RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13360
(1161 letters)
>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 = 678 bits (1752), Expect = 0.0
Identities = 214/411 (52%), Positives = 298/411 (72%), Gaps = 22/411 (5%)
Query: 345 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVT 404
+S +SSI++L+GL+AVRKRP MYIGDT DGTGLHH VFE++DNAIDE+LAG+C +I VT
Sbjct: 2 NSSDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVT 61
Query: 405 IYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 464
I++DNS+S+ D+GRGIP I + SAAE++MT LHAGGKF+ NSYK+SGGLHG+
Sbjct: 62 IHADNSVSVQDDGRGIPTGIH----PEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGV 117
Query: 465 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTK 524
G+S VN LS+ L+L I R KIH + +G+ +P+ + G+T K GT
Sbjct: 118 GVSVVNALSQKLELVIQREGKIHRQIYE------------HGVPQAPLAVTGETEKTGTM 165
Query: 525 IHFWVDEKIFSNI-EFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFV 583
+ FW + F+N+ EF YEIL KR+RELSFL++GV I L D+R K++ F ++GG FV
Sbjct: 166 VRFWPSLETFTNVTEFEYEILAKRLRELSFLDSGVSIRLRDKRDGKEDHFHYEGGIKAFV 225
Query: 584 SYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTH 643
Y+NK+K +HP IF S +K+ I ++V++QWN+ + ENI CFTNNI Q DGGTH
Sbjct: 226 EYLNKNKTPIHPNIFY-----FSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTH 280
Query: 644 LTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLV 703
L G R+ +TR +N Y+++ + KK+K+ G+D REGL V+S+K+PDPKF+SQTK+KLV
Sbjct: 281 LAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLV 340
Query: 704 SSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELT 754
SSEV+ VE+ + + L ++L ENP ++K++ KII+AAR+REAAR+ RE+T
Sbjct: 341 SSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMT 391
>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 = 650 bits (1680), Expect = 0.0
Identities = 156/410 (38%), Positives = 241/410 (58%), Gaps = 24/410 (5%)
Query: 346 SYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTI 405
SY AS+I++L+GLE VR RP MYIG T G HH EILDNA+DE+LAGY T+I V +
Sbjct: 2 SYDASAIRVLKGLEGVRHRPAMYIGGTGV-EGYHHLFKEILDNAVDEALAGYATEILVRL 60
Query: 406 YSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIG 465
D S+++ DNGRGIP+D+ + + A E++ LH+GGKF + +YK+SGGLHG+G
Sbjct: 61 NEDGSLTVEDNGRGIPVDLM----PEEGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVG 116
Query: 466 LSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDT--NKQGT 523
S VN LS + + + R K H + F G P++++G+ K GT
Sbjct: 117 ASVVNALSEWTVVEVFREGKHHRIAFSRGE------------VTEPLRVVGEAPRGKTGT 164
Query: 524 KIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFV 583
++ F D +IF N+ F ++ R+RE+++L G+ + D + K+E+F KGG + F
Sbjct: 165 RVTFKPDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEEVFLDKGGVASFA 224
Query: 584 SYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTH 643
+ + + +++ F I + ++V YN IL + N I DGGTH
Sbjct: 225 KALAEGEDLLYEKPFL-----IRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTH 279
Query: 644 LTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLV 703
LT +S +RA+N+Y ++ K+ + G+D+ EGL V+S+K+P+P+F QTK KL+
Sbjct: 280 LTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLL 339
Query: 704 SSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTREL 753
+ E V +++ + L + L+ENP +K + EK + AA++REAARK REL
Sbjct: 340 NPEAGTAVGQVVYERLLEILEENPRIAKAVYEKALRAAQAREAARKAREL 389
>3lnu_A Topoisomerase IV subunit B; PARE, ATP-binding, nucleotide-BI
topoisomerase; 2.20A {Xanthomonas oryzae PV} PDB:
3lps_A*
Length = 408
Score = 619 bits (1600), Expect = 0.0
Identities = 133/421 (31%), Positives = 225/421 (53%), Gaps = 32/421 (7%)
Query: 340 QDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCT 399
+ + + Y+A+ I++L GL+ V++RP MY D +H E++DN++DE+LAG+
Sbjct: 17 RGSHNTRYNAADIEVLSGLDPVKRRPGMYT----DTARPNHLAQEVIDNSVDEALAGHAK 72
Query: 400 KINVTIYSDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKIS 458
+I VT+Y D S +SD+GRG+P+DI H + K E+++T LHAGGKFN +Y S
Sbjct: 73 QIEVTLYKDGSCEVSDDGRGMPVDI-----HPEEKIPGVELILTRLHAGGKFNNRNYTFS 127
Query: 459 GGLHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDT 518
GGLHG+G+S VN LS ++L I R H MEFR +G + S ++++G
Sbjct: 128 GGLHGVGVSVVNALSTKVELFIKREGSEHRMEFR------------DGNAASKLEVVGTV 175
Query: 519 NKQ--GTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFK 576
K+ GT++ FW D K F +F+ L+ +R + L G+ + L DE +++ + F+
Sbjct: 176 GKKNTGTRLRFWADPKYFDTPKFNVRALRHLLRAKAVLCPGLTVKLHDEATGEQDSWYFE 235
Query: 577 GGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNIL 636
G ++ ++ +F S KK+ +D + W + N I
Sbjct: 236 NGLRDYLKGEMAEHEMLPADLFV-----GSLKKDTEIVDWAAGWVPEGELVQESYVNLIP 290
Query: 637 QVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNS 696
GTH+ GLRSG+T A+ ++ + L + +++ ED+ + +T VLS+K+ DP+F+
Sbjct: 291 TAQHGTHVNGLRSGLTDALREFCDFRNLLPR-GVKLAPEDVWDRVTFVLSLKMTDPQFSG 349
Query: 697 QTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRK 756
QTK +L S + +E +L +N + I + I+ A +R + +++ RK
Sbjct: 350 QTKERLSSRQAAGFIEGAAHDAFSLYLNQNVEIGEKIAQIAIDRASAR--LKTEKQIVRK 407
Query: 757 K 757
K
Sbjct: 408 K 408
>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 = 606 bits (1564), Expect = 0.0
Identities = 126/417 (30%), Positives = 224/417 (53%), Gaps = 33/417 (7%)
Query: 345 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVT 404
+Y+A +I++L GLE VR+RP MY D T +H E++DN++DE+LAG+ +++V
Sbjct: 3 QTYNADAIEVLTGLEPVRRRPGMYT----DTTRPNHLGQEVIDNSVDEALAGHAKRVDVI 58
Query: 405 IYSDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHG 463
+++D S+ + D+GRG+P+DI H + A E+++ LHAGGKF+ +Y+ SGGLHG
Sbjct: 59 LHADQSLEVIDDGRGMPVDI-----HPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHG 113
Query: 464 IGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ-- 521
+G+S VN LS+ +++ + R+ +++ + F NG V ++++G K+
Sbjct: 114 VGISVVNALSKRVEVNVRRDGQVYNIAFE------------NGEKVQDLQVVGTCGKRNT 161
Query: 522 GTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSG 581
GT +HFW DE F + F L ++ + L GV IT DE ++ + ++ G +
Sbjct: 162 GTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQDGLND 221
Query: 582 FVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENIL-CFTNNILQVDG 640
+++ + F + + +D ++ W E + + N I + G
Sbjct: 222 YLAEAVNGLPTLPEKPFI-----GNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQG 276
Query: 641 GTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKN 700
GTH+ GLR G+ A+ ++ E L + +++ EDI + VLS+K+ DP+F QTK
Sbjct: 277 GTHVNGLRQGLLDAMREFCEYRNILPR-GVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKE 335
Query: 701 KLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKK 757
+L S + V ++ +L +N ++L+ E I +A+ R R +++ RKK
Sbjct: 336 RLSSRQCAAFVSGVVKDAFILWLNQNVQAAELLAEMAISSAQRR--MRAAKKVVRKK 390
>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 = 553 bits (1428), Expect = 0.0
Identities = 80/386 (20%), Positives = 161/386 (41%), Gaps = 37/386 (9%)
Query: 357 GLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYSDNSISISDN 416
+E VRKRP MY GD + GLHH V+ +LD A +E+ G C + + + D SI++
Sbjct: 11 IVENVRKRPGMYCGDVGE-YGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCT 69
Query: 417 GRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFL 476
R + AE ++ G + G L LS
Sbjct: 70 SRTVT---------------AENLVRVATGAGFLGRPPGDGWGWDSM--LVVSLALSSRY 112
Query: 477 QLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSN 536
Q+ I + + + +G Q G +V+P++ + + ++G ++HF D IF
Sbjct: 113 QVDIWADGRQWRVMGEHGHPQGE------GAAVTPMEPMPVSAERGVRVHFVPDATIFEV 166
Query: 537 IEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPT 596
+ F L +R EL+ L G+ ++ D + ++ ++ GG + + + +++ +HP
Sbjct: 167 LAFDRARLSRRCNELAALAPGLRVSFADLQRGERTLWHLPGGVAQWAHVLTEARPQLHPE 226
Query: 597 IFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAIN 656
+ + + ++QW + +L F N + V G H+ G+ + A+
Sbjct: 227 PVV-----FDFTWDGLRVQCALQWCEDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALA 281
Query: 657 KYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPK--FNSQTKNKLVSSEVRKPVEEI 714
K +++ + +GLT ++++ P + F TK L + + + +
Sbjct: 282 KL------SGETRGAFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQ 335
Query: 715 IIKTLFDFLQENPGESKLICEKIIEA 740
+ + L+E+P L+ + +
Sbjct: 336 LQPLFIELLREHPVTPALLARRTSGS 361
>3nuh_B DNA gyrase subunit B; topoisomerase, supercoiling, specialization,
isomera; HET: DNA; 3.10A {Escherichia coli}
Length = 420
Score = 495 bits (1276), Expect = e-165
Identities = 181/424 (42%), Positives = 276/424 (65%), Gaps = 13/424 (3%)
Query: 747 ARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVL 806
+ RE+TR+K +D L KLADCQE++P L ELY+VEGDSAGGS KQGR+R+ QA+L
Sbjct: 1 SNAAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAIL 60
Query: 807 PLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGA 866
PL+GK+LN+EKARF+K++ S+++ TLI+ LG GI +DE+N +KLRYH IIIMTDAD+DG+
Sbjct: 61 PLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGS 120
Query: 867 HIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNV 926
HIR LLLTFFYR+MP+++E G++YIAQPPLYK+K G E Y++DD ++Y + IA
Sbjct: 121 HIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGA 180
Query: 927 KLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVILN---LDTRE 983
L + + + KL+ +YN T ++++R+++ ++L ++ L L +
Sbjct: 181 TLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQ 240
Query: 984 NAEQFAKKIIKKLND-----SNIEIIVEFDQLNNKYLLNIKKKFL-KKKNYIIDINFINN 1037
++ ++ +LND S + V + N + ++ + +Y +D FI
Sbjct: 241 TVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITG 300
