RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 007003
(622 letters)
>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 = 619 bits (1599), Expect = 0.0
Identities = 168/399 (42%), Positives = 236/399 (59%), Gaps = 11/399 (2%)
Query: 76 TYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALL 135
+Y + I+VL+GLE VR RPAMYIG TG G HHL EILDNAVDEA AGYA+ I V L
Sbjct: 2 SYDASAIRVLKGLEGVRHRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATEILVRLN 61
Query: 136 ADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSV 195
D S++V DNGRGIP+DL P K A+E + LH+GGKF + Y VSGGLHGVG SV
Sbjct: 62 EDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYNTLHSGGKFEQGA--YKVSGGLHGVGASV 119
Query: 196 VNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTT 255
VNALSE V V+R+G + +SRG+ L V+ + + GTR+ F PD ++F
Sbjct: 120 VNALSEWTVVEVFREGKHHRIAFSRGEVTEPL--RVVGEAPRGKTGTRVTFKPDPEIFGN 177
Query: 256 AIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKK 315
++FD + I R+RE+A+L L + + E+ + GG+ + + L +
Sbjct: 178 -LRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEE----VFLDKGGVASFAKALAEGED 232
Query: 316 PLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTL 374
L+ R + +++ Y+ +L YAN I T DGGTH+ K++ +R L
Sbjct: 233 LLYEKPFLIRGTHGEVEVEVGFLHT-QGYNAEILTYANMIPTRDGGTHLTAFKSAYSRAL 291
Query: 375 NSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV 434
N KK+ K+K +G+ + EGL ++SV++PNP+FEGQTK +L NPE V Q V
Sbjct: 292 NQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVV 351
Query: 435 QEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLV 473
E L E LE +P + ++ K+L A +A AA++AR+LV
Sbjct: 352 YERLLEILEENPRIAKAVYEKALRAAQAREAARKARELV 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 = 602 bits (1554), Expect = 0.0
Identities = 175/401 (43%), Positives = 257/401 (64%), Gaps = 13/401 (3%)
Query: 74 SKTYGSEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEV 132
S + S I+VL+GL+AVRKRP MYIG T GLHH+V+E++DNA+DEA AG+ I V
Sbjct: 1 SNSSDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIV 60
Query: 133 ALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVG 192
+ ADNSVSV D+GRGIP +HP SA E ++TVLHAGGKF +S Y VSGGLHGVG
Sbjct: 61 TIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNS--YKVSGGLHGVG 118
Query: 193 LSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQV 252
+SVVNALS+ LE+ + R+G + Q Y G P L ++ GT +RFWP +
Sbjct: 119 VSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLET 174
Query: 253 FTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNT 312
FT +F++ +A R+REL+FL+ ++I LR + E + + GG++ +V++LN
Sbjct: 175 FTNVTEFEYEILAKRLRELSFLDSGVSIRLRDKRDGKED----HFHYEGGIKAFVEYLNK 230
Query: 313 DKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLT 371
+K P+H ++ F + DGI +++ALQW D + + + + N+I DGGTH+ G +A++T
Sbjct: 231 NKTPIHPNIFYFSTEKDGIGVEVALQWN-DGFQENIYCFTNNIPQRDGGTHLAGFRAAMT 289
Query: 372 RTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVD 431
RTLN+ K K +S +G+ REGL ++SV+VP+P+F QTK +L + EV+ V+
Sbjct: 290 RTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVE 349
Query: 432 QSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDL 472
Q + E L EYL +P ++ K + A +A AA+RAR++
Sbjct: 350 QQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREM 390
>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 = 579 bits (1494), Expect = 0.0
Identities = 133/404 (32%), Positives = 214/404 (52%), Gaps = 16/404 (3%)
Query: 74 SKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVA 133
++TY ++ I+VL GLE VR+RP MY +T +HL E++DN+VDEA AG+A ++V
Sbjct: 2 TQTYNADAIEVLTGLEPVRRRPGMYTDTTR---PNHLGQEVIDNSVDEALAGHAKRVDVI 58
Query: 134 LLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGL 193
L AD S+ V D+GRG+P+D+HP A+E +L LHAGGKF + Y SGGLHGVG+
Sbjct: 59 LHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKN--YQFSGGLHGVGI 116
Query: 194 SVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVF 253
SVVNALS+ +EV V RDG Y+ + G+ V L V+ K GT + FWPD+ F
Sbjct: 117 SVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDL--QVVGTCGKRNTGTSVHFWPDETFF 174
Query: 254 TTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTD 313
+ +F + + ++ A L P + I + E ++ E+ + + GL +Y+
Sbjct: 175 DS-PRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQ----RWCYQDGLNDYLAEAVNG 229
Query: 314 KKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTR 372
L D +D AL W + Y N I T+ GGTH+ G++ L
Sbjct: 230 LPTLPEKPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLD 289
Query: 373 TLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQ 432
+ + + + + LS E + + ++SV++ +P+F GQTK RL + + V
Sbjct: 290 AMREFCEYRNILP-RGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSG 348
Query: 433 SVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQK 476
V++ +L + + + ++S+ + + A+ +VR+K
Sbjct: 349 VVKDAFILWLNQNVQAAELLAEMAISSAQR--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 = 576 bits (1488), Expect = 0.0
Identities = 132/413 (31%), Positives = 215/413 (52%), Gaps = 17/413 (4%)
Query: 65 TEAFKENPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQA 124
+ + Y + I+VL GL+ V++RP MY + +HL E++DN+VDEA A
Sbjct: 12 SGLVPRGSHNTRYNAADIEVLSGLDPVKRRPGMYTDTAR---PNHLAQEVIDNSVDEALA 68
Query: 125 GYASNIEVALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSV 184
G+A IEV L D S V+D+GRG+P+D+HP +E +LT LHAGGKF + Y+
Sbjct: 69 GHAKQIEVTLYKDGSCEVSDDGRGMPVDIHPEEKIPGVELILTRLHAGGKFNNRN--YTF 126
Query: 185 SGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRI 244
SGGLHGVG+SVVNALS +E+ + R+G E+ ++ G + L V+ K GTR+
Sbjct: 127 SGGLHGVGVSVVNALSTKVELFIKREGSEHRMEFRDGNAASKLE--VVGTVGKKNTGTRL 184
Query: 245 RFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLE 304
RFW D + F T +F+ + +R A L P LT+ L E + + ++F GL
Sbjct: 185 RFWADPKYFDT-PKFNVRALRHLLRAKAVLCPGLTVKLHDEATGEQD----SWYFENGLR 239
Query: 305 EYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHI 363
