RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 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|31393 COG1200, RecG, RecG-like helicase [DNA replication, recombination, and repair / Transcription]. Length = 677 Score = 726 bits (1876), Expect = 0.0 Identities = 315/691 (45%), Positives = 443/691 (64%), Gaps = 20/691 (2%) Query: 1 MRPSFLNPLFAPLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPK 60 M S L+P F PLST +G+G K + L K+ DLL Y P + DR P Sbjct: 1 MMLSLLDP-FVPLSTLKGIGPKTAEKLKKL------GIHTVQDLLLYLPRRYEDRTLLPG 53 Query: 61 ISEISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEG 120 I+E IVTI G + H F KR+ K+ L+DGTG +TL+FF LK G Sbjct: 54 IAEARPGEIVTIEGTVLSHEKFPFGKRKLLKVTLSDGTGVLTLVFFNFPA-YLKKKLKVG 112 Query: 121 RKITVTGKIKKLKNRIIMVHPHYIFHNSQDVNFPLIEAVYSLPTGLSVDLFKKIIVEALS 180 ++ V GK+K+ K + + HP YI ++ + VY L GL +K+I +AL Sbjct: 113 ERVIVYGKVKRFKGGLQITHPEYIVNDDGSELEERLTPVYPLTEGLKQKTLRKLIQQALE 172 Query: 181 RLP-VLPEWIEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIA 239 LP L E + ++LL+K PS+ EA +H P KD E AR RLA++ELLA Q++ Sbjct: 173 VLPSELEELLPEELLEKYGLPSLDEALRTLHFP---KDEEDLKRARRRLAFEELLALQLS 229 Query: 240 LLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQ 299 LLL R + +K GIP+ G++ K L +PF T +Q+ IK+IL D++ M R+LQ Sbjct: 230 LLLRRAKRQKRSGIPLPANGELLAKFLAALPFKLTNAQKRVIKEILADLASPVPMNRLLQ 289 Query: 300 GDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNM 359 GDVGSGKT+VAL+AM AA+EAG QA +MAP ILA+QHYE ++K+ + I V ++TG++ Sbjct: 290 GDVGSGKTVVALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSL 349 Query: 360 PQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKA- 418 R++ LE++A G+ I++GTHAL QD ++++ L LVI+DEQHRFGV QRL L +K Sbjct: 350 KGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLVIIDEQHRFGVHQRLALREKGE 409 Query: 419 TAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVV 478 PHVL+MTATPIPRTL LT+ GD+D+S I E P GRKPI TV+IP R EV ER++ Sbjct: 410 QNPHVLVMTATPIPRTLALTAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIREE 469 Query: 479 LSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFT-SSIAIIHGRMSDIDKESVMDSF 537 +++G++AY +CP IEE ++ ++ E + L + ++HGRM +K++VM++F Sbjct: 470 IAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAF 529 Query: 538 KNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYH 597 K G +L+ATTVIEVG+DV +A++++IENAE FGLAQLHQLRGRVGRG+ S C+LLY Sbjct: 530 KEGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYK 589 Query: 598 PPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSGMPKFLIAQPELHDSLLE 657 PPLS+ + RL +++ T DGF+IAEEDLK R GE+LG +QSG+P+F +A +LE Sbjct: 590 PPLSEVAKQRLKIMRETTDGFVIAEEDLKLRGPGELLGTRQSGLPEFRVADLVRDYDILE 649 Query: 658 IARKDAKHILTQDPDLTSVRGQSIRILLYLY 688 ARKDA +L++DP G+++ LL + Sbjct: 650 EARKDAAKLLSRDP------GEALEALLKRF 674 >gnl|CDD|31390 COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]. Length = 1139 Score = 322 bits (827), Expect = 2e-88 Identities = 149/426 (34%), Positives = 236/426 (55%), Gaps = 26/426 (6%) Query: 224 ARERLAYDELLAGQIALLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKD 283 AR+++ +A ++ L ++Q KK G + + ++ + P+ T Q AI++ Sbjct: 551 