Query: 1038 KDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANNFYKIINYLRNEAENMVIKQRYK 1097
+Y+++ ++ + ++ + I++ ++ +F + +++L E+ + QRYK
Sbjct: 301 GEYRRICTLGEKLRGLLEEDAFIER----GERRQPVASFEQALDWLVKESRRGLSIQRYK 356
Query: 1098 GLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNALHAK 1157
GLGEMNP QLWETTM+P R +L+V +KDAI+AD++F TLMGD VE RR FIE NAL A
Sbjct: 357 GLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAA 416
Query: 1158 NIDI 1161
NIDI
Sbjct: 417 NIDI 420
>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 = 428 bits (1102), Expect = e-139
Identities = 87/433 (20%), Positives = 162/433 (37%), Gaps = 55/433 (12%)
Query: 342 TQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGT----------------------GLH 379
+ E ++ Q + LE + KRP+ YIG GL
Sbjct: 7 STEPVSASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLF 66
Query: 380 HFVFEILDNAIDESLAG-YCTKINVTIYSD-NSISISDNGRGIPIDIKIDDKH-KPKRSA 436
EIL NA D + +I+V I+++ ++I + ++G+GIPI+I H K
Sbjct: 67 KIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEI-----HNKENIYI 121
Query: 437 AEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTIN--RNKKIHYMEFRYG 494
E++ L ++ + K++GG +G G N S L + + ++
Sbjct: 122 PEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENN 181
Query: 495 VLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFL 554
+ I P TK+ F D F E +IL R + +
Sbjct: 182 M----------SICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDI 231
Query: 555 NNGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKI--SEKKNNI 612
N V + K +I FK ++ + K + + + A + ++ N
Sbjct: 232 NGSVRDINVYLNGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINN 291
Query: 613 NIDVSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEI 672
+V+ ++ + I F N+I GGTH+ + I + I++ ++ KK K +
Sbjct: 292 RWEVAFAVSDISFQQI-SFVNSIATTMGGTHVNYITDQIVKKISEILK-----KKKKKSV 345
Query: 673 IGEDIREGLTCVLSIKIPDPKFNSQTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKL 732
I+ + ++ I +P F SQTK +L + I + + +
Sbjct: 346 KSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTD----- 400
Query: 733 ICEKIIEAARSRE 745
+ ++ E A + E
Sbjct: 401 LATRMFEIADANE 413
>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 = 394 bits (1015), Expect = e-130
Identities = 126/234 (53%), Positives = 169/234 (72%), Gaps = 17/234 (7%)
Query: 345 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVT 404
+SY +SSI++L+GL+AVRKRP MYIGDT DGTGLHH VFE++DNAIDE+LAG+C +I VT
Sbjct: 3 NSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVT 62
Query: 405 IYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 464
I++DNS+S+ D+GRGIP I + SAAE++MT LHAGGKF+ NSYK+SGGLHG+
Sbjct: 63 IHADNSVSVQDDGRGIPTGI----HPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGV 118
Query: 465 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTK 524
G+S VN LS+ L+L I R KIH + +G+ +P+ + G+T K GT
Sbjct: 119 GVSVVNALSQKLELVIQREGKIHRQIYE------------HGVPQAPLAVTGETEKTGTM 166
Query: 525 IHFWVDEKIFSNI-EFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKG 577
+ FW + F+N+ EF YEIL KR+RELSFLN+GV I L D+R K++ F ++G
Sbjct: 167 VRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEG 220
>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-120
Identities = 99/239 (41%), Positives = 146/239 (61%), Gaps = 19/239 (7%)
Query: 340 QDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCT 399
++ ++Y+ +IQ+LEGL+AVRKRP MYIG T DG GLHH V+EI+DNA+DE+L+G+
Sbjct: 4 KEININNYNDDAIQVLEGLDAVRKRPGMYIGST-DGAGLHHLVWEIVDNAVDEALSGFGD 62
Query: 400 KINVTIYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISG 459
+I+VTI D S+++ D+GRG+P + H E++ T LHAGGKF + YK SG
Sbjct: 63 RIDVTINKDGSLTVQDHGRGMPTGM-----HAMGIPTVEVIFTILHAGGKFGQGGYKTSG 117
Query: 460 GLHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDT- 518
GLHG+G S VN LS +L++ I R+ ++ F G G V+ +K IG
Sbjct: 118 GLHGVGSSVVNALSSWLEVEITRDGAVYKQRFENG-----------GKPVTTLKKIGTAL 166
Query: 519 -NKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFK 576
+K GTK+ F D IFS +F Y + +R+ E +FL V ++L D+R + F ++
Sbjct: 167 KSKTGTKVTFMPDATIFSTTDFKYNTISERLNESAFLLKNVTLSLTDKRTDEAIEFHYE 225
>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 = 371 bits (955), Expect = e-118
Identities = 77/432 (17%), Positives = 146/432 (33%), Gaps = 64/432 (14%)
Query: 351 SIQILEGLEAVRKRPEMYIGDTSDGT---------------------GLHHFVFEILDNA 389
Q LE + RP+ YIG T GL+ EIL NA
Sbjct: 5 IYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVNA 64
Query: 390 IDESLAG-YCTKINVTIYSD-NSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAG 447
D + I VTI + N ISI +NG+GIP+ K ++ +L
Sbjct: 65 ADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEH----KVEKMYVPALIFGQLLTS 120
Query: 448 GKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTI--NRNKKIHYMEFRYGVLQNRIIKTIN 505
++ + K++GG +G G N S + KK+ + + +
Sbjct: 121 SNYDDDEKKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGR-------- 172
Query: 506 GISVSPIKIIGDTNKQGTKIHFWVDEKIFSNIEFHYEILK---KRIRELSFLNNGVCITL 562
+++ + T I F D F +I+ +R +++ V + L
Sbjct: 173 ---AGEMELKPFNGEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFL 229
Query: 563 IDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNN 622
++ K +V K KL K+ ++ N +V + +
Sbjct: 230 NGNKLPVKGFRS-------YVDMYLKDKLDETGNSL-----KVIHEQVNHRWEVCLTMSE 277
Query: 623 SYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLT 682
+ I F N+I GG H+ + I + +++ K + + ++ +
Sbjct: 278 KGFQQI-SFVNSIATSKGGRHVDYVADQIVTKLVDVVKKK---NKGGVAVKAHQVKNHMW 333
Query: 683 CVLSIKIPDPKFNSQTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAAR 742
++ I +P F+SQTK + + + I E I+ +
Sbjct: 334 IFVNALIENPTFDSQTKENMTLQPKSFGSTCQLSEKFIKAAIGCG-----IVESILNWVK 388
Query: 743 SREAARKTRELT 754
+ + ++ +
Sbjct: 389 FKAQVQLNKKCS 400
>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 = 334 bits (859), Expect = e-107
Identities = 77/222 (34%), Positives = 129/222 (58%), Gaps = 24/222 (10%)
Query: 357 GLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYSDNSISISDN 416
GLE VR+RP MY D T +H E++DN++DE+LAG+ +++V +++D S+ + D+
Sbjct: 1 GLEPVRRRPGMYT----DTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDD 56
Query: 417 GRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRF 475
GRG+P+DI H + A E+++ LHAGGKF+ +Y+ SGGLHG+G+S VN LS+
Sbjct: 57 GRGMPVDI-----HPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKR 111
Query: 476 LQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ--GTKIHFWVDEKI 533
+++ + R+ +++ + F NG V ++++G K+ GT +HFW DE
Sbjct: 112 VEVNVRRDGQVYNIAFE------------NGEKVQDLQVVGTCGKRNTGTSVHFWPDETF 159
Query: 534 FSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEF 575
F + F L ++ + L GV IT DE ++ + +
Sbjct: 160 FDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCY 201
>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding clamp,
DNA replication, rational drug design, antibiotic
target, transferase; HET: DNA 322; 1.64A {Escherichia
coli} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A*
1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 3q4j_A*
3q4k_A* 3qsb_A* 3q4l_A* 2xur_A* 1jql_A* 1jqj_A* 3f1v_A*
3pwe_A*
Length = 366
Score = 335 bits (861), Expect = e-105
Identities = 112/318 (35%), Positives = 186/318 (58%), Gaps = 4/318 (1%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ V + +L PLQ V + + LPIL N+L+ +S TD E+++ A
Sbjct: 1 MKFTVE--REHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVA 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
+ + V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P
Sbjct: 59 LVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPN 118
Query: 121 MTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL 180
+ + + + EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL
Sbjct: 119 LD-DWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRL 177
Query: 181 TYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKL 240
+ I + S S +I+PRK V L R+L+ +NP+ ++I +N I+ + SKL
Sbjct: 178 AVCSMPIGQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKL 236
Query: 241 IDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSS 300
+DG+F DY+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++
Sbjct: 237 VDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANN 296
Query: 301 SNREKASEELEINYNGKD 318
+E+A E L++ Y+G +
Sbjct: 297 PEQEEAEEILDVTYSGAE 314
>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 = 316 bits (811), Expect = 1e-99
Identities = 91/186 (48%), Positives = 115/186 (61%), Gaps = 5/186 (2%)
Query: 740 AARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRD 799
+ + KN D LS KL Q KNP ELY+VEGDSAGGS KQGRD
Sbjct: 8 HHHHHSSGHIDDDDKHMKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRD 67
Query: 800 RRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMT 859
R+FQA+LPLRGKV+N KA+ I+ +E+I T+I T+G G+ +F++E Y +IIIMT
Sbjct: 68 RKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGV-GADFSIEDANYDKIIIMT 126
Query: 860 DADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNEC----YLRDDIEEE 915
DAD DGAHI+ LLLTFFYR M L+E G++YIA PPLYK+ G + Y D E E
Sbjct: 127 DADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELE 186
Query: 916 RYMLKI 921
+
Sbjct: 187 ELRKQF 192
Score = 123 bits (312), Expect = 2e-31
Identities = 42/101 (41%), Positives = 53/101 (52%), Gaps = 11/101 (10%)
Query: 1067 KIKKYTANNFYKIINYLRNEAE-NMVIK--------QRYKGLGEMNPGQLWETTMNPMIR 1117
K+ K + + Y + E + K QRYKGLGEMN QLWETTMNP R