+Y++ + + L D+ D +D A W Y N I T GTH+
Sbjct: 240 DYLKGEMAEHEMLPADLFVGSLKKDTEIVDWAAGWV-PEGELVQESYVNLIPTAQHGTHV 298
Query: 364 EGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGN 423
G+++ LT L + + + L+ E V + +T ++S+++ +P+F GQTK RL +
Sbjct: 299 NGLRSGLTDALREFCDFRNLLP-RGVKLAPEDVWDRVTFVLSLKMTDPQFSGQTKERLSS 357
Query: 424 PEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQK 476
+ ++ + + + YL + ++ + I ++ A K + +VR+K
Sbjct: 358 RQAAGFIEGAAHDAFSLYLNQNVEIGEKIAQIAIDRASA--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 = 531 bits (1371), Expect = 0.0
Identities = 102/378 (26%), Positives = 162/378 (42%), Gaps = 32/378 (8%)
Query: 87 GLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNG 146
+E VRKRP MY G G GLHHLVY +LD A +EA+ G ++ + + D S+++
Sbjct: 11 IVENVRKRPGMYCGDVGEYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCTS 70
Query: 147 RGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVT 206
R + E ++ V G G G + V ALS +V
Sbjct: 71 RTVTA-----------ENLVRVATGAGFLGR--PPGDGWGWDSML--VVSLALSSRYQVD 115
Query: 207 VWRDGMEYHQKYSRGKPVTTLTCH--VLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTI 264
+W DG ++ G P + P+ +G R+ F PD +F + FD +
Sbjct: 116 IWADGRQWRVMGEHGHPQGEGAAVTPMEPMPVSAERGVRVHFVPDATIFEV-LAFDRARL 174
Query: 265 AGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGF 323
+ R ELA L P L ++ + GG+ ++ L + LH + V F
Sbjct: 175 SRRCNELAALAPGLRVSFADLQRGERT----LWHLPGGVAQWAHVLTEARPQLHPEPVVF 230
Query: 324 RKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKT 383
DG+ + ALQWC + T+L +AN++RT+ G H++GV +L L L +
Sbjct: 231 DFTWDGLRVQCALQWC-EDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGE--- 286
Query: 384 VKDKDISLSGEHVREGLTCIISVRVPNP--EFEGQTKTRLGNPEVRKVVDQSVQEYLTEY 441
+ V +GLT I++V P F G TK L P + + + + +Q E
Sbjct: 287 ---TRGAFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIEL 343
Query: 442 LELHPDVLDSILSKSLSA 459
L HP + ++ +
Sbjct: 344 LREHPVTPALLARRTSGS 361
>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 = 408 bits (1051), Expect = e-138
Identities = 83/422 (19%), Positives = 154/422 (36%), Gaps = 64/422 (15%)
Query: 74 SKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPR-----------------------GLHHL 110
S++ Q + LE + KRP YIGS + GL +
Sbjct: 9 EPVSASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKI 68
Query: 111 VYEILDNAVDEAQAG-YASNIEVALLAD-NSVSVADNGRGIPIDLHPATNKSALETVLTV 168
EIL NA D I+V + A+ +++ V ++G+GIPI++H N E +
Sbjct: 69 FDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGH 128
Query: 169 LHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTV--WRDGMEYHQKYSRGKPVTT 226
L + V+GG +G G + N S + G +Y QK+ +
Sbjct: 129 LLTSSNYDDDE--KKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICH 186
Query: 227 LTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKED 286
+ K T++ F PD F + D++ + R + +N + +
Sbjct: 187 P--PKITSYKKGPSYTKVTFKPDLTRFGM-KELDNDILGVMRRRVYDINGSVRDINVYLN 243
Query: 287 SDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH--------DVVGFRKDVDGITIDLALQW 338
K F +E Y++ L ++ + D+ + ++A
Sbjct: 244 GKSLK----IRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWEVAFAV 299
Query: 339 CSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVRE 398
SD + + NSI T GGTH+ + + + ++ + K K K S+ ++
Sbjct: 300 -SDISFQ-QISFVNSIATTMGGTHVNYITDQIVKKISEILK-----KKKKKSVKSFQIKN 352
Query: 399 GLTCIISVRVPNPEFEGQTKTRLGNPE-------------VRKVVDQSVQEYLTEYLELH 445
+ I+ + NP F QTK +L + K++ + + E + +
Sbjct: 353 NMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIADAN 412
Query: 446 PD 447
+
Sbjct: 413 EE 414
>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 = 369 bits (950), Expect = e-126
Identities = 111/232 (47%), Positives = 147/232 (63%), Gaps = 11/232 (4%)
Query: 69 KENPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYAS 128
K+ Y + IQVLEGL+AVRKRP MYIGST GLHHLV+EI+DNAVDEA +G+
Sbjct: 3 KKEININNYNDDAIQVLEGLDAVRKRPGMYIGSTDGAGLHHLVWEIVDNAVDEALSGFGD 62
Query: 129 NIEVALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGL 188
I+V + D S++V D+GRG+P +H +E + T+LHAGGKFG GY SGGL
Sbjct: 63 RIDVTINKDGSLTVQDHGRGMPTGMHA-MGIPTVEVIFTILHAGGKFGQ--GGYKTSGGL 119
Query: 189 HGVGLSVVNALSESLEVTVWRDGMEYHQKYSR-GKPVTTLTCHVLPVDSKDRQGTRIRFW 247
HGVG SVVNALS LEV + RDG Y Q++ GKPVTTL + K + GT++ F
Sbjct: 120 HGVGSSVVNALSSWLEVEITRDGAVYKQRFENGGKPVTTLK--KIGTALKSKTGTKVTFM 177
Query: 248 PDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFF 299
PD +F+T F +NTI+ R+ E AFL +T++L + +D E+ +
Sbjct: 178 PDATIFST-TDFKYNTISERLNESAFLLKNVTLSLTDKRTDEAI----EFHY 224
>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 = 375 bits (965), Expect = e-125
Identities = 81/420 (19%), Positives = 135/420 (32%), Gaps = 55/420 (13%)
Query: 79 SEQIQVLEGLEAVRKRPAMYIGSTGPR----------------------GLHHLVYEILD 116
Q LE + RP YIGS GL+ + EIL
Sbjct: 3 ERIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILV 62
Query: 117 NAVDEAQAG-YASNIEVALLAD-NSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGK 174
NA D Q S I V + + N +S+ +NG+GIP+ H + L
Sbjct: 63 NAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSN 122
Query: 175 FGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVW--RDGMEYHQKYSRGKPVTTLTCHVL 232
+ V+GG +G G + N S V + Q + +
Sbjct: 123 YDDDE--KKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGE---ME 177
Query: 233 PVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAG---RIRELAFLNPKLTIALRKEDSDP 289
T I F PD F D + +A R ++A + + L
Sbjct: 178 LKPFNGEDYTCITFQPDLSKFKM-QSLDKDIVALMVRRAYDIAGSTKDVKVFLN------ 230
Query: 290 EKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTML 348
G YV DK + + + ++ L S+ +
Sbjct: 231 -----GNKLPVKGFRSYVDMYLKDKLDETGNSLKVIHEQVNHRWEVCLTM-SEKGF-QQI 283
Query: 349 GYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRV 408
+ NSI T GG H++ V + L + KK +++ V+ + ++ +
Sbjct: 284 SFVNSIATSKGGRHVDYVADQIVTKLVDVVKKKN---KGGVAVKAHQVKNHMWIFVNALI 340