ARKKV---RDIAAELIKLYAKRQAKK--GFAFPPDTEWQEEFEASFPYEETPDQLKAIEE 605 Query: 284 ILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKK 343 + +DM M R++ GDVG GKT VA+ A AV G Q ++ P +LAQQHYE K+ Sbjct: 606 VKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKE 665 Query: 344 YTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQ 403 + +E+++ +++ L+ +A G+ I+IGTH L +++ L L+I+DE+ Sbjct: 666 RFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLIIDEE 725 Query: 404 HRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVII 463 RFGV+ + KL + VL ++ATPIPRTL ++ G D+S I P R P+KT + Sbjct: 726 QRFGVKHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVS 785 Query: 464 PINR--IDEVIERLKVVLSEGKKAYWICPQIE--EKKESNFRSVVERFNSLHEHFTSSIA 519 + I E I R L G + +++ ++E EKK R +V + IA Sbjct: 786 EYDDLLIREAILR---ELLRGGQVFYVHNRVESIEKKAERLRELVP---------EARIA 833 Query: 520 IIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQL 579 + HG+M + + E VM F NG +L+ TT+IE GID+ +A+ IIIE A+ FGLAQL+QL Sbjct: 834 VAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQL 893 Query: 580 RGRVGRGEEISSCILLYHPP--LSKNSYTRLSVLKNTED---GFLIAEEDLKQRKEGEIL 634 RGRVGR + + LY P L++++ RL + + + GF +A DL+ R G +L Sbjct: 894 RGRVGRSNKQAYAYFLYPPQKALTEDAEKRLEAIASFTELGAGFKLAMHDLEIRGAGNLL 953 Query: 635 GIKQSG 640 G +QSG Sbjct: 954 GEEQSG 959 >gnl|CDD|144015 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Length = 167 Score = 116 bits (293), Expect = 2e-26 Identities = 47/171 (27%), Positives = 77/171 (45%), Gaps = 23/171 (13%) Query: 274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV---EAGGQAVIMAPI 330 T Q AI IL+ ++Q GSGKTL L+ A+ G QA+++AP Sbjct: 1 TPIQAEAIPAILEGKD------VLVQAPTGSGKTLAFLLPALQALLKNPDGPQALVLAPT 54 Query: 331 GILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSI 390 LA+Q YE +KK + + V ++ G + + L++ I++GT D + Sbjct: 55 RELAEQIYEELKKLGKYLGLKVALLYGGDSPKEQLRKLKK----GPDILVGTPGRLLDLL 110 Query: 391 QYYKLIL-----VIVDEQHR-----FGVQQRLKLTQKATAPHVLLMTATPI 431 + L+L +++DE HR FG L + +LL++AT Sbjct: 111 ERGGLLLKNLKLLVLDEAHRLLDQGFGDDLEEILRRLPPKRQILLLSATLP 161 >gnl|CDD|30859 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]. Length = 513 Score = 91.0 bits (225), Expect = 1e-18 Identities = 82/412 (19%), Positives = 155/412 (37%), Gaps = 39/412 (9%) Query: 272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGG-----QAVI 326 PT Q +AI IL R + Q G+GKT L+ + + A+I Sbjct: 51 EPTPIQLAAIPLILA-----GRDVLG-QAQTGTGKTAAFLLPLLQKILKSVERKYVSALI 104 Query: 327 MAPIGILAQQHYEFIKKYTQNT-QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHAL 385 +AP LA Q E ++K +N + V ++ G + + +AL+R I++ T Sbjct: 105 LAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKR----GVDIVVATPGR 160 Query: 386 FQDSIQYYKLIL-----VIVDEQHRF---GVQQRLKLTQKATAP--HVLLMTATPIPRTL 435 D I+ KL L +++DE R G ++ KA P LL +AT Sbjct: 161 LLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIR 220 Query: 436 VLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEK 495 L D +I + + + +I + ++ + + + +E Sbjct: 221 ELARRYLNDPVEIEVSV------EKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDEG 274 Query: 496 KESNFRSVVERFNSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIE 552 + F L E +A +HG + +++ ++ FK+G ++L+AT V Sbjct: 275 RVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAA 334 Query: 553 VGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLK 612 G+D+ D S +I + +H++ GR GR I + +L ++ Sbjct: 335 RGLDIPDVSHVINYDLPLDPEDYVHRI-GRTGRAGRKGVAISFVTE---EEEVKKLKRIE 390 Query: 613 NTEDGFLIAEEDLKQRKEGEILGIKQSGMPKFLIAQPELHDSLLEIARKDAK 664 + L + L + + +K + + L+ ++K Sbjct: 391 KRLERKLPSAVLLPLDEPEDAKLLKTTRPGLEEESDISDEIKKLKSSKKALL 442 >gnl|CDD|28960 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process. Length = 131 Score = 84.2 bits (208), Expect = 1e-16 Identities = 39/141 (27%), Positives = 69/141 (48%), Gaps = 12/141 (8%) Query: 457 PIKTVIIPIN--RIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHF 514 PIK ++P+ +++ ++E LK L +G K CP + +++ L Sbjct: 1 PIKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCP---------SKKMLDELAELLRKP 51 Query: 515 TSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLA 574 +A +HG S ++E V+ F+ G +L+AT VI GID+ + S++I + + + Sbjct: 52 GIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDL-PWSPS 110 Query: 575 QLHQLRGRVGRGEEISSCILL 595 Q GR GR + + ILL Sbjct: 111 SYLQRIGRAGRAGQKGTAILL 131 >gnl|CDD|28927 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.. Length = 144 Score = 83.2 bits (205), Expect = 2e-16 Identities = 44/147 (29%), Positives = 65/147 (44%), Gaps = 17/147 (11%) Query: 296 RILQGDVGSGKTLVALIAMAAAV--EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVE 353 +L GSGKTL AL+ + + GGQ +++AP LA Q E +K+ I V Sbjct: 3 VLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGE-GIKVG 61 Query: 354 IITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQ-----YYKLILVIVDEQHRFGV 408 + G + K L + I++GT D ++ KL L+I+DE HR Sbjct: 62 YLIGGTSIKQQEKLLSG----KTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLN 117 Query: 409 QQR-----LKLTQKATAPHVLLMTATP 430 Q L + VLL++ATP Sbjct: 118 QGFGLLGLKILLKLPKDRQVLLLSATP 144 >gnl|CDD|31391 COG1198, PriA, Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]. Length = 730 Score = 80.0 bits (197), Expect = 2e-15 Identities = 121/653 (18%), Positives = 216/653 (33%), Gaps = 157/653 (24%) Query: 159 VYSLPTGLSVDLFK-KIIVEALSRLPVLP-EWIE-KDLLQKKSFPSIAEAF------NII 209 V L + VD K K I L PVL E + + + + + Sbjct: 46 VVELSSESDVDGRKLKEIERVLDTEPVLTPELLRLIEWAADYYLSPLGDVLRLALPVLLR 105 Query: 210 HNPRKAKDFEW----TSPARERLAYDELLAGQIALLLMRKQFKKEIGIPINVEGKIAQKI 265 K T R L + Q +L Q + + ++ + Sbjct: 106 QGYAKPSLPVLFYRLTERGRAALPDLKRAKKQARVLEALLQGGEWTRSALAHAAGVSLSV 165 Query: 266 LRNI--------------------------PFSPTKSQESAIKDILQDMSQKNRMLRILQ 299 L+ + + + Q++A++ IL + L L Sbjct: 166 LKGLEKKGLIEIIELEPPLVVAPPDPSLSEWLALNQEQQAAVEAILSSLGGFAPFL--LD 223 Query: 300 GDVGSGKTLVALIAMAAAVEAGGQAVIMAP-IGILAQQHYEFIKKYTQNTQIIVEIITGN 358 G GSGKT V L A+A + G Q +++ P I + Q F ++ V ++ Sbjct: 224 GVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAK----VAVLHSG 279 Query: 359 MPQAHRRKALERIAHGQAHIIIGTH-ALFQDSIQYYKLILVIVDEQHRFGVQQR------ 411 + R + R G+A ++IGT ALF + + L L+IVDE+H +Q Sbjct: 280 LSPGERYRVWRRARRGEARVVIGTRSALF---LPFKNLGLIIVDEEHDSSYKQEDGPRYH 