RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780945|ref|YP_003065358.1| ATP-dependent DNA helicase RecG [Candidatus Liberibacter asiaticus str. psy62] (700 letters) >gnl|CDD|182836 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional. Length = 681 Score = 819 bits (2119), Expect = 0.0 Identities = 303/675 (44%), Positives = 430/675 (63%), Gaps = 12/675 (1%) Query: 3 PSFLNPLFAPLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPKIS 62 PS L L APL++ +GVG K + L+K+ DLL + P + DR I+ Sbjct: 1 PSLLLLLDAPLTSLKGVGPKTAEKLAKL------GIHTVQDLLLHLPRRYEDRTRLKPIA 54 Query: 63 EISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRK 122 E+ VT+ G + KRR + ++DGTG +TL FF LK G++ Sbjct: 55 ELRPGEKVTVEGEVLSAEVVF-GKRRRLTVTVSDGTGNLTLRFFNFNQPYLKKQLKVGKR 113 Query: 123 ITVTGKIKKLKNRIIMVHPHYIFHNS-QDVNFPLIEAVYSLPTGLSVDLFKKIIVEALSR 181 + V GK+K+ K + MVHP Y + VY L GL +K+I +AL Sbjct: 114 VAVYGKVKRGKYGLEMVHPEYEVLEEESPELEGRLTPVYPLTEGLKQKTLRKLIKQALEL 173 Query: 182 LPVLPEWIEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIALL 241 L LPE + ++LL+K S+AEA IH P E PAR RL ++EL A Q++LL Sbjct: 174 LDALPELLPEELLEKYGLLSLAEALRAIHFP---PSDEDLHPARRRLKFEELFALQLSLL 230 Query: 242 LMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGD 301 L+R + + P+ +G++ +K L ++PF T +Q+ + +IL D++ M R+LQGD Sbjct: 231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGD 290 Query: 302 VGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQ 361 VGSGKT+VA +A AA+EAG QA +MAP ILA+QHYE +KK + I V ++TG++ Sbjct: 291 VGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKG 350 Query: 362 AHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKATAP 421 RR+ LE IA G+A I+IGTHAL QD ++++ L LVI+DEQHRFGV+QRL L +K P Sbjct: 351 KERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHRFGVEQRLALREKGENP 410 Query: 422 HVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSE 481 HVL+MTATPIPRTL +T+ GD+D+S I E P GRKPI TV+IP +R DEV ER++ +++ Sbjct: 411 HVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEIAK 470 Query: 482 GKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNG 540 G++AY +CP IEE ++ + +S E + L E F + ++HGRM +K++VM +FK G Sbjct: 471 GRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAG 530 Query: 541 TCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPL 600 +L+ATTVIEVG+DV +A++++IENAE FGLAQLHQLRGRVGRG S C+LLY PL Sbjct: 531 EIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPL 590 Query: 601 SKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSGMPKFLIAQPELHDSLLEIAR 660 S+ + RL +++ T DGF+IAE+DL+ R GE+LG +QSG+P+F +A + LLE AR Sbjct: 591 SETARERLKIMRETNDGFVIAEKDLELRGPGELLGTRQSGLPEFKVADLVRDEELLEEAR 650 Query: 661 KDAKHILTQDPDLTS 675 KDA+ +L +DP+L Sbjct: 651 KDARELLERDPELAE 665 >gnl|CDD|161975 TIGR00643, recG, ATP-dependent DNA helicase RecG. Length = 630 Score = 603 bits (1558), Expect = e-173 Identities = 264/628 (42%), Positives = 385/628 (61%), Gaps = 12/628 (1%) Query: 43 DLLFYHPSSFIDRHYRPKISEISEERIVTITGYISQHSSFQLQKRRPYKILLND-GTGEI 101 DLLFY P + DR I E+ TI G + H F ++R+ K+ L D G ++ Sbjct: 8 DLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKL 67 Query: 102 TLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPHYIFHNSQDVNFPLIEAVYS 161 L FF R LK F G K+ V GK+K K + ++HP +I I VY Sbjct: 68 ELRFFNR--AFLKKKFKVGSKVVVYGKVKSSKFKAYLIHPEFISEKDGVEFELKILPVYP 125 Query: 162 LPTGLSVDLFKKIIVEALSRLP-VLPEWIEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEW 220 L GL+ +K+I +AL +L L + + ++L +K S+ +A IH P K Sbjct: 126 LTEGLTQKKLRKLIQQALDQLDKSLEDPLPEELREKYGLLSLEDALRAIHFP---KTLSL 182 Query: 221 TSPARERLAYDELLAGQIALL-LMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQES 279 AR RL +DE Q+A+L + ++ P N ++ K L ++PF T++Q+ Sbjct: 183 LELARRRLIFDEFFYLQLAMLARRLGEKQQFSAPPANPSEELLTKFLASLPFKLTRAQKR 242 Query: 280 AIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYE 339 +K+ILQD+ M R+LQGDVGSGKTLVA +AM AA+EAG Q +MAP ILA+QHY Sbjct: 243 VVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYN 302 Query: 340 FIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVI 399 ++ I V ++TG++ R++ LE IA GQ H+++GTHAL Q+ +++ +L LVI Sbjct: 303 SLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVI 362 Query: 400 VDEQHRFGVQQRLKLTQKA---TAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRK 456 +DEQHRFGV+QR KL +K PHVL+M+ATPIPRTL LT GD+D S I E P GRK Sbjct: 363 IDEQHRFGVEQRKKLREKGQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRK 422 Query: 457 PIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS 516 PI TV+I + D V E ++ +++G++AY + P IEE ++ + ++ + L + F Sbjct: 423 PITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPK 482 Query: 517 -SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQ 575 ++ ++HGRM +KE+VM+ F+ G +L+ATTVIEVG+DV +A++++IE+AE FGL+Q Sbjct: 483 YNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQ 542 Query: 576 LHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILG 635 LHQLRGRVGRG+ S C+L+Y P S+++ RL V+ +T DGF+IAEEDL+ R G++LG Sbjct: 543 LHQLRGRVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLG 602 Query: 636 IKQSGMPKFLIAQPELHDSLLEIARKDA 663 KQSG P+F +A +L AR+DA Sbjct: 603 TKQSGYPEFRVADLVRDREILVEAREDA 630 >gnl|CDD|161938 TIGR00580, mfd, transcription-repair