Query: 409 PNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAAKR 468
NP F+ QTK + + E + +++SIL + KA + +
Sbjct: 341 ENPTFDSQTKENMTLQPKSFGSTCQLSEKFIKAAIGCG-IVESIL--NWVKFKAQVQLNK 397
>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 = 357 bits (919), Expect = e-121
Identities = 111/230 (48%), Positives = 149/230 (64%), Gaps = 11/230 (4%)
Query: 73 VSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIE 131
+S +Y S I+VL+GL+AVRKRP MYIG T GLHH+V+E++DNA+DEA AG+ I
Sbjct: 1 MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEII 60
Query: 132 VALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGV 191
V + ADNSVSV D+GRGIP +HP SA E ++TVLHAGGKF +S Y VSGGLHGV
Sbjct: 61 VTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNS--YKVSGGLHGV 118
Query: 192 GLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 251
G+SVVNALS+ LE+ + R+G + Q Y G P L ++ GT +RFWP +
Sbjct: 119 GVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLE 174
Query: 252 VFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAG 301
FT +F++ +A R+REL+FLN ++I LR + E + + G
Sbjct: 175 TFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKED----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 = 329 bits (845), Expect = e-110
Identities = 89/205 (43%), Positives = 126/205 (61%), Gaps = 8/205 (3%)
Query: 87 GLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNG 146
GLE VR+RP MY +T P +HL E++DN+VDEA AG+A ++V L AD S+ V D+G
Sbjct: 1 GLEPVRRRPGMYTDTTRP---NHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDG 57
Query: 147 RGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVT 206
RG+P+D+HP A+E +L LHAGGKF + Y SGGLHGVG+SVVNALS+ +EV
Sbjct: 58 RGMPVDIHPEEGVPAVELILCRLHAGGKFSNKN--YQFSGGLHGVGISVVNALSKRVEVN 115
Query: 207 VWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAG 266
V RDG Y+ + G+ V L V+ K GT + FWPD+ F + +F + +
Sbjct: 116 VRRDGQVYNIAFENGEKVQDLQ--VVGTCGKRNTGTSVHFWPDETFFDS-PRFSVSRLTH 172
Query: 267 RIRELAFLNPKLTIALRKEDSDPEK 291
++ A L P + I + E ++ E+
Sbjct: 173 VLKAKAVLCPGVEITFKDEINNTEQ 197
>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 = 322 bits (829), Expect = e-108
Identities = 105/227 (46%), Positives = 135/227 (59%), Gaps = 30/227 (13%)
Query: 77 YGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLA 136
YG+ QIQVLEGLEAVRKRP MYIGST RGLHHLV+EI+DN++DEA AGYA+ IEV +
Sbjct: 2 YGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEK 61
Query: 137 DNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVV 196
DN + V DNGRGIP+D+ + A+E +LT SVV
Sbjct: 62 DNWIKVTDNGRGIPVDIQEKMGRPAVEVILTS-------------------------SVV 96
Query: 197 NALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTA 256
NALS+ LEV V R+ YHQ Y +G P L V + D+ GT IRF D ++FT
Sbjct: 97 NALSQDLEVYVHRNETIYHQAYKKGVPQFDLKE----VGTTDKTGTVIRFKADGEIFTET 152
Query: 257 IQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGL 303
+++ T+ RIRELAFLN + I LR E + + + Y + GG+
Sbjct: 153 TVYNYETLQQRIRELAFLNKGIQITLRDERDEENVRE-DSYHYEGGI 198
>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 = 310 bits (797), Expect = e-102
Identities = 82/161 (50%), Positives = 104/161 (64%), Gaps = 1/161 (0%)
Query: 458 SALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGR 517
+ D K+ L GKL S P ++E+++VEGDSAGGSAKQGR
Sbjct: 7 HHHHHHSSGHIDDDDKHMKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGR 66
Query: 518 DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIIL 577
DR+FQAILPLRGK++N + A + KNEEI +I +G GV G DF E Y KIII+
Sbjct: 67 DRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGV-GADFSIEDANYDKIIIM 125
Query: 578 TDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKV 618
TDAD DGAHI+TLLLTFFYRY + L + G +Y+ +PPLYK+
Sbjct: 126 TDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKM 166
>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 = 277 bits (711), Expect = 8e-90
Identities = 70/138 (50%), Positives = 95/138 (68%), Gaps = 1/138 (0%)
Query: 481 SSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEA 540
+ + D T P +SE+++VEGDSAGGSAK GRD FQAILPLRGKI+NVE+
Sbjct: 2 AHHHHHHVDDDDKTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARID 61
Query: 541 AMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 600
+ KN E+Q +I ALG G+ ++F LRYHKI+++ DADVDG HI TLLLT +R+ +
Sbjct: 62 RVLKNTEVQAIITALGTGI-HDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMR 120
Query: 601 TLFDEGCIYVGVPPLYKV 618
L + G +++ PPLYK+
Sbjct: 121 PLIENGHVFLAQPPLYKL 138
>3nuh_B DNA gyrase subunit B; topoisomerase, supercoiling, specialization,
isomera; HET: DNA; 3.10A {Escherichia coli}
Length = 420
Score = 278 bits (713), Expect = 7e-88
Identities = 86/153 (56%), Positives = 112/153 (73%)
Query: 466 AKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAIL 525
+ AR++ R+K L + LPGKLADC P SE+++VEGDSAGGSAKQGR+R+ QAIL
Sbjct: 1 SNAAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAIL 60
Query: 526 PLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGA 585
PL+GKILNVE+ M ++E+ LI ALG G+ +++ + LRYH III+TDADVDG+
Sbjct: 61 PLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGS 120
Query: 586 HIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKV 618
HIRTLLLTFFYR + + G +Y+ PPLYKV
Sbjct: 121 HIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKV 153
>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 = 193 bits (490), Expect = 8e-53
Identities = 50/169 (29%), Positives = 74/169 (43%), Gaps = 12/169 (7%)
Query: 461 KAALAAKRARDL----VRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQG 516
K A + D + S ++ D E + + EGDSA A G
Sbjct: 11 KGADDDDKVPDPTSVDSVKYSKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSG 70
Query: 517 R---DRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA----L 569
R + PLRGKILNV + +N EI N+I+ +GL + + L
Sbjct: 71 LGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQY-KKSYDDAESLKTL 129
Query: 570 RYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKV 618