336 Query: 412 -----LKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPIN 466 + +K AP V+L +ATP + G + ++T + + + II + Sbjct: 337 ARDVAVLRAKKENAP-VVLGSATPSLESYANAESGKYKLLRLTNRAGRARLPRVEIIDMR 395 Query: 467 RID---------EVIERLKVVLSEGKKA------------------YWI----------- 488 + ++E ++ L G++ +I Sbjct: 396 KEPLETGRSLSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLT 455 Query: 489 ----------------------CPQIEEKKESNFRSVVER-FNSLHEHFTSSIAIIHGRM 525 CP+ + ER L F + I Sbjct: 456 LHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPGTERIEEELKRLFPGARIIRIDSD 515 Query: 526 SDIDKESVMDSFK---NGTCKLLIATTVIEVGIDVVDASIIIIENA------------EH 570 + K ++ D NG +LI T +I G D + +++ + +A E Sbjct: 516 TTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASER 575 Query: 571 FGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKE 630 L Q+ GR GR + ++ + P + ++ + + F E++L +RKE Sbjct: 576 T-FQLLMQVAGRAGRAGKPGEVVIQTYNP---DHPAIQALKRGDYEAF--YEQELAERKE 629 Query: 631 GEILGIKQSGMPKF-----LIAQPELHDSLLEIARKDAKHILTQDPDLTSVRG 678 G+P F +IA + + LE AR + + P V G Sbjct: 630 L--------GLPPFSRLAAVIASAKNEEKALEFARALRELLKEALPVDVEVLG 674 >gnl|CDD|144016 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Length = 78 Score = 75.6 bits (187), Expect = 4e-14 Identities = 24/69 (34%), Positives = 41/69 (59%), Gaps = 1/69 (1%) Query: 517 SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQL 576 +A +HG +S ++E +++ F+NG K+L+AT V GID+ D +++I + + A Sbjct: 9 KVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNVVINYDL-PWNPASY 67 Query: 577 HQLRGRVGR 585 Q GR GR Sbjct: 68 IQRIGRAGR 76 Score = 31.3 bits (72), Expect = 0.96 Identities = 9/36 (25%), Positives = 18/36 (50%) Query: 350 IIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHAL 385 I V + G + Q R + LE +G++ +++ T Sbjct: 8 IKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVA 43 >gnl|CDD|31394 COG1201, Lhr, Lhr-like helicases [General function prediction only]. Length = 814 Score = 75.3 bits (185), Expect = 5e-14 Identities = 85/354 (24%), Positives = 146/354 (41%), Gaps = 47/354 (13%) Query: 272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV--------EAGGQ 323 S T Q AI +I + ++ GSGKT A + + + E G Sbjct: 22 SLTPPQRYAIPEIHSGENV------LIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIY 75 Query: 324 AVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH 383 A+ ++P+ L +++ + I V + G+ PQ+ ++K L+ H I+I T Sbjct: 76 ALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPH----ILITTP 131 Query: 384 ALFQDSI------QYYK-LILVIVDEQHRF-----GVQQRL---KLTQKATAPHVLLMTA 428 + + + + VIVDE H GVQ L +L + A + ++A Sbjct: 132 ESLAILLNSPKFRELLRDVRYVIVDEIHALAESKRGVQLALSLERLRELAGDFQRIGLSA 191 Query: 429 TPIPRTLVLTSL-GDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYW 487 T P V L G D +I + A +K VI P+ + E + Sbjct: 192 TVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISPVEDLIYDEELWAALYER------ 245 Query: 488 ICPQIEEKKES----NFRSVVER-FNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTC 542 I +++ + + N RS ER L + I + HG +S + V + K G Sbjct: 246 IAELVKKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGEL 305 Query: 543 KLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVG-RGEEISSCILL 595 K ++AT+ +E+GID+ D ++I + + + Q GR G R E+S I++ Sbjct: 306 KAVVATSSLELGIDIGDIDLVIQLGSPK-SVNRFLQRIGRAGHRLGEVSKGIII 358 >gnl|CDD|31261 COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]. Length = 442 Score = 74.0 bits (181), Expect = 1e-13 Identities = 74/368 (20%), Positives = 133/368 (36%), Gaps = 67/368 (18%) Query: 264 KILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQ 323 K++ F QE A+ ++++ + R + +L G+GKT+V A A E Sbjct: 28 KLIVAFEFELRPYQEEALDALVKNRRTERRGVIVLP--TGAGKTVV---AAEAIAELKRS 82 Query: 324 AVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT- 382 +++ P L Q E +KK+ I A + + T Sbjct: 83 TLVLVPTKELLDQWAEALKKFLLLNDEIGIY------------GGGEKELEPAKVTVATV 130 Query: 383 --HALFQDSIQYY--KLILVIVDEQHRFGVQQRLKLTQKATAPHVLL-MTATPIPRT--- 434 A Q ++ + L+I DE H ++ + +A + L +TATP R Sbjct: 131 QTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILELLSAAYPRLGLTATP-EREDGG 189 Query: 435 ---LVLTSLGDIDISKITEKPAGRK---PIKTVIIPIN-------------RIDEVIERL 475 + +G I ++ P K V I + + R Sbjct: 190 RIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRA 249 Query: 476 KVVLSEGKKAYWICPQIEEKKESN---------------FRSVVERFNSLHEHFTSS--I 518 + L +A I E K + F S VE + + F + + Sbjct: 250 RGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGIV 309 Query: 519 AIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQ 578 I G ++E++++ F+ G K+L+ V++ G+D+ DA ++II G + Sbjct: 310 EAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLII--LRPTGSRR--L 365 Query: 579 LRGRVGRG 586 R+GRG Sbjct: 366 FIQRLGRG 373 >gnl|CDD|33855 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]. Length = 441 Score = 68.4 bits (167), Expect = 6e-12 Identities = 77/347 (22%), Positives = 153/347 (44%), Gaps = 43/347 (12%) Query: 274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGIL 333 + Q+ A ++Q + QK L + G+GKT + + A+ GG+ I +P + Sbjct: 99 SPGQKKASNQLVQYIKQKEDTL--VWAVTGAGKTEMIFQGIEQALNQGGRVCIASPRVDV 156 Query: 334 AQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-HALFQDSIQY 392 + Y +K+ N I +++ G+ + +A +++ T H L + + Sbjct: 157 CLELYPRLKQAFSNCDI--DLLYGDSDS-----------YFRAPLVVATTHQLLR----F 199 Query: 393 YKLI-LVIVDEQHRF------GVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDI 445 + L+I+DE F +Q +K +K + +TATP + G++ I Sbjct: 200 KQAFDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGA-TIYLTATPTKKLERKILKGNLRI 258 Query: 446 SKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKE-----SNF 500 K+ + G+ + I ++ ++R K+ L K W+ Q + + Sbjct: 259 LKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPL---KLKRWLEKQRKTGRPVLIFFPEI 315 Query: 501 RSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVD 559 ++ + +L + +IA +H D ++ +++F++G LLI TT++E G+ + Sbjct: 316 ETMEQVAAALKKKLPKETIASVHS--EDQHRKEKVEAFRDGKITLLITTTILERGVTFPN 373 Query: 560 ASIIIIENAEH--FGLAQLHQLRGRVGRG-EEISSCILLYHPPLSKN 603 + ++ AEH F + L Q+ GRVGR E + +L +H SK Sbjct: 374 VDVFVL-GAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHYGKSKA 419 >gnl|CDD|35553 KOG0332, KOG0332, KOG0332, ATP-dependent RNA helicase [RNA processing and modification]. Length = 477 