 LWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 507
LWETT+NPE R L Q+ +EDA EA+ F LMG V+ R++ I++ A NLD ++
Sbjct: 149 LWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAEL 205
>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 = 185 bits (472), Expect = 8e-54
Identities = 43/260 (16%), Positives = 82/260 (31%), Gaps = 27/260 (10%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAG---RIR 58
+ Q + + T I F PD F D + +A R
Sbjct: 161 MFKQTWMDNMGRAGE---MELKPFNGEDYTCITFQPDLSKFKM-QSLDKDIVALMVRRAY 216
Query: 59 ELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVD 117
++A + + L G YV DK + + +
Sbjct: 217 DIAGSTKDVKVFLN-----------GNKLPVKGFRSYVDMYLKDKLDETGNSLKVIHEQV 265
Query: 118 GITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKD 177
++ L S+ + + NSI T GG H++ V + L + KK
Sbjct: 266 NHRWEVCLTM-SEKGF-QQISFVNSIATSKGGRHVDYVADQIVTKLVDVVKKKN---KGG 320
Query: 178 ISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDV 237
+++ V+ + ++ + NP F+ QTK + + E + +
Sbjct: 321 VAVKAHQVKNHMWIFVNALIENPTFDSQTKENMTLQPKSFGSTCQLSEKFIKAAIGCG-I 379
Query: 238 LDSILSKSLSALKAALAAKR 257
++SIL + KA + +
Sbjct: 380 VESIL--NWVKFKAQVQLNK 397
>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 = 150 bits (381), Expect = 3e-39
Identities = 63/239 (26%), Positives = 108/239 (45%), Gaps = 11/239 (4%)
Query: 276 KLADCS---STTPEESEIFIVEGDSAGGSAKQGR---DRRFQAILPLRGKILNVERKDEA 329
KL D + + + + + EGDSA A G R + PLRGK+LNV
Sbjct: 8 KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASAD 67
Query: 330 AMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 389
+ KN EIQ + + +GL + + ++LRY ++I+TD D DG+HI+ L++ F
Sbjct: 68 QILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFP 127
Query: 390 TLFD-EGCIYVGVPPLYKVERGKQVQYC---YDDAELKKVKSSFPSNALYSIQRFKGLGE 445
L D +G + + P+ KV K + Y+ + +K + + + +KGLG
Sbjct: 128 GLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGT 187
Query: 446 MMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDH 504
+ ++ 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 = 98.7 bits (247), Expect = 4e-24
Identities = 34/90 (37%), Positives = 49/90 (54%), Gaps = 5/90 (5%)
Query: 3 YHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAF 62
YHQ Y +G P L V + D+ GT IRF D ++FT +++ T+ RIRELAF
Sbjct: 114 YHQAYKKGVPQFDLKE----VGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAF 169
Query: 63 LNPKLTIALRKEDSDPEKNQYNEYFFAGGL 92
LN + I LR E + + + Y + GG+
Sbjct: 170 LNKGIQITLRDERDEENVRE-DSYHYEGGI 198
>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 = 88.7 bits (221), Expect = 2e-20
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 8/89 (8%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
+ Q Y G P L ++ GT +RFWP + FT +F++ +A R+REL+
Sbjct: 140 IHRQIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELS 195
Query: 62 FLNPKLTIALRKEDSDPEKNQYNEYFFAG 90
FLN ++I LR + E + + G
Sbjct: 196 FLNSGVSIRLRDKRDGKED----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 = 86.0 bits (214), Expect = 1e-19
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 2 EYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELA 61
Y+ + G+ V L V+ K GT + FWPD+ F + +F + + ++ A
Sbjct: 122 VYNIAFENGEKVQDLQ--VVGTCGKRNTGTSVHFWPDETFFDS-PRFSVSRLTHVLKAKA 178
Query: 62 FLNPKLTIALRKEDSDPEK 80
L P + I + E ++ E+
Sbjct: 179 VLCPGVEITFKDEINNTEQ 197
>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 = 85.7 bits (213), Expect = 3e-19
Identities = 30/88 (34%), Positives = 48/88 (54%), Gaps = 8/88 (9%)
