RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13357
(833 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 = 679 bits (1754), Expect = 0.0
Identities = 214/411 (52%), Positives = 299/411 (72%), Gaps = 22/411 (5%)
Query: 17 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKINVT 76
+S +SSI++L+GL+AVRKRP MYIGDT DGTGLHH+VFE++DNAIDE+LAG+C +I VT
Sbjct: 2 NSSDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVT 61
Query: 77 IYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 136
I++DNS+S+ D+GRGIP I + SAAE++MT LHAGGKF+ NSYK+SGGLHG+
Sbjct: 62 IHADNSVSVQDDGRGIPTGIH----PEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGV 117
Query: 137 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTK 196
G+S VN LS+ L+L I R KIH + +G+ +P+ + G+T K GT
Sbjct: 118 GVSVVNALSQKLELVIQREGKIHRQIYE------------HGVPQAPLAVTGETEKTGTM 165
Query: 197 IHFWVDEKIFSNI-EFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFV 255
+ FW + F+N+ EF YEIL KR+RELSFL++GV I L D+R K++ F ++GG FV
Sbjct: 166 VRFWPSLETFTNVTEFEYEILAKRLRELSFLDSGVSIRLRDKRDGKEDHFHYEGGIKAFV 225
Query: 256 SYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTH 315
Y+NK+K +HP IF S +K+ I ++V++QWN+ + ENI CFTNNI Q DGGTH
Sbjct: 226 EYLNKNKTPIHPNIFY-----FSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTH 280
Query: 316 LTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLV 375
L G R+ +TR +N Y+++ + KK+K+ G+D REGL V+S+K+PDPKF+SQTK+KLV
Sbjct: 281 LAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLV 340
Query: 376 SSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELT 426
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 = 651 bits (1683), Expect = 0.0
Identities = 157/410 (38%), Positives = 242/410 (59%), Gaps = 24/410 (5%)
Query: 18 SYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKINVTI 77
SY AS+I++L+GLE VR RP MYIG T G HHL EILDNA+DE+LAGY T+I V +
Sbjct: 2 SYDASAIRVLKGLEGVRHRPAMYIGGTGV-EGYHHLFKEILDNAVDEALAGYATEILVRL 60
Query: 78 YSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIG 137
D S+++ DNGRGIP+D+ + + A E++ LH+GGKF + +YK+SGGLHG+G
Sbjct: 61 NEDGSLTVEDNGRGIPVDLM----PEEGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVG 116
Query: 138 LSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDT--NKQGT 195
S VN LS + + + R K H + F G P++++G+ K GT
Sbjct: 117 ASVVNALSEWTVVEVFREGKHHRIAFSRGE------------VTEPLRVVGEAPRGKTGT 164
Query: 196 KIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFV 255
++ F D +IF N+ F ++ R+RE+++L G+ + D + K+E+F KGG + F
Sbjct: 165 RVTFKPDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEEVFLDKGGVASFA 224
Query: 256 SYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTH 315
+ + + +++ F I + ++V YN IL + N I DGGTH
Sbjct: 225 KALAEGEDLLYEKPFL-----IRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTH 279
Query: 316 LTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLV 375
LT +S +RA+N+Y ++ K+ + G+D+ EGL V+S+K+P+P+F QTK KL+
Sbjct: 280 LTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLL 339
Query: 376 SSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTREL 425
+ 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 = 620 bits (1602), Expect = 0.0
Identities = 134/421 (31%), Positives = 226/421 (53%), Gaps = 32/421 (7%)
Query: 12 QDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCT 71
+ + + Y+A+ I++L GL+ V++RP MY D +HL E++DN++DE+LAG+
Sbjct: 17 RGSHNTRYNAADIEVLSGLDPVKRRPGMYT----DTARPNHLAQEVIDNSVDEALAGHAK 72
Query: 72 KINVTIYSDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKIS 130
+I VT+Y D S +SD+GRG+P+DI H + K E+++T LHAGGKFN +Y S
Sbjct: 73 QIEVTLYKDGSCEVSDDGRGMPVDI-----HPEEKIPGVELILTRLHAGGKFNNRNYTFS 127
Query: 131 GGLHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDT 190
GGLHG+G+S VN LS ++L I R H MEFR +G + S ++++G
Sbjct: 128 GGLHGVGVSVVNALSTKVELFIKREGSEHRMEFR------------DGNAASKLEVVGTV 175
Query: 191 NKQ--GTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFK 248
K+ GT++ FW D K F +F+ L+ +R + L G+ + L DE +++ + F+
Sbjct: 176 GKKNTGTRLRFWADPKYFDTPKFNVRALRHLLRAKAVLCPGLTVKLHDEATGEQDSWYFE 235
Query: 249 GGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNIL 308
G ++ ++ +F S KK+ +D + W + N I
Sbjct: 236 NGLRDYLKGEMAEHEMLPADLFV-----GSLKKDTEIVDWAAGWVPEGELVQESYVNLIP 290
Query: 309 QVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNS 368
GTH+ GLRSG+T A+ ++ + L + +++ ED+ + +T VLS+K+ DP+F+
Sbjct: 291 TAQHGTHVNGLRSGLTDALREFCDFRNLLPR-GVKLAPEDVWDRVTFVLSLKMTDPQFSG 349
Query: 369 QTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRK 428
QTK +L S + +E +L +N + I + I+ A +R + +++ RK
Sbjct: 350 QTKERLSSRQAAGFIEGAAHDAFSLYLNQNVEIGEKIAQIAIDRASAR--LKTEKQIVRK 407
Query: 429 K 429
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 (1566), Expect = 0.0
Identities = 127/417 (30%), Positives = 225/417 (53%), Gaps = 33/417 (7%)
Query: 17 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKINVT 76
+Y+A +I++L GLE VR+RP MY D T +HL E++DN++DE+LAG+ +++V
Sbjct: 3 QTYNADAIEVLTGLEPVRRRPGMYT----DTTRPNHLGQEVIDNSVDEALAGHAKRVDVI 58
Query: 77 IYSDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHG 135
+++D S+ + D+GRG+P+DI H + A E+++ LHAGGKF+ +Y+ SGGLHG
Sbjct: 59 LHADQSLEVIDDGRGMPVDI-----HPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHG 113
Query: 136 IGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ-- 193
+G+S VN LS+ +++ + R+ +++ + F NG V ++++G K+
Sbjct: 114 VGISVVNALSKRVEVNVRRDGQVYNIAFE------------NGEKVQDLQVVGTCGKRNT 161
Query: 194 GTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSG 253
GT +HFW DE F + F L ++ + L GV IT DE ++ + ++ G +
Sbjct: 162 GTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQDGLND 221
Query: 254 FVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNNSYNENIL-CFTNNILQVDG 312
+++ + F + + +D ++ W E + + N I + G
Sbjct: 222 YLAEAVNGLPTLPEKPFI-----GNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQG 276
Query: 313 GTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKN 372
GTH+ GLR G+ A+ ++ E L + +++ EDI + VLS+K+ DP+F QTK
Sbjct: 277 GTHVNGLRQGLLDAMREFCEYRNILPR-GVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKE 335
Query: 373 KLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKK 429
+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 = 554 bits (1430), Expect = 0.0
Identities = 81/386 (20%), Positives = 162/386 (41%), Gaps = 37/386 (9%)
Query: 29 GLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKINVTIYSDNSISISDN 88
+E VRKRP MY GD + GLHHLV+ +LD A +E+ G C + + + D SI++
Sbjct: 11 IVENVRKRPGMYCGDVGE-YGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCT 69
Query: 89 GRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFL 148
R + AE ++ G + G L LS
Sbjct: 70 SRTVT---------------AENLVRVATGAGFLGRPPGDGWGWDSM--LVVSLALSSRY 112
Query: 149 QLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSN 208
Q+ I + + + +G Q G +V+P++ + + ++G ++HF D IF
Sbjct: 113 QVDIWADGRQWRVMGEHGHPQGE------GAAVTPMEPMPVSAERGVRVHFVPDATIFEV 166
Query: 209 IEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPT 268
+ F L +R EL+ L G+ ++ D + ++ ++ GG + + + +++ +HP