Sbjct: 165 KMSK--GKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETR 222
Query: 1118 CLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNALHAKN 1158
L++V I+D A++ LMGD VE RRK+IE N
Sbjct: 223 TLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTLE 263
>1vpk_A DNA polymerase III, beta subunit; TM0262, structural genomic center
for structural genomics, JCSG, protein structure INI
PSI, transferase; HET: DNA; 2.00A {Thermotoga maritima}
SCOP: d.131.1.1 d.131.1.1 d.131.1.1
Length = 378
Score = 315 bits (810), Expect = 4e-98
Identities = 68/319 (21%), Positives = 150/319 (47%), Gaps = 7/319 (2%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M++ V + + + + KK++ PIL+ L +TD E +
Sbjct: 13 MKVTVT--TLELKDKITIASKALAKKSVKPILAGFLFEVKDGNFYICATDLETGVKATVN 70
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
+ +V +++ LP+ + +E + I SG + F + T+ A E+P
Sbjct: 71 AAEISGEARFVVPGDVIQKMVKVLPDEI-TELSLEGDALVISSGSTVFRITTMPADEFPE 129
Query: 121 MTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL 180
+T F + L+ ++ V F+ A+ + LNG+ K + V+SDG RL
Sbjct: 130 ITPAES-GITFEVDTSLLEEMVEKVIFAAAKDEFMRNLNGVFWELHKNLLRLVASDGFRL 188
Query: 181 TYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLEN-KENPVELKISNNQIKIIFSNIEIISK 239
+ I+ + + ++ K++ +Q +L+N E + ++ ++ + +++E + +
Sbjct: 189 ALAEEQIENEEEA--SFLLSLKSMKEVQNVLDNTTEPTITVRYDGRRVSLSTNDVETVMR 246
Query: 240 LIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVS 299
++D +F DYK VI ++ +V+R +L SL+R+ +I++ + V+ I+ N +++
Sbjct: 247 VVDAEFPDYKRVIPETFKTKVVVSRKELRESLKRVMVIASKGSESVKFEIEENVMRLVSK 306
Query: 300 SSNREKASEELEINYNGKD 318
S + + +E+E+ G+D
Sbjct: 307 SPDYGEVVDEVEVQKEGED 325
>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 = 300 bits (770), Expect = 7e-95
Identities = 99/237 (41%), Positives = 139/237 (58%), Gaps = 46/237 (19%)
Query: 347 YSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIY 406
Y A IQ+LEGLEAVRKRP MYIG TS+ GLHH V+EI+DN+IDE+LAGY +I V I
Sbjct: 2 YGAGQIQVLEGLEAVRKRPGMYIGSTSE-RGLHHLVWEIVDNSIDEALAGYANQIEVVIE 60
Query: 407 SDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIG 465
DN I ++DNGRGIP+DI K R A E+++T
Sbjct: 61 KDNWIKVTDNGRGIPVDI-----QEKMGRPAVEVILT----------------------- 92
Query: 466 LSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKI 525
S VN LS+ L++ ++RN+ I++ ++ GV +K +G T+K GT I
Sbjct: 93 SSVVNALSQDLEVYVHRNETIYHQAYKKGV------------PQFDLKEVGTTDKTGTVI 140
Query: 526 HFWVDEKIFSN-IEFHYEILKKRIRELSFLNNGVCITLIDER---IKKKEIFEFKGG 578
F D +IF+ ++YE L++RIREL+FLN G+ ITL DER +++ + ++GG
Sbjct: 141 RFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEGG 197
>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp,
replication, transferase; HET: DNA; 2.00A {Streptococcus
pyogenes} PDB: 2awa_A*
Length = 378
Score = 302 bits (775), Expect = 5e-93
Identities = 83/327 (25%), Positives = 157/327 (48%), Gaps = 13/327 (3%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
+Q +N + +H L + KN +PILS+I + S ++ ++ ++ I
Sbjct: 2 IQFSIN--RTLFIHALNTTKRAISTKNAIPILSSIKIEVTSTGVTLTGSNGQISIENTIP 59
Query: 61 VGYGNSSINII------VAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLD 114
V N+ + I + A FI+I+ SLP+ IE + + SGKS+ TL+ D
Sbjct: 60 VSNENAGLLITSPGAILLEASFFINIISSLPDISINVKEIEQHQVVLTSGKSEITLKGKD 119
Query: 115 AKEYPIMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQ-KKNIIAV 173
+YP + S + L K LK I+ F+ + Q+ R L G+ + K+ AV
Sbjct: 120 VDQYPRLQEVST-ENPLILKTKLLKSIIAETAFAASLQESRPILTGVHIVLSNHKDFKAV 178
Query: 174 SSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSN 233
++D HR++ + +D + +++P K++ + + VE+ S +QI +
Sbjct: 179 ATDSHRMSQRLITLDNTSAD-FMVVLPSKSLREFSAVFTDDIETVEVFFSPSQILFRSEH 237
Query: 234 IEIISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKG-VRLVIKPN 292
I ++L++G + D ++ ++E + N L +++R +ISN G V+L I N
Sbjct: 238 ISFYTRLLEGNYPDTDRLLMTEFETEVVFNTQSLRHAMERAFLISNATQNGTVKLEITQN 297
Query: 293 YLKITVSSSNREKASEELEI-NYNGKD 318
++ V+S K +E+L+I + +G D
Sbjct: 298 HISAHVNSPEVGKVNEDLDIVSQSGSD 324
>3t0p_A DNA polymerase III, beta subunit; DNA clamp, structural genomics,
joint center for structural JCSG, protein structure
initiative; HET: DNA MSE; 2.26A {Eubacterium rectale}
Length = 371
Score = 299 bits (769), Expect = 3e-92
Identities = 74/320 (23%), Positives = 155/320 (48%), Gaps = 8/320 (2%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+L+ + K +L + +V V + + IL IL+ ++ +I ++ D E+ I T
Sbjct: 2 MKLICS--KANLLKGVNIVSKAVPTRTTMAILECILIDASANEIKLMANDMELGIETIID 59
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
I + A+ F +I+R LP+ + + I K+KF + ++
Sbjct: 60 GT-IEERGIIALDAKIFSEIVRKLPDNDVTIETDASFKTVISCEKAKFNIIGKSGDDFSY 118
Query: 121 MTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL 180
+ + + LSQ TLK ++ FSIA D + G L ++ + VS DGHR+
Sbjct: 119 IPYVER-NESIVLSQFTLKEVIRQTIFSIADNDNNKLMTGELFEIEENKLRVVSLDGHRI 177
Query: 181 TYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLEN-KENPVELKISNNQIKIIFSNIEIISK 239
+ + + + S +++P KT+ + +++ + V + I+NN I F N ++S+
Sbjct: 178 SIRYIEMKNHYDS-KKVVVPGKTLQEISKIIPGSADEDVVIYITNNHIVFEFENTTVVSR 236
Query: 240 LIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISND-KLKGVRLVIKPNYLKITV 298
LI+G++ ++S+ Y+ +N+ +LL + R +++ + K + + I +++
Sbjct: 237 LIEGEYFKIDQMLSSDYDTKVRINKRELLDCIDRATLLVKEGDKKPIIMNITDGNMELR- 295
Query: 299 SSSNREKASEELEINYNGKD 318
+S +E+++I+ +GKD
Sbjct: 296 INSFIGSMNEDIDIDKDGKD 315
>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 = 286 bits (734), Expect = 3e-89
Identities = 75/162 (46%), Positives = 111/162 (68%), Gaps = 2/162 (1%)
Query: 768 KLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSE 827
+ D + +P ELY+VEGDSAGGS K GRD FQA+LPLRGK++N+EKAR ++++ +
Sbjct: 8 HVDDDDKTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNT 67
Query: 828 QITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYG 887
++ +I+ LG GI DEF++ KLRYH+I++M DAD+DG HI LLLT +R M LIE G
Sbjct: 68 EVQAIITALGTGI-HDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENG 126
Query: 888 YIYIAQPPLYKIKYGNNEC-YLRDDIEEERYMLKIAFKNVKL 928
++++AQPPLYK+K+ ++ + D E + + K+
Sbjct: 127 HVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKI 168
Score = 134 bits (340), Expect = 2e-35
Identities = 35/68 (51%), Positives = 50/68 (73%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 1153
QRYKGLGEM+ +LWETTM+P +R L +V + DA +AD++F LMG++V+ RR FI NA
Sbjct: 175 QRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNA 234
Query: 1154 LHAKNIDI 1161
+ +D+
Sbjct: 235 KDVRFLDV 242
>3p16_A DNA polymerase III subunit beta; DNA polymerase III sliding clamp,
transferase; HET: DNA; 2.89A {Mycobacterium
tuberculosis} PDB: 3rb9_A*
Length = 408
Score = 290 bits (745), Expect = 2e-88
Identities = 49/326 (15%), Positives = 140/326 (42%), Gaps = 16/326 (4%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
+ + + + + V + + +P+LS +L+ + ++ D EV
Sbjct: 19 LTFRLL--RESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVG 76
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
S +++V+ R DI R+LP V +++E + + G ++F+L T+ ++YP
Sbjct: 77 AE-IVSPGSVLVSGRLLSDITRALPNKP-VDVHVEGNRVALTCGNARFSLPTMPVEDYPT 134
Query: 121 MTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL 180
+ + L + ++ V + + D L G+ + + ++ ++D RL
Sbjct: 135 LPTLP--EETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRL 192
Query: 181 TYYQVNIDKKFSSCS-DIIIPRKTVFTLQRLLENKENPVELKIS-------NNQIKIIFS 232
++ +++P KT+ + + V L + + + I +
Sbjct: 193 AVRELKWSASSPDIEAAVLVPAKTLAEAAKAGIG-GSDVRLSLGTGPGVGKDGLLGISGN 251
Query: 233 NIEIISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPN 292
++L+D +F ++ ++ ++ ++ +L+ +++ ++++++ VR+
Sbjct: 252 GKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVADRG-AQVRMEFADG 310
Query: 293 YLKITVSSSNREKASEELEINYNGKD 318
++++ + + +A E+L ++Y G+
Sbjct: 311 SVRLSAGADDVGRAEEDLVVDYAGEP 336
>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 = 191 bits (487), Expect = 1e-50
Identities = 58/216 (26%), Positives = 95/216 (43%), Gaps = 13/216 (6%)
Query: 725 ENPGESKLICEKIIEAARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYI 784
+P K + + T + K + I I D K+ C L +
Sbjct: 5 SHPQFEKGADDD-------DKVPDPTSVDSVKYSKIKGIPKLDDANDAGGKHSLECTLIL 57
Query: 785 VEGDSAGGSVKQGR---DRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIE 841
EGDSA G R V PLRGK+LN+ +A ++I+ + +I +I +G+ +
Sbjct: 58 TEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYK 117
Query: 842 Q---DEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYK 898
+ D +L+ LRY +I+IMTD D DG+HI+ LL+ F + P L+++G++ P+ K
Sbjct: 118 KSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPIVK 177
Query: 899 IKYGNNECYLRDDIEEERYMLKIAFKNVKLISIENG 934
E E + + I + I G
Sbjct: 178 ASKNKQELSFYSIPEFDEWKKHIENQKAWKIKYYKG 213
Score = 41.7 bits (97), Expect = 0.002
Identities = 9/67 (13%), Positives = 22/67 (32%), Gaps = 1/67 (1%)
Query: 1094 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 1153
+ YKGLG + E + +L + I + ++ R++++
Sbjct: 209 KYYKGLGTSTAKEAKEYFADMERHRILF-RYAGPEDDAAITLAFSKKKIDDRKEWLTNFM 267
Query: 1154 LHAKNID 1160
+
Sbjct: 268 EDRRQRR 274
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 189 bits (483), Expect = 4e-50
Identities = 77/195 (39%), Positives = 114/195 (58%), Gaps = 8/195 (4%)
Query: 737 IIEAARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQ 796
I +A R +AA+K +K ++ L KLADC + E EL+IVEGDSAGGS KQ
Sbjct: 5 ISKAGRRLKAAKKVE----RKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQ 60