Query: 2 EYHQKYSR-GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIREL 60
Y Q++ GKPVTTL + K + GT++ F PD +F+T F +NTI+ R+ E
Sbjct: 144 VYKQRFENGGKPVTTLK--KIGTALKSKTGTKVTFMPDATIFST-TDFKYNTISERLNES 200
Query: 61 AFLNPKLTIALRKEDSDPEKNQYNEYFF 88
AFL +T++L + +D E+ +
Sbjct: 201 AFLLKNVTLSLTDKRTDEAI----EFHY 224
>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 = 64.9 bits (157), Expect = 3e-11
Identities = 86/557 (15%), Positives = 168/557 (30%), Gaps = 162/557 (29%)
Query: 23 VDSKDR-QGTRIRFW-----PDKQV---FTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 73
+ SKD GT FW ++ V ++ ++ + I+ P + +
Sbjct: 55 IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT-EQRQPSMMTRMYI 113
Query: 74 EDSDPEKNQYNEYF---FAGGLEEYVQ---WLNTDKKP----LHDVVGFRKDVDGITIDL 123
E D N N+ F L+ Y++ L + + V+G K +
Sbjct: 114 EQRDRLYND-NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW------V 166
Query: 124 ALQWCSDAYSDTM---------LGYANSIRTI-------------------DGGT----H 151
AL C L NS T+ D +
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR 226
Query: 152 IEGVKASLTRTL------NSL---------------GKKSKTV---KDKDIS-------- 179
I ++A L R L N L K + + K ++
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT 286
Query: 180 --LSGEHVREGLTC---------IISVRVPN-PEFEGQTKTRLGNPEVRKVVDQSVQEYL 227
+S +H LT + R + P + T NP ++ +S+++ L
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR---EVLT--TNPRRLSIIAESIRDGL 341
Query: 228 T---EYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSS-LPGKL-----A 278
+ ++ D L +I+ SL+ L+ A K L SV S+ +P L
Sbjct: 342 ATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL----SVFPPSAHIPTILLSLIWF 397
Query: 279 DCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAI----LPLRGKILN--------VERK 326
D + +V ++ +I L L+ K+ N V+
Sbjct: 398 DVIKSDVMV----VVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHY 453
Query: 327 DEAAMYKNEEIQNL-------------IRALGLGVKGEDFKKEALRYH----KIIILTDA 369
+ + ++++ ++ + + F+ L + KI + A
Sbjct: 454 NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTA 513
Query: 370 DVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYK--VERGKQVQYCYDDAELKKVKS 427
I L + Y+ + D Y + + + ++ C +L ++
Sbjct: 514 WNASGSILNTLQQLKF-YKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIAL 572
Query: 428 SFPSNALYS-----IQR 439
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 = 52.4 bits (125), Expect = 4e-07
Identities = 70/427 (16%), Positives = 137/427 (32%), Gaps = 167/427 (39%)
Query: 29 QGTRIRFWPD-KQVFTTAIQFDHNTIAGRIRELAF--LNPKLTIALRKEDSDPEKNQYNE 85
QG ++ + + ++ T ++ + G + + + L+ L + D EK
Sbjct: 163 QGNTDDYFEELRDLYQT-----YHVLVGDLIKFSAETLSE-----LIRTTLDAEK----- 207
Query: 86 YFFAGGLEEYVQWL-NTDKKPLHD-------------------------VVG-----FRK 114
F GL ++WL N P D ++G R
Sbjct: 208 -VFTQGLN-ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRS 265
Query: 115 DVDGIT-----------IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTL 163
+ G T I W +++ + + + I I GV+
Sbjct: 266 YLKGATGHSQGLVTAVAIAETDSW--ESF------FVSVRKAITVLFFI-GVRCYEAYPN 316
Query: 164 NSLGKKSKTVKDKDISLSGEHVREGL-TCIISVR-VPNPEFE---GQTKTRL-------- 210
SL ++D S E+ EG+ + ++S+ + + + +T + L
Sbjct: 317 TSL--PPSILED-----SLEN-NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 211 ------------GNPE--------VRKV-----VDQS-----------VQEYL------- 227
G P+ +RK +DQS +L
Sbjct: 369 SLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFH 428
Query: 228 TEYLE-----LHPDVLDSILSKSLSALKAAL-AAKRARDLVRQKSVLRSSSLPGKLADCS 281
+ L ++ D++ + +S + ++ + DL R S S+ ++ DC
Sbjct: 429 SHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDL-RVLS----GSISERIVDCI 483