Sbjct: 167 LAFDRARLSRRCNELAALAPGLRVSFADLQRGERTLWHLPGGVAQWAHVLTEARPQLHPE 226
Query: 269 IFQAIGNKISEKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAIN 328
+ + + ++QW + +L F N + V G H+ G+ + A+
Sbjct: 227 PVV-----FDFTWDGLRVQCALQWCEDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALA 281
Query: 329 KYIEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPK--FNSQTKNKLVSSEVRKPVEEI 386
K +++ + +GLT ++++ P + F TK L + + + +
Sbjct: 282 KL------SGETRGAFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQ 335
Query: 387 IIKTLFDFLQENPGESKLICEKIIEA 412
+ + 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 = 492 bits (1267), Expect = e-168
Identities = 181/424 (42%), Positives = 276/424 (65%), Gaps = 13/424 (3%)
Query: 419 ARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVL 478
+ RE+TR+K +D L KLADCQE++P L ELY+VEGDSAGGS KQGR+R+ QA+L
Sbjct: 1 SNAAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAIL 60
Query: 479 PLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGA 538
PL+GK+LN+EKARF+K++ S+++ TLI+ LG GI +DE+N +KLRYH IIIMTDAD+DG+
Sbjct: 61 PLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGS 120
Query: 539 HIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNV 598
HIR LLLTFFYR+MP+++E G++YIAQPPLYK+K G E Y++DD ++Y + IA
Sbjct: 121 HIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGA 180
Query: 599 KLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVILN---LDTRE 655
L + + + KL+ +YN T ++++R+++ ++L ++ L L +
Sbjct: 181 TLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQ 240
Query: 656 NAEQFAKKIIKKLND-----SNIEIIVEFDQLNNKYLLNIKKKFL-KKKNYIIDINFINN 709
++ ++ +LND S + V + N + ++ + +Y +D FI
Sbjct: 241 TVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITG 300
Query: 710 KDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANNFYKIINYLRNEAENMVIKQRYK 769
+Y+++ ++ + ++ + I++ ++ +F + +++L E+ + QRYK
Sbjct: 301 GEYRRICTLGEKLRGLLEEDAFIER----GERRQPVASFEQALDWLVKESRRGLSIQRYK 356
Query: 770 GLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNALHAK 829
GLGEMNP QLWETTM+P R +L+V +KDAI+AD++F TLMGD VE RR FIE NAL A
Sbjct: 357 GLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAA 416
Query: 830 NIDI 833
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 = 430 bits (1109), Expect = e-144
Identities = 87/433 (20%), Positives = 163/433 (37%), Gaps = 55/433 (12%)
Query: 14 TQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGT----------------------GLH 51
+ E ++ Q + LE + KRP+ YIG GL
Sbjct: 7 STEPVSASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLF 66
Query: 52 HLVFEILDNAIDESLAG-YCTKINVTIYSD-NSISISDNGRGIPIDIKIDDKH-KPKRSA 108
+ EIL NA D + +I+V I+++ ++I + ++G+GIPI+I H K
Sbjct: 67 KIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEI-----HNKENIYI 121
Query: 109 AEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTIN--RNKKIHYMEFRYG 166
E++ L ++ + K++GG +G G N S L + + ++
Sbjct: 122 PEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENN 181
Query: 167 VLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFL 226
+ I P TK+ F D F E +IL R + +
Sbjct: 182 M----------SICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDI 231
Query: 227 NNGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKI--SEKKNNI 284
N V + K +I FK ++ + K + + + A + ++ N
Sbjct: 232 NGSVRDINVYLNGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINN 291
Query: 285 NIDVSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEI 344
+V+ ++ + I F N+I GGTH+ + I + I++ ++ KK K +
Sbjct: 292 RWEVAFAVSDISFQQI-SFVNSIATTMGGTHVNYITDQIVKKISEILK-----KKKKKSV 345
Query: 345 IGEDIREGLTCVLSIKIPDPKFNSQTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKL 404
I+ + ++ I +P F SQTK +L + I + + +
Sbjct: 346 KSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTD----- 400
Query: 405 ICEKIIEAARSRE 417
+ ++ 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 (1016), Expect = e-133
Identities = 126/234 (53%), Positives = 170/234 (72%), Gaps = 17/234 (7%)
Query: 17 SSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKINVT 76
+SY +SSI++L+GL+AVRKRP MYIGDT DGTGLHH+VFE++DNAIDE+LAG+C +I VT
Sbjct: 3 NSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVT 62
Query: 77 IYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGI 136
I++DNS+S+ D+GRGIP I + SAAE++MT LHAGGKF+ NSYK+SGGLHG+
Sbjct: 63 IHADNSVSVQDDGRGIPTGI----HPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGV 118
Query: 137 GLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTK 196
G+S VN LS+ L+L I R KIH + +G+ +P+ + G+T K GT
Sbjct: 119 GVSVVNALSQKLELVIQREGKIHRQIYE------------HGVPQAPLAVTGETEKTGTM 166
Query: 197 IHFWVDEKIFSNI-EFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKG 249
+ 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 = 370 bits (952), Expect = e-123
Identities = 100/239 (41%), Positives = 147/239 (61%), Gaps = 19/239 (7%)
Query: 12 QDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCT 71
++ ++Y+ +IQ+LEGL+AVRKRP MYIG T DG GLHHLV+EI+DNA+DE+L+G+
Sbjct: 4 KEININNYNDDAIQVLEGLDAVRKRPGMYIGST-DGAGLHHLVWEIVDNAVDEALSGFGD 62
Query: 72 KINVTIYSDNSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISG 131
+I+VTI D S+++ D+GRG+P + H E++ T LHAGGKF + YK SG
Sbjct: 63 RIDVTINKDGSLTVQDHGRGMPTGM-----HAMGIPTVEVIFTILHAGGKFGQGGYKTSG 117
Query: 132 GLHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDT- 190
GLHG+G S VN LS +L++ I R+ ++ F G G V+ +K IG
Sbjct: 118 GLHGVGSSVVNALSSWLEVEITRDGAVYKQRFENG-----------GKPVTTLKKIGTAL 166
Query: 191 -NKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFK 248
+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 = 374 bits (962), Expect = e-122
Identities = 77/432 (17%), Positives = 147/432 (34%), Gaps = 64/432 (14%)
Query: 23 SIQILEGLEAVRKRPEMYIGDTSDGT---------------------GLHHLVFEILDNA 61
Q LE + RP+ YIG T GL+ + EIL NA
Sbjct: 5 IYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVNA 64
Query: 62 IDESLAG-YCTKINVTIYSD-NSISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAG 119
D + I VTI + N ISI +NG+GIP+ K ++ +L
Sbjct: 65 ADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEH----KVEKMYVPALIFGQLLTS 120
Query: 120 GKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTI--NRNKKIHYMEFRYGVLQNRIIKTIN 177
++ + K++GG +G G N S + KK+ + + +
Sbjct: 121 SNYDDDEKKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGR-------- 172
Query: 178 GISVSPIKIIGDTNKQGTKIHFWVDEKIFSNIEFHYEILK---KRIRELSFLNNGVCITL 234
+++ + T I F D F +I+ +R +++ V + L
Sbjct: 173 ---AGEMELKPFNGEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFL 229
Query: 235 IDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVSMQWNN 294
++ K +V K KL K+ ++ N +V + +
Sbjct: 230 NGNKLPVKGFRS-------YVDMYLKDKLDETGNSL-----KVIHEQVNHRWEVCLTMSE 277
Query: 295 SYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKSKIEIIGEDIREGLT 354
+ I F N+I GG H+ + I + +++ K + + ++ +
Sbjct: 278 KGFQQI-SFVNSIATSKGGRHVDYVADQIVTKLVDVVKKK---NKGGVAVKAHQVKNHMW 333
Query: 355 CVLSIKIPDPKFNSQTKNKLVSSEVRKPVEEIIIKTLFDFLQENPGESKLICEKIIEAAR 414
++ I +P F+SQTK + + + I E I+ +
Sbjct: 334 IFVNALIENPTFDSQTKENMTLQPKSFGSTCQLSEKFIKAAIGCG-----IVESILNWVK 388