coupling factor (mfd). All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. Length = 926 Score = 310 bits (796), Expect = 7e-85 Identities = 149/410 (36%), Positives = 232/410 (56%), Gaps = 21/410 (5%) Query: 240 LLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQ 299 L+ + + K G + + Q+ + PF T Q AI++I DM M R++ Sbjct: 419 LIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVC 478 Query: 300 GDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNM 359 GDVG GKT VA+ A AV G Q ++ P +LAQQH+E K+ N + +E+++ Sbjct: 479 GDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFR 538 Query: 360 PQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKAT 419 + + L+ +A G+ I+IGTH L Q +++ L L+I+DE+ RFGV+Q+ KL + T Sbjct: 539 SAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRT 598 Query: 420 APHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINR--IDEVIERLKV 477 + VL ++ATPIPRTL ++ G D+S I P R P++T ++ + + E I R Sbjct: 599 SVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEYDPELVREAIRR--- 655 Query: 478 VLSEGKKAYWICPQIE--EKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMD 535 L G + +++ +IE EK + R +V + IAI HG+M++ + E VM Sbjct: 656 ELLRGGQVFYVHNRIESIEKLATQLRELVPE---------ARIAIAHGQMTENELEEVML 706 Query: 536 SFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILL 595 F G ++L+ TT+IE GID+ +A+ IIIE A+ FGLAQL+QLRGRVGR ++ + LL Sbjct: 707 EFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLL 766 Query: 596 YHP--PLSKNSYTRLSVLKNTED---GFLIAEEDLKQRKEGEILGIKQSG 640 Y L++++ RL ++ + GF IA DL+ R G +LG +QSG Sbjct: 767 YPHQKALTEDAQKRLEAIQEFSELGAGFKIALHDLEIRGAGNLLGEEQSG 816 >gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor; Provisional. Length = 1147 Score = 253 bits (647), Expect = 1e-67 Identities = 146/379 (38%), Positives = 211/379 (55%), Gaps = 19/379 (5%) Query: 270 PFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP 329 PF T Q AI +L DM Q M R++ GDVG GKT VA+ A AVE Q ++ P Sbjct: 598 PFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVP 657 Query: 330 IGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDS 389 +LAQQHY+ + N + +E+++ + + L A G+ I+IGTH L Q Sbjct: 658 TTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSD 717 Query: 390 IQYYKLILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKIT 449 +++ L L+IVDE+HRFGV+ + ++ +L +TATPIPRTL + G D+S I Sbjct: 718 VKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIA 777 Query: 450 EKPAGRKPIKTVIIPINRIDEVIER---LKVVLSEGKKAYWICPQIEEKKESNFRSVVER 506 PA R +KT + D ++ R L+ +L G + Y++ +E N + ER Sbjct: 778 TPPARRLAVKTF---VREYDSLVVREAILREIL-RGGQVYYLYNDVE-----NIQKAAER 828 Query: 507 FNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE 566 L + IAI HG+M + + E VM+ F + +L+ TT+IE GID+ A+ IIIE Sbjct: 829 LAELVPE--ARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIE 886 Query: 567 NAEHFGLAQLHQLRGRVGRGEEISSCILLYHPP--LSKNSYTRLSVLKNTED---GFLIA 621 A+HFGLAQLHQLRGRVGR + LL P ++ ++ RL + + ED GF +A Sbjct: 887 RADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALA 946 Query: 622 EEDLKQRKEGEILGIKQSG 640 DL+ R GE+LG +QSG Sbjct: 947 THDLEIRGAGELLGEEQSG 965 >gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. Length = 201 Score = 104 bits (260), Expect = 1e-22 Identities = 53/207 (25%), Positives = 84/207 (40%), Gaps = 20/207 (9%) Query: 265 ILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV--EAGG 322 I + Q+ AI+ +L IL GSGKTL AL+ A+ G Sbjct: 1 IEKFGFEPLRPYQKEAIEALLS-----GLRDVILAAPTGSGKTLAALLPALEALKRGKGK 55 Query: 323 QAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT 382 + +++ P LA+Q E +KK + + V + G +R+ L ++ G+ I++ T Sbjct: 56 RVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDS---KREQLRKLESGKTDILVTT 112 Query: 383 -----HALFQDSIQYYKLILVIVDEQHRFGVQQRLK-----LTQKATAPHVLLMTATPIP 432 L D ++ + LVI+DE HR L +LL++ATP Sbjct: 113 PGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPE 172 Query: 433 RTLVLTSLGDIDISKITEKPAGRKPIK 459 L L D I P +PI+ Sbjct: 173 EIENLLELFLNDPVFIDVGPTPLEPIE 199 >gnl|CDD|161946 TIGR00595, priA, primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 505 Score = 74.3 bits (183), Expect = 1e-13 Identities = 92/422 (21%), Positives = 157/422 (37%), Gaps = 105/422 (24%) Query: 298 LQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP-IGILAQQHYEFIKKYTQNTQIIVEIIT 356 L G GSGKT V L A+ + G +++ P I + Q F KY +Q V ++ Sbjct: 2 LFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRF--KYRFGSQ--VAVLH 57 Query: 357 GNMPQAHRRKALERIAHGQAHIIIGTH-ALFQDSIQYYKLILVIVDEQHRFGVQQR---- 411 + + + +A ++ +G+ ++IGT ALF + + L L+IVDE+H +Q Sbjct: 58 SGLSDSEKLQAWRKVKNGEILVVIGTRSALF---LPFKNLGLIIVDEEHDSSYKQEEGPR 114 Query: 412 -------LKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIP 464 + +K P V+L +ATP + + +T + +GRKP + +I Sbjct: 115 YHARDVAVYRAKKFNCP-VVLGSATPSLESYHNAKQKAYRLLVLTRRVSGRKPPEVKLID 173 Query: 465 INR-------IDEVIERLKVVLSEGKKA------------------YWI----------- 488 + + E+I ++ L+ G+++ +I Sbjct: 174 MRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLT 233 Query: 489 ----------------------CPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRM- 525 CPQ + E+ I R+ Sbjct: 234 YHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIA--RID 291 