Query: 282 STTP---EESEIF----IVE---GDSAG-GS----AKQGRDRRFQAILPLRGKILNVERK 326
P E + F I++ G ++G G K G R I+ G L++
Sbjct: 484 IRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRV--IVA--GT-LDINPD 538
Query: 327 DEAAMYK 333
D+ +K
Sbjct: 539 DDYG-FK 544
Score = 47.4 bits (112), Expect = 1e-05
Identities = 69/386 (17%), Positives = 122/386 (31%), Gaps = 118/386 (30%)
Query: 194 SVRVPNP----------EFEGQTKTRLGNPEVRKVVDQ---SVQEYLTEYL-----ELHP 235
+ VP +F K L P D + E + ++L + P
Sbjct: 19 VLLVPTASFFIASQLQEQF---NKI-LPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEP 74
Query: 236 DV---LDSILSKSLS-------------ALKAALAAKRARDLVRQKSVLRSSSLPGKLAD 279
D +L+ L+ AL A L + LV+ K ++++ +A
Sbjct: 75 SKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAK 134
Query: 280 CSSTTPEESEIF--IVEGDSA-----GGSAKQG-RDRRFQAILPLRGKILNVERKDE-AA 330
S +F + EG++ GG QG D F +E
Sbjct: 135 RPFDKKSNSALFRAVGEGNAQLVAIFGG---QGNTDDYF----------------EELRD 175
Query: 331 MYK--NEEIQNLIRALG-----LGVKGEDFKKEALRYHKIII---LTDADV--DGAHIRT 378
+Y+ + + +LI+ L D +K + + I L + D ++ +
Sbjct: 176 LYQTYHVLVGDLIKFSAETLSELIRTTLDAEK--VFTQGLNILEWLENPSNTPDKDYLLS 233
Query: 379 -------LLLTFFYRYQKTLFDEGCIYVGVPP--LYKVERGKQVQYCYDD----AELKKV 425
+ + Y T +G P L +G + +
Sbjct: 234 IPISCPLIGVIQLAHYVVT-----AKLLGFTPGELRSYLKG--ATGHSQGLVTAVAIAET 286
Query: 426 KS--SFPSNALYSIQRFKGLG----EMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFS 479
S SF + +I +G E P T+L P ++ED+ E N
Sbjct: 287 DSWESFFVSVRKAITVLFFIGVRCYEAYPN----TSLPPS-------ILEDSLENNEGVP 335
Query: 480 SLMGARVDTRKELIQNAANLVNLDHL 505
S M + + +E +Q+ N N HL
Sbjct: 336 SPMLSISNLTQEQVQDYVNKTN-SHL 360
Score = 42.7 bits (100), Expect = 3e-04
Identities = 42/293 (14%), Positives = 82/293 (27%), Gaps = 128/293 (43%)
Query: 91 GLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGT 150
G++ Y +DV + A D + G+ SI I
Sbjct: 1632 GMDLYKT---------SKAA---QDV----WNRA-----DNHFKDTYGF--SILDI---- 1664
Query: 151 HIEGVKASLTR-TLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTR 209
V + T++ G+K K +++ ++ E + +G
Sbjct: 1665 ----VINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDG--------------------- 1699
Query: 210 LGNPEVRKVVDQSVQEYLTEYLELHP-DVLDS-------ILSKSLSALK----------- 250
+ + + + E+ T Y +L + + +A +
Sbjct: 1700 ---KLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPAD 1756
Query: 251 -----------AALAA-------KRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFI 292
AALA+ + ++V R G +
Sbjct: 1757 ATFAGHSLGEYAALASLADVMSIESLVEVVFY----R-----GMTMQVA----------- 1796
Query: 293 VEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALG 345
V D G S + AI P G++ AA + E +Q ++ +G
Sbjct: 1797 VPRDELGRS-----NYGMIAINP--GRV--------AASFSQEALQYVVERVG 1834
Score = 39.3 bits (91), Expect = 0.004
Identities = 44/260 (16%), Positives = 70/260 (26%), Gaps = 109/260 (41%)
Query: 9 RGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRI--------REL 60
P LT H +G RIR +F T + D +I
Sbjct: 1666 INNP-VNLTIHFGG-----EKGKRIRENYSAMIFETIV--DGKLKTEKIFKEINEHSTSY 1717
Query: 61 AFLNPK----LT-----------IA----LRKEDSDPEKNQYNEYFFAG---GLEEY--- 95
F + K T A L+ + P + FAG G EY
Sbjct: 1718 TFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPA-----DATFAGHSLG--EYAAL 1770
Query: 96 -----VQWLNTDKKPLHD---VVGFRKDVDGITIDLAL---------------------- 125
V + + VV +R G+T+ +A+
Sbjct: 1771 ASLADV--M-----SIESLVEVVFYR----GMTMQVAVPRDELGRSNYGMIAINPGRVAA 1819
Query: 126 --------QWCSDAYSDTMLGY----AN----SIRTIDGGTHIEGVKASLTRTLNSLGKK 169
T G+ N + + + G + + +T LN + +