Score = 66.9 bits (163), Expect = 2e-11 Identities = 65/316 (20%), Positives = 128/316 (40%), Gaps = 49/316 (15%) Query: 273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG---GQAVIMAP 329 P+K QE+A+ +L + Q I Q G+GKT ++ M + V+ Q + +AP Sbjct: 113 PSKIQETALPLLLAEPPQN----LIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAP 168 Query: 330 IGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDS 389 LA Q E +++ + T++ R +R I+IGT D Sbjct: 169 TRELAPQTGEVVEEMGKFTELTASYAI-------RGSKAKRGNKLTEQIVIGTPGTVLDL 221 Query: 390 IQYYKLILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKIT 449 + K I + + + TQ + +M + P + L+L S ++ Sbjct: 222 MLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVE----- 276 Query: 450 EKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERF-- 507 I+P N +++R ++ L K+ Y +C ++ ++++V + Sbjct: 277 ----KVAAFALKIVP-NANVIILKREELALDNIKQLYVLCA----CRDDKYQALVNLYGL 327 Query: 508 ----------------NSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGTCKLLIAT 548 L+E + ++++HG ++ + +++D F+ G K+LI T Sbjct: 328 LTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITT 387 Query: 549 TVIEVGIDVVDASIII 564 V GIDV S+++ Sbjct: 388 NVCARGIDVAQVSVVV 403 >gnl|CDD|31398 COG1205, COG1205, Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]. Length = 851 Score = 67.0 bits (163), Expect = 2e-11 Identities = 66/414 (15%), Positives = 135/414 (32%), Gaps = 45/414 (10%) Query: 207 NIIHNPRKAKDFEWTSPARERLAYDELLAGQIALLLMRKQFKKEIGIPINVEGKIAQKIL 266 +++ + R A F E + + + + K P + + ++ Sbjct: 5 SVVASLRSAFKFITEYLEDEFKDAEGQEGSILRDPEIEARPGKTSEFPELRDESLKSALV 64 Query: 267 RNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAM--AAAVEAGGQA 324 + Q A++ I + + ++ GSGKT L+ + + +A Sbjct: 65 KAGIERLYSHQVDALRLIREGRNV------VVTTGTGSGKTESFLLPILDHLLRDPSARA 118 Query: 325 VIMAPIGILAQQHYEFIKKYTQNT--QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT 382 +++ P LA E +++ + ++ TG+ P RR + I++ Sbjct: 119 LLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIR----NPPDILLTN 174 Query: 383 HALFQDSI---------QYYKLILVIVDEQHRF-GVQ--------QRLKLTQKA--TAPH 422 + + L ++VDE H + GVQ +RL + + Sbjct: 175 PDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRRLRRYGSPLQ 234 Query: 423 VLLMTAT-PIPRTLVLTSLGDIDISKITEKPAGRKPIKTVII-PINRID---------EV 471 ++ +AT P G + E + R V P R Sbjct: 235 IICTSATLANPGEFAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAE 294 Query: 472 IERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKE 531 + L +L + + ++ E + S R +++ + ++ Sbjct: 295 LATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERR 354 Query: 532 SVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGR 585 + FK G +IAT +E+GID+ +I + Q GR GR Sbjct: 355 RIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGR 408 >gnl|CDD|35565 KOG0344, KOG0344, KOG0344, ATP-dependent RNA helicase [RNA processing and modification]. Length = 593 Score = 65.4 bits (159), Expect = 5e-11 Identities = 88/495 (17%), Positives = 184/495 (37%), Gaps = 63/495 (12%) Query: 188 WIEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIALLLMRKQF 247 EK+ LQ S E + + +K K + + +A + L LL +RK Sbjct: 59 