Query: 415 SREAARKTRELT 426
+ + ++ +
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 = 335 bits (861), Expect = e-110
Identities = 78/222 (35%), Positives = 130/222 (58%), Gaps = 24/222 (10%)
Query: 29 GLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKINVTIYSDNSISISDN 88
GLE VR+RP MY D T +HL E++DN++DE+LAG+ +++V +++D S+ + D+
Sbjct: 1 GLEPVRRRPGMYT----DTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDD 56
Query: 89 GRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRF 147
GRG+P+DI H + A E+++ LHAGGKF+ +Y+ SGGLHG+G+S VN LS+
Sbjct: 57 GRGMPVDI-----HPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKR 111
Query: 148 LQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQ--GTKIHFWVDEKI 205
+++ + R+ +++ + F NG V ++++G K+ GT +HFW DE
Sbjct: 112 VEVNVRRDGQVYNIAFE------------NGEKVQDLQVVGTCGKRNTGTSVHFWPDETF 159
Query: 206 FSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEF 247
F + F L ++ + L GV IT DE ++ + +
Sbjct: 160 FDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCY 201
>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 = 313 bits (805), Expect = e-101
Identities = 91/186 (48%), Positives = 115/186 (61%), Gaps = 5/186 (2%)
Query: 412 AARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRD 471
+ + KN D LS KL Q KNP ELY+VEGDSAGGS KQGRD
Sbjct: 8 HHHHHSSGHIDDDDKHMKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRD 67
Query: 472 RRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMT 531
R+FQA+LPLRGKV+N KA+ I+ +E+I T+I T+G G+ +F++E Y +IIIMT
Sbjct: 68 RKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGV-GADFSIEDANYDKIIIMT 126
Query: 532 DADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNEC----YLRDDIEEE 587
DAD DGAHI+ LLLTFFYR M L+E G++YIA PPLYK+ G + Y D E E
Sbjct: 127 DADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELE 186
Query: 588 RYMLKI 593
+
Sbjct: 187 ELRKQF 192
Score = 123 bits (310), Expect = 2e-31
Identities = 42/101 (41%), Positives = 53/101 (52%), Gaps = 11/101 (10%)
Query: 739 KIKKYTANNFYKIINYLRNEAE-NMVIK--------QRYKGLGEMNPGQLWETTMNPMIR 789
K+ K + + Y + E + K QRYKGLGEMN QLWETTMNP R
Sbjct: 165 KMSK--GKGKKEEVAYAWTDGELEELRKQFGKGATLQRYKGLGEMNADQLWETTMNPETR 222
Query: 790 CLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNALHAKN 830
L++V I+D A++ LMGD VE RRK+IE N
Sbjct: 223 TLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFTLE 263
>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 = 301 bits (774), Expect = 1e-97
Identities = 100/237 (42%), Positives = 140/237 (59%), Gaps = 46/237 (19%)
Query: 19 YSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGYCTKINVTIY 78
Y A IQ+LEGLEAVRKRP MYIG TS+ GLHHLV+EI+DN+IDE+LAGY +I V I
Sbjct: 2 YGAGQIQVLEGLEAVRKRPGMYIGSTSE-RGLHHLVWEIVDNSIDEALAGYANQIEVVIE 60
Query: 79 SDNSISISDNGRGIPIDIKIDDKH-KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIG 137
DN I ++DNGRGIP+DI K R A E+++T
Sbjct: 61 KDNWIKVTDNGRGIPVDI-----QEKMGRPAVEVILT----------------------- 92
Query: 138 LSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKI 197
S VN LS+ L++ ++RN+ I++ ++ GV +K +G T+K GT I
Sbjct: 93 SSVVNALSQDLEVYVHRNETIYHQAYKKGV------------PQFDLKEVGTTDKTGTVI 140
Query: 198 HFWVDEKIFSN-IEFHYEILKKRIRELSFLNNGVCITLIDER---IKKKEIFEFKGG 250
F D +IF+ ++YE L++RIREL+FLN G+ ITL DER +++ + ++GG
Sbjct: 141 RFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEGG 197
>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 = 284 bits (730), Expect = 1e-90
Identities = 75/162 (46%), Positives = 111/162 (68%), Gaps = 2/162 (1%)
Query: 440 KLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSE 499
+ D + +P ELY+VEGDSAGGS K GRD FQA+LPLRGK++N+EKAR ++++ +
Sbjct: 8 HVDDDDKTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNT 67
Query: 500 QITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYG 559
++ +I+ LG GI DEF++ KLRYH+I++M DAD+DG HI LLLT +R M LIE G
Sbjct: 68 EVQAIITALGTGI-HDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENG 126
Query: 560 YIYIAQPPLYKIKYGNNEC-YLRDDIEEERYMLKIAFKNVKL 600
++++AQPPLYK+K+ ++ + D E + + K+
Sbjct: 127 HVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKI 168
Score = 133 bits (338), Expect = 2e-35
Identities = 35/68 (51%), Positives = 50/68 (73%)
Query: 766 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 825
QRYKGLGEM+ +LWETTM+P +R L +V + DA +AD++F LMG++V+ RR FI NA
Sbjct: 175 QRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNA 234
Query: 826 LHAKNIDI 833
+ +D+
Sbjct: 235 KDVRFLDV 242
>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 (486), Expect = 4e-51
Identities = 58/216 (26%), Positives = 95/216 (43%), Gaps = 13/216 (6%)
Query: 397 ENPGESKLICEKIIEAARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYI 456
+P K + + T + K + I I D K+ C L +
Sbjct: 5 SHPQFEKGADDD-------DKVPDPTSVDSVKYSKIKGIPKLDDANDAGGKHSLECTLIL 57
Query: 457 VEGDSAGGSVKQGR---DRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIE 513
EGDSA G R V PLRGK+LN+ +A ++I+ + +I +I +G+ +
Sbjct: 58 TEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYK 117
Query: 514 Q---DEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYK 570
+ D +L+ LRY +I+IMTD D DG+HI+ LL+ F + P L+++G++ P+ K
Sbjct: 118 KSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPIVK 177
Query: 571 IKYGNNECYLRDDIEEERYMLKIAFKNVKLISIENG 606
E E + + I + I G
Sbjct: 178 ASKNKQELSFYSIPEFDEWKKHIENQKAWKIKYYKG 213
Score = 41.7 bits (97), Expect = 0.001
Identities = 9/67 (13%), Positives = 22/67 (32%), Gaps = 1/67 (1%)
Query: 766 QRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRKFIELNA 825
+ YKGLG + E + +L + I + ++ R++++
Sbjct: 209 KYYKGLGTSTAKEAKEYFADMERHRILF-RYAGPEDDAAITLAFSKKKIDDRKEWLTNFM 267
Query: 826 LHAKNID 832
+
Sbjct: 268 EDRRQRR 274
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 188 bits (480), Expect = 2e-50
Identities = 77/195 (39%), Positives = 114/195 (58%), Gaps = 8/195 (4%)
Query: 409 IIEAARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQ 468
I +A R +AA+K +K ++ L KLADC + E EL+IVEGDSAGGS KQ
Sbjct: 5 ISKAGRRLKAAKKVE----RKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQ 60
Query: 469 GRDRRFQAVLPLRGKVLNIEKARFEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRII 528
RD+ FQA++P+RGK+LN + ++++ S+++ + +G+ D+ L +LRY +I
Sbjct: 61 ARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSDD--LSELRYGKIC 118
Query: 529 IMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEER 588
I+ DAD DG HI LL F + P L+E G++Y+A PPL++I G + Y DD E E
Sbjct: 119 ILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELET 178
Query: 589 YMLKIAFKNVKLISI 603
+ K K I
Sbjct: 179 --ILKNVKGNKNPQI 191
Score = 54.7 bits (132), Expect = 9e-08
Identities = 22/53 (41%), Positives = 30/53 (56%)
Query: 767 RYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMGDNVELRRK 819
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 = 177 bits (451), Expect = 8e-47
Identities = 86/136 (63%), Positives = 106/136 (77%), Gaps = 1/136 (0%)
Query: 432 IDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQGRDRRFQAVLPLRGKVLNIEKAR 491
+D L KLADC K+PE CE+++VEGDSAGGS K GRD R QA+LPLRGK+LN+EKAR