RY KI+I+TD D DG+HI+ LL+ F + +L G + + P+ K
Sbjct: 130 RYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPIVKA 178
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 185 bits (471), Expect = 4e-50
Identities = 78/170 (45%), Positives = 108/170 (63%), Gaps = 9/170 (5%)
Query: 449 LDSILSKSLSALKAALAAKRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDS 508
++ +SK+ LKAA +R K ++ +LPGKLADC T EESE+FIVEGDS
Sbjct: 1 MEMAISKAGRRLKAAKKVER-------KKIVSGPALPGKLADCVGQTREESELFIVEGDS 53
Query: 509 AGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA 568
AGGSAKQ RD+ FQAI+P+RGKILN + ++E+ ++ A+G+ +D +
Sbjct: 54 AGGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSDDLSE-- 111
Query: 569 LRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVPPLYKV 618
LRY KI IL DAD DG HI TLL F ++ L +EG +YV +PPL+++
Sbjct: 112 LRYGKICILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRI 161
>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 = 179 bits (456), Expect = 2e-48
Identities = 86/133 (64%), Positives = 101/133 (75%), Gaps = 1/133 (0%)
Query: 482 SSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAA 541
+SLPGKLADCSS +PEE EIF+VEGDSAGGS K GRD R QAILPLRGKILNVE+
Sbjct: 4 ASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDR 63
Query: 542 MYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKT 601
+ N EI+ +I A G G+ G DF RYHKI+I+TDADVDGAHIRTLLLTFFYR+ +
Sbjct: 64 ILNNNEIRQMITAFGTGIGG-DFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 602 LFDEGCIYVGVPP 614
L + G +Y+ PP
Sbjct: 123 LIEAGYVYIAQPP 135
>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 = 123 bits (311), Expect = 1e-29
Identities = 45/139 (32%), Positives = 71/139 (51%), Gaps = 7/139 (5%)
Query: 487 KLADCS---STTPEESEIFIVEGDSAGGSAKQGR---DRRFQAILPLRGKILNVERKDEA 540
KL D + + + + + EGDSA A G R + PLRGK+LNV
Sbjct: 8 KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASAD 67
Query: 541 AMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 600
+ KN EIQ + + +GL + + ++LRY ++I+TD D DG+HI+ L++ F
Sbjct: 68 QILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFP 127
Query: 601 TLFD-EGCIYVGVPPLYKV 618
L D +G + + P+ KV
Sbjct: 128 GLLDIQGFLLEFITPIIKV 146
>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 = 65.8 bits (160), Expect = 3e-11
Identities = 108/650 (16%), Positives = 190/650 (29%), Gaps = 251/650 (38%)
Query: 23 CSF--SSSLFFKPRTNFAIRGVSSQVLTRSNVVLPRAFLSS-SIATEAFKENPVSKTYGS 79
++ FF ++SQ L F TE F +
Sbjct: 18 HVLLVPTASFF----------IASQ--------LQEQFNKILPEPTEGFAAD-------D 52
Query: 80 EQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEV-----AL 134
E E L + Y+ S ++L+ + E + Y ++ L
Sbjct: 53 EPTTPAE-LVG---KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKL 108
Query: 135 LADNSVSVADNGRGI------------PIDLHPATNKSALETVLTVLHAGGK-----FGG 177
L +N ++ I P D SAL + G FGG
Sbjct: 109 LQENDTTLVKTKELIKNYITARIMAKRPFDKKS---NSAL---FRAVGEGNAQLVAIFGG 162
Query: 178 SSSG----------YSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSRGKPVTTL 227
+ Y L VG ++ +E+L + R ++ + +++G
Sbjct: 163 QGNTDDYFEELRDLYQTYHVL--VG-DLIKFSAETLSELI-RTTLDAEKVFTQG------ 212
Query: 228 TCHVLPVDSKDRQGTRIRFW-------PDKQVFTTA---------IQFDHNTIAGRIREL 271
++ I W PDK + IQ H + ++
Sbjct: 213 ------LN--------ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGF 258
Query: 272 AFLNPK--------LT---------IALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDK 314
P T +A+ + DS F + + + L
Sbjct: 259 ---TPGELRSYLKGATGHSQGLVTAVAIAETDSWES--------FFVSVRKAITVL---- 303
Query: 315 KPLHDVVGFRKDVDGITIDLALQWCSDAYSDT--------------------MLGYANSI 354
+G R C +AY +T ML SI
Sbjct: 304 --FF--IGVR--------------CYEAYPNTSLPPSILEDSLENNEGVPSPML----SI 341
Query: 355 RTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL---------SGEHVR--EGLTCI 403
E V+ + +T NS K V+ ISL SG + GL
Sbjct: 342 S----NLTQEQVQDYVNKT-NSHLPAGKQVE---ISLVNGAKNLVVSG-PPQSLYGLN-- 390
Query: 404 ISVR-VPNPEFEGQTKTRLGNPEVRKVVDQSVQEYL-------TEYLE-----LHPDVLD 450
+++R P Q++ RK+ + +L + L ++ D++
Sbjct: 391 LTLRKAKAPSGLDQSRIPFSE---RKLKFSN--RFLPVASPFHSHLLVPASDLINKDLVK 445
Query: 451 SILSKSLSALKAAL-AAKRARDLVRQKSVLRSSSLPGKLADCSSTTP---EESEIF---- 502
+ +S + ++ + DL R S S+ ++ DC P E + F
Sbjct: 446 NNVSFNAKDIQIPVYDTFDGSDL-RVLS----GSISERIVDCIIRLPVKWETTTQFKATH 500
Query: 503 IVE---GDSAG-GS----AKQGRDRRFQAILPLRGKILNVERKDEAAMYK 544
I++ G ++G G K G R I+ G L++ D+ +K
Sbjct: 501 ILDFGPGGASGLGVLTHRNKDGTGVRV--IVA--GT-LDINPDDDYG-FK 544
Score = 50.4 bits (120), Expect = 2e-06
Identities = 63/385 (16%), Positives = 112/385 (29%), Gaps = 111/385 (28%)
Query: 5 LLKAPY-LHIRVLMASRCFCSFSSSLFFKPRTNFAIRGVSSQVLTRSNVVLPRAFLSSSI 63
LL P + ++ + + L F P +R S ++ ++ +
Sbjct: 231 LLSIPISCPLIGVIQLAHYVVTAKLLGFTPG---ELRSYLKGATGHSQGLVTAVAIAETD 287
Query: 64 ATEAFKENPVSKTYGSEQIQVL--EGLEAVRKRPAMYI-----------GSTGP------ 104
+ E+F + + I VL G+ P + P
Sbjct: 288 SWESFFVS------VRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSI 341
Query: 105 RGLHHLVYEILDNAVDEAQAGYASN--IEVALL--ADNSVSVADNGRGIPIDLHPATNKS 160
L E + + V++ + + +E++L+ A N V V+ G P L+
Sbjct: 342 SNLTQ---EQVQDYVNKTNSHLPAGKQVEISLVNGAKNLV-VS----GPPQSLY------ 387
Query: 161 ALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGMEYHQKYSR 220
L L A S +S L N L V +H
Sbjct: 388 GLNLTLRKAKAPSGLDQSRIPFS------ERKLKFSNRF---LPVAS-----PFHSHLL- 432
Query: 221 GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGR-IRELAF-LNPKL 278
P + L L ++ I+ P V+ T FD G +R L+ ++ ++
Sbjct: 433 -VPASDLINKDLVKNNVSFNAKDIQI-P---VYDT---FD-----GSDLRVLSGSISERI 479
Query: 279 TIALRKEDSDPEKNQYNEYFFAGGLEEYVQW-LNTDKKPLHDVVGF-RKDVDGITIDLAL 336
+ + V+W T K H ++ F G+ L
Sbjct: 480 VDCI--------------------IRLPVKWETTTQFKATH-ILDFGPGGASGLG-VLT- 516
Query: 337 QWCSDAYSDTMLGYANSIRTIDGGT 361
G +R I GT
Sbjct: 517 -------HRNKDGT--GVRVIVAGT 532
Score = 43.5 bits (102), Expect = 2e-04
Identities = 58/369 (15%), Positives = 104/369 (28%), Gaps = 139/369 (37%)