Query: 797 GRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRII 856
RD+ FQA++P+RGK+LN + ++++ S+++ + +G+ D+ L +LRY +I
Sbjct: 61 ARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSDD--LSELRYGKIC 118
Query: 857 IMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEER 916
I+ DAD DG HI LL F + P L+E G++Y+A PPL++I G + Y DD E E
Sbjct: 119 ILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELET 178
Query: 917 YMLKIAFKNVKLISI 931
+ K K I
Sbjct: 179 --ILKNVKGNKNPQI 191
Score = 55.1 bits (133), Expect = 1e-07
Identities = 22/53 (41%), Positives = 30/53 (56%)
Query: 1095 RYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRK 1147
R+KGLGEMN QL ETTM+P R L+++ + DA + L+ RK
Sbjct: 193 RFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADRK 245
>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 = 178 bits (453), Expect = 1e-46
Identities = 86/136 (63%), Positives = 106/136 (77%), Gaps = 1/136 (0%)
Query: 760 IDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKAR 819
+D L KLADC K+PE CE+++VEGDSAGGS K GRD R QA+LPLRGK+LN+EKAR
Sbjct: 1 MDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKAR 60
Query: 820 FEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRK 879
++I+ + +I +I+ G GI D F+L K RYH+I+IMTDAD+DGAHIR LLLTFFYR
Sbjct: 61 LDRILNNNEIRQMITAFGTGIGGD-FDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRF 119
Query: 880 MPKLIEYGYIYIAQPP 895
M LIE GY+YIAQPP
Sbjct: 120 MRPLIEAGYVYIAQPP 135
Score = 53.8 bits (130), Expect = 3e-07
Identities = 51/97 (52%), Positives = 62/97 (63%), Gaps = 4/97 (4%)
Query: 1065 GEKIKKYTANNFYKIINYLRNEAENMVIKQ---RYKGLGEMNPGQLWETTMNPMIRCLLK 1121
G I+ FY+ + L EA + I Q YKGLGEMN QLWETTMNP R LL+
Sbjct: 105 GAHIRTLLLTFFYRFMRPLI-EAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQ 163
Query: 1122 VKIKDAISADKIFMTLMGDNVELRRKFIELNALHAKN 1158
VK++DAI AD+ F LMGD VE RR+FIE NA++A
Sbjct: 164 VKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANL 200
>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 = 121 bits (305), Expect = 3e-28
Identities = 43/146 (29%), Positives = 72/146 (49%), Gaps = 7/146 (4%)
Query: 767 TKLADCQE---KNPELCELYIVEGDSAGGSVKQGR---DRRFQAVLPLRGKVLNIEKARF 820
KL D + K C L + EGDSA G R + PLRGK+LN+ +A
Sbjct: 7 PKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASA 66
Query: 821 EKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKM 880
++I+ + +I + +G+ + + + LRY ++IMTD D DG+HI+ L++ F
Sbjct: 67 DQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSF 126
Query: 881 PKLIEY-GYIYIAQPPLYKIKYGNNE 905
P L++ G++ P+ K+
Sbjct: 127 PGLLDIQGFLLEFITPIIKVSITKPT 152
>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 = 78.4 bits (192), Expect = 1e-14
Identities = 112/722 (15%), Positives = 219/722 (30%), Gaps = 201/722 (27%)
Query: 379 HHFVFEILDNAIDESLAGYCTKINVTIYSDNSIS------ISDNGRGIPIDIKIDD--KH 430
HH FE Y K ++++ D + + D + I +ID
Sbjct: 5 HHMDFET--GEHQ-----YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMS 57
Query: 431 KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTINRNKKIHYME 490
K S + L + + + +F++ + N
Sbjct: 58 KDAVSGTLRLFWTLLSKQE--------------------EMVQKFVEEVLRIN------- 90
Query: 491 FRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFS----NIEFHYEILKK 546
Y L + I S+ I ++ + D ++F+ + Y L++
Sbjct: 91 --YKFLMSPIKTEQRQPSMMTRMYIEQRDR------LYNDNQVFAKYNVSRLQPYLKLRQ 142
Query: 547 RIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKIS 606
+ EL V I G G K+ + + +
Sbjct: 143 ALLELR-PAKNVLID----------------GVLGS----GKTWVAL-----DVCLSYKV 176
Query: 607 EKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLK 666
+ K + I W N N N +L+ L L I + ++
Sbjct: 177 QCKMDFKI----FWLNLKNCNS---PETVLE-----MLQKLLYQIDP---NWTSRSDHSS 221
Query: 667 KSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKL-VSSEVRKPVEEIIIKTLFDFLQE 725
K+ I I+ L +L K +N L V V+ F+
Sbjct: 222 NIKLRI--HSIQAELRRLLKSK--------PYENCLLVLLNVQNAK---AWNA-FNLS-- 265
Query: 726 NPGESKLICEKIIEAARSREAARKTRELTRKKNLIDDIELS-TKLADCQEKNPELCELYI 784
C KI+ R ++ T +D ++ T ++ L Y+
Sbjct: 266 --------C-KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP-----DEVKSLLLKYL 311
Query: 785 VEGDSAGGSVKQGRDRRFQA--VLPLR----GKVLNIEKARFE--KIILSEQITTLISTL 836
+ R + P R + + A ++ K + +++TT+I
Sbjct: 312 --------DCRPQDLPR-EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIE-- 360
Query: 837 GIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPL 896
+ E + + R+ + AHI +LL+ + + I+ + +
Sbjct: 361 -SSLNVLEPAEYRKMFDRLSVFPP----SAHIPTILLSLIWFDV---IKSDVMVVV---- 408
Query: 897 YKIKYGNNECY----LRDDIEEERY-----MLKIAFKNVKLISIENGDIIKENYFFKLID 947
N+ + + +E L++ K ++ ++D
Sbjct: 409 -------NKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR----------SIVD 451
Query: 948 KYN--KTIEIVHRLKQIIDISILSAIMSDVILNLDTRENAEQFA--KKIIKKLNDSNIE- 1002
YN KT + + +D S I +L E+ E+ + + L+ +E
Sbjct: 452 HYNIPKTFDSDDLIPPYLDQYFYSHIGH----HLKNIEHPERMTLFRMVF--LDFRFLEQ 505
Query: 1003 -IIVEFDQLNNK-YLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKKIIGKGVII 1060
I + N +LN ++ K YI D N+ Y++LV+ I F I + +I
Sbjct: 506 KIRHDSTAWNASGSILNTLQQLKFYKPYICD----NDPKYERLVNAILDFLPKIEENLIC 561
Query: 1061 QK 1062
K
Sbjct: 562 SK 563
Score = 77.6 bits (190), Expect = 2e-14
Identities = 79/558 (14%), Positives = 164/558 (29%), Gaps = 173/558 (31%)
Query: 659 IEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLVSSEVRK----PVEEI 714
E+++ K + + + + C + D K+ L E+
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDNFDCK---DVQD-----MPKSILSKEEIDHIIMSKDAVS 62
Query: 715 IIKTLFDFLQENPGES-------------KLICEKIIEAARSREAARKTRELTRKKN-LI 760
LF L E K + I R+ + TR +++ L
Sbjct: 63 GTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPI--KTEQRQPSMMTRMYIEQRDRLY 120
Query: 761 DDIELSTKLADCQEKNPE-----LCEL----YI-VEGDSAGGSVKQGRDRRFQAVLPLRG 810
+D ++ K + + L EL + ++G GS G
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGV--LGS----------------G 162
Query: 811 K-VLNIEKARFEKIILSEQITTLISTLGIGIEQDEF--NLEKLRYHRIIIMTDADIDGAH 867
K + ++ K+ + I F NL+ ++
Sbjct: 163 KTWVALDVCLSYKVQ---------CKMDFKI----FWLNLKNCNSPETVLE--------- 200
Query: 868 IRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVK 927
+L Y+ P K++ + + LR ++ + Y +N
Sbjct: 201 ---MLQKLLYQIDPNWTSRS----DHSSNIKLRIHSIQAELRRLLKSKPY------ENCL 247
Query: 928 LI--SIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVILN-----LD 980
L+ +++N F + K + + R KQ+ D + +A + + L+ L
Sbjct: 248 LVLLNVQNAKAWN--AF----NLSCKIL-LTTRFKQVTD-FLSAATTTHISLDHHSMTLT 299
Query: 981 TRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDY 1040
E K + + D E+ N L+I + ++ + + + + +
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREV-----LTTNPRRLSIIAESIR--DGLATWDNWKHVNC 352
Query: 1041 KKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANNFYKIINYLRNEAENMVIKQRYKGLG 1100
KL +II + +N L AE ++ + L
Sbjct: 353 DKLTTIIESS-----------------------------LNVL-EPAE---YRKMFDRLS 379
Query: 1101 EMN-----PGQ----LW--------ETTMNPMI-RCLLKVKIKDAISADKIFMTLMGDNV 1142
P +W +N + L++ K + +++ +
Sbjct: 380 VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE---KQP---KESTISIPSIYL 433
Query: 1143 ELRRKFIELNALHAKNID 1160
EL+ K ALH +D
Sbjct: 434 ELKVKLENEYALHRSIVD 451
Score = 74.1 bits (181), Expect = 2e-13
Identities = 102/658 (15%), Positives = 198/658 (30%), Gaps = 151/658 (22%)
Query: 26 KNILPILSNILV----CKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFIDIL 81
K+IL + + V CK+ + D I + + + S + + + L
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQ-------DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTL 71
Query: 82 RSLPETEKVTIYIENKHM----FIKSGKSKFTLQ-TLDAKEYPIMTLNSKYDFEFTLSQK 136
S E E V ++E F+ S Q ++ + Y + D + +Q
Sbjct: 72 LSKQE-EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMY-----IEQRDRLYNDNQV 125
Query: 137 TLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDG------HRLTYYQVNIDKK 190
K +++++ L LL + + + DG + V + K
Sbjct: 126 FAK-------YNVSRLQPYLKLRQALLELRPAKNVLI--DGVLGSGKTWVAL-DVCLSYK 175
Query: 191 FSSCSDIII----------PRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKL 240
D I P + LQ+LL +I N + I ++
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEMLQKLL--------YQIDPNWTSRSDHSSNIKLRI 227
Query: 241 IDGKFLDYKYVISNKYEKSFLVNRN----KLLRSLQ---RISIISNDKLKGVRLVIKPNY 293
+ + + S YE LV N K + +I + + K V +
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK--QVTDFLSAAT 285
Query: 294 LKITVSSSNREKA---SEELEINYNGKDKNFIKFL-IKIMLLKNKNSYDIQDTQESSYSA 349
+S + E + +K+L + L + +
Sbjct: 286 TTH-ISLDHHSMTLTPDEVKSL--------LLKYLDCRPQDLPR------EVLTTNPRRL 330
Query: 350 SSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYSDN 409
S I E++R T D H + L I+ SL ++
Sbjct: 331 SIIA-----ESIRDGL-----ATWDN--WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL 378
Query: 410 SISISDNGRGIPIDIKIDDK------HKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHG 463
S+ P I +S +V+ +LH K + + +
Sbjct: 379 SV--------FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS 430
Query: 464 IGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKI-------IG 516
I L L++ + +H R V I KT + + P + IG
Sbjct: 431 IYLE--------LKVKLENEYALH----RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG 478
Query: 517 ---DTNKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNN---GVCITLIDERIKKK 570
+ ++ + +F + F L+++IR S N + TL + K
Sbjct: 479 HHLKNIEHPERMTLF--RMVFLDFRF----LEQKIRHDSTAWNASGSILNTLQQLKFYKP 532
Query: 571 EIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNS--YNE 626