Sbjct: 1820 SFSQEALQYVVERVGKRT--GWLVEIVNYNVENQQYVAAG-DLRALDT-VTNVLNFIKLQ 1875
Query: 170 SKTVKDKDISLSGEHVREGL 189
+ + SLS E V L
Sbjct: 1876 KIDIIELQKSLSLEEVEGHL 1895
Score = 38.9 bits (90), Expect = 0.004
Identities = 36/192 (18%), Positives = 61/192 (31%), Gaps = 55/192 (28%)
Query: 4 HQKYSRGKPVTTLTCHVLPVDSKDR-QGT-----RIRFWPDKQVFTTAIQFD-------- 49
++ Y P T+L +L DS + +G I +QV + +
Sbjct: 311 YEAY----PNTSLPPSIL-EDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ 365
Query: 50 -----HNT-----IAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWL 99
N ++G + L LN + LRK + +Q F L+ ++L
Sbjct: 366 VEISLVNGAKNLVVSGPPQSLYGLN----LTLRKAKAPSGLDQSRIPFSERKLKFSNRFL 421
Query: 100 NTDKKPLH-----DVVGFRKDVDGITIDLALQWCSDAYSDTMLG---YANSIRTIDGGTH 151
P H D I DL S D + Y T D G+
Sbjct: 422 PVA-SPFHSHLLVPA------SDLINKDLVKNNVSFNAKD--IQIPVYD----TFD-GSD 467
Query: 152 IEGVKASLTRTL 163
+ + S++ +
Sbjct: 468 LRVLSGSISERI 479
>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 = 31.2 bits (71), Expect = 0.76
Identities = 4/44 (9%), Positives = 16/44 (36%), Gaps = 10/44 (22%)
Query: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
+ + 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 = 0.96
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 10/44 (22%)
Query: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
++ 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 = 30.7 bits (70), Expect = 1.0
Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 10/44 (22%)
Query: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
+ 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 = 1.1
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 10/44 (22%)
Query: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
RM K L + + + S +G+ T +L
Sbjct: 83 RMYKMLNEAGSGASGAILSPPALFGTLVSFYLGSLDPTASQLQT 126
>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 = 30.4 bits (69), Expect = 1.4
Identities = 10/64 (15%), Positives = 23/64 (35%), Gaps = 9/64 (14%)
Query: 69 IALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRK------DVDGITID 122
+ + K+ N + + ++N +K PL FR+ + + I +
Sbjct: 243 VPVLKKAYGIVTWYENAPYMLPANTAGI-YINVNKYPLSIPE-FRRAMAYAINPEKI-VT 299
Query: 123 LALQ 126
A +
Sbjct: 300 RAYE 303
>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 = 29.5 bits (65), Expect = 1.6
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 11/26 (42%)
Query: 411 KQVQYCYDDAELKKVKSSFPSNALYS 436
KQ LKK+++S LY+
Sbjct: 19 KQ--------ALKKLQASL---KLYA 33
>3k7d_A Glutamate-ammonia-ligase adenylyltransferase; nucleotidyl
transferase domain, ATP-binding, nucleotide-BIND
nucleotidyltransferase; 2.40A {Escherichia coli}
Length = 498
Score = 30.3 bits (68), Expect = 1.8
Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 11/56 (19%)
Query: 225 EYLTEYLELHPDVLDSILS-------KSLSALKAALAAKRAR----DLVRQKSVLR 269
+ 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 = 28.6 bits (64), Expect = 1.8
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 355 KEALRYHKIIILTDADVDGAHIRTLLLTFF 384
+ L + + +L DAD G +R F
Sbjct: 45 ADELEGYDVYLLADADEAGEKLRRQFRRMF 74
>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 = 3.5
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 11/44 (25%)
Query: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
+ 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 = 3.6
Identities = 9/44 (20%), Positives = 20/44 (45%), Gaps = 11/44 (25%)
Query: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
+ +QL + + N+ FS + +G + DT E+++