Query: 526 SDIDK-----ESVMDSFKNGTCKLLIATTVIEVGID--------VVDASIIIIEN----A 568 SD E++++ F NG +LI T +I G V+DA + A Sbjct: 292 SDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAA 351 Query: 569 EHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQR 628 E G L Q+ GR GR E+ I+ + P N + L + F E++L QR Sbjct: 352 ER-GFQLLTQVAGRAGRAEDPGQVIIQTYNP---NHPAIQAALTGDYEAFY--EQELAQR 405 Query: 629 KE 630 + Sbjct: 406 RA 407 >gnl|CDD|128766 smart00490, HELICc, helicase superfamily c-terminal domain. Length = 82 Score = 71.5 bits (176), Expect = 8e-13 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 1/69 (1%) Query: 517 SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQL 576 +A +HG +S ++E +++ F NG K+L+AT V E G+D+ ++II + + A Sbjct: 13 KVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASY 71 Query: 577 HQLRGRVGR 585 Q GR GR Sbjct: 72 IQRIGRAGR 80 Score = 32.6 bits (75), Expect = 0.40 Identities = 10/47 (21%), Positives = 22/47 (46%) Query: 339 EFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHAL 385 E + + + I V + G + Q R + LE+ +G+ +++ T Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVA 47 >gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional. Length = 773 Score = 60.7 bits (148), Expect = 1e-09 Identities = 42/144 (29%), Positives = 70/144 (48%), Gaps = 26/144 (18%) Query: 303 GSGKTLVALIAMAAAVEA-GGQAVIMAPIGILAQQHYEFIKKYTQ--NTQIIVEIITGNM 359 G GKT +AL+ +A + GG+ +I+AP L +QH EF +K+ +I+V TG + Sbjct: 39 GLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVV--FTGEV 96 Query: 360 PQAHRRKALERIAHGQAHIIIGTHALFQDSI--QYYKL---ILVIVDEQHR--------F 406 R + E+ A +I+ T + ++ + L L+I DE HR + Sbjct: 97 SPEKRAELWEK-----AKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVY 151 Query: 407 GVQQRLKLTQKATAPHVLLMTATP 430 + +R + A P VL +TA+P Sbjct: 152 -IAERYH--EDAKNPLVLGLTASP 172 Score = 34.8 bits (81), Expect = 0.070 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 23/67 (34%) Query: 533 VMDSFKNGTCKLLIATTVIEVGIDV-----------VDASIIIIENAEHFGLAQLHQLRG 581 ++D F+ G +L++T+V E G+D+ V + I I Q +G Sbjct: 415 ILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSI------------QRKG 462 Query: 582 RVGRGEE 588 R GR EE Sbjct: 463 RTGRQEE 469 >gnl|CDD|180144 PRK05580, PRK05580, primosome assembly protein PriA; Validated. Length = 679 Score = 59.4 bits (145), Expect = 3e-09 Identities = 37/133 (27%), Positives = 63/133 (47%), Gaps = 12/133 (9%) Query: 274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP-IGI 332 Q +A+ + ++ + + L L G GSGKT V L A+A + G QA+++ P I Sbjct: 146 NPEQAAAV-EAIRAAAGFSPFL--LDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIA- 201 Query: 333 LAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH-ALFQDSIQ 391 L Q + ++ V ++ + R + G+A ++IG ALF + Sbjct: 202 LTPQ---MLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF---LP 255 Query: 392 YYKLILVIVDEQH 404 + L L+IVDE+H Sbjct: 256 FKNLGLIIVDEEH 268 >gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional. Length = 401 Score = 47.5 bits (113), Expect = 1e-05 Identities = 86/343 (25%), Positives = 144/343 (41%), Gaps = 74/343 (21%) Query: 260 KIAQKILRNIPFS-----PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAM 314 K+ + +LR I +S P+ Q+ IK IL + I Q G+GKT +IA Sbjct: 34 KLNEDLLRGI-YSYGFEKPSAIQQRGIKPIL------DGYDTIGQAQSGTGKTATFVIAA 86 Query: 315 AAAVE---AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERI 371 ++ QA+I+AP LAQQ + + ++ G R + ++ Sbjct: 87 LQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVV---RDDINKL 143 Query: 372 AHGQAHIIIGTHALFQDSIQYY-----KLILVIVDEQHRF---GVQQRLKLTQKATAP-- 421 G H+++GT D I L L I+DE G + ++ K P Sbjct: 144 KAGV-HMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDV 202 Query: 422 HVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSE 481 V L +AT +P +I ++T K R P + ++ + DE+ E Sbjct: 203 QVALFSAT-MPN----------EILELTTKFM-RDPKRILV----KKDELT-------LE 239 Query: 482 GKKAYWICPQIEEKK--------ES----------NFRSVVERFNS-LHEH-FTSSIAII 521 G + +++ + EE K E+ N R V+ +HE FT S + Sbjct: 240 GIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSC--M 297 Query: 522 HGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII 564 HG M D++ +M F++G+ ++LI T ++ GIDV S++I Sbjct: 298 HGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVI 340 >gnl|CDD|162177 TIGR01054, rgy, reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA. Length = 1171 Score = 47.5 bits (113), Expect = 1e-05 Identities = 29/123 (23%), Positives = 47/123 (38%), Gaps = 14/123 (11%) Query: 290 QKNRMLRILQGD-------VGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIK 342 QK R+L+GD G GKT L + G + I+ P +L Q E I Sbjct: 83 QKMWAKRVLRGDSFAIIAPTGVGKTTFGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKIS 142 Query: 343 KYTQNTQIIVEIIT---GNMPQAHRRKALERIAHGQAHIIIGT----HALFQDSIQYYKL 395 + + I +P +++ +ERI +G I+I T + + + Sbjct: 143 SLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDF 202 Query: 396 ILV 398 I V Sbjct: 203 IFV 205 Score = 34.4 bits (79), Expect = 0.10 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 14/75 (18%) Query: 481 EGKKAYWICP------QIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVM 534 +GK+ Y I P Q+ EK S+ E+ T +I H R+ +K+ M Sbjct: 120 