Query: 60 SSSIATEAFKE--NPVSKTYGSEQIQVLEGLEAVRKRP-AMYIGSTGPRGLH------HL 110
+S A + + N TYG L+ V P + I G +G +
Sbjct: 1638 TSKAAQDVWNRADNHFKDTYG------FSILDIVINNPVNLTIHFGGEKGKRIRENYSAM 1691
Query: 111 VYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDL-------HPA---TNKS 160
++E + + + + + + ++S S L PA K+
Sbjct: 1692 IFETIVDGKLKTEKIFKE------INEHSTSYTFRS---EKGLLSATQFTQPALTLMEKA 1742
Query: 161 ALETVLTVLHAGGK------FGGSSSG-YS--VSGGLHGVGLSVVNALSESLEVTVWRDG 211
A E L + G F G S G Y+ S V +S + +EV
Sbjct: 1743 AFE----DLKSKGLIPADATFAGHSLGEYAALASLA--DV-MS----IESLVEVV----- 1786
Query: 212 MEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIREL 271
+ RG +P D R + IA
Sbjct: 1787 ------FYRGM----TMQVAVPRDELGRSNYGM-------------------IA------ 1811
Query: 272 AFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGIT 331
+NP A +++ L+ V+ + L ++V + +V+
Sbjct: 1812 --INPGRVAASFSQEA---------------LQYVVERVGKRTGWLVEIVNY--NVENQQ 1852
Query: 332 IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL 391
+ G + + +T LN + + + + SL
Sbjct: 1853 Y------------------------VAAG-DLRALDT-VTNVLNFIKLQKIDIIELQKSL 1886
Query: 392 SGEHVREGL 400
S E V L
Sbjct: 1887 SLEEVEGHL 1895
Score = 42.0 bits (98), Expect = 7e-04
Identities = 42/293 (14%), Positives = 82/293 (27%), Gaps = 128/293 (43%)
Query: 302 GLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGT 361
G++ Y +DV + A D + G+ SI I
Sbjct: 1632 GMDLYKT---------SKAA---QDV----WNRA-----DNHFKDTYGF--SILDI---- 1664
Query: 362 HIEGVKASLTR-TLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTR 420
V + T++ G+K K +++ ++ E + +G
Sbjct: 1665 ----VINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDG--------------------- 1699
Query: 421 LGNPEVRKVVDQSVQEYLTEYLELHP-DVLDS-------ILSKSLSALK----------- 461
+ + + + E+ T Y +L + + +A +
Sbjct: 1700 ---KLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPAD 1756
Query: 462 -----------AALAA-------KRARDLVRQKSVLRSSSLPGKLADCSSTTPEESEIFI 503
AALA+ + ++V R G +
Sbjct: 1757 ATFAGHSLGEYAALASLADVMSIESLVEVVFY----R-----GMTMQVA----------- 1796
Query: 504 VEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALG 556
V D G S + AI P G++ AA + E +Q ++ +G
Sbjct: 1797 VPRDELGRS-----NYGMIAINP--GRV--------AASFSQEALQYVVERVG 1834
Score = 40.4 bits (94), Expect = 0.002
Identities = 34/178 (19%), Positives = 55/178 (30%), Gaps = 56/178 (31%)
Query: 26 SSSLFFKP------RTNFAIRGVSSQVLTRSNVVLPRAFLSSSIATEAFKEN---PVSKT 76
S+S F+ T F Q P L A E K P T
Sbjct: 1714 STSYTFRSEKGLLSATQFT------Q---------PALTLMEKAAFEDLKSKGLIPADAT 1758
Query: 77 Y-----G--------SEQIQVLEGLEAVRKRPAMYIGSTGPRG-LHHLVYEILDNAVDEA 122
+ G ++ + + +E V R M + PR L Y ++ A++
Sbjct: 1759 FAGHSLGEYAALASLADVMSIESLVEVVFYR-GMTMQVAVPRDELGRSNYGMI--AINPG 1815
Query: 123 QAGYASNIE-----VALLADNS---VSVA-DNGRG--IPIDLHPATNKSALETVLTVL 169
+ + + E V + + V + N A + AL+TV VL
Sbjct: 1816 RVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVA----AGDLRALDTVTNVL 1869
>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 = 64.5 bits (156), Expect = 8e-11
Identities = 78/493 (15%), Positives = 145/493 (29%), Gaps = 167/493 (33%)
Query: 234 VDSKDR-QGTRIRFW-----PDKQV---FTTAIQFDHNTIAGRIRELAFLNPKLTIALRK 284
+ SKD GT FW ++ V ++ ++ + I+
Sbjct: 55 IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT-------------- 100
Query: 285 EDSDPEKN--QYNEY---FFAGG----------LEEYVQ---WLNTDKKP----LHDVVG 322
E P Y E + L+ Y++ L + + V+G
Sbjct: 101 EQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLG 160
Query: 323 FRKDVDGITIDLALQWCSDAYSDTM---------LGYANSIRTI---------------- 357
K +AL C L NS T+
Sbjct: 161 SGKTW------VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214
Query: 358 ---DGGT----HIEGVKASLTRTL------NSL---------------GKKSKTV---KD 386
D + I ++A L R L N L K + +
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRF 274
Query: 387 KDIS----------LSGEHVREGLTC---------IISVRVPN-PEFEGQTKTRLGNPEV 426
K ++ +S +H LT + R + P + T NP
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR---EVLT--TNPRR 329
Query: 427 RKVVDQSVQEYLT---EYLELHPDVLDSILSKSLSALKAALAAKRARDLVRQKSVLRSSS 483
++ +S+++ L + ++ D L +I+ SL+ L+ A K L SV S+
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL----SVFPPSA 385
Query: 484 -LPGKLADC--SSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEA 540
+P L + + + + KQ ++ +P L V+ ++E
Sbjct: 386 HIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS--IPSIYLELKVKLENEY 443
Query: 541 AMYKNEEIQNLIRA--LGLGVKGEDFKKEALR--------YHKIIILTDADVDG--AHIR 588
A+++ +++ + +D L +H L + + R
Sbjct: 444 ALHR-----SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHH----LKNIEHPERMTLFR 494
Query: 589 TLLLTF-FYRYQK 600
+ L F F QK
Sbjct: 495 MVFLDFRFLE-QK 506
Score = 59.1 bits (142), Expect = 3e-09
Identities = 96/591 (16%), Positives = 168/591 (28%), Gaps = 176/591 (29%)
Query: 58 FLSSSIATEAFKENPVSKTYGSEQ------IQVL--------EGLEAVRK-----RPAMY 98
FL S I TE + + +++ Y ++ QV + +R+ RPA
Sbjct: 93 FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKN 152
Query: 99 IGSTGPRGL--HHLVYEIL-DNAVDEAQA--------GYASNIEVAL---------LADN 138
+ G G + ++ V ++ E L + N
Sbjct: 153 VLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN 212
Query: 139 SVSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNA 198
S +D+ I + +H ++ L +L S Y L V
Sbjct: 213 WTSRSDHSSNIKLRIHSI--QAELRRLL-----------KSKPYENC-------LLV--- 249
Query: 199 LSESLEVTVWR----DGMEYHQKY---SRGKPVT-----TLTCHVLPVDSKDRQGTRIRF 246
L V + K +R K VT T H+
Sbjct: 250 LLN-----VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM------TL 298
Query: 247 WPD--KQVFTTAIQFDHNTIAGRIRELAF-LNPKL--TIALRKEDSDPEKNQYNEYFFAG 301
PD K + + + + NP+ IA D ++
Sbjct: 299 TPDEVKSLLLKYL----DCRPQDLPREVLTTNPRRLSIIAESIRD-GLATWDNWKHVNCD 353
Query: 302 GLEEYVQ----WLNTD--KKPLHDVVGFRKDVDGITID-LALQWCSDAYSDTMLGYANSI 354
L ++ L +K + F I L+L W SD M+ N +
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH-IPTILLSLIWFDVIKSDVMV-VVNKL 411