Sbjct: 21 SLYRQLAHQSNST-NIFFSPVSIATAFAMLSLGTKADTHDEILE 63
>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 = 29.0 bits (65), Expect = 3.8
Identities = 9/52 (17%), Positives = 16/52 (30%), Gaps = 7/52 (13%)
Query: 225 EYLTEYLELHPDVLDSILS-----KSLSALKAALAAKRAR--DLVRQKSVLR 269
+++ + + HP+ L + S A L D LR
Sbjct: 40 DFVQDSVIAHPEWLTELESQPPQADEWQHYAAWLQEALCNVSDEAGLMRELR 91
>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: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
+ 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 = 4.5
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 11/44 (25%)
Query: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
+ K LV + N+ S + +G TR +L+Q
Sbjct: 17 SLYKHLVALSPKK-NIFISPVSISMALAMLSLGTCGHTRAQLLQ 59
>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 = 4.7
Identities = 9/44 (20%), Positives = 20/44 (45%), Gaps = 11/44 (25%)
Query: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
+ +QL + + N+ FS + +G + DT E+++
Sbjct: 66 SLYRQLAHQSNST-NIFFSPVSIATAFAMLSLGTKADTHDEILE 108
>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 = 4.7
Identities = 7/50 (14%), Positives = 12/50 (24%), Gaps = 10/50 (20%)
Query: 86 YFFAGGLEEYVQWLNTDK--------KPLHDVVGFRKDVDGITIDLALQW 127
Y + +L K L +G + +D A
Sbjct: 317 YLIQD--TKVYVFLTKGGYTLVNGYPKRLEKELGSPPVISLEAVDAAFVC 364
>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 = 4.8
Identities = 7/44 (15%), Positives = 19/44 (43%), Gaps = 11/44 (25%)
Query: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
+ + 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 = 5.5
Identities = 7/44 (15%), Positives = 18/44 (40%), Gaps = 10/44 (22%)
Query: 461 RMLKQLVIEDAAEANVVFSSL----------MGARVDTRKELIQ 494
+ 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 = 28.2 bits (62), Expect = 7.8
Identities = 24/179 (13%), Positives = 48/179 (26%), Gaps = 14/179 (7%)
Query: 204 GQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILS-KSLSALKAALAAKRARDLV 262
+ R ++ Q Q+ + +L+ H D S K+ + A A+R +
Sbjct: 10 SFGQQRQQQQPQQQKQQQRDQDSVEAWLDDHWDFTFSYFVRKATREMVNAWFAERVHTIP 69
Query: 263 RQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGG-----------SAKQGRDRRFQ 311
K +R + S + S + +G
Sbjct: 70 VCKEGIRGHTESCSCPLQQSPRADNSVPGTPTRKISASEFDRPLRPIVVKDSEGTVSFLS 129
Query: 312 AILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDAD 370
L R D + + L++ + + + + I L AD
Sbjct: 130 DSEKKEQMPLTPPRFDHDEGDQCSRLLELVKDISSHLDVTALCHKIFLH--IHGLISAD 186
>1bs0_A Protein (8-amino-7-oxonanoate synthase); PLP-dependent acyl-COA
synthase, biotin biosynthesis, 8-AMIN oxonanoate
synthase; 1.65A {Escherichia coli} SCOP: c.67.1.4 PDB:
2g6w_A* 1dje_A* 1dj9_A*
Length = 384
Score = 27.9 bits (63), Expect = 8.6
Identities = 10/51 (19%), Positives = 21/51 (41%), Gaps = 3/51 (5%)
Query: 227 LTEYLELHPDVLDSILSKSLSALKAALAAKRA-RDLVRQKS--VLRSSSLP 274
++ P++L K AA+ D + Q + ++ S+S+P
Sbjct: 219 SCWLQKVKPELLVVTFGKGFGVSGAAVLCSSTVADYLLQFARHLIYSTSMP 269
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
0.318 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: 7,821,944
Number of extensions: 493318
Number of successful extensions: 1194
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1127
Number of HSP's successfully gapped: 52
Length of query: 507
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 409
Effective length of database: 3,965,535
Effective search space: 1621903815
Effective search space used: 1621903815
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: 59 (26.3 bits)