KGKRCYIILPTTLLVIQVAEK----ISSLAEKAGVG----TVNIGAYHSRLPTKEKKEFM 171 Query: 535 DSFKNGTCKLLIATT 549 + +NG +LI TT Sbjct: 172 ERIENGDFDILITTT 186 >gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 470 Score = 47.1 bits (112), Expect = 2e-05 Identities = 52/236 (22%), Positives = 88/236 (37%), Gaps = 31/236 (13%) Query: 379 IIGTHALFQDSIQYYKLILVIVDEQH---RFGVQQRLKLTQ----KATAPHVLLM----T 427 ++ L Q + + L+ VDE H ++G R K P+V +M T Sbjct: 112 CSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQKFPNVPIMALTAT 171 Query: 428 ATPIPRTLVLTSLGDIDISKITEKPAGRKPIK-TVIIPINRIDEVIERLKVVLSEGKKAY 486 A+P R +L L + +I R + V +I E + R +GK Sbjct: 172 ASPSVREDILRQLN-LKNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRKEFKGKSGI 230 Query: 487 WICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLI 546 CP R E+ + ++ + H + ++ V F+ ++++ Sbjct: 231 IYCPS---------RKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVV 281 Query: 547 ATTVIEVGIDVVDASIIIIENAEHFGLAQ----LHQLRGRVGRGEEISSCILLYHP 598 AT +GI+ D +I H+ L + +Q GR GR S C L Y P Sbjct: 282 ATVAFGMGINKPDVRFVI-----HYSLPKSMESYYQESGRAGRDGLPSECHLFYAP 332 >gnl|CDD|162437 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model. Length = 358 Score = 47.1 bits (112), Expect = 2e-05 Identities = 46/222 (20%), Positives = 81/222 (36%), Gaps = 42/222 (18%) Query: 380 IGTHALFQDSIQYYK-----LILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRT 434 I L D + +Y LIL +++ V +LLM+AT +P+ Sbjct: 123 IANSLLIFDEVHFYDEYTLALILAVLEVLKDNDVP-------------ILLMSAT-LPKF 168 Query: 435 LVLTSLG-DIDISKITE--KPAGRKPIKTVIIPINRIDE---VIERLKVVLSEGKKAYWI 488 L + K R I + +ERL + +G K I Sbjct: 169 LKEYAEKIGYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAII 228 Query: 489 CPQIEEKKESNFRSVVERFNSLHEHF-TSSIAIIHGRMSDIDKES----VMDSFKNGTCK 543 ++ E + L E+ I ++H R ++ D+ +++ K Sbjct: 229 VNTVDR--------AQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKF 280 Query: 544 LLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGR 585 +++AT VIE +D + A ++I E + L Q GR+ R Sbjct: 281 VIVATQVIEASLD-ISADVMI---TELAPIDSLIQRLGRLHR 318 >gnl|CDD|177796 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional. Length = 518 Score = 42.9 bits (101), Expect = 3e-04 Identities = 99/421 (23%), Positives = 168/421 (39%), Gaps = 105/421 (24%) Query: 234 LAGQIALLLMRKQFKKEIGIPINVEG-------------KIAQKILRNIPFS----PTKS 276 L+ A LL RK + I+V+G + K+L N+ + PT Sbjct: 95 LSSSQAELLRRK-------LEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPI 147 Query: 277 QESAIKDILQDMSQKNRMLRILQGDVGSGKT---LVALIAMAAAVEAGGQ-------AVI 326 Q AI L R L ++ D GSGKT LV +I+ + +G A++ Sbjct: 148 QMQAIPAAL-----SGRSL-LVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMV 201 Query: 327 MAPIGILAQQHYEFIKKYTQNTQIIVEIITGN--MPQAHRRKALERIAHGQAHIIIGTHA 384 + P L Q + K + ++ G MPQ L RI G +I+GT Sbjct: 202 LTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQ-----LYRIQQG-VELIVGTPG 255 Query: 385 -----LFQDSIQYYKLILVIVDE-----QHRFGVQQRLKLTQKATAPHVLLMTATPIPRT 434 L + I+ + ++++DE + F Q +++ Q + P VLL +AT Sbjct: 256 RLIDLLSKHDIELDNVSVLVLDEVDCMLERGFR-DQVMQIFQALSQPQVLLFSAT----- 309 Query: 435 LVLTSLGDIDISKITEKPAG---RKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQ 491 +S EK A + I I NR ++ +++L A W+ + Sbjct: 310 ----------VSPEVEKFASSLAKDIILISIGNPNRPNKAVKQL---------AIWVETK 350 Query: 492 IEEKK-------ESNFRS-VVERFNS------LHEHFTSSIAI----IHGRMSDIDKESV 533 +++K + +F+ V +S L T + IHG S ++ V Sbjct: 351 QKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREV 410 Query: 534 MDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCI 593 M SF G +++AT V+ G+D++ +II + + +HQ+ GR R E + I Sbjct: 411 MKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQI-GRASRMGEKGTAI 469 Query: 594 L 594 + Sbjct: 470 V 470 >gnl|CDD|179415 PRK02362, PRK02362, ski2-like helicase; Provisional. Length = 737 Score = 41.1 bits (97), Expect = 0.001 Identities = 20/55 (36%), Positives = 35/55 (63%), Gaps = 1/55 (1%) Query: 304 SGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGN 358 SGKTL+A +AM A+ GG+A+ + P+ LA + +E +++ + + V I TG+ Sbjct: 50 SGKTLIAELAMLKAIARGGKALYIVPLRALASEKFEEFERFEE-LGVRVGISTGD 103 >gnl|CDD|181823 PRK09401, PRK09401, reverse gyrase; Reviewed. Length = 1176 Score = 37.6 bits (88), Expect = 0.010 Identities = 29/120 (24%), Positives = 54/120 (45%), Gaps = 16/120 (13%) Query: 296 RILQGD-------VGSGKTLVALIAMAA--AVEAGGQAVIMAPIGILAQQHYEFIKKYTQ 346 R+L G+ G GKT + M+ A + G ++ I+ P +L +Q E ++K+ + Sbjct: 91 RLLLGESFAIIAPTGVGKT-TFGLVMSLYLAKK-GKKSYIIFPTRLLVEQVVEKLEKFGE 148 Query: 347 NTQIIVEII--TGNMPQAHRRKALERIAHGQAHIIIGTHALFQ---DSIQYYKLILVIVD 401 V+I+ ++ + + + LER+ G I++ T D + K V VD Sbjct: 149 KVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDELPKKKFDFVFVD 208 Score = 31.4 bits (72), Expect = 0.80 Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 7/72 (9%) Query: 480 SEGKKAYWICPQIEEKKESNFRSVVERFNSLHE--HFTSSIAIIHGRMSDIDKESVMDSF 537 +GKK+Y I P VVE+ E I H + +KE ++ Sbjct: 121 KKGKKSYIIFP-----TRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERL 175 Query: 538 KNGTCKLLIATT 549 K G +L+ T+ Sbjct: 176 KEGDFDILVTTS 187 >gnl|CDD|166873 PRK00254, PRK00254, ski2-like helicase; Provisional. Length = 720 Score = 37.1 bits (86), Expect = 0.015 Identities = 36/115 (31%), Positives = 52/115 (45%), Gaps = 16/115 (13%) Query: 304 SGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQA 362 SGKTLVA I M + GG+AV + P+ LA++ Y K + + + V + TG+ Sbjct: 50 SGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYREFKDW-EKLGLRVAMTTGDYDST 108 Query: 363 HRRKALERIAHGQAHIIIGTHALFQDSIQYYK------LILVIVDEQHRFGVQQR 411 G+ III T F DS+ + + LV+ DE H G R Sbjct: 109 DEWL-------GKYDIIIATAEKF-DSLLRHGSSWIKDVKLVVADEIHLIGSYDR 155 Score = 34.4 bits (79), Expect = 0.11 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 7/83 (8%) Query: 510 LHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII--IEN 567 L + +A H + ++ + D+F+ G K++ AT + GI++ +II + Sbjct: 290 LKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKR 349 Query: 568 AEHFGLA-----QLHQLRGRVGR 585 +FG ++ Q+ GR GR Sbjct: 350 YSNFGWEDIPVLEIQQMMGRAGR 372 >gnl|CDD|183308 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional. Length = 460 Score = 36.7 bits (86), Expect = 0.022 Identities = 30/102 (29%), Positives = 50/102 (49%), Gaps = 10/102 (9%) Query: 501 RSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDA 560 + E ++L+ S++A+ HG + D++ V+ F N +C +L+AT V G+D+ Sbjct: 253 KECQEVADALNAQGFSALAL-HGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKAL 311 Query: 561 SIIIIENAEHFGLA---QLHQLR-GRVGRGEEISSCILLYHP 598 +I N E LA ++H R GR GR + L P Sbjct: 312 EAVI--NYE---LARDPEVHVHRIGRTGRAGSKGLALSLVAP 348 Score = 34.4 bits (80), Expect = 0.098 Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 12/92 (13%) Query: 297 ILQGDVGSGKTLVALIAMAAAVEA---GGQAVIMAPIGILAQQHYEFIKK---YTQNTQI 350 I Q GSGKT + + ++ QA+++ P LA Q + I++ + N ++ Sbjct: 45 IAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKV 104 Query: 351 IVEIITGNMPQAHRRKALERIAHGQAHIIIGT 382 + + G +P + +LE HG AHII+GT Sbjct: 105 LT--LCGGVPMGPQIDSLE---HG-AHIIVGT 130 >gnl|CDD|185453 PTZ00110, PTZ00110, helicase; Provisional. Length = 545 Score = 35.9 bits (83), Expect = 0.039 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 15/73 (20%) Query: 521 IHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII-------IENAEHFGL 573 IHG ++ V++ FK G ++IAT V G+DV D +I IE+ Sbjct: 407 IHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIED------ 460 Query: 574 AQLHQLRGRVGRG 586 +H++ GR GR Sbjct: 461 -YVHRI-GRTGRA 471 >gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ. Length = 591 Score = 34.7 bits (80), Expect = 0.081 Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 9/86 (10%) Query: 517 SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII----IENAEHFG 572 S H +S+ + + F K+++AT +GID + +I N E + Sbjct: 250 SALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESY- 308 Query: 573 LAQLHQLRGRVGRGEEISSCILLYHP 598 +Q GR GR + ILLY P Sbjct: 309 ----YQEAGRAGRDGLPAEAILLYSP 330 >gnl|CDD|183029 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional. Length = 434 Score = 34.5 bits (80), Expect = 0.091 Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 8/78 (10%) Query: 495 KKESNFRSVV-----ERFNSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGTCKLLI 546 K+ RS+V ER + L + + G M + + +G +L+ Sbjct: 241 KQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLV 300 Query: 547 ATTVIEVGIDVVDASIII 564 AT V GID+ D S +I Sbjct: 301 ATDVAARGIDIDDVSHVI 318 >gnl|CDD|179861 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional. Length = 572 Score = 34.2 bits (78), Expect = 0.13 Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 7/68 (10%) Query: 352 VEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQDSIQY---YKLILVIVDEQH 404 V +++G++PQ R L R GQ I++ T L D ++Y Y L D H Sbjct: 284 VGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVH 343 Query: 405 RFGVQQRL 412 R G RL Sbjct: 344 RIGRTARL 351 Score = 33.4 bits (76), Expect = 0.21 Identities = 61/287 (21%), Positives = 118/287 (41%), Gaps = 43/287 (14%) Query: 299 QGDVGSGKTLVALI----------AMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNT 348 Q G+GKTL L+ A+A +A+I+AP LA Q ++ K+ + Sbjct: 52 QAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADL 111 Query: 349 QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLI------LVIVDE 402 + ++ G + +R+ L++ +II T D ++ +K++ + ++DE Sbjct: 112 GLRFALVYGGVDYDKQRELLQQ----GVDVIIATPGRLIDYVKQHKVVSLHACEICVLDE 167 Query: 403 QHRF-------GVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKI---TEKP 452 R ++ L+ + LL +AT R L L + K+ TE Sbjct: 168 ADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETI 227 Query: 453 AGRKPIKTVIIPINRIDEVIERLKVVL--SEGKKAYWICPQIEEKKESNFRSVVERFNSL 510 + + + P + +E L +L SEG + N ++ VER Sbjct: 228 TAARVRQRIYFPAD--EEKQTLLLGLLSRSEGARTMVFV---------NTKAFVERVART 276 Query: 511 HEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV 557 E + ++ G + +ES+++ F+ G ++L+AT V G+ + Sbjct: 277 LERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHI 323 >gnl|CDD|183441 PRK12326, PRK12326, preprotein translocase subunit SecA; Reviewed. Length = 764 Score = 33.0 bits (76), Expect = 0.25 Identities = 18/38 (47%), Positives = 21/38 (55%), Gaps = 8/38 (21%) Query: 294 MLRILQGDV-----GSGKTLVALIAMAAAVEA-GGQAV 325 LR+L GDV G GKTL A+AAA A G+ V Sbjct: 87 ALRLLAGDVIEMATGEGKTLAG--AIAAAGYALQGRRV 