Query: 355 RTIDGGTHIEGVKASL--------TRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISV 406
K SL T ++ S+ + K + + +L H +
Sbjct: 412 -----------HKYSLVEKQPKESTISIPSIYLELKVKLENEYAL---HRS----IVDHY 453
Query: 407 RVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILSKSLSALKAALAA 466
+P KT + + +DQ Y ++ H L + L
Sbjct: 454 NIP--------KTFDSDDLIPPYLDQ----YFYSHIGHH-------LKNIEHPERMTLFR 494
Query: 467 KRARDL--VRQKSVLRSSSLPGKLADCSSTTPEESEI-----FIVEGDSAGGSAKQGRDR 519
D + QK +R S S ++ +I + D +R
Sbjct: 495 MVFLDFRFLEQK--IRHDSTA--WNASGSILNTLQQLKFYKPYICDNDPK-------YER 543
Query: 520 RFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALR 570
AIL L K E + ++ +L+R + L + E +EA +
Sbjct: 544 LVNAIL----DFL---PKIEENLICSKYT-DLLR-IALMAEDEAIFEEAHK 585
>2q2e_B Type 2 DNA topoisomerase 6 subunit B; DNA-binding, SPO11, ATPase;
4.00A {Methanosarcina mazei}
Length = 621
Score = 59.4 bits (143), Expect = 2e-09
Identities = 48/236 (20%), Positives = 78/236 (33%), Gaps = 36/236 (15%)
Query: 70 ENPVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEA-QAGYAS 128
E P+++ +Q + + E K + + PR L V E +DNA+D +AG
Sbjct: 2 ETPIAEELAKKQ-KSISVAEFFEKNRQILGFDSAPRSLITTVKEAVDNALDACEEAGILP 60
Query: 129 NIEVALLADNS----VSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSV 184
+I V + V + DNG GI + + V L G +F
Sbjct: 61 DILVQVERTGPDYVTVIIEDNGPGIVRE--------QIPKVFAKLLYGSRFHALKQ---- 108
Query: 185 SGGLHGVGLSVVNALSESLE------VTVWRDG-----MEYHQKYSRGKPVTTLTCHVLP 233
S G G+G+S ++ ++ E S +P +
Sbjct: 109 SRGQQGIGISAAVLYAQMTAGRHTKILSKTSPTAPAHYYELMINTSTNEPDILVDE---V 165
Query: 234 VDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDP 289
D GT+I Q I ++ A +NP I L D +
Sbjct: 166 RDWFRPHGTQIELEMRAAYVKGRRQS----IYEYLKATAIVNPHARITLIDPDGNE 217
>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 = 51.7 bits (123), Expect = 4e-07
Identities = 34/220 (15%), Positives = 68/220 (30%), Gaps = 40/220 (18%)
Query: 89 EAVRKRPAMYIGSTGPRGLHHLVYEILDNAVD---EAQAGYASNIEVALLADNS----VS 141
E ++ P + R L+ V E+++N++D I + L+ D V+
Sbjct: 14 EFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVN 73
Query: 142 VADNGRGIPIDLHPATNKSALETVLTVLHAGGKFG-GSSSGYSVSGGLHGVGLSVVNALS 200
V DNG GIP P +A G+ S + G++G+G+ S
Sbjct: 74 VVDNGIGIPPQEVP--------------NAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYS 119
Query: 201 ESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVD--------SKDRQGTRIRFWPDKQV 252
+ + + + + L +D + R + V
Sbjct: 120 QM-------HQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSV 172
Query: 253 FTTA---IQFDHNTIAGRIRELAFLNPKLTIALRKEDSDP 289
+ + I I+ + P + + +
Sbjct: 173 AISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNV 212
>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix
two-turns helix; 2.00A {Sulfolobus shibatae} SCOP:
a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A*
1z5a_A* 1z59_A* 1z5c_A* 2hkj_A*
Length = 471
Score = 43.6 bits (102), Expect = 2e-04
Identities = 33/202 (16%), Positives = 68/202 (33%), Gaps = 36/202 (17%)
Query: 105 RGLHHLVYEILDNAVD-EAQAGYASNIEVALLADN------SVSVADNGRGIPIDLHPAT 157
R L+ V E+++N++D G NI++ + + V+V DNG GIP P
Sbjct: 31 RALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVP-- 88
Query: 158 NKSALETVLTVLHAGGKFG-GSSSGYSVSGGLHGVGLSVVNALSESL---EVTVWRDGME 213
+A G+ S + G++G+G+ S+ + + +
Sbjct: 89 ------------NAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVN 136
Query: 214 YHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGR------ 267
+ Y+ + P+ + R + V AI + +
Sbjct: 137 SKRIYTFKLKIDINKNE--PIIVERGSVENTRGFHGTSV---AISIPGDWPKAKSRIYEY 191
Query: 268 IRELAFLNPKLTIALRKEDSDP 289
I+ + P + + +
Sbjct: 192 IKRTYIITPYAEFIFKDPEGNV 213
>1y8o_A [pyruvate dehydrogenase [lipoamide]] kinase isozy; pyruvate
dehydrogenase kinase 3, lipoyl-bearing domain; HET: RED
ADP; 2.48A {Homo sapiens} SCOP: a.29.5.1 d.122.1.4 PDB:
1y8n_A* 1y8p_A* 2pnr_A* 2q8i_A*
Length = 419
Score = 38.6 bits (89), Expect = 0.006
Identities = 16/119 (13%), Positives = 40/119 (33%), Gaps = 17/119 (14%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASN------IEVALLADN---SVSVADNGRGIPIDLH 154
P L H+++E+ N++ Y ++ + S+ ++D G G+P
Sbjct: 251 PSHLFHMLFELFKNSMRATVELYEDRKEGYPAVKTLVTLGKEDLSIKISDLGGGVP---- 306
Query: 155 PATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTVWRDGME 213
++ + +++ + G GL + + + + ME
Sbjct: 307 ----LRKIDRLFNYMYSTAPRPSLEPTRAAPLAGFGYGLPISRLYARYFQGDLKLYSME 361
>1ysr_A Sensor-type histidine kinase PRRB; ATP-binding domain, structural
genomics, mycobacterium tuberculosis structural
proteomics project; 1.78A {Mycobacterium tuberculosis}
SCOP: d.122.1.3 PDB: 1ys3_A
Length = 150
Score = 33.3 bits (77), Expect = 0.080
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNS---VSVADNGRGIPIDLHP 155
P GL V + NAV A ++++ ++ + +++ DNG G+P
Sbjct: 44 PAGLRLAVDNAIANAVKHGGAT---LVQLSAVSSRAGVEIAIDDNGSGVPEGERQ 95
>1gkz_A [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase;
transferase, mitochondrial protein kinase, potassium;
HET: ADP; 2.2A {Rattus norvegicus} SCOP: a.29.5.1
d.122.1.4 PDB: 1gjv_A 1gkx_A*
Length = 388
Score = 34.6 bits (79), Expect = 0.10
Identities = 22/115 (19%), Positives = 38/115 (33%), Gaps = 15/115 (13%)
Query: 104 PRGLHHLVYEILDNAV------DEAQAGYASNIEVALLADNS---VSVADNGRGIPIDLH 154
P L +++ E+L NA+ ++ + + ++ + ++D G GI
Sbjct: 236 PMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDL 295
Query: 155 PA------TNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESL 203
T A + G S G S G GL A +E L
Sbjct: 296 DRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFGFGLPTSRAYAEYL 350
>3jz3_A Sensor protein QSEC; helix-turn-helix, kinase domain, ATP-binding,
cell inner MEM cell membrane, kinase, membrane,
nucleotide-binding; 2.50A {Escherichia coli}
Length = 222
Score = 33.7 bits (78), Expect = 0.11
Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 107 LHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHP 155