Sbjct: 1 MDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKAR 60
Query: 492 FEKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRK 551
++I+ + +I +I+ G GI D F+L K RYH+I+IMTDAD+DGAHIR LLLTFFYR
Sbjct: 61 LDRILNNNEIRQMITAFGTGIGGD-FDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRF 119
Query: 552 MPKLIEYGYIYIAQPP 567
M LIE GY+YIAQPP
Sbjct: 120 MRPLIEAGYVYIAQPP 135
Score = 53.5 bits (129), Expect = 2e-07
Identities = 51/97 (52%), Positives = 62/97 (63%), Gaps = 4/97 (4%)
Query: 737 GEKIKKYTANNFYKIINYLRNEAENMVIKQ---RYKGLGEMNPGQLWETTMNPMIRCLLK 793
G I+ FY+ + L EA + I Q YKGLGEMN QLWETTMNP R LL+
Sbjct: 105 GAHIRTLLLTFFYRFMRPLI-EAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQ 163
Query: 794 VKIKDAISADKIFMTLMGDNVELRRKFIELNALHAKN 830
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 (304), Expect = 2e-28
Identities = 43/146 (29%), Positives = 72/146 (49%), Gaps = 7/146 (4%)
Query: 439 TKLADCQE---KNPELCELYIVEGDSAGGSVKQGR---DRRFQAVLPLRGKVLNIEKARF 492
KL D + K C L + EGDSA G R + PLRGK+LN+ +A
Sbjct: 7 PKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASA 66
Query: 493 EKIILSEQITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKM 552
++I+ + +I + +G+ + + + LRY ++IMTD D DG+HI+ L++ F
Sbjct: 67 DQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSF 126
Query: 553 PKLIEY-GYIYIAQPPLYKIKYGNNE 577
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 = 79.1 bits (194), Expect = 3e-15
Identities = 112/722 (15%), Positives = 220/722 (30%), Gaps = 201/722 (27%)
Query: 51 HHLVFEILDNAIDESLAGYCTKINVTIYSDNSIS------ISDNGRGIPIDIKIDD--KH 102
HH+ FE Y K ++++ D + + D + I +ID
Sbjct: 5 HHMDFET--GEHQ-----YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMS 57
Query: 103 KPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTINRNKKIHYME 162
K S + L + + + +F++ + N
Sbjct: 58 KDAVSGTLRLFWTLLSKQE--------------------EMVQKFVEEVLRIN------- 90
Query: 163 FRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFS----NIEFHYEILKK 218
Y L + I S+ I ++ + D ++F+ + Y L++
Sbjct: 91 --YKFLMSPIKTEQRQPSMMTRMYIEQRDR------LYNDNQVFAKYNVSRLQPYLKLRQ 142
Query: 219 RIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQAIGNKIS 278
+ EL V I G G K+ + + +
Sbjct: 143 ALLELR-PAKNVLID----------------GVLGS----GKTWVAL-----DVCLSYKV 176
Query: 279 EKKNNINIDVSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLK 338
+ K + I W N N N +L+ L L I + ++
Sbjct: 177 QCKMDFKI----FWLNLKNCNS---PETVLE-----MLQKLLYQIDP---NWTSRSDHSS 221
Query: 339 KSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKL-VSSEVRKPVEEIIIKTLFDFLQE 397
K+ I I+ L +L K +N L V V+ F+
Sbjct: 222 NIKLRI--HSIQAELRRLLKSK--------PYENCLLVLLNVQNAK---AWNA-FNLS-- 265
Query: 398 NPGESKLICEKIIEAARSREAARKTRELTRKKNLIDDIELS-TKLADCQEKNPELCELYI 456
C KI+ R ++ T +D ++ T ++ L Y+
Sbjct: 266 --------C-KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP-----DEVKSLLLKYL 311
Query: 457 VEGDSAGGSVKQGRDRRFQA--VLPLR----GKVLNIEKARFE--KIILSEQITTLISTL 508
+ R + P R + + A ++ K + +++TT+I
Sbjct: 312 --------DCRPQDLPR-EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIE-- 360
Query: 509 GIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPL 568
+ E + + R+ + AHI +LL+ + + I+ + +
Sbjct: 361 -SSLNVLEPAEYRKMFDRLSVFPP----SAHIPTILLSLIWFDV---IKSDVMVVV---- 408
Query: 569 YKIKYGNNECY----LRDDIEEERY-----MLKIAFKNVKLISIENGDIIKENYFFKLID 619
N+ + + +E L++ K ++ ++D
Sbjct: 409 -------NKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR----------SIVD 451
Query: 620 KYN--KTIEIVHRLKQIIDISILSAIMSDVILNLDTRENAEQFA--KKIIKKLNDSNIE- 674
YN KT + + +D S I +L E+ E+ + + L+ +E
Sbjct: 452 HYNIPKTFDSDDLIPPYLDQYFYSHIGH----HLKNIEHPERMTLFRMVF--LDFRFLEQ 505
Query: 675 -IIVEFDQLNNK-YLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKKIIGKGVII 732
I + N +LN ++ K YI D N+ Y++LV+ I F I + +I
Sbjct: 506 KIRHDSTAWNASGSILNTLQQLKFYKPYICD----NDPKYERLVNAILDFLPKIEENLIC 561
Query: 733 QK 734
K
Sbjct: 562 SK 563
Score = 77.2 bits (189), Expect = 1e-14
Identities = 79/558 (14%), Positives = 164/558 (29%), Gaps = 173/558 (31%)
Query: 331 IEENEFLKKSKIEIIGEDIREGLTCVLSIKIPDPKFNSQTKNKLVSSEVRK----PVEEI 386
E+++ K + + + + C + D K+ L E+
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDNFDCK---DVQD-----MPKSILSKEEIDHIIMSKDAVS 62
Query: 387 IIKTLFDFLQENPGES-------------KLICEKIIEAARSREAARKTRELTRKKN-LI 432
LF L E K + I R+ + TR +++ L
Sbjct: 63 GTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPI--KTEQRQPSMMTRMYIEQRDRLY 120
Query: 433 DDIELSTKLADCQEKNPE-----LCEL----YI-VEGDSAGGSVKQGRDRRFQAVLPLRG 482
+D ++ K + + L EL + ++G GS G
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGV--LGS----------------G 162
Query: 483 K-VLNIEKARFEKIILSEQITTLISTLGIGIEQDEF--NLEKLRYHRIIIMTDADIDGAH 539
K + ++ K+ + I F NL+ ++
Sbjct: 163 KTWVALDVCLSYKVQ---------CKMDFKI----FWLNLKNCNSPETVLE--------- 200
Query: 540 IRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVK 599
+L Y+ P K++ + + LR ++ + Y +N
Sbjct: 201 ---MLQKLLYQIDPNWTSRS----DHSSNIKLRIHSIQAELRRLLKSKPY------ENCL 247
Query: 600 LI--SIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILSAIMSDVILN-----LD 652
L+ +++N F + K + + R KQ+ D + +A + + L+ L
Sbjct: 248 LVLLNVQNAKAWN--AF----NLSCKIL-LTTRFKQVTD-FLSAATTTHISLDHHSMTLT 299
Query: 653 TRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDY 712
E K + + D E+ N L+I + ++ + + + + +
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREV-----LTTNPRRLSIIAESIR--DGLATWDNWKHVNC 352
Query: 713 KKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANNFYKIINYLRNEAENMVIKQRYKGLG 772
KL +II + +N L AE ++ + L
Sbjct: 353 DKLTTIIESS-----------------------------LNVL-EPAE---YRKMFDRLS 379
Query: 773 EMN-----PGQ----LW--------ETTMNPMI-RCLLKVKIKDAISADKIFMTLMGDNV 814
P +W +N + L++ K + +++ +
Sbjct: 380 VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE---KQP---KESTISIPSIYL 433
Query: 815 ELRRKFIELNALHAKNID 832
EL+ K ALH +D
Sbjct: 434 ELKVKLENEYALHRSIVD 451
Score = 58.3 bits (140), Expect = 8e-09
Identities = 87/620 (14%), Positives = 189/620 (30%), Gaps = 135/620 (21%)
Query: 2 LLKNKNSYDIQDTQESSYSASSIQ--ILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILD 59
+ N + D+QD +S S I I+ + + + V E+L
Sbjct: 29 FVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLR 88
Query: 60 ---NAIDESLAGYC--TKINVTIYSDN-SISISDNGRGIPIDIKIDDKHKPKRSAAEIVM 113
+ + + +Y + +DN ++ + R A +
Sbjct: 89 INYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQA----L 144
Query: 114 TELHAGGKFNKNSYKISGGLHGIGLSC-VNGLSRFLQLTINRNKKIHYMEFRYGVLQNRI 172
EL + G+ G G + + ++ + KI ++ + +
Sbjct: 145 LEL------RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198
Query: 173 IKTINGISVSPIKIIGDTNKQGTKIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCI 232
++ + + +I + + SNI+ ++ +R L +
Sbjct: 199 LEMLQKLLY---QIDPNWTSRS---------DHSSNIKLRIHSIQAELRRL-LKSKPYEN 245
Query: 233 TLI--DERIKKKEIFE-FKGGTSGFVSYINKSKLVVHPTIFQAIGNKISEKKNNINIDVS 289
L+ ++ + + F K+++ T F+ + + +S
Sbjct: 246 CLLVLLN-VQNAKAWNAFNLS----------CKILL-TTRFKQVTDFLSAAT-------- 285
Query: 290 MQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAI-NKYIEEN------EFLKKS-- 340
T +I H L +++ KY++ E L +