I + V+ I + + N I K ++ + +++ + + E
Sbjct: 533 YICDNDPKYERLVNAILD-------FLPKIEENLICSKYTDL-LRIALMAEDEAIFEE 582
Score = 66.4 bits (161), Expect = 4e-11
Identities = 95/701 (13%), Positives = 214/701 (30%), Gaps = 191/701 (27%)
Query: 246 LDYKY-VISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNRE 304
+D++ +Y+ V + + + + D K + ++
Sbjct: 7 MDFETGEHQYQYKDILSVFEDAFVDNFDCKDV--QDMPKSI----------LS------- 47
Query: 305 KASEELEINYNGKD-KNFIKFLIKIMLLKNKNSYD--IQDTQESSYSASSIQILEGLEAV 361
EE++ KD + L +L K + +++ +Y ++ ++
Sbjct: 48 --KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKF----LMSPIKTE 101
Query: 362 RKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGYCTKINVTIYSDNSISISDN-GRGI 420
+++P M T Y + + +Y+DN + N R
Sbjct: 102 QRQPSM---MTRM----------------------YIEQRDR-LYNDNQVFAKYNVSRLQ 135
Query: 421 PIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSC-VNGLSRFLQLT 479
P K+ R A ++ + G+ G G + + ++
Sbjct: 136 PYL-KLRQALLELRPAKNVL---ID--------------GVLGSGKTWVALDVCLSYKVQ 177
Query: 480 INRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSNIEF 539
+ KI ++ + +++ + + +I + + SNI+
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLY---QIDPNWTSRS---------DHSSNIKL 225
Query: 540 HYEILKKRIRELSFLNNGVCITLI--DERIKKKEIFE-FKGGTSGFVSYINKSKLVVHPT 596
++ +R L + L+ ++ + + F K+++ T
Sbjct: 226 RIHSIQAELRRL-LKSKPYENCLLVLLN-VQNAKAWNAFNLS----------CKILL-TT 272
Query: 597 IFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAI- 655
F+ + + +S T +I H L +++
Sbjct: 273 RFKQVTDFLSAAT----------------------TTHISLDH---HSMTLTPDEVKSLL 307
Query: 656 NKYIEEN------EFLKKS--KIEIIGEDIREGLTCVLSIKIPD--PKFNSQTKNKLVSS 705
KY++ E L + ++ II E IR+G + D N ++ S
Sbjct: 308 LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDG------LATWDNWKHVNCDKLTTIIES 361
Query: 706 --EVRKPVEEIIIKTLFDFL---QEN---PGESKLIC-----------EKIIEAARSREA 746
V +P E + +FD L + P + L+ ++
Sbjct: 362 SLNVLEPAE---YRKMFDRLSVFPPSAHIP--TILLSLIWFDVIKSDVMVVVNKLHKYSL 416
Query: 747 ARKTRELTRKKNL---IDDI--ELSTKLADCQEKNPELCELY-IVEGDSAGGSVKQGRDR 800
K + K I I EL KL + + + + Y I + + + D+
Sbjct: 417 VEK-----QPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471
Query: 801 RFQAVLP--LRGKVLNIEKARFEKIILS----EQ--ITTLISTLGIGIEQDEFNLEKLRY 852
F + + L+ F + L EQ + G + L++L++
Sbjct: 472 YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN--TLQQLKF 529
Query: 853 HRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQ 893
++ I + + A +L F + LI Y + +
Sbjct: 530 YKPYICDNDPKYERLVNA-ILDFLPKIEENLICSKYTDLLR 569
Score = 54.5 bits (130), Expect = 2e-07
Identities = 67/411 (16%), Positives = 139/411 (33%), Gaps = 129/411 (31%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNI----------LVCK------NSEKISFLSTDT 51
++I L+ ++ +N L +L N+ L CK + FLS T
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285
Query: 52 EVQITT-YTAVGYGNSSINIIVAARKFIDI-LRSLPETEKVTIY---------------- 93
I+ + ++ + ++ K++D + LP E +T
Sbjct: 286 TTHISLDHHSMTLTPDEVKSLLL--KYLDCRPQDLPR-EVLTTNPRRLSIIAESIRDGLA 342
Query: 94 -IEN-KHMFIKSGKS--KFTLQTLDAKEY----------------PIMTL-----NSKYD 128
+N KH+ + + +L L+ EY P + L +
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402
Query: 129 FEFTLSQKTLKCILNMVYFSIAQQD---IRYYLNGLLLSFQKK--NIIAVSSDGHR--LT 181
+ K + +S+ ++ + + L + K N A+ HR +
Sbjct: 403 DVMVVVNK-------LHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL----HRSIVD 451
Query: 182 YYQVNIDKKFSSCSDIIIPRKTVFTLQRL---LENKENPVELKISNNQIKIIFSNIEIIS 238
+Y NI K F S D+I P + + L+N E+P + +F +
Sbjct: 452 HY--NIPKTFDS-DDLIPPYLDQYFYSHIGHHLKNIEHPERMT--------LFRMV---- 496
Query: 239 KLIDGKFLDYKYVISNK--YEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLK- 295
FLD+++ + K ++ + +L +LQ++ Y
Sbjct: 497 ------FLDFRF-LEQKIRHDSTAWNASGSILNTLQQLK----------------FYKPY 533
Query: 296 ITVSSSNREKASEELEINYNGKDKNFI--KF--LIKIMLLKNKNSYDIQDT 342
I + E+ + ++N I K+ L++I L+ ++ ++
Sbjct: 534 ICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALM-AEDEAIFEEA 583
>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 = 57.8 bits (139), Expect = 2e-08
Identities = 99/649 (15%), Positives = 187/649 (28%), Gaps = 262/649 (40%)
Query: 131 FTLSQKTLKCILNM---VYFSIAQ-QDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVN 186
TLS +L+ +L + +F +Q Q+ F K I+ ++G
Sbjct: 9 LTLSHGSLEHVLLVPTASFFIASQLQE----------QFNK--ILPEPTEGFAA------ 50
Query: 187 IDKKFSSCSDIIIPRKTVFTLQRLLENKENPVE--LKISNNQIKIIF-SNIEI---ISKL 240
D + ++ ++++ + + + +K + L + + + + +I +KL
Sbjct: 51 -DDEPTTPAELVG-KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKL 108
Query: 241 I---DGKFLDYKYVISNKYEKSFLVNR-------NKLLRSLQRISIISNDKLKGVRLV-- 288
+ D + K +I N + R + L R++ +LV
Sbjct: 109 LQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGE---------GNAQLVAI 159
Query: 289 -----IKPNYLKITVSSSNREKASEELEINYNGKDKNFIKFLIKIM--LLKN--KNSYDI 339
+Y EEL Y + LIK L + + D
Sbjct: 160 FGGQGNTDDYF-------------EELRDLYQ-TYHVLVGDLIKFSAETLSELIRTTLD- 204
Query: 340 QDTQESSYSASSIQILEGLEAVRKRPEM-Y----------IGDTSDGTGLHHFVFEILDN 388
E ++ + ILE LE P+ Y IG
Sbjct: 205 ---AEKVFTQ-GLNILEWLENPSNTPDKDYLLSIPISCPLIGVI---------------- 244
Query: 389 AIDESLAGYCTKINVTIYS-----DNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTE 443
LA Y + ++ + + +G+ +A I
Sbjct: 245 ----QLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLV-------------TAVAI---- 283
Query: 444 LHAGGK----FNKNSYKISGGLHGIGLSC------------------------------V 469
A F + K L IG+ C +
Sbjct: 284 --AETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSI 341
Query: 470 NGLSR-FLQLTINR-------NKKIHYMEFRYGVLQNRIIKTING-----ISVSPI---- 512
+ L++ +Q +N+ K++ I +NG +S P
Sbjct: 342 SNLTQEQVQDYVNKTNSHLPAGKQVE-------------ISLVNGAKNLVVSGPPQSLYG 388
Query: 513 ------KIIGDTNKQGTKIHFWVDEKI-FSN----IE--FHYEILKKRIRELSFLNNGVC 559
K + ++I F + K+ FSN + FH +L
Sbjct: 389 LNLTLRKAKAPSGLDQSRIPF-SERKLKFSNRFLPVASPFHSHLLVP------------A 435
Query: 560 ITLIDERIKKKEIFEFKGGTSGFVSYINKSKLV--VHPTI----FQAIGNKISEKKNNIN 613
LI++ + K + F + V+ T + + ISE+ +
Sbjct: 436 SDLINKDLVKNNV-SFNA-----------KDIQIPVYDTFDGSDLRVLSGSISERIVDCI 483
Query: 614 IDVSMQWNNSYNEN---ILCF-----------TNNILQVDGGTHLTGLR 648
I + ++W + IL F T+ DG TG+R
Sbjct: 484 IRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRN--KDG----TGVR 526
Score = 47.0 bits (111), Expect = 5e-05
Identities = 78/478 (16%), Positives = 150/478 (31%), Gaps = 162/478 (33%)
Query: 740 AARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYI------VEGDSAGGS 793
A++ +E K + D E +T EL ++ VE G
Sbjct: 30 ASQLQEQFNKILP-EPTEGFAADDEPTTPA--------ELVGKFLGYVSSLVEPSKVG-- 78
Query: 794 VKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQ-ITTLISTLGIGIEQDEFNLEK--- 849
+F VL L L FE L I L + L +++++ L K
Sbjct: 79 -------QFDQVLNL---CLT----EFENCYLEGNDIHALAAKL---LQENDTTLVKTKE 121
Query: 850 -LR-YHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIA-----QPPLYKIKYG 902
++ Y IM D AL + + G + Q G
Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALF---------RAVGEGNAQLVAIFGGQ--------G 164
Query: 903 NNECYLRDDIEE--ERY------MLKIAFKNVKLIS---------IENG-DIIK------ 938
N + Y +++ + + Y ++K + + + + G +I++
Sbjct: 165 NTDDYF-EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPS 223
Query: 939 ----ENYF------FKLID-----KYNKTI--------EIVHRLKQIIDIS--ILSAIMS 973
++Y LI Y T E+ LK S +++A+
Sbjct: 224 NTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAV-- 281
Query: 974 DVILNLDTRENAEQFAKKIIKKL-----------NDSNIEIIVEFDQLNNK-----YLLN 1017
I D+ E+ +K I L ++++ + D L N +L+
Sbjct: 282 -AIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS 340
Query: 1018 IK-------KKFLKKKN-YI-----IDINFINNKD-------YKKLVSIISTFKKIIGKG 1057
I + ++ K N ++ ++I+ +N + L + T +K
Sbjct: 341 ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPS 400
Query: 1058 VIIQKSI---GEKIKKYTANNFYKII-----NYLRNEAENMVIKQRYKGLGEMNPGQL 1107
+ Q I K+K +N F + + L A +++ K K N +
Sbjct: 401 GLDQSRIPFSERKLK--FSNRFLPVASPFHSHLLV-PASDLINKDLVKNNVSFNAKDI 455
Score = 45.4 bits (107), Expect = 1e-04
Identities = 46/301 (15%), Positives = 86/301 (28%), Gaps = 120/301 (39%)
Query: 910 DDIEEERY---MLKIAFKNVKLISI----ENGDIIKENYFFKLIDKYNKTIEIVHRLKQI 962
D+ ++ Y +L I N ++I E G I+ENY + + ++ +
Sbjct: 1650 DNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKE 1709
Query: 963 IDISILSAIMS--DVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKK 1020
I+ S +L+ T + Q A L
Sbjct: 1710 INEHSTSYTFRSEKGLLSA-T-QFT-QPA-------------------------LT---- 1737
Query: 1021 KFLKKKNYIIDINFINNKDYKKLVSIISTFKKIIGKGVIIQK------SIGEKIKKYTA- 1073
L+ + F+ + KG+I S+GE Y A
Sbjct: 1738 ----------------------LME-KAAFEDLKSKGLIPADATFAGHSLGE----YAAL 1770
Query: 1074 ---------NNFYKIINYLRNEAENMVIKQRYKGLGE--M---NPGQLWETTMNPMIRCL 1119
+ +++ Y R + + + G M NPG++ + ++
Sbjct: 1771 ASLADVMSIESLVEVVFY-RGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQ-- 1827
Query: 1120 LKVKIKDAISADKIFMTLMG-------DNV---------ELR--RKFIE-LNALHAKNID 1160
+ + + G NV +LR LN + + ID
Sbjct: 1828 ---YVVERVGKRT------GWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKID 1878
Query: 1161 I 1161
I
Sbjct: 1879 I 1879
Score = 41.2 bits (96), Expect = 0.003
Identities = 79/463 (17%), Positives = 150/463 (32%), Gaps = 133/463 (28%)
Query: 45 SFLSTDTEVQITTYTAVGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSG 104
F E T A ++ +V KF+ + SL E KV + + +
Sbjct: 36 QFNKILPEP--TEGFAADDEPTTPAELVG--KFLGYVSSLVEPSKVGQFDQ----VLNLC 87
Query: 105 KSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCILNMVYFS---IAQQDIRYYLNGL 161