L LV +LDNAV + G S ++V L ADN V DNG G+ +
Sbjct: 118 LSLLVRNLLDNAVRYSPQG--SVVDVTLNADN-FIVRDNGPGVTPEALA 163
>2e0a_A Pyruvate dehydrogenase kinase isozyme 4; PDK4, ATP-binding,
structural genomics, NPPSFA, NATI project on protein
structural and functional analyses; HET: ANP; 1.86A
{Homo sapiens} PDB: 2zdx_A* 2zdy_A* 2zkj_A* 3d2r_A*
Length = 394
Score = 34.4 bits (78), Expect = 0.11
Identities = 17/89 (19%), Positives = 35/89 (39%), Gaps = 16/89 (17%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASN-----IEVALLADN---SVSVADNGRGIPIDLHP 155
P LHH+++E+ NA+ + IEV ++ ++ ++D G G+P+ +
Sbjct: 228 PSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIID 287
Query: 156 --------ATNKSALETVLTVLHAGGKFG 176
++ AG +G
Sbjct: 288 RLFSYTYSTAPTPVMDNSRNAPLAGFGYG 316
>1b63_A MUTL; DNA mismatch repair, ATPase; HET: ANP; 1.90A {Escherichia
coli K12} SCOP: d.14.1.3 d.122.1.2 PDB: 1nhh_A* 1nhi_A*
1bkn_A 1nhj_A* 1b62_A*
Length = 333
Score = 34.0 bits (79), Expect = 0.11
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 111 VYEILDNAVDEAQAGYASNIEVALLA--DNSVSVADNGRGIPID 152
V E+++N++D AG A+ I++ + + + DNG GI D
Sbjct: 29 VKELVENSLD---AG-ATRIDIDIERGGAKLIRIRDNGCGIKKD 68
>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 = 33.2 bits (75), Expect = 0.23
Identities = 24/117 (20%), Positives = 44/117 (37%), Gaps = 18/117 (15%)
Query: 107 LHHLVYEILDNAV-----DEAQAGYASNIEVALLADNS---VSVADNGRGIPID------ 152
L+H+V+E+ NA+ A G I+V + N V ++D G G+P+
Sbjct: 244 LYHMVFELFKNAMRATMEHHANRGVYPPIQVHVTLGNEDLTVKMSDRGGGVPLRKIDRLF 303
Query: 153 --LHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESLEVTV 207
++ + +ET V AG +G S L + + + +
Sbjct: 304 NYMYSTAPRPRVETSRAVPLAGFGYGLPISRLYAQ--YFQGDLKLYSLEGYGTDAVI 358
>1id0_A PHOQ histidine kinase; PHOQ/PHOP, signal transduction, transferase;
HET: ANP; 1.60A {Escherichia coli} SCOP: d.122.1.3 PDB:
3cgz_A 3cgy_A
Length = 152
Score = 31.8 bits (73), Expect = 0.27
Identities = 24/129 (18%), Positives = 44/129 (34%), Gaps = 28/129 (21%)
Query: 83 QVLEGLEAVRKRPAMYIGSTGPRGLH-----HLVYEILDNAVDEAQAGYA-SNIEVALLA 136
+ L V +R + I + + E++ N +D A Y +E++
Sbjct: 12 NLTSALNKVYQRKGVNISLDISPEISFVGEQNDFVEVMGNVLDNA-CKYCLEFVEISARQ 70
Query: 137 DNS---VSVADNGRGIPIDLHPATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGL 193
+ + V D+G GIP+ + G + G GVGL
Sbjct: 71 TDEHLYIVVEDDGPGIPLSKREV-----------IFDRGQRVDTLRPG-------QGVGL 112
Query: 194 SVVNALSES 202
+V ++E
Sbjct: 113 AVAREITEQ 121
>1h7s_A PMS1 protein homolog 2; DNA repair, GHL ATPase, mismatch repair,
HNPCC; 1.95A {Homo sapiens} SCOP: d.14.1.3 d.122.1.2
PDB: 1h7u_A* 1ea6_A*
Length = 365
Score = 32.5 bits (75), Expect = 0.43
Identities = 15/43 (34%), Positives = 27/43 (62%), Gaps = 8/43 (18%)
Query: 113 EILDNAVDEAQAGYASNIEVALLADN---SVSVADNGRGIPID 152
E+++N++D AG A+NI++ L D + V+DNG G+ +
Sbjct: 41 ELVENSLD---AG-ATNIDL-KLKDYGVDLIEVSDNGCGVEEE 78
>1th8_A Anti-sigma F factor; SPOIIAB, SPOIIAA, anti-ANTI-sigma,
sporulation, serine kinase, transcription; HET: ADP;
2.40A {Geobacillus stearothermophilus} SCOP: d.122.1.3
PDB: 1thn_A* 1til_A* 1l0o_A* 1tid_A*
Length = 145
Score = 31.1 bits (71), Expect = 0.45
Identities = 10/44 (22%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 111 VYEILDNAVDEAQAGYAS-NIEVALLADN---SVSVADNGRGIP 150
V E + NA+ + + ++++ ++ ++V D G GIP
Sbjct: 44 VSEAVTNAIIHGYNNDPNGIVSISVIIEDGVVHLTVRDEGVGIP 87
>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 = 32.1 bits (72), Expect = 0.56
Identities = 21/106 (19%), Positives = 46/106 (43%), Gaps = 17/106 (16%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASN-----IEVALLA---DNSVSVADNGRGIPIDLHP 155
P L+H+++E+ NA+ + S+ I+V + D S+ ++D G G+P
Sbjct: 229 PSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVP----- 283
Query: 156 ATNKSALETVLTVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSE 201
+E + + +++ +G + G G GL + ++
Sbjct: 284 ---LRKIERLFSYMYSTAPTPQPGTGGTPLAGF-GYGLPISRLYAK 325
>3zxq_A Hypoxia sensor histidine kinase response regulato; transferase;
1.90A {Mycobacterium tuberculosis}
Length = 124
Score = 30.3 bits (69), Expect = 0.72
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 113 EILDNAVDEAQAGYASNIEVALLADNSV--SVADNGRGIPID 152
E + NAV A A +++ + + ++ V V D+G GI D
Sbjct: 46 EAVSNAVRHANA---TSLAINVSVEDDVRVEVVDDGVGISGD 84
>3h4l_A DNA mismatch repair protein PMS1; ATP binding, DNA repair, DNA
damage, nucleus, phosphop DNA binding protein, protein
binding; HET: DNA ANP; 2.50A {Saccharomyces cerevisiae}
Length = 367
Score = 31.4 bits (72), Expect = 0.76
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 8/43 (18%)
Query: 113 EILDNAVDEAQAGYASNIEVALLADN---SVSVADNGRGIPID 152
E++DN++D A A+ IE+ + D S+ +DNG GI
Sbjct: 32 ELVDNSID---AN-ANQIEI-IFKDYGLESIECSDNGDGIDPS 69
>3na3_A DNA mismatch repair protein MLH1; MUTL protein homolog 1, DNA damag
repair, structural genomics consortium, SGC, protein
bindin; HET: DNA ATP; 2.50A {Homo sapiens}
Length = 348
Score = 31.3 bits (72), Expect = 0.96
Identities = 11/43 (25%), Positives = 25/43 (58%), Gaps = 8/43 (18%)
Query: 113 EILDNAVDEAQAGYASNIEVALLAD---NSVSVADNGRGIPID 152
E+++N +D A +++I+V ++ + + + DNG GI +
Sbjct: 35 EMIENCLD---AK-STSIQV-IVKEGGLKLIQIQDNGTGIRKE 72
>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 = 31.2 bits (71), Expect = 1.2
Identities = 10/64 (15%), Positives = 23/64 (35%), Gaps = 9/64 (14%)
Query: 280 IALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRK------DVDGITID 333
+ + K+ N + + ++N +K PL FR+ + + I +
Sbjct: 243 VPVLKKAYGIVTWYENAPYMLPANTAGI-YINVNKYPLSIPE-FRRAMAYAINPEKI-VT 299
Query: 334 LALQ 337
A +
Sbjct: 300 RAYE 303
>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 = 29.4 bits (66), Expect = 1.4
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 566 KEALRYHKIIILTDADVDGAHIRTLLLTFF 595
+ L + + +L DAD G +R F
Sbjct: 45 ADELEGYDVYLLADADEAGEKLRRQFRRMF 74