Sbjct: 286 --------------TTHISLDH---HSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328
Query: 341 KIEIIGEDIREGLTCVLSIKIPD--PKFNSQTKNKLVSS--EVRKPVEEIIIKTLFDFL- 395
++ II E IR+G + D N ++ S V +P E + +FD L
Sbjct: 329 RLSIIAESIRDG------LATWDNWKHVNCDKLTTIIESSLNVLEPAE---YRKMFDRLS 379
Query: 396 --QEN---PGESKLIC-----------EKIIEAARSREAARKTRELTRKKNL---IDDI- 435
+ P + L+ ++ K + K I I
Sbjct: 380 VFPPSAHIP--TILLSLIWFDVIKSDVMVVVNKLHKYSLVEK-----QPKESTISIPSIY 432
Query: 436 -ELSTKLADCQEKNPELCELY-IVEGDSAGGSVKQGRDRRFQAVLP--LRGKVLNIEKAR 491
EL KL + + + + Y I + + + D+ F + + L+
Sbjct: 433 LELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL 492
Query: 492 FEKIILS----EQ--ITTLISTLGIGIEQDEFNLEKLRYHRIIIMTDADIDGAHIRALLL 545
F + L EQ + G + L++L++++ I + + A +L
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNASGSILN--TLQQLKFYKPYICDNDPKYERLVNA-IL 549
Query: 546 TFFYRKMPKLIEYGYIYIAQ 565
F + LI Y + +
Sbjct: 550 DFLPKIEENLICSKYTDLLR 569
Score = 51.0 bits (121), Expect = 2e-06
Identities = 42/268 (15%), Positives = 85/268 (31%), Gaps = 55/268 (20%)
Query: 52 HLVFEILDNAIDESLAGYCTKINVTIYSDNSISISDNGRGIPIDIKIDDK------HKPK 105
H+ + L I+ SL ++ S+ P I
Sbjct: 349 HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV--------FPPSAHIPTILLSLIWFDVI 400
Query: 106 RSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQLTINRNKKIHYMEFRY 165
+S +V+ +LH K + + + I L L++ + +H R
Sbjct: 401 KSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLE--------LKVKLENEYALH----RS 448
Query: 166 GVLQNRIIKTINGISVSPIKI-------IG---DTNKQGTKIHFWVDEKIFSNIEFHYEI 215
V I KT + + P + IG + ++ + +F + F
Sbjct: 449 IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLF--RMVFLDFRF---- 502
Query: 216 LKKRIRELSFLNN---GVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLVVHPTIFQA 272
L+++IR S N + TL + K I + V+ I + +
Sbjct: 503 LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILD-------FLPKI 555
Query: 273 IGNKISEKKNNINIDVSMQWNNS--YNE 298
N I K ++ + +++ + + E
Sbjct: 556 EENLICSKYTDL-LRIALMAEDEAIFEE 582
>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 = 46.6 bits (110), Expect = 4e-05
Identities = 78/478 (16%), Positives = 150/478 (31%), Gaps = 162/478 (33%)
Query: 412 AARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPELCELYI------VEGDSAGGS 465
A++ +E K + D E +T EL ++ VE G
Sbjct: 30 ASQLQEQFNKILP-EPTEGFAADDEPTTPA--------ELVGKFLGYVSSLVEPSKVG-- 78
Query: 466 VKQGRDRRFQAVLPLRGKVLNIEKARFEKIILSEQ-ITTLISTLGIGIEQDEFNLEK--- 521
+F VL L L FE L I L + L +++++ L K
Sbjct: 79 -------QFDQVLNL---CLT----EFENCYLEGNDIHALAAKL---LQENDTTLVKTKE 121
Query: 522 -LR-YHRIIIMTDADIDGAHIRALLLTFFYRKMPKLIEYGYIYIA-----QPPLYKIKYG 574
++ Y IM D AL + + G + Q G
Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALF---------RAVGEGNAQLVAIFGGQ--------G 164
Query: 575 NNECYLRDDIEE--ERY------MLKIAFKNVKLIS---------IENG-DIIK------ 610
N + Y +++ + + Y ++K + + + + G +I++
Sbjct: 165 NTDDYF-EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPS 223
Query: 611 ----ENYF------FKLID-----KYNKTI--------EIVHRLKQIIDIS--ILSAIMS 645
++Y LI Y T E+ LK S +++A+
Sbjct: 224 NTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAV-- 281
Query: 646 DVILNLDTRENAEQFAKKIIKKL-----------NDSNIEIIVEFDQLNNK-----YLLN 689
I D+ E+ +K I L ++++ + D L N +L+
Sbjct: 282 -AIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS 340
Query: 690 IK-------KKFLKKKN-YI-----IDINFINNKD-------YKKLVSIISTFKKIIGKG 729
I + ++ K N ++ ++I+ +N + L + T +K
Sbjct: 341 ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPS 400
Query: 730 VIIQKSI---GEKIKKYTANNFYKII-----NYLRNEAENMVIKQRYKGLGEMNPGQL 779
+ Q I K+K +N F + + L A +++ K K N +
Sbjct: 401 GLDQSRIPFSERKLK--FSNRFLPVASPFHSHLLV-PASDLINKDLVKNNVSFNAKDI 455
Score = 45.0 bits (106), Expect = 1e-04
Identities = 46/301 (15%), Positives = 86/301 (28%), Gaps = 120/301 (39%)
Query: 582 DDIEEERY---MLKIAFKNVKLISI----ENGDIIKENYFFKLIDKYNKTIEIVHRLKQI 634
D+ ++ Y +L I N ++I E G I+ENY + + ++ +
Sbjct: 1650 DNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKE 1709
Query: 635 IDISILSAIMS--DVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKK 692
I+ S +L+ T + Q A L
Sbjct: 1710 INEHSTSYTFRSEKGLLSA-T-QFT-QPA-------------------------LT---- 1737
Query: 693 KFLKKKNYIIDINFINNKDYKKLVSIISTFKKIIGKGVIIQK------SIGEKIKKYTA- 745
L+ + F+ + KG+I S+GE Y A
Sbjct: 1738 ----------------------LME-KAAFEDLKSKGLIPADATFAGHSLGE----YAAL 1770
Query: 746 ---------NNFYKIINYLRNEAENMVIKQRYKGLGE--M---NPGQLWETTMNPMIRCL 791
+ +++ Y R + + + G M NPG++ + ++
Sbjct: 1771 ASLADVMSIESLVEVVFY-RGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQ-- 1827
Query: 792 LKVKIKDAISADKIFMTLMG-------DNV---------ELR--RKFIE-LNALHAKNID 832
+ + + G NV +LR LN + + ID
Sbjct: 1828 ---YVVERVGKRT------GWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKID 1878
Query: 833 I 833
I
Sbjct: 1879 I 1879
Score = 43.5 bits (102), Expect = 4e-04
Identities = 65/433 (15%), Positives = 120/433 (27%), Gaps = 188/433 (43%)
Query: 5 NKNSY--DIQDTQESSYSA-------SSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVF 55
N + Y +++D ++ Y S + L L E GL+ +
Sbjct: 165 NTDDYFEELRDLYQT-YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQ-----GLN--IL 216
Query: 56 EILDNAIDE-------------------SLAGYCTKINVTIYS-----DNSISISDNGRG 91
E L+N + LA Y + ++ + + +G
Sbjct: 217 EWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQG 276
Query: 92 IPIDIKIDDKHKPKRSAAEIVMTELHAGGK----FNKNSYKISGGLHGIGLSC------- 140
+ +A I A F + K L IG+ C
Sbjct: 277 LV-------------TAVAI------AETDSWESFFVSVRKAITVLFFIGVRCYEAYPNT 317
Query: 141 -----------------------VNGLSR-FLQLTINR-------NKKIHYMEFRYGVLQ 169
++ L++ +Q +N+ K++
Sbjct: 318 SLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVE---------- 367
Query: 170 NRIIKTING-----ISVSPI----------KIIGDTNKQGTKIHFWVDEKI-FSN----I 209
I +NG +S P K + ++I F + K+ FSN +
Sbjct: 368 ---ISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPF-SERKLKFSNRFLPV 423
Query: 210 E--FHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVSYINKSKLV--V 265
FH +L LI++ + K + F + V
Sbjct: 424 ASPFHSHLLVP------------ASDLINKDLVKNNV-SFNA-----------KDIQIPV 459
Query: 266 HPTI----FQAIGNKISEKKNNINIDVSMQWNNSYNEN---ILCF-----------TNNI 307
+ T + + ISE+ + I + ++W + IL F T+
Sbjct: 460 YDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRN 519
Query: 308 LQVDGGTHLTGLR 320
DG TG+R
Sbjct: 520 --KDG----TGVR 526
Score = 40.8 bits (95), Expect = 0.003
Identities = 41/260 (15%), Positives = 82/260 (31%), Gaps = 90/260 (34%)
Query: 149 QLTIN----RNKKIH--YMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKIHFWVD 202
LTI+ + K+I Y + +TI + KI + N+ T F +
Sbjct: 1671 NLTIHFGGEKGKRIRENYSAMIF--------ETIVDGKLKTEKIFKEINEHSTSYTFRSE 1722
Query: 203 EKIFSNIEF-----------HYEILKKR--IRELSF-----LNNG-----VC-------- 231
+ + S +F +E LK + I + L G
Sbjct: 1723 KGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSL--GEYAALASLADVMSIE 1780
Query: 232 --ITLIDER--IKKKEIFEFKGGTSGF-VSYINKSKLVVHPT--IFQAIGNKISEKKNNI 284
+ ++ R + + + G S + + IN ++ + Q + ++ ++ +
Sbjct: 1781 SLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWL 1840