++F L+ + I L +K E + K ++ Y + +A++ N
Sbjct: 88 LTEFENCYLEGND--IHALAAKLLQENDTTLVKTKELIK-NYITARIMAKRPFDKKSNSA 144
Query: 162 LL---SFQKKNIIAV-----SSDGH----RLTY--YQVNIDKKFSSCSDIIIP------- 200
L ++A+ ++D + R Y Y V + ++ +
Sbjct: 145 LFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLD 204
Query: 201 RKTVFT----LQRLLENKEN----------PVELKISNNQIKII-FSNIEIISKLID--- 242
+ VFT + LEN N P+ + I +I ++ + +KL+
Sbjct: 205 AEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPL----IGVIQLAHYVVTAKLLGFTP 260
Query: 243 GKFLDY--------KYVIS------NKYEKSFLVNRNKLL--------RSLQ---RISI- 276
G+ Y + +++ +SF V+ K + R + S+
Sbjct: 261 GELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLP 320
Query: 277 --ISNDKLKGVR------LVIK---PNYLKITVSSSNREKASEE-LEI-NYNGKDKNFI- 322
I D L+ L I ++ V+ +N + + +EI NG N +
Sbjct: 321 PSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAK-NLVV 379
Query: 323 ----KFL--IKIMLLKNKNSYDI-QD----TQE----------------SSY--SASSIQ 353
+ L + + L K K + Q ++ S AS
Sbjct: 380 SGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASD-L 438
Query: 354 ILEGLEAVR---KRPEMYIG--DTSDGTGLHHFVFEILDNAID 391
I + L ++ I DT DG+ L I + +D
Sbjct: 439 INKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVD 481
Score = 40.8 bits (95), Expect = 0.003
Identities = 41/260 (15%), Positives = 82/260 (31%), Gaps = 90/260 (34%)
Query: 477 QLTIN----RNKKIH--YMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVD 530
LTI+ + K+I Y + +TI + KI + N+ T F +
Sbjct: 1671 NLTIHFGGEKGKRIRENYSAMIF--------ETIVDGKLKTEKIFKEINEHSTSYTFRSE 1722
Query: 531 EKIFSNIEF-----------HYEILKKR--IRELSF-----LNNG-----VC-------- 559
+ + S +F +E LK + I + L G
Sbjct: 1723 KGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSL--GEYAALASLADVMSIE 1780
Query: 560 --ITLIDER--IKKKEIFEFKGGTSGF-VSYINKSKLVVHPT--IFQAIGNKISEKKNNI 612
+ ++ R + + + G S + + IN ++ + Q + ++ ++ +
Sbjct: 1781 SLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWL 1840
Query: 613 ----NIDVSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKS 668
N N N+ + +G RA++ F+K
Sbjct: 1841 VEIVN-------YNVENQQYVA------------------AGDLRALDTVTNVLNFIKLQ 1875
Query: 669 KIEIIG-------EDIREGL 681
KI+II E++ L
Sbjct: 1876 KIDIIELQKSLSLEEVEGHL 1895
Score = 38.1 bits (88), Expect = 0.024
Identities = 55/306 (17%), Positives = 95/306 (31%), Gaps = 99/306 (32%)
Query: 739 EAARSREAARKTRELTR-KKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQG 797
+ ++ +AA+ R + D S + D NP L I G G +++
Sbjct: 1634 DLYKTSKAAQDVWN--RADNHFKDTYGFS--ILDIVINNPV--NLTIHFGGEKGKRIREN 1687
Query: 798 RDR-RFQAVLPLRGKVLNIEKARFE---KIILSEQITTL---------ISTLGIGIEQDE 844
F+ ++ + K I K E + L ++ +
Sbjct: 1688 YSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAA---- 1743
Query: 845 FNLEKLRYHRIIIMTDADIDGAH----IRAL-----LLTF-------FYR------KMPK 882
E L+ + +I DA G H AL +++ FYR +P+
Sbjct: 1744 --FEDLK-SKGLIPADATFAG-HSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPR 1799
Query: 883 LIEYG---YIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISIENGDIIKE 939
E G Y IA P + E L+ +E + + L+ I N
Sbjct: 1800 -DELGRSNYGMIAINPGRVAASFSQEA-LQYVVER------VGKRTGWLVEIVN------ 1845
Query: 940 NYFFKLIDKYNKTIEIVHRLKQIIDIS-ILSAIMSDVILNLDTRENAEQFAKKIIKKLND 998
YN +E +Q + + L A LDT ++ +
Sbjct: 1846 ---------YN--VEN----QQYV-AAGDLRA--------LDT-------VTNVLNFIKL 1874
Query: 999 SNIEII 1004
I+II
Sbjct: 1875 QKIDII 1880
Score = 37.3 bits (86), Expect = 0.033
Identities = 86/609 (14%), Positives = 174/609 (28%), Gaps = 226/609 (37%)
Query: 63 YGNSSINIIVAARKFI--DILR-----SLPE-TEKVTIYIENKHM------FIKSGKSKF 108
+G+ ++V F L+ LPE TE E F+ +
Sbjct: 13 HGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLG-----Y 67
Query: 109 TLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKK 168
++ + ++D + L L F YL G
Sbjct: 68 VSSLVEPSK------VGQFD-------QVLNLCLT--EFE------NCYLEG-------N 99
Query: 169 NI--IAVSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVF----TLQRLLENKENPVELK- 221
+I +A D ++I K +R + K N +
Sbjct: 100 DIHALAAKLLQEN--------DTTLVKTKELI---KNYITARIMAKRPFDKKSNSALFRA 148
Query: 222 ISNNQIKI--IF---SNIEI----ISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQ 272
+ ++ IF N + + L + Y ++ + + L L
Sbjct: 149 VGEGNAQLVAIFGGQGNTDDYFEELRDL----YQTYHVLV-----GDLIKFSAETLSELI 199
Query: 273 RISIISNDKL--KGVRLV-------IKPN--YLK-ITVS--------SSNREKASEELEI 312
R ++ +K+ +G+ ++ P+ YL I +S ++ ++ L
Sbjct: 200 RTTL-DAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGF 258
Query: 313 NYNGKDKNFIKFLIKIMLLKNKNSYDIQ--------DTQESSYSASSIQILE-----GLE 359
G+ ++++K S + D+ ES + + + + G+
Sbjct: 259 TP-GELRSYLKGATGH-------SQGLVTAVAIAETDSWESFFVSVR-KAITVLFFIGVR 309
Query: 360 AVRKRPEMYI-----GDTSDG-----------TGLHHFVFEILDNAIDESLAGYCTKINV 403
P + D+ + + L E + + ++ K N
Sbjct: 310 CYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQ---EQVQDYVN--------KTNS 358
Query: 404 TIYSDNSISIS-DNGR------GIPID----------IKID---DKH-------KPK--- 433
+ + + IS NG G P K D+ K K
Sbjct: 359 HLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSN 418
Query: 434 --------------RSAAEIVMTELHAGG-KFNKNSYKI------SGG-LHGIGLSCVNG 471
A++++ +L FN +I G L + S
Sbjct: 419 RFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISER 478
Query: 472 LSR-FLQLTIN-----RNKKIHYMEF------RYGVLQNRI-----IKTING--ISVSPI 512
+ ++L + + K H ++F GVL +R ++ I + ++P
Sbjct: 479 IVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPD 538
Query: 513 KIIGDTNKQ 521
G KQ
Sbjct: 539 DDYG--FKQ 545
>2q2e_B Type 2 DNA topoisomerase 6 subunit B; DNA-binding, SPO11, ATPase;
4.00A {Methanosarcina mazei}
Length = 621
Score = 44.8 bits (105), Expect = 2e-04
Identities = 47/233 (20%), Positives = 79/233 (33%), Gaps = 26/233 (11%)
Query: 349 ASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDES-LAGYCTKINVTIYS 407
A + + E K ++ +G S L V E +DNA+D AG I V +
Sbjct: 10 AKKQKSISVAEFFEKNRQI-LGFDSAPRSLITTVKEAVDNALDACEEAGILPDILVQVER 68
Query: 408 DNS----ISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHG 463
+ I DNG GI + PK V +L G +F ++ K S G G
Sbjct: 69 TGPDYVTVIIEDNGPGIV------REQIPK------VFAKLLYGSRF--HALKQSRGQQG 114
Query: 464 IGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGT 523
IG+S ++ + + I + N + ++ GT
Sbjct: 115 IGISAAVLYAQMTAGRHTKILSKTSPTAPAHYYELMINTSTNEPDILVDEVRDWFRPHGT 174
Query: 524 KIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFK 576
+I + + + ++ + +N ITLID F+
Sbjct: 175 QIELEMRAAYVKGRRQS---IYEYLKATAIVNPHARITLID---PDGNEEVFE 221
>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 = 39.6 bits (92), Expect = 0.005
Identities = 24/100 (24%), Positives = 42/100 (42%), Gaps = 11/100 (11%)
Query: 378 LHHFVFEILDNAIDESLAGY------CTKINVTIYSDNS---ISISDNGRGIPIDI--KI 426
L + + E+L NA+ ++ + + +TI +++ I ISD G GI ++
Sbjct: 239 LDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRV 298
Query: 427 DDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGL 466
D H A+ G + +S SG +HG G
Sbjct: 299 MDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFGF 338
>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 = 39.4 bits (91), Expect = 0.007
Identities = 30/165 (18%), Positives = 54/165 (32%), Gaps = 23/165 (13%)
Query: 369 IGDTSDGTGLHHFVFEILDNAID-ESLAGYCTKINVTIYSDN------SISISDNGRGIP 421
G + L+ V E+++N++D + G I +TI + +++ DNG GIP
Sbjct: 23 AGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 82
Query: 422 IDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQ-LTI 480
P + K+ + G++G+G+ S+ Q I
Sbjct: 83 PQ------EVPN------AFGRVLYSSKYVNRQ---TRGMYGLGVKAAVLYSQMHQDKPI 127
Query: 481 NRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKI 525
+ Y I I V + GT +
Sbjct: 128 EIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSV 172
>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 = 39.0 bits (90), Expect = 0.009
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 9/55 (16%)
Query: 378 LHHFVFEILDNAIDESLAGYCTK------INVTIYSDN---SISISDNGRGIPID 423
L H +FE+ N++ ++ Y + + + SI ISD G G+P+
Sbjct: 254 LFHMLFELFKNSMRATVELYEDRKEGYPAVKTLVTLGKEDLSIKISDLGGGVPLR 308
>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 = 38.2 bits (88), Expect = 0.015
Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 10/95 (10%)
Query: 338 DIQDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAIDESLAGY 397
+ + Y +S L + ++I + LHH +FE+ NA+ ++
Sbjct: 193 CSRMLCDQYYLSSPELKLTQVNGKFPDQPIHI--VYVPSHLHHMLFELFKNAMRATVEHQ 250
Query: 398 C-----TKINVTIYSDN---SISISDNGRGIPIDI 424
T I V + +I ISD G G+P+ I
Sbjct: 251 ENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRI 285
>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 = 37.4 bits (88), Expect = 0.021
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 384 EILDNAIDESLAGYCTKINVTIYS--DNSISISDNGRGIPID 423
E+++N++D AG T+I++ I I I DNG GI D
Sbjct: 31 ELVENSLD---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 = 37.4 bits (86), Expect = 0.022
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 10/94 (10%)
Query: 338 DIQDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHFVFEILDNAI-----DE 392
+ + + Y S LE L A + + + L+H VFE+ NA+
Sbjct: 206 NARRLCDLYYINSPELELEELNAKSPGQPIQV--VYVPSHLYHMVFELFKNAMRATMEHH 263
Query: 393 SLAGYCTKINVTIYSDNS---ISISDNGRGIPID 423
+ G I V + N + +SD G G+P+
Sbjct: 264 ANRGVYPPIQVHVTLGNEDLTVKMSDRGGGVPLR 297
>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 = 36.7 bits (84), Expect = 0.040
Identities = 22/112 (19%), Positives = 43/112 (38%), Gaps = 22/112 (19%)