>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 = 1.8
Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 11/56 (19%)
Query: 436 EYLTEYLELHPDVLDSILS-------KSLSALKAALAAKRAR----DLVRQKSVLR 480
+ L +P +LD +L + A + L R D +Q LR
Sbjct: 115 PMIASQLARYPLLLDELLDPNTLYQPTATDAYRDELRQYLLRVPEDDEEQQLEALR 170
>3zxo_A Redox sensor histidine kinase response regulator; transferase; HET:
MSE; 1.90A {Mycobacterium tuberculosis}
Length = 129
Score = 29.1 bits (66), Expect = 1.8
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 113 EILDNAVDEAQAGYASNIEVALLADNSV--SVADNGRGIP 150
E + NAV A A S + V + D+ + V DNGRG+P
Sbjct: 50 EAVSNAVRHAAA---STLTVRVKVDDDLCIEVTDNGRGMP 86
>2c2a_A Sensor histidine kinase; phosphotransfer, PHOQ, selenomethionyl
MAD, two-component systems, transferase; HET: ADP; 1.9A
{Thermotoga maritima} SCOP: a.30.2.1 d.122.1.3 PDB:
3dge_A*
Length = 258
Score = 29.8 bits (68), Expect = 2.4
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 114 ILDNAV---DEAQAGYASNIEVALLADNS---VSVADNGRGIP 150
+L+N V + ++V L + + V DNG GIP
Sbjct: 146 LLNNGVKYSKKD--APDKYVKVILDEKDGGVLIIVEDNGIGIP 186
>1wvf_A 4-cresol dehydrogenase [hydroxylating] flavoprote subunit;
flavoprotein, electron-transfer, FAD, oxidoreductase;
HET: FAD; 1.30A {Pseudomonas putida} SCOP: d.58.32.1
d.145.1.1 PDB: 1wve_A* 1dii_A* 1diq_A*
Length = 520
Score = 30.0 bits (68), Expect = 2.4
Identities = 9/56 (16%), Positives = 20/56 (35%), Gaps = 10/56 (17%)
Query: 161 ALETVL---TVLHAGGKFGGSSSGYSVSGGLHGVGLSVVNALSESL-----EVTVW 208
+E VL V G S+ + + G G ++ +++ ++ W
Sbjct: 183 GMEVVLANGDVYRTGMGGVPGSNTWQIFK--WGYGPTLDGMFTQANYGICTKMGFW 236
>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 = 4.0
Identities = 9/52 (17%), Positives = 16/52 (30%), Gaps = 7/52 (13%)
Query: 436 EYLTEYLELHPDVLDSILS-----KSLSALKAALAAKRAR--DLVRQKSVLR 480
+++ + + HP+ L + S A L D LR
Sbjct: 40 DFVQDSVIAHPEWLTELESQPPQADEWQHYAAWLQEALCNVSDEAGLMRELR 91
>1bxd_A ENVZ(290-450), protein (osmolarity sensor protein (ENVZ));
histidine kinase, osmosensor, His-Asp phosphorelay
system, signal transduction; HET: ANP; NMR {Escherichia
coli BL21} SCOP: d.122.1.3
Length = 161
Score = 28.4 bits (64), Expect = 4.2
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYA-SNIEVALLADNS---VSVADNGRGIPID 152
P + V ++ NA Y I+V+ + + V D+G GI +
Sbjct: 45 PLSIKRAVANMVVNAAR-----YGNGWIKVSSGTEPNRAWFQVEDDGPGIAPE 92
>3a0y_A Sensor protein; ATP-LID, kinase, phosphoprotein, transferase,
two-component regulatory system; 1.57A {Thermotoga
maritima} PDB: 3a0t_A* 3a0x_A 3a0w_A 3a0z_A
Length = 152
Score = 28.3 bits (64), Expect = 4.5
Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 5/40 (12%)
Query: 114 ILDNAVDEAQAGYASNIEVALLADNS---VSVADNGRGIP 150
++ NA++ I++ + VSV ++G IP
Sbjct: 55 LVQNAIEATGEN--GKIKITSEDMYTKVRVSVWNSGPPIP 92
>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 = 27.6 bits (61), Expect = 4.8
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 3/72 (4%)
Query: 528 RGKILNVE-RKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAH 586
R ++ VE + D+ A+ I+N+I G + ++ K+I+L D D G
Sbjct: 20 REAVILVEGKNDKKAL-SKFSIKNVIDLSGKRYA-DVVDMLEGKWEKVILLFDLDTHGER 77
Query: 587 IRTLLLTFFYRY 598
I +
Sbjct: 78 INQKMKELLSSQ 89
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase,
phosphoprotein, transfe two-component regulatory system;
3.80A {Thermotoga maritima}
Length = 349
Score = 28.8 bits (65), Expect = 5.1
Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 5/40 (12%)
Query: 114 ILDNAVDEAQAGYASNIEVALLADNS---VSVADNGRGIP 150
++ NA++ I++ + VSV ++G IP
Sbjct: 252 LVQNAIEATGEN--GKIKITSEDMYTKVRVSVWNSGPPIP 289
>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 = 29.0 bits (64), Expect = 5.6
Identities = 24/179 (13%), Positives = 48/179 (26%), Gaps = 14/179 (7%)
Query: 415 GQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDVLDSILS-KSLSALKAALAAKRARDLV 473
+ R ++ Q Q+ + +L+ H D S K+ + A A+R +
Sbjct: 10 SFGQQRQQQQPQQQKQQQRDQDSVEAWLDDHWDFTFSYFVRKATREMVNAWFAERVHTIP 69
Query: 474 RQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGG-----------SAKQGRDRRFQ 522
K +R + S + S + +G
Sbjct: 70 VCKEGIRGHTESCSCPLQQSPRADNSVPGTPTRKISASEFDRPLRPIVVKDSEGTVSFLS 129
Query: 523 AILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDAD 581
L R D + + L++ + + + + I L AD
Sbjct: 130 DSEKKEQMPLTPPRFDHDEGDQCSRLLELVKDISSHLDVTALCHKIFLH--IHGLISAD 186
>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 = 5.8
Identities = 7/50 (14%), Positives = 12/50 (24%), Gaps = 10/50 (20%)
Query: 297 YFFAGGLEEYVQWLNTDK--------KPLHDVVGFRKDVDGITIDLALQW 338
Y + +L K L +G + +D A
Sbjct: 317 YLIQD--TKVYVFLTKGGYTLVNGYPKRLEKELGSPPVISLEAVDAAFVC 364
>3sl2_A Sensor histidine kinase YYCG; ATP binding, intact ATP, bergerat
fold, TR; HET: ATP; 1.61A {Bacillus subtilis}
Length = 177
Score = 28.0 bits (63), Expect = 6.6
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 114 ILDNAVDEAQAGYASNIEVALLADNS---VSVADNGRGIP 150
I+ NA+ + G + + + +SV D G GIP
Sbjct: 51 IISNALKYSPEGGHVTFSIDVNEEEELLYISVKDEGIGIP 90
>1r62_A Nitrogen regulation protein NR(II); PII, histidine kinase, two
component system, transfera; 1.60A {Escherichia coli}
SCOP: d.122.1.3
Length = 160
Score = 27.5 bits (62), Expect = 7.7
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 140 VSVADNGRGIPIDLHP 155
+ V DNG GIP L
Sbjct: 94 IDVEDNGPGIPPHLQD 109
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 0.390
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: 9,530,619
Number of extensions: 601751
Number of successful extensions: 1488
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1392
Number of HSP's successfully gapped: 66
Length of query: 622
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 523
Effective length of database: 3,937,614
Effective search space: 2059372122
Effective search space used: 2059372122
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)