Query: 285 ----NIDVSMQWNNSYNENILCFTNNILQVDGGTHLTGLRSGITRAINKYIEENEFLKKS 340
N N N+ + +G RA++ F+K
Sbjct: 1841 VEIVN-------YNVENQQYVA------------------AGDLRALDTVTNVLNFIKLQ 1875
Query: 341 KIEIIG-------EDIREGL 353
KI+II E++ L
Sbjct: 1876 KIDIIELQKSLSLEEVEGHL 1895
Score = 37.7 bits (87), Expect = 0.019
Identities = 55/306 (17%), Positives = 95/306 (31%), Gaps = 99/306 (32%)
Query: 411 EAARSREAARKTRELTR-KKNLIDDIELSTKLADCQEKNPELCELYIVEGDSAGGSVKQG 469
+ ++ +AA+ R + D S + D NP L I G G +++
Sbjct: 1634 DLYKTSKAAQDVWN--RADNHFKDTYGFS--ILDIVINNPV--NLTIHFGGEKGKRIREN 1687
Query: 470 RDR-RFQAVLPLRGKVLNIEKARFE---KIILSEQITTL---------ISTLGIGIEQDE 516
F+ ++ + K I K E + L ++ +
Sbjct: 1688 YSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAA---- 1743
Query: 517 FNLEKLRYHRIIIMTDADIDGAH----IRAL-----LLTF-------FYR------KMPK 554
E L+ + +I DA G H AL +++ FYR +P+
Sbjct: 1744 --FEDLK-SKGLIPADATFAG-HSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPR 1799
Query: 555 LIEYG---YIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIAFKNVKLISIENGDIIKE 611
E G Y IA P + E L+ +E + + L+ I N
Sbjct: 1800 -DELGRSNYGMIAINPGRVAASFSQEA-LQYVVER------VGKRTGWLVEIVN------ 1845
Query: 612 NYFFKLIDKYNKTIEIVHRLKQIIDIS-ILSAIMSDVILNLDTRENAEQFAKKIIKKLND 670
YN +E +Q + + L A LDT ++ +
Sbjct: 1846 ---------YN--VEN----QQYV-AAGDLRA--------LDT-------VTNVLNFIKL 1874
Query: 671 SNIEII 676
I+II
Sbjct: 1875 QKIDII 1880
Score = 34.6 bits (79), Expect = 0.17
Identities = 40/270 (14%), Positives = 80/270 (29%), Gaps = 100/270 (37%)
Query: 13 DTQESSYSASSIQILE-----GLEAVRKRPEMYI--------GDTSDGT-----GLHHLV 54
D+ ES + + + + G+ P + + ++G + +L
Sbjct: 287 DSWESFFVSVR-KAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLT 345
Query: 55 FEILDNAIDESLAGYCTKINVTIYSDNSISIS-DNGR------GIPID----------IK 97
E + + ++ K N + + + IS NG G P K
Sbjct: 346 QEQVQDYVN--------KTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK 397
Query: 98 IDD----------KHKPK-----------------RSAAEIVMTELHAGG-KFNKNSYKI 129
+ K K A++++ +L FN +I
Sbjct: 398 APSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQI 457
Query: 130 ------SGG-LHGIGLSCVNGLSR-FLQLTIN-----RNKKIHYMEF------RYGVLQN 170
G L + S + ++L + + K H ++F GVL +
Sbjct: 458 PVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTH 517
Query: 171 RI-----IKTING--ISVSPIKIIGDTNKQ 193
R ++ I + ++P G KQ
Sbjct: 518 RNKDGTGVRVIVAGTLDINPDDDYG--FKQ 545
Score = 31.2 bits (70), Expect = 2.2
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 15/64 (23%)
Query: 2 LLKNKNSYDIQDTQES--SYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILD 59
LL + +D ++ S++A IQI P +Y DT DG+ L L I +
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDIQI----------P-VY--DTFDGSDLRVLSGSISE 477
Query: 60 NAID 63
+D
Sbjct: 478 RIVD 481
>2q2e_B Type 2 DNA topoisomerase 6 subunit B; DNA-binding, SPO11, ATPase;
4.00A {Methanosarcina mazei}
Length = 621
Score = 46.0 bits (108), Expect = 5e-05
Identities = 47/233 (20%), Positives = 79/233 (33%), Gaps = 26/233 (11%)
Query: 21 ASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDES-LAGYCTKINVTIYS 79
A + + E K ++ +G S L V E +DNA+D AG I V +
Sbjct: 10 AKKQKSISVAEFFEKNRQI-LGFDSAPRSLITTVKEAVDNALDACEEAGILPDILVQVER 68
Query: 80 DNS----ISISDNGRGIPIDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHG 135
+ I DNG GI + PK V +L G +F ++ K S G G
Sbjct: 69 TGPDYVTVIIEDNGPGIV------REQIPK------VFAKLLYGSRF--HALKQSRGQQG 114
Query: 136 IGLSCVNGLSRFLQLTINRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGT 195
IG+S ++ + + I + N + ++ GT
Sbjct: 115 IGISAAVLYAQMTAGRHTKILSKTSPTAPAHYYELMINTSTNEPDILVDEVRDWFRPHGT 174
Query: 196 KIHFWVDEKIFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFK 248
+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 = 41.2 bits (96), Expect = 0.001
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 11/100 (11%)
Query: 50 LHHLVFEILDNAIDESLAGY------CTKINVTIYSDNS---ISISDNGRGIPIDI--KI 98
L +++ E+L NA+ ++ + + +TI +++ I ISD G GI ++
Sbjct: 239 LDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRV 298
Query: 99 DDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGL 138
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 = 40.6 bits (94), Expect = 0.002
Identities = 30/165 (18%), Positives = 54/165 (32%), Gaps = 23/165 (13%)
Query: 41 IGDTSDGTGLHHLVFEILDNAID-ESLAGYCTKINVTIYSDN------SISISDNGRGIP 93
G + L+ V E+++N++D + G I +TI + +++ DNG GIP
Sbjct: 23 AGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 82
Query: 94 IDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLSRFLQ-LTI 152
P + K+ + G++G+G+ S+ Q I
Sbjct: 83 PQ------EVPN------AFGRVLYSSKYVNRQ---TRGMYGLGVKAAVLYSQMHQDKPI 127
Query: 153 NRNKKIHYMEFRYGVLQNRIIKTINGISVSPIKIIGDTNKQGTKI 197
+ 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 = 40.1 bits (93), Expect = 0.002
Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 9/55 (16%)
Query: 50 LHHLVFEILDNAIDESLAGYCTK------INVTIYSDN---SISISDNGRGIPID 95
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 = 39.4 bits (91), Expect = 0.004
Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 10/95 (10%)
Query: 10 DIQDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAIDESLAGY 69
+ + Y +S L + ++I + LHH++FE+ NA+ ++
Sbjct: 193 CSRMLCDQYYLSSPELKLTQVNGKFPDQPIHI--VYVPSHLHHMLFELFKNAMRATVEHQ 250
Query: 70 C-----TKINVTIYSDN---SISISDNGRGIPIDI 96
T I V + +I ISD G G+P+ I
Sbjct: 251 ENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRI 285
>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 = 39.0 bits (90), Expect = 0.005
Identities = 22/94 (23%), Positives = 38/94 (40%), Gaps = 10/94 (10%)
Query: 10 DIQDTQESSYSASSIQILEGLEAVRKRPEMYIGDTSDGTGLHHLVFEILDNAI-----DE 64
+ + + Y S LE L A + + + L+H+VFE+ NA+
Sbjct: 206 NARRLCDLYYINSPELELEELNAKSPGQPIQV--VYVPSHLYHMVFELFKNAMRATMEHH 263
Query: 65 SLAGYCTKINVTIYSDNS---ISISDNGRGIPID 95
+ 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 = 37.8 bits (87), Expect = 0.012
Identities = 22/112 (19%), Positives = 43/112 (38%), Gaps = 22/112 (19%)
Query: 41 IGDTSDGTGLHHLVFEILDNAID-ESLAGYCTKINVTIYSDN------SISISDNGRGIP 93
G + L+ V E+++N++D + G I +TI + +++ DNG GIP
Sbjct: 24 AGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 83
Query: 94 IDIKIDDKHKPKRSAAEIVMTELHAGGKFNKNSYKISGGLHGIGLSCVNGLS 145
+ 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 = 37.9 bits (87), Expect = 0.012
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 8/54 (14%)
Query: 50 LHHLVFEILDNAIDESLAGYCTK-----INVTI---YSDNSISISDNGRGIPID 95
L+H++FE+ NA+ ++ + + I V + D SI +SD G G+P+
Sbjct: 232 LYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLR 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 = 0.016
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 56 EILDNAIDESLAGYCTKINVTIYS--DNSISISDNGRGIPID 95
E+++N++D AG T+I++ I I I DNG GI D
Sbjct: 31 ELVENSLD---AG-ATRIDIDIERGGAKLIRIRDNGCGIKKD 68
>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 = 34.1 bits (79), Expect = 0.20
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 6/42 (14%)
Query: 56 EILDNAIDESLAGYCTKINVTI--YSDNSISISDNGRGIPID 95
E+++N++D AG T I++ + Y + I +SDNG G+ +