Query: 369 IGDTSDGTGLHHFVFEILDNAID-ESLAGYCTKINVTIYSDN------SISISDNGRGIP 421
G + L+ V E+++N++D + G I +TI + +++ DNG GIP
Sbjct: 24 AGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 83
Query: 422 IDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLS 473
+ P + K+ + G++G+G+ S
Sbjct: 84 ------PQEVPN------AFGRVLYSSKYVNRQTR---GMYGLGVKAAVLYS 120
>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 = 36.3 bits (83), Expect = 0.048
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 8/54 (14%)
Query: 378 LHHFVFEILDNAIDESLAGYCTK-----INVTI---YSDNSISISDNGRGIPID 423
L+H +FE+ NA+ ++ + + I V + D SI +SD G G+P+
Sbjct: 232 LYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLR 285
>2vrw_B P95VAV, VAV1, proto-oncogene VAV; lipoprotein, GTP-binding,
metal-binding, phosphoprotein, exchange factor, RAC,
GTPase, membrane domain; 1.85A {Mus musculus} PDB:
3bji_A 1f5x_A
Length = 406
Score = 34.0 bits (78), Expect = 0.26
Identities = 21/142 (14%), Positives = 43/142 (30%), Gaps = 25/142 (17%)
Query: 201 RKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYVISNKYEKSF 260
K TL + ++ P++ + ++ IF NIE + F
Sbjct: 38 EKYTDTLGSIQQHFMKPLQRFLKPQDMETIFVNIEEL----------------------F 75
Query: 261 LVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKI-TVSSSNREKASEELEINYNGKDK 319
V+ L+ L+ + + S E AS+ L+ +
Sbjct: 76 SVHT-HFLKELKDALAGPGATTLYQVFIKYKERFLVYGRYCSQVESASKHLD-QVATARE 133
Query: 320 NFIKFLIKIMLLKNKNSYDIQD 341
+ L + N + ++D
Sbjct: 134 DVQMKLEECSQRANNGRFTLRD 155
>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 = 33.7 bits (78), Expect = 0.30
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 6/42 (14%)
Query: 384 EILDNAIDESLAGYCTKINVTI--YSDNSISISDNGRGIPID 423
E+++N++D AG T I++ + Y + I +SDNG G+ +
Sbjct: 41 ELVENSLD---AG-ATNIDLKLKDYGVDLIEVSDNGCGVEEE 78
>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 = 33.6 bits (78), Expect = 0.31
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 384 EILDNAIDESLAGYCTKINVTIYS--DNSISISDNGRGIPID 423
E+++N +D A T I V + I I DNG GI +
Sbjct: 35 EMIENCLD---AK-STSIQVIVKEGGLKLIQIQDNGTGIRKE 72
>3pie_A 5'->3' exoribonuclease (XRN1); beta berrel, tudor domain, chromo
domain, mRNA turnover, RRN processing, RNA binding, DNA
binding; 2.90A {Kluyveromyces lactis} PDB: 3pif_A
Length = 1155
Score = 34.2 bits (77), Expect = 0.36
Identities = 34/261 (13%), Positives = 79/261 (30%), Gaps = 27/261 (10%)
Query: 901 YGNNECYLRDDIEEERYMLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLK 960
+ ++ C LR+++ + + + + + I++E + + + +
Sbjct: 217 HDHHFCLLREEVTFGKRSSSVKTLETQNFFLLHLSILREYLALEFEEITDSVQFEYDFER 276
Query: 961 QIIDISILSAIMS-DVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIK 1019
+ D + + D + NL + F L + K
Sbjct: 277 VLDDFIFVLFTIGNDFLPNLPDLHLKKGA------------------FPVLLQTF----K 314
Query: 1020 KKFLKKKNYIIDINFINNKDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANNFYKI 1079
+ YI + IN + + +S F+ + +K I + N
Sbjct: 315 EALQHMDGYINEQGKINLARFSIWLKYLSDFEYLN----FEKKDIDVEWFNQQLENISLE 370
Query: 1080 INYLRNEAENMVIKQRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMG 1139
R ++ ++ K L L +T + L + DK +
Sbjct: 371 GERKRTRMGKKLLMKQQKKLIGAVKPWLLKTVQRKVTSELQDADFEIFPLEDKELVRANL 430
Query: 1140 DNVELRRKFIELNALHAKNID 1160
D ++ + L H+K+ D
Sbjct: 431 DFLKEFAFDLGLILAHSKSKD 451
>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 = 33.7 bits (78), Expect = 0.38
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 384 EILDNAIDESLAGYCTKINVTI--YSDNSISISDNGRGIPID 423
E++DN+ID A +I + Y SI SDNG GI
Sbjct: 32 ELVDNSID---AN-ANQIEIIFKDYGLESIECSDNGDGIDPS 69
>3sl2_A Sensor histidine kinase YYCG; ATP binding, intact ATP, bergerat
fold, TR; HET: ATP; 1.61A {Bacillus subtilis}
Length = 177
Score = 32.3 bits (74), Expect = 0.47
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 385 ILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIP 421
I+ NA+ S G ++ + + IS+ D G GIP
Sbjct: 51 IISNALKYSPEGGHVTFSIDVNEEEELLYISVKDEGIGIP 90
>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 = 32.1 bits (74), Expect = 0.73
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 386 LDNAIDESLAGYCTKINVTIYSDNSISISDNGRGIP 421
LDNA+ S G + ++VT+ +DN + DNG G+
Sbjct: 126 LDNAVRYSPQG--SVVDVTLNADN-FIVRDNGPGVT 158
>3ky9_A Proto-oncogene VAV; calponin homology domain, DBL homology domain,
pleckst homology domain, C1 domain, guanine-nucleotide
releasing FA metal-binding; 2.73A {Homo sapiens} PDB:
2d86_A
Length = 587
Score = 32.7 bits (74), Expect = 0.77
Identities = 21/142 (14%), Positives = 43/142 (30%), Gaps = 25/142 (17%)
Query: 201 RKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYVISNKYEKSF 260
K TL + ++ P++ + I+IIF NIE +
Sbjct: 210 EKYTDTLGSIQQHFLKPLQRFLKPQDIEIIFINIEDL----------------------L 247
Query: 261 LVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKI-TVSSSNREKASEELEINYNGKDK 319
V+ L+ ++ + + S E AS+ L+ +
Sbjct: 248 RVHT-HFLKEMKEALGTPGAANLYQVFIKYKERFLVYGRYCSQVESASKHLD-RVAAARE 305
Query: 320 NFIKFLIKIMLLKNKNSYDIQD 341
+ L + N + ++D
Sbjct: 306 DVQMKLEECSQRANNGRFTLRD 327
>3qw4_B UMP synthase; N-terminal orotidine monophosphate decarboxylase
domain C-TE orotate phosphoribosyltransferase domain,
transferase, LYAS; HET: U5P; 3.00A {Leishmania donovani}
Length = 453
Score = 31.3 bits (71), Expect = 1.9
Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 5/79 (6%)
Query: 540 HYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVS--YINKSKLVVHPTI 597
IR + + L+D + F K SG S YI+ +LV +P I
Sbjct: 244 ELCEEINAIRFAKGASVELAKALVDSHCVRFGNFTLK---SGKSSPIYIDLRRLVTYPAI 300
Query: 598 FQAIGNKISEKKNNINIDV 616
+ + + ++ + D
Sbjct: 301 MRLVAREYAKVLRHYKFDR 319
>2hgc_A YJCQ protein; SR346, structure, autostructure, NESG, PSI-2, northeast
structural genomics consortium, protein structure
initiative; NMR {Bacillus subtilis} SCOP: a.4.5.77
Length = 102
Score = 29.6 bits (66), Expect = 1.9
Identities = 12/68 (17%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 984 NAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKL 1043
N ++ I+K++ + N + + + FLK++ YII +++ +++ +
Sbjct: 2 NKDKLRYAILKEIFEGNTPLSENDIGVTEDQFDDAVN-FLKREGYIIGVHYSDDRPHLYK 60
Query: 1044 VSIISTFK 1051
+ T K
Sbjct: 61 LGPELTEK 68
>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 = 30.0 bits (68), Expect = 2.1
Identities = 10/49 (20%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 382 VFEILDNAIDESLAGYCT-KINVTIYSDN---SISISDNGRGIPIDIKI 426
V E + NAI +++++ ++ +++ D G GIP +
Sbjct: 44 VSEAVTNAIIHGYNNDPNGIVSISVIIEDGVVHLTVRDEGVGIPDIEEA 92
>2lju_A Putative oxidoreductase; structural genomics, seattle structural GENO
center for infectious disease, ssgcid; NMR {Ehrlichia
chaffeensis}
Length = 108
Score = 29.3 bits (66), Expect = 2.4
Identities = 15/68 (22%), Positives = 22/68 (32%), Gaps = 19/68 (27%)
Query: 972 MSDVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIID 1031
V L+ TRE A +A I+ V D + + K+Y
Sbjct: 59 KQQVCLSFTTRELAIAYAVA-------HKIDYTVLQD----------NPRTIVPKSYA-- 99
Query: 1032 INFINNKD 1039
NF +D
Sbjct: 100 DNFTKPRD 107
>1g55_A DNA cytosine methyltransferase DNMT2; human DNA methyltransferase
homologue; HET: DNA SAH; 1.80A {Homo sapiens} SCOP:
c.66.1.26
Length = 343
Score = 30.9 bits (70), Expect = 2.6
Identities = 34/233 (14%), Positives = 72/233 (30%), Gaps = 32/233 (13%)
Query: 77 FIDILRSLPETEKV--TIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLS 134
F+ IL LP +K+ I +EN F S +QT++ N + ++
Sbjct: 98 FLHILDILPRLQKLPKYILLENVKGFEVSSTRDLLIQTIE---------NCGFQYQEF-- 146
Query: 135 QKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSC 194
+L+ I +RY+L + + + G L K
Sbjct: 147 ------LLSPTSLGIPNSRLRYFLIA----KLQSEPLPFQAPGQVLM----EFPKIEIHR 192
Query: 195 SDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYVISN 254
+ +V L+ LE+ + + + + ++I+ K S
Sbjct: 193 KNQQDSDLSVKMLKDFLEDDTDVNQYLLPPKSLLRYALLLDIVQPTCRRSVCFTKGYGSY 252
Query: 255 KYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYL-KITVSSSNREKA 306
++ + ++ ++N + + L T +E A
Sbjct: 253 IEGTGSVLQTAEDVQVENIYKSLTNLSQEEQITKLLILKLRYFTP----KEIA 301
>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA
complex, transcription/DNA complex; 3.00A {Homo sapiens}
SCOP: h.1.3.1
Length = 61
Score = 28.1 bits (63), Expect = 2.6
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 742 RSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPEL 779
R+R AA ++R+ ++K + +E K D N +L
Sbjct: 8 RNRAAASRSRQ--KRKVWVQSLE--KKAEDLSSLNGQL 41
>2d6y_A Putative TETR family regulatory protein; helix-turn-helix, gene
regulation; HET: TLA; 2.30A {Streptomyces coelicolor}
SCOP: a.4.1.9 a.121.1.1
Length = 202
Score = 30.2 bits (68), Expect = 2.7
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 705 SEVRKPVEEI--IIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRE--LTRKKNLI 760
V ++I I L D+ +P +L+ + +E + R+ RK +
Sbjct: 69 ISVPVDPDDIEGWIDRLLDYHAAHPELLRLLFWEGMEYGTAELPHEAERQEHYARKVAAV 128
Query: 761 DD 762
D
Sbjct: 129 RD 130
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex;
HET: DNA D3T; 2.40A {Mus musculus}
Length = 360
Score = 30.7 bits (68), Expect = 2.8
Identities = 12/107 (11%), Positives = 33/107 (30%), Gaps = 10/107 (9%)
Query: 996 LNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKKIIG 1055
L N + + L + + ++ + + K V+ +S +
Sbjct: 13 LTHHNTLLSEALETLAE--AAGFEANEGRLLSFSRAASVL--KSLPCPVASLSQLHGLPY 68
Query: 1056 KGVIIQKSIGEKIKKYTANNFYKIINYLRNEAENMVIKQ--RYKGLG 1100
G + I++ + + + +R +K + G+G