122 >gnl|CDD|184873 PRK14873, PRK14873, primosome assembly protein PriA; Provisional. Length = 665 Score = 33.0 bits (76), Expect = 0.29 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 2/72 (2%) Query: 313 AMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIA 372 A AA + AG A+++ P + ++ + V ++ + A R + + Sbjct: 180 AAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAV--LSAGLGPADRYRRWLAVL 237 Query: 373 HGQAHIIIGTHA 384 GQA +++GT + Sbjct: 238 RGQARVVVGTRS 249 >gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional. Length = 674 Score = 32.9 bits (75), Expect = 0.29 Identities = 20/86 (23%), Positives = 44/86 (51%), Gaps = 9/86 (10%) Query: 508 NSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIEN 567 +SL+E +A H +S+ + + + F+N K+++AT + G++ + A ++I+ + Sbjct: 278 DSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVN-LPARLVIVRD 336 Query: 568 AEHFGLA--------QLHQLRGRVGR 585 +G ++ Q+ GR GR Sbjct: 337 ITRYGNGGIRYLSNMEIKQMIGRAGR 362 >gnl|CDD|162952 TIGR02621, cas3_GSU0051, CRISPR-associated helicase Cas3, Anaes-subtype. This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs. Length = 844 Score = 32.7 bits (74), Expect = 0.30 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 5/61 (8%) Query: 545 LIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSC-ILLYHPPLSKN 603 L+ T+ EVG++ + A ++ + A + Q GRV R E+ +C I + H L K+ Sbjct: 340 LVCTSAGEVGVN-ISADHLVCDLAPFESMQQRF---GRVNRFGELQACQIAVVHLDLGKD 395 Query: 604 S 604 Sbjct: 396 Q 396 >gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148 Score = 32.7 bits (74), Expect = 0.32 Identities = 34/174 (19%), Positives = 57/174 (32%), Gaps = 32/174 (18%) Query: 297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIIT 356 ++ G GSGKT +A GG + + IL + Q IIV Sbjct: 6 LIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEV-------LDQLLLIIVGGKK 58 Query: 357 GNMPQAHR-RKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLT 415 + R R AL + K ++I+DE ++ L Sbjct: 59 ASGSGELRLRLALAL-------------------ARKLKPDVLILDEITSLLDAEQEALL 99 Query: 416 QKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRID 469 +LL+ + T++LT+ + D+ PA + I + I Sbjct: 100 LLLEELRLLLLLKSEKNLTVILTTNDEKDL-----GPALLRRRFDRRIVLLLIL 148 >gnl|CDD|162382 TIGR01479, GMP_PMI, mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase. This enzyme is known to be bifunctional, as both mannose-6-phosphate isomerase (EC 5.3.1.8) (PMI) and mannose-1-phosphate guanylyltransferase (EC 2.7.7.22) in Pseudomonas aeruginosa, Xanthomonas campestris, and Gluconacetobacter xylinus. The literature on the enzyme from E. coli attributes mannose-6-phosphate isomerase activity to an adjacent gene, but the present sequence has not been shown to lack the activity. The PMI domain is C-terminal. Length = 468 Score = 32.7 bits (75), Expect = 0.36 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 9/64 (14%) Query: 375 QAHIIIGTHALFQDSIQY-----YKLILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTAT 429 Q ++G + Q +++ LVI +E+HRF V ++L+ A +++L Sbjct: 25 QFLALVGDLTMLQQTLKRLAGLPCSSPLVICNEEHRFIVAEQLR-EIGKLASNIIL---E 80 Query: 430 PIPR 433 P+ R Sbjct: 81 PVGR 84 >gnl|CDD|183247 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional. Length = 629 Score = 32.5 bits (74), Expect = 0.37 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 9/71 (12%) Query: 519 AIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASII----IIENAEHFGLA 574 A ++G M+ +E ++ K+G +LIAT V G+DV S++ I ++E + Sbjct: 273 AALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESY--- 329 Query: 575 QLHQLRGRVGR 585 +H++ GR GR Sbjct: 330 -VHRI-GRTGR 338 Score = 28.7 bits (64), Expect = 5.1 Identities = 12/28 (42%), Positives = 18/28 (64%) Query: 355 ITGNMPQAHRRKALERIAHGQAHIIIGT 382 + G+M QA R + LER+ G+ I+I T Sbjct: 275 LNGDMNQALREQTLERLKDGRLDILIAT 302 >gnl|CDD|178682 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional. Length = 1195 Score = 32.2 bits (73), Expect = 0.45 Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 9/82 (10%) Query: 519 AIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQ--- 575 A HG M + V + ++ AT +GI+ D +I H L + Sbjct: 708 AFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVI-----HHSLPKSIE 762 Query: 576 -LHQLRGRVGRGEEISSCILLY 596 HQ GR GR + SSC+L Y Sbjct: 763 GYHQECGRAGRDGQRSSCVLYY 784 >gnl|CDD|162351 TIGR01420, pilT_fam, pilus retraction protein PilT. This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation. Length = 343 Score = 31.9 bits (73), Expect = 0.57 Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 12/98 (12%) Query: 226 ERLAYDELLAGQIALLLMRKQFKKEIGIP------INV---EGKIAQKILRNIPFSPTKS 276 ++L + L Q + +P +N G +A +LR IP Sbjct: 47 QKLLREILSEKQREEFEENGELDFSYSLPGVSRFRVNAFKQRGGVAL-VLRLIPSKIPTF 105 Query: 277 QESAIKDILQDMSQKNRMLRILQGDVGSGK--TLVALI 312 +E + +L++++++ R L ++ G GSGK TL ++I Sbjct: 106 EELGLPPVLRELAERPRGLILVTGPTGSGKSTTLASMI 143 >gnl|CDD|163066 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC. Length = 615 Score = 31.7 bits (72), Expect = 0.65 Identities = 23/58 (39%), Positives = 29/58 (50%) Query: 260 KIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAA 317 K AQ +LR FS QE AIK +L ++ IL G G GKT A +A+ A Sbjct: 142 KSAQSLLRPRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEA 199 >gnl|CDD|114722 pfam06016, Reovirus_L2, Reovirus core-spike protein lambda-2 (L2). This family consists of several Reovirus core-spike protein lambda-2 (L2) sequences. The reovirus L2 genome segment encodes the core spike protein lambda-2, which mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts. Length = 1289 Score = 31.7 bits (72), Expect = 0.72 Identities = 12/38 (31%), Positives = 17/38 (44%) Query: 407 GVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDID 444 GVQQ + A+ + L P+P L L +ID Sbjct: 907 GVQQLISQIVDASVKTLWLQLNCPLPSVGSLPGLLEID 944 >gnl|CDD|183476 PRK12366, PRK12366, replication factor A; Reviewed. Length = 637 Score = 30.8 bits (70), Expect = 1.2 Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 9/96 (9%) Query: 49 PSSFIDRHYRPKISEISEERI-VTITGY---ISQHSSFQLQKRRPYK---ILLNDGTGEI 101 + KIS+I E +I V ITG IS +F + K I + D TG I Sbjct: 54 EYGQEEEEEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTGTI 113 Query: 102 TLLFFYRKTEMLKNVFFEGRKITVTG-KIKKLKNRI 136 L + ++LK EG I + + +K N + Sbjct: 114 RLTLWNDNAKLLKG-LKEGDVIKIENARSRKWNNDV 148 Score = 30.0 bits (68), Expect = 1.9 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 7/83 (8%) Query: 60 KISEISEERIVTITGY---ISQHSSFQLQKRRPY--KILLNDGTGEITLLFFYRKTEMLK 114 +++E + V + G IS + R I L DGTG + + F+ K ++L+ Sbjct: 284 ELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGTGRVRVSFWGEKAKILE 343 Query: 115 NVFFEGRKITVTG-KIKKLKNRI 136 N+ EG + + K++ + Sbjct: 344 NL-KEGDAVKIENCKVRTYYDNE 365 >gnl|CDD|181223 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated. Length = 928 Score = 30.7 bits (70), Expect = 1.3 Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 11/48 (22%) Query: 364 RRKALERIAHGQAHIIIGTHA-LFQDSIQYYKLI----LVIVDEQHRF 406 + +A A ++I HA L D L+ +I+DE H F Sbjct: 426 KNRAKF------ADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHF 467 >gnl|CDD|179884 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional. Length = 423 Score = 30.3 bits (69), Expect = 1.9 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 17/106 (16%) Query: 299 QGDVGSGKTLVALIA-----MAAAVEAGGQ-----AVIMAPIGILAQQHYEFIKKYTQNT 348 Q G+GKT+ L A ++ + A+IMAP LA Q + + Q T Sbjct: 51 QAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQAT 110 Query: 349 QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYK 394 + + + G + K LE I+IGT I Y K Sbjct: 111 GLKLGLAYGGDGYDKQLKVLES----GVDILIGTTGRL---IDYAK 149 >gnl|CDD|183820 PRK12898, secA, preprotein translocase subunit SecA; Reviewed. Length = 656 Score = 30.0 bits (68), Expect = 1.9 Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 6/87 (6%) Query: 296 RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEII 355 R+ + G GKTL A + A AG ++ LA++ E ++ + + V + Sbjct: 119 RLAEMQTGEGKTLTATLPAGTAALAGLPVHVITVNDYLAERDAELMRPLYEALGLTVGCV 178 Query: 356 TGNMPQAHRRKALERIAHGQAHIIIGT 382 + RR A A I T Sbjct: 179 VEDQSPDERRAAY------GADITYCT 199 >gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr; Provisional. Length = 1490 Score = 29.9 bits (67), Expect = 2.5 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 5/65 (7%) Query: 522 HGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV--VDASIIIIENAEHFGLAQLHQL 579 HG +S + + K+G + ++AT+ +E+GID+ VD ++I+ A +A Q Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVD---LVIQVATPLSVASGLQR 364 Query: 580 RGRVG 584 GR G Sbjct: 365 IGRAG 369 >gnl|CDD|150847 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29). Length = 274 Score = 29.1 bits (66), Expect = 3.7 Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 1/36 (2%) Query: 286 QDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG 321 D S+K +L G+ GSGK+++ AMA A+ G Sbjct: 17 ADASKKVVR-FVLTGERGSGKSVLLAQAMAYALTQG 51 >gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated. Length = 233 Score = 29.0 bits (65), Expect = 3.8 Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%) Query: 298 LQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPI 330 L G G+GKT +AL A+ AA E G++ P+ Sbjct: 46 LSGPAGTGKTHLAL-ALCAAAEQAGRSSAYLPL 77 >gnl|CDD|184957 PRK14995, PRK14995, methyl viologen resistance protein SmvA; Provisional. Length = 495 Score = 29.3 bits (66), Expect = 3.9 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%) Query: 160 YSLPTGLSVDLFKKIIVEALSRLPVLPEWIEKDLLQKKSFPSIAEAFNIIHN 211 Y L GL + +F ++ + S LP + L++K S SI EA + ++ Sbjct: 396 YELGAGLGIAIFGLLLSRSYSASIRLPAGLPAQLIEKAS-SSIGEAVQLANS 446 >gnl|CDD|162340 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model. Length = 1213 Score = 28.9 bits (65), Expect = 4.3 Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 7/75 (9%) Query: 64 ISEERIVTITGYISQHSSFQLQ-KRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRK 122 EE V I GYI + +L+ R KI + D T + L F + E + F+G K Sbjct: 4 NEEENRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPE--KFDGIK 61 Query: 123 IT----VTGKIKKLK 133 I GKI+ Sbjct: 62 IGKWVRARGKIELDN 76 >gnl|CDD|149617 pfam08623, TIP120, TATA-binding protein interacting (TIP20). TIP120 (also known as cullin-associated and neddylation-dissociated protein 1) is a TATA binding protein