Sbjct: 41 ELVENSLD---AG-ATNIDLKLKDYGVDLIEVSDNGCGVEEE 78
>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 = 0.20
Identities = 34/261 (13%), Positives = 79/261 (30%), Gaps = 27/261 (10%)
Query: 573 YGNNECYLRDDIEEERYMLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLK 632
+ ++ C LR+++ + + + + + I++E + + + +
Sbjct: 217 HDHHFCLLREEVTFGKRSSSVKTLETQNFFLLHLSILREYLALEFEEITDSVQFEYDFER 276
Query: 633 QIIDISILSAIMS-DVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIK 691
+ D + + D + NL + F L + K
Sbjct: 277 VLDDFIFVLFTIGNDFLPNLPDLHLKKGA------------------FPVLLQTF----K 314
Query: 692 KKFLKKKNYIIDINFINNKDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTANNFYKI 751
+ YI + IN + + +S F+ + +K I + N
Sbjct: 315 EALQHMDGYINEQGKINLARFSIWLKYLSDFEYLN----FEKKDIDVEWFNQQLENISLE 370
Query: 752 INYLRNEAENMVIKQRYKGLGEMNPGQLWETTMNPMIRCLLKVKIKDAISADKIFMTLMG 811
R ++ ++ K L L +T + L + DK +
Sbjct: 371 GERKRTRMGKKLLMKQQKKLIGAVKPWLLKTVQRKVTSELQDADFEIFPLEDKELVRANL 430
Query: 812 DNVELRRKFIELNALHAKNID 832
D ++ + L H+K+ D
Sbjct: 431 DFLKEFAFDLGLILAHSKSKD 451
>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 = 0.22
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 56 EILDNAIDESLAGYCTKINVTIYS--DNSISISDNGRGIPID 95
E+++N +D A T I V + I I DNG GI +
Sbjct: 35 EMIENCLD---AK-STSIQVIVKEGGLKLIQIQDNGTGIRKE 72
>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 = 33.3 bits (77), Expect = 0.25
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 46 DGTGLHHLVFEILDNAIDESLAGYCTKINVTIYSDNSISISDNGRGIP 93
L LV +LDNA+ S G + ++VT+ +DN + DNG G+
Sbjct: 114 QPLLLSLLVRNLLDNAVRYSPQG--SVVDVTLNADN-FIVRDNGPGVT 158
>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 = 0.25
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 56 EILDNAIDESLAGYCTKINVTI--YSDNSISISDNGRGIPID 95
E++DN+ID A +I + Y SI SDNG GI
Sbjct: 32 ELVDNSID---AN-ANQIEIIFKDYGLESIECSDNGDGIDPS 69
>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 = 32.2 bits (74), Expect = 0.33
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 46 DGTGLHHLVFEILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIP 93
GL V + NA+ A + ++ S + I+I DNG G+P
Sbjct: 43 LPAGLRLAVDNAIANAVKHGGAT---LVQLSAVSSRAGVEIAIDDNGSGVP 90
>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 = 0.39
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 57 ILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIP 93
I+ NA+ S G ++ + + IS+ D G GIP
Sbjct: 51 IISNALKYSPEGGHVTFSIDVNEEEELLYISVKDEGIGIP 90
>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 = 29.3 bits (65), Expect = 1.4
Identities = 12/68 (17%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 656 NAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKL 715
N ++ I+K++ + N + + + FLK++ YII +++ +++ +
Sbjct: 2 NKDKLRYAILKEIFEGNTPLSENDIGVTEDQFDDAVN-FLKREGYIIGVHYSDDRPHLYK 60
Query: 716 VSIISTFK 723
+ T K
Sbjct: 61 LGPELTEK 68
>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 = 1.4
Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 5/79 (6%)
Query: 212 HYEILKKRIRELSFLNNGVCITLIDERIKKKEIFEFKGGTSGFVS--YINKSKLVVHPTI 269
IR + + L+D + F K SG S YI+ +LV +P I
Sbjct: 244 ELCEEINAIRFAKGASVELAKALVDSHCVRFGNFTLK---SGKSSPIYIDLRRLVTYPAI 300
Query: 270 FQAIGNKISEKKNNINIDV 288
+ + + ++ + D
Sbjct: 301 MRLVAREYAKVLRHYKFDR 319
>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 = 1.6
Identities = 15/68 (22%), Positives = 22/68 (32%), Gaps = 19/68 (27%)
Query: 644 MSDVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIID 703
V L+ TRE A +A I+ V D + + K+Y
Sbjct: 59 KQQVCLSFTTRELAIAYAVA-------HKIDYTVLQD----------NPRTIVPKSYA-- 99
Query: 704 INFINNKD 711
NF +D
Sbjct: 100 DNFTKPRD 107
>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 = 1.8
Identities = 10/49 (20%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 54 VFEILDNAIDESLAGYCT-KINVTIYSDN---SISISDNGRGIPIDIKI 98
V E + NAI +++++ ++ +++ D G GIP +
Sbjct: 44 VSEAVTNAIIHGYNNDPNGIVSISVIIEDGVVHLTVRDEGVGIPDIEEA 92
>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 = 1.9
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 414 RSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPEL 451
R+R AA ++R+ ++K + +E K D N +L
Sbjct: 8 RNRAAASRSRQ--KRKVWVQSLE--KKAEDLSSLNGQL 41
>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 = 2.4
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 57 ILDNAIDESLAG-YCTKINVTIYSDNS---ISISDNGRGIP 93
+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 = 29.4 bits (67), Expect = 2.4
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 83 ISISDNGRGIPIDIK 97
I + DNG GIP ++
Sbjct: 94 IDVEDNGPGIPPHLQ 108
>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 = 29.8 bits (67), Expect = 2.6
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 377 SEVRKPVEEI--IIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRE--LTRKKNLI 432
V ++I I L D+ +P +L+ + +E + R+ RK +
Sbjct: 69 ISVPVDPDDIEGWIDRLLDYHAAHPELLRLLFWEGMEYGTAELPHEAERQEHYARKVAAV 128
Query: 433 DD 434
D
Sbjct: 129 RD 130
>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 = 2.7
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 413 ARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPEL 451
R+R AA K+R+ RK I +E K+ + +N EL
Sbjct: 7 MRNRIAASKSRK--RKLERIARLE--EKVKTLKAQNSEL 41
>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 = 27.5 bits (61), Expect = 2.7
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 413 ARSREAARKTRELTRKKNLIDDIELSTKLADCQEKNPEL 451
AR+ EAAR++R RK + +E K+ + KN L
Sbjct: 15 ARNTEAARRSRA--RKLQRMKQLE--DKVEELLSKNYHL 49
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA
complex; HET: DNA D3T; 2.40A {Mus musculus}
Length = 360
Score = 30.3 bits (67), Expect = 2.7
Identities = 12/107 (11%), Positives = 33/107 (30%), Gaps = 10/107 (9%)
Query: 668 LNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKKIIG 727
L N + + L + + ++ + + K V+ +S +
Sbjct: 13 LTHHNTLLSEALETLAE--AAGFEANEGRLLSFSRAASVL--KSLPCPVASLSQLHGLPY 68
Query: 728 KGVIIQKSIGEKIKKYTANNFYKIINYLRNEAENMVIKQ--RYKGLG 772
G + I++ + + + +R +K + G+G
Sbjct: 69 FG----EHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVG 111
>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 = 29.1 bits (66), Expect = 2.8
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 46 DGTGLHHLVFEILDNAIDESLAGYC-TKINVTIYSDNS---ISISDNGRGIP 93
+ ++ +LDNA YC + ++ + I + D+G GIP
Sbjct: 41 EQNDFVEVMGNVLDNACK-----YCLEFVEISARQTDEHLYIVVEDDGPGIP 87
>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 = 30.4 bits (69), Expect = 2.9
Identities = 11/94 (11%), Positives = 23/94 (24%), Gaps = 17/94 (18%)
Query: 654 RENAEQFAKKIIKKLNDSNIEIIVE-----------FDQLNNKYL-----LNIKKKFLKK 697
RE+ A+ + IVE + ++L + K +K
Sbjct: 89 REHFAMLARDFLATELTGPDPFIVEIGCNDGIMLRTIQEAGVRHLGFEPSSGVAAKAREK 148
Query: 698 KNYIIDINFINNKDYKKLVSIISTFKKIIGKGVI 731
+ +F + I +
Sbjct: 149 GIRVR-TDFFEKATADDVRRTEGPANVIYAANTL 181
Score = 28.8 bits (65), Expect = 8.7
Identities = 7/89 (7%), Positives = 27/89 (30%), Gaps = 2/89 (2%)
Query: 661 AKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIIS 720
+ + K + I + +F ++++ + + ++ +