Sbjct: 69 FG----EHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVG 111
>2dgc_A Protein (GCN4); basic domain, leucine zipper, DNA binding,
eukaryotic regulatory protein, transcription/DNA
complex; HET: DNA; 2.20A {Saccharomyces cerevisiae}
SCOP: h.1.3.1 PDB: 1dgc_A* 1ld4_E 1ysa_C* 3p8m_D
Length = 63
Score = 27.9 bits (62), Expect = 2.9
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 741 ARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPEL 779
AR+ EAAR++R RK + +E K+ + KN L
Sbjct: 15 ARNTEAARRSRA--RKLQRMKQLE--DKVEELLSKNYHL 49
>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 = 29.5 bits (67), Expect = 3.0
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 9/41 (21%)
Query: 385 ILDNAIDESLAGYC-TKINVTIYSDNS---ISISDNGRGIP 421
+LDNA YC + ++ + I + D+G GIP
Sbjct: 52 VLDNACK-----YCLEFVEISARQTDEHLYIVVEDDGPGIP 87
>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 = 30.2 bits (69), Expect = 3.2
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 385 ILDNAIDESLAG-YCTKINVTIYSDNS---ISISDNGRGIP 421
+L+N + S + V + + I + DNG GIP
Sbjct: 146 LLNNGVKYSKKDAPDKYVKVILDEKDGGVLIIVEDNGIGIP 186
>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 = 29.8 bits (68), Expect = 3.2
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 411 ISISDNGRGIPIDIK 425
I + DNG GIP ++
Sbjct: 94 IDVEDNGPGIPPHLQ 108
>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA
complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F
2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A
Length = 62
Score = 27.7 bits (62), Expect = 3.4
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 741 ARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPEL 779
R+R AA K+R+ RK I +E K+ + +N EL
Sbjct: 7 MRNRIAASKSRK--RKLERIARLE--EKVKTLKAQNSEL 41
>3sso_A Methyltransferase; macrolide, natural product, rossman fold; HET:
SAH; 1.90A {Micromonospora griseorubida} PDB: 3ssn_A*
3ssm_A*
Length = 419
Score = 30.3 bits (67), Expect = 3.8
Identities = 14/86 (16%), Positives = 26/86 (30%)
Query: 863 IDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIA 922
DG+HI A + T F P + G I + ++ +LK
Sbjct: 294 DDGSHINAHVRTSFAALFPHVRPGGLYVIEDMWTAYWPGFGGQADPQECSGTSLGLLKSL 353
Query: 923 FKNVKLISIENGDIIKENYFFKLIDK 948
++ + + Y + I
Sbjct: 354 IDAIQHQELPSDPNRSPGYVDRNIVG 379
>3l7y_A Putative uncharacterized protein SMU.1108C; hydrolase; 2.00A
{Streptococcus mutans}
Length = 304
Score = 30.3 bits (69), Expect = 3.9
Identities = 15/100 (15%), Positives = 32/100 (32%), Gaps = 10/100 (10%)
Query: 908 LRDDIEEERYMLKIAFKNVKLI-SIENGDIIKEN---YFFKLIDKYNKTIEIVHRLKQII 963
R+DI Y ++ + + S E +K+ K++ + +E+V+ +
Sbjct: 119 QREDIASIIYFIEEKYPQAVIALSGEKKGYLKKGVSENIVKMLSPFFPVLELVNSFSPLP 178
Query: 964 DISILSAIMSDVILNLDTRENAEQFAKKIIKKLNDSNIEI 1003
D + E + Q K I +
Sbjct: 179 DERFFKLTL------QVKEEESAQIMKAIADYKTSQRLVG 212
>2jya_A AGR_C_3324P, uncharacterized protein ATU1810; protein with unknown
function ATU1810, ontario centre for ST proteomics, OCSP;
NMR {Agrobacterium tumefaciens str}
Length = 106
Score = 28.5 bits (64), Expect = 4.5
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 19/67 (28%)
Query: 972 MSDVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIID 1031
V L +T+E AE +A++ IE V K+ K +Y
Sbjct: 51 KQQVKLTFETQEQAEAYAQR-------KGIEYRVILP----------KEATRKVVSYT-- 91
Query: 1032 INFINNK 1038
NF N+
Sbjct: 92 DNFRFNR 98
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase,
phosphoprotein, transfe two-component regulatory system;
3.80A {Thermotoga maritima}
Length = 349
Score = 29.9 bits (68), Expect = 4.7
Identities = 10/43 (23%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 385 ILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIPIDI 424
++ NAI+ + KI +T + +S+ ++G IP ++
Sbjct: 252 LVQNAIEATGEN--GKIKITSEDMYTKVRVSVWNSGPPIPEEL 292
>4e2x_A TCAB9; kijanose, tetronitrose, tetradeoxy sugar, sugar methylation,
transferase; HET: SAH TYD; 1.40A {Micromonospora chalcea}
PDB: 3ndi_A* 3ndj_A* 4e32_A* 4e33_A* 4e2y_A* 4e31_A*
4e2w_A* 4e2z_A* 4e30_A*
Length = 416
Score = 30.0 bits (68), Expect = 5.0
Identities = 11/94 (11%), Positives = 23/94 (24%), Gaps = 17/94 (18%)
Query: 982 RENAEQFAKKIIKKLNDSNIEIIVE-----------FDQLNNKYL-----LNIKKKFLKK 1025
RE+ A+ + IVE + ++L + K +K
Sbjct: 89 REHFAMLARDFLATELTGPDPFIVEIGCNDGIMLRTIQEAGVRHLGFEPSSGVAAKAREK 148
Query: 1026 KNYIIDINFINNKDYKKLVSIISTFKKIIGKGVI 1059
+ +F + I +
Sbjct: 149 GIRVR-TDFFEKATADDVRRTEGPANVIYAANTL 181
>2qtq_A Transcriptional regulator, TETR family; transcription regulator,
DNA/RNA-binding 3-helical bundle FO turn helix motif,
HTH motif; HET: MSE; 1.85A {Novosphingobium
aromaticivorans} PDB: 2rha_A*
Length = 213
Score = 29.2 bits (66), Expect = 5.6
Identities = 6/56 (10%), Positives = 18/56 (32%), Gaps = 2/56 (3%)
Query: 710 PVEEI--IIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKNLIDDI 763
P ++ I D + P ++L+ + ++ + + L +
Sbjct: 90 PEAKLRRHISKCIDTYYDYPYLNRLLMRLVRDSDEAEAKRIADQYLLPLHRAYNRF 145
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.4 bits (65), Expect = 5.9
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 8/75 (10%)
Query: 737 IIEAARSR---EAARKTRELTRKKNLID-DIELSTKLADCQEK-NPELCELYIVEGDSAG 791
I +A R E+ RK RE ++K L + D + +EK +L E + +
Sbjct: 74 IAQADRLTQEPESIRKWRE-EQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVE 132
Query: 792 GSVKQGR--DRRFQA 804
+ R D+ F
Sbjct: 133 KNKINNRIADKAFYQ 147
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis,
mutation, deletion, streisinger, slippage, transferase,
lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP:
a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A*
2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A*
1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A*
3hx0_A* 3mdc_A* 3mda_A* ...
Length = 335
Score = 29.5 bits (65), Expect = 6.2
Identities = 19/116 (16%), Positives = 43/116 (37%), Gaps = 8/116 (6%)
Query: 994 KKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKKI 1053
+K + N+ I + + L +++ + Y IN + K + K V+ I
Sbjct: 7 QKATNHNLHITEKLEVLAK--AYSVQGDKWRALGYAKAINAL--KSFHKPVTSYQEACSI 62
Query: 1054 IGKGVIIQKSIGEKIKKYTANNFYKIINYLRNEAENMVIKQRYKGLGEMNPGQLWE 1109
G G K + EKI + + + ++++ + + G G ++
Sbjct: 63 PGIG----KRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQ 114
>2p1z_A Phosphoribosyltransferase; STRU genomics, PSI-2, protein structure
initiative, midwest CENT structural genomics, MCSG;
2.44A {Corynebacterium diphtheriae}
Length = 180
Score = 28.8 bits (65), Expect = 7.0
Identities = 7/40 (17%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 579 TSGFVS--YINKSKLVVHPTIFQAIGNKISEKKNNINIDV 616
+SG + Y++ + +H + IG + E + +
Sbjct: 27 SSGKEADYYVDLRRATLHARASRLIGELLRELTADWDYVA 66
>3mpx_A FYVE, rhogef and PH domain-containing protein 5; structural
genomics consortium, DH domain, SGC, L binding protein;
2.80A {Homo sapiens}
Length = 434
Score = 29.2 bits (65), Expect = 8.0
Identities = 4/31 (12%), Positives = 15/31 (48%)
Query: 207 LQRLLENKENPVELKISNNQIKIIFSNIEII 237
+ R L++ ++ ++ +++ S + I
Sbjct: 52 VMRALDDMDHEGRDTLAREELRQGLSELPAI 82
>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation,
GTP-binding domain, maturation enzyme, oxidoreductase;
2.99A {Thermotoga neapolitana}
Length = 423
Score = 29.2 bits (66), Expect = 8.9
Identities = 10/86 (11%), Positives = 25/86 (29%), Gaps = 13/86 (15%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
+ ++V ++ + + L + LV K E +
Sbjct: 212 LVILVVPIDLGAPKGRLIMPQVHAIREALDREAIALVVKERELRYVMENI---------- 261
Query: 61 VGYGNSSINIIVAARKFIDILRSLPE 86
G +I ++ + + +PE
Sbjct: 262 ---GMKPKLVITDSQVAMKVASDVPE 284
>1by1_A Protein (PIX); RHO-GTPase exchange factor, transport protein; NMR
{Homo sapiens} SCOP: a.87.1.1
Length = 209
Score = 28.8 bits (65), Expect = 9.0
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 201 RKTVFTLQRLLENKENPVELK--ISNNQIKIIFSNIEII 237
+ LQ +L P++ +S+ I + N+E I
Sbjct: 26 NEYSKELQTVLSTYLRPLQTSEKLSSANISYLMGNLEEI 64
>3bma_A D-alanyl-lipoteichoic acid synthetase; structural genomics,
D-alanyl-lipoteichoic acid biosynthesis structure
initiative, PSI-2; 2.24A {Streptococcus pneumoniae}
Length = 407
Score = 29.2 bits (65), Expect = 9.1
Identities = 28/179 (15%), Positives = 60/179 (33%), Gaps = 16/179 (8%)
Query: 910 DDIEEERYMLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILS 969
++ + + K+A +L + +N I F + + + + ++
Sbjct: 155 PNVAMKDLVQKLA-SKEELSTADNEMIELLARFNERQASFFGQFSVRGYVNYDKHVAKYL 213
Query: 970 AIMSDVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYI 1029
I + + + + E K +K +N E N Y IKK K K+
Sbjct: 214 KI----LPDQFSYQAIEDVVKADAEKNTSNN-----EMGMENYFYNEQIKKDLKKLKDSQ 264
Query: 1030 IDINFINNKDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTA------NNFYKIINY 1082
++ + +Y L +++ F K + I + +K Y + I Y
Sbjct: 265 KSFTYLKSPEYNDLQLVLTQFSKSKVNPIFIIPPVNKKWMDYAGLREDMYQQTVQKIRY 323
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
0.319 0.138 0.382
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 17,660,924
Number of extensions: 1144430
Number of successful extensions: 3320
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3141
Number of HSP's successfully gapped: 173
Length of query: 1161
Length of database: 6,701,793
Length adjustment: 104
Effective length of query: 1057
Effective length of database: 3,798,009
Effective search space: 4014495513
Effective search space used: 4014495513
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (28.1 bits)