interacting protein that enhances transcription. Length = 169 Score = 28.7 bits (65), Expect = 5.3 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 1/56 (1%) Query: 467 RIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIH 522 R+D + E L+ LS+ K + +IE+++E RSV+ SL+ + H Sbjct: 103 RLDSLAEPLRKTLSKKVKEKAVKQEIEKQQELI-RSVLRLVVSLNLKLPEAEDSPH 157 >gnl|CDD|149922 pfam09015, NgoMIV_restric, NgoMIV restriction enzyme. Members of this family are prokaryotic DNA restriction enzymes, exhibiting an alpha/beta structure, with a central region comprising a mixed six-stranded beta-sheet with alpha-helices on each side. A long 'arm' protrudes out of the core of the domain between strands beta2 and beta3 and is mainly involved in the tetramerisation interface of the protein. These restriction enzymes recognize the double-stranded sequence GCCGGC and cleave after G-1. Length = 277 Score = 28.6 bits (64), Expect = 5.8 Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 2/31 (6%) Query: 416 QKATAPHVLLMTATPIPRTLVLTSL--GDID 444 +K PH++++TA P+P + +L GDID Sbjct: 200 RKGRLPHIVVVTAEPLPSRIASLALGTGDID 230 >gnl|CDD|173333 PTZ00036, PTZ00036, glycogen synthase kinase; Provisional. Length = 440 Score = 28.5 bits (63), Expect = 6.3 Identities = 12/24 (50%), Positives = 17/24 (70%) Query: 276 SQESAIKDILQDMSQKNRMLRILQ 299 S++ AIK +LQD KNR L I++ Sbjct: 91 SEKVAIKKVLQDPQYKNRELLIMK 114 >gnl|CDD|179031 PRK00448, polC, DNA polymerase III PolC; Validated. Length = 1437 Score = 28.3 bits (64), Expect = 7.0 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 8/76 (10%) Query: 60 KISEIS-EERIVTITGYISQHSSFQLQKRRP-YKILLNDGTGEITLLFFYRKTEMLKNVF 117 + EI+ EER V + GY+ + +L+ R + D T I + F R E LK Sbjct: 228 PMKEINEEERRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLK--K 285 Query: 118 FEGRK----ITVTGKI 129 F+ K + V G + Sbjct: 286 FDEIKKGDWVKVRGSV 301 >gnl|CDD|148880 pfam07517, SecA_DEAD, SecA DEAD-like domain. SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the pfam00270. Length = 381 Score = 28.3 bits (64), Expect = 7.8 Identities = 32/127 (25%), Positives = 53/127 (41%), Gaps = 27/127 (21%) Query: 295 LRILQGDV-----GSGKTLVALIAMAAAVEA-GGQAVIMAPIG-ILAQQHYEFIKKYTQN 347 L + +G + G GKTL A + A + A G+ V + + LA++ E++ + Sbjct: 87 LVLHEGKIAEMKTGEGKTLTA--TLPAYLNALSGKGVHVVTVNDYLAKRDAEWMGPLYEF 144 Query: 348 TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQ-----DSIQYYK-------L 395 + V +IT +M RR+A I GT++ D++ K L Sbjct: 145 LGLSVGVITSDMSPEERREAY------NCDITYGTNSELGFDYLRDNMALSKEDKVQRGL 198 Query: 396 ILVIVDE 402 IVDE Sbjct: 199 NFAIVDE 205 >gnl|CDD|184796 PRK14701, PRK14701, reverse gyrase; Provisional. Length = 1638 Score = 28.3 bits (63), Expect = 7.9 Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 7/71 (9%) Query: 481 EGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAII--HGRMSDIDKESVMDSFK 538 +GKK Y I P K+ VE+ S E + ++ H + +KE ++ + Sbjct: 121 KGKKCYIILPTTLLVKQ-----TVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIE 175 Query: 539 NGTCKLLIATT 549 NG +L+ T Sbjct: 176 NGDFDILVTTA 186 >gnl|CDD|135660 PRK05927, PRK05927, hypothetical protein; Provisional. Length = 350 Score = 27.9 bits (62), Expect = 8.5 Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 1/39 (2%) Query: 497 ESNFRSVVERFNSLHEHFTSSIAIIHG-RMSDIDKESVM 534 E R V+ F SLH HF S++ I H ++S I E + Sbjct: 112 EELVRITVKEFPSLHPHFFSAVEIAHAAQVSGISTEQAL 150 >gnl|CDD|182572 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional. Length = 456 Score = 27.8 bits (62), Expect = 9.3 Identities = 13/39 (33%), Positives = 22/39 (56%) Query: 519 AIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV 557 A IHG S + + FK+G ++L+AT + G+D+ Sbjct: 273 AAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDI 311 >gnl|CDD|132559 TIGR03520, GldE, gliding motility-associated protein GldE. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. GldE was discovered because of its adjacency to GldD in F. johnsonii. Overexpression of GldE partially supresses the effects of a GldB point mutant suggesting that GldB and GldE interact. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility and in fact some do not appear to express the gliding phenotype. Length = 408 Score = 27.7 bits (62), Expect = 9.4 Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 24/66 (36%) Query: 169 DLFKKIIVEALSRLPVLPEWIE--------KDLLQKKSFPSIAEAFNIIHNPRKAKDFEW 220 ++ KII SR+PV E I+ KDLL P + K+F+W Sbjct: 214 EIIPKIIENGYSRIPVYKETIDNITGVLYIKDLL-----PHL-----------NKKNFDW 257 Query: 221 TSPARE 226 S RE Sbjct: 258 QSLLRE 263 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.322 0.138 0.393 Gapped Lambda K H 0.267 0.0710 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 11,728,270 Number of extensions: 804150 Number of successful extensions: 1968 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1927 Number of HSP's successfully gapped: 92 Length of query: 700 Length of database: 5,994,473 Length adjustment: 100 Effective length of query: 600 Effective length of database: 3,833,673 Effective search space: 2300203800 Effective search space used: 2300203800 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 (21.9 bits) S2: 61 (27.3 bits)