Sbjct: 138 SSGVAAKAREKGIRVRTDF--FEKATADDVRRTEGPANVIYAANTLCHIPYVQSVLEGVD 195
Query: 721 TFKKIIGKGVIIQKSIGEKIKKYTANNFY 749
G V +G+ + K + + +
Sbjct: 196 ALLAPDGVFVFEDPYLGDIVAKTSFDQIF 224
>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 = 3.0
Identities = 14/86 (16%), Positives = 26/86 (30%)
Query: 535 IDGAHIRALLLTFFYRKMPKLIEYGYIYIAQPPLYKIKYGNNECYLRDDIEEERYMLKIA 594
DG+HI A + T F P + G I + ++ +LK
Sbjct: 294 DDGSHINAHVRTSFAALFPHVRPGGLYVIEDMWTAYWPGFGGQADPQECSGTSLGLLKSL 353
Query: 595 FKNVKLISIENGDIIKENYFFKLIDK 620
++ + + Y + I
Sbjct: 354 IDAIQHQELPSDPNRSPGYVDRNIVG 379
>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 = 3.0
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 19/67 (28%)
Query: 644 MSDVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIID 703
V L +T+E AE +A++ IE V K+ K +Y
Sbjct: 51 KQQVKLTFETQEQAEAYAQR-------KGIEYRVILP----------KEATRKVVSYT-- 91
Query: 704 INFINNK 710
NF N+
Sbjct: 92 DNFRFNR 98
>3l7y_A Putative uncharacterized protein SMU.1108C; hydrolase; 2.00A
{Streptococcus mutans}
Length = 304
Score = 29.9 bits (68), Expect = 3.0
Identities = 15/100 (15%), Positives = 32/100 (32%), Gaps = 10/100 (10%)
Query: 580 LRDDIEEERYMLKIAFKNVKLI-SIENGDIIKEN---YFFKLIDKYNKTIEIVHRLKQII 635
R+DI Y ++ + + S E +K+ K++ + +E+V+ +
Sbjct: 119 QREDIASIIYFIEEKYPQAVIALSGEKKGYLKKGVSENIVKMLSPFFPVLELVNSFSPLP 178
Query: 636 DISILSAIMSDVILNLDTRENAEQFAKKIIKKLNDSNIEI 675
D + E + Q K I +
Sbjct: 179 DERFFKLTL------QVKEEESAQIMKAIADYKTSQRLVG 212
>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 = 3.6
Identities = 10/43 (23%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 57 ILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIPIDI 96
++ NAI+ + KI +T + +S+ ++G IP ++
Sbjct: 252 LVQNAIEATGEN--GKIKITSEDMYTKVRVSVWNSGPPIPEEL 292
>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 = 29.6 bits (66), Expect = 4.6
Identities = 28/179 (15%), Positives = 60/179 (33%), Gaps = 16/179 (8%)
Query: 582 DDIEEERYMLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILS 641
++ + + K+A +L + +N I F + + + + ++
Sbjct: 155 PNVAMKDLVQKLA-SKEELSTADNEMIELLARFNERQASFFGQFSVRGYVNYDKHVAKYL 213
Query: 642 AIMSDVILNLDTRENAEQFAKKIIKKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYI 701
I + + + + E K +K +N E N Y IKK K K+
Sbjct: 214 KI----LPDQFSYQAIEDVVKADAEKNTSNN-----EMGMENYFYNEQIKKDLKKLKDSQ 264
Query: 702 IDINFINNKDYKKLVSIISTFKKIIGKGVIIQKSIGEKIKKYTA------NNFYKIINY 754
++ + +Y L +++ F K + I + +K Y + I Y
Sbjct: 265 KSFTYLKSPEYNDLQLVLTQFSKSKVNPIFIIPPVNKKWMDYAGLREDMYQQTVQKIRY 323
>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 = 4.7
Identities = 6/56 (10%), Positives = 18/56 (32%), Gaps = 2/56 (3%)
Query: 382 PVEEI--IIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRELTRKKNLIDDI 435
P ++ I D + P ++L+ + ++ + + L +
Sbjct: 90 PEAKLRRHISKCIDTYYDYPYLNRLLMRLVRDSDEAEAKRIADQYLLPLHRAYNRF 145
>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 = 5.5
Identities = 7/40 (17%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 251 TSGFVS--YINKSKLVVHPTIFQAIGNKISEKKNNINIDV 288
+SG + Y++ + +H + IG + E + +
Sbjct: 27 SSGKEADYYVDLRRATLHARASRLIGELLRELTADWDYVA 66
>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 = 29.1 bits (64), Expect = 5.8
Identities = 19/116 (16%), Positives = 43/116 (37%), Gaps = 8/116 (6%)
Query: 666 KKLNDSNIEIIVEFDQLNNKYLLNIKKKFLKKKNYIIDINFINNKDYKKLVSIISTFKKI 725
+K + N+ I + + L +++ + Y IN + K + K V+ I
Sbjct: 7 QKATNHNLHITEKLEVLAK--AYSVQGDKWRALGYAKAINAL--KSFHKPVTSYQEACSI 62
Query: 726 IGKGVIIQKSIGEKIKKYTANNFYKIINYLRNEAENMVIKQRYKGLGEMNPGQLWE 781
G G K + EKI + + + ++++ + + G G ++
Sbjct: 63 PGIG----KRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQ 114
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 28.2 bits (62), Expect = 8.1
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 8/75 (10%)
Query: 409 IIEAARSR---EAARKTRELTRKKNLID-DIELSTKLADCQEK-NPELCELYIVEGDSAG 463
I +A R E+ RK RE ++K L + D + +EK +L E + +
Sbjct: 74 IAQADRLTQEPESIRKWRE-EQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVE 132
Query: 464 GSVKQGR--DRRFQA 476
+ R D+ F
Sbjct: 133 KNKINNRIADKAFYQ 147
>1pb6_A Hypothetical transcriptional regulator YCDC; helix-loop-helix,
dimer, structural genomics, PSI, protein structure
initiative; 2.50A {Escherichia coli} SCOP: a.4.1.9
a.121.1.1 PDB: 3loc_A*
Length = 212
Score = 28.5 bits (64), Expect = 8.1
Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 5/68 (7%)
Query: 382 PVEEI--IIKTLFDFLQENPGESKLIC-EKIIEAARSREAARKTRE--LTRKKNLIDDIE 436
P+ I I+ + ++ P S+L C E + A + + + K LI
Sbjct: 90 PLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWV 149
Query: 437 LSTKLADC 444
S KLA
Sbjct: 150 KSGKLAPI 157
>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 = 27.9 bits (63), Expect = 8.2
Identities = 10/43 (23%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 57 ILDNAIDESLAGYCTKINVTIYSDNS---ISISDNGRGIPIDI 96
++ NAI+ + KI +T + +S+ ++G IP ++
Sbjct: 55 LVQNAIEATGEN--GKIKITSEDMYTKVRVSVWNSGPPIPEEL 95
>3jrx_A Acetyl-COA carboxylase 2; BC domain, soraphen A, alternative
splicing, ATP-binding, biotin, fatty acid biosynthesis,
ligase, lipid synthesis; HET: S1A; 2.50A {Homo sapiens}
PDB: 3jrw_A*
Length = 587
Score = 28.8 bits (65), Expect = 9.1
Identities = 9/38 (23%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 205 IFSNIEFHYEILKKRIRELSFLNNGVCITLIDERIKKK 242
+ +E+ +L+ SF NN + +D I +K
Sbjct: 526 FRTTVEYLINLLETE----SFQNNDIDTGWLDYLIAEK 559
>3bq9_A Predicted rossmann fold nucleotide-binding domain containing
protein; structural genomics, PSI-2, protein structure
initiative; 1.80A {Idiomarina baltica}
Length = 460
Score = 28.8 bits (64), Expect = 9.3
Identities = 14/89 (15%), Positives = 30/89 (33%), Gaps = 14/89 (15%)
Query: 582 DDIEEERYMLKIAFKNVKLISIENGDIIKENYFFKLIDKYNKTIEIVHRLKQIIDISILS 641
DD + VK ++GD N+ K+ +++ + H
Sbjct: 317 DDPAAVAQHMHAGMAAVKQYRRDSGDAYYFNWTLKINEEFQRPFSPTH------------ 364
Query: 642 AIMSDVILNLDTRENAEQFAKKIIKKLND 670
++ LNL + E+ A + + +
Sbjct: 365 ENVAA--LNLHPDQPKERLAADLRRAFSA 391
>2jj7_A Hemolysin II regulatory protein; DNA-binding protein, transcription
regulation, DNA-binding, family, transcription,
transcriptional regulator; 2.10A {Bacillus cereus} PDB:
2wv1_A 2jk3_A 2fx0_A
Length = 186
Score = 28.1 bits (63), Expect = 9.6
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 382 PVEEI--IIKTLFDFLQENPGESKLICEKIIEAARSREAARKTRE 424
P+ + + ++ENP L E+II+ + E +
Sbjct: 79 PINALREYLTVFTTHIKENPEIGTLAYEEIIKESARLEKIKPYFI 123
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 0.139 0.387
Gapped
Lambda K H
0.267 0.0814 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 12,977,503
Number of extensions: 855293
Number of successful extensions: 2471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2346
Number of HSP's successfully gapped: 170
Length of query: 833
Length of database: 6,701,793
Length adjustment: 102
Effective length of query: 731
Effective length of database: 3,853,851
Effective search space: 2817165081
Effective search space used: 2817165081
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: 61 (27.1 bits)