SEEKEKLQNSDSSSPLEDIDRRGSSKKTKPKMEEKLSEDVIAAKKKLQTSEKLLGIRKSN 118 Query: 248 K-----KEIGIPI----------NVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKN 292 K + P+ ++ ++ + + PT Q+ AI L+ Sbjct: 119 KINVDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLE-----K 173 Query: 293 RMLRILQGDVGSGKTLVALIAM--------AAAVEAGGQAVIMAPIGILAQQHYEFIKKY 344 R + + GSGKTL + + + G +A+I++P LA Q Y ++KY Sbjct: 174 RDV-LACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKY 232 Query: 345 TQN--TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLIL----- 397 + + T + + + + L + I+I T + KL + Sbjct: 233 SIDEGTSLRAAQFSKPAYPSQKPAFLSDE---KYDILISTPMRIVGLLGLGKLNIDLSKV 289 Query: 398 --VIVDEQHR-----FGVQQRLKLTQKATAPHVL--LMTAT-PIPRTLVLTSLGDIDISK 447 ++VDE F V+Q + +P + L +AT + + Sbjct: 290 EWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRV 349 Query: 448 I-TEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVER 506 I + + + + ++ + L+ +++ G K + +++ +E Sbjct: 350 IVGLRNSANETVDQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEELEI 409 Query: 507 FNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE 566 +++++ + +IHG S ++ M+ F+ G +LI T ++ GID +++I Sbjct: 410 YDNIN------VDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVINY 463 Query: 567 NAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNT--EDGFLIAEED 624 + L+ +H++ GR GR I Y + R+ + + G + E+ Sbjct: 464 DFPQSDLSYIHRI-GRTGRAGRSGKAITFY----TDQDMPRIRSIAEVMEQSGCEVPEKI 518 Query: 625 LKQRKEGEILGIKQS 639 + +K + K Sbjct: 519 MGIKKLSRLKKKKLL 533 Score = 43.8 bits (103), Expect = 2e-04 Identities = 51/283 (18%), Positives = 92/283 (32%), Gaps = 52/283 (18%) Query: 294 MLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQN----TQ 349 + Q V G L+A+ V +G P ++ Q E K+ + Sbjct: 358 NETVDQELVFCGSEKGKLLALRQLVASG-----FKPPVLIFVQSKERAKQLFEELEIYDN 412 Query: 350 IIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQ 409 I V++I G Q R + +ER G+ ++I T L I + + LVI + + + Sbjct: 413 INVDVIHGERSQKQRDETMERFRIGKIWVLICT-DLLARGIDFKGVNLVINYDFPQSDLS 471 Query: 410 QRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRID 469 H + T +T D D P R + + + Sbjct: 472 Y----------IHRIGRTGRAGRSGKAITFYTDQD------MPRIRSIAEVMEQSGCEVP 515 Query: 470 EVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDID 529 E I +K + KK+ ++ +R I + Sbjct: 516 EKIMGIKKLSR-------------LKKKKLLKAASKR-----------EEISTKKFPKYK 551 Query: 530 KESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFG 572 K+ ++ K+ K+L E+ + +EN E+FG Sbjct: 552 KKEALEKAKSQEKKIL--KQETEIAVKKEGKIKKKVENKENFG 592 >gnl|CDD|35556 KOG0335, KOG0335, KOG0335, ATP-dependent RNA helicase [RNA processing and modification]. Length = 482 Score = 65.3 bits (159), Expect = 5e-11 Identities = 76/376 (20%), Positives = 141/376 (37%), Gaps = 59/376 (15%) Query: 253 IPINVEGKIAQKILRNIPFS----PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTL 308 IP E + + + NI S PT Q+ +I I R L + GSGKT Sbjct: 73 IPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIIS-----GGRDL-MACAQTGSGKTA 126 Query: 309 VALI-AMAAAVE------------AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEII 355 LI ++ ++ +A+I+AP L Q Y +K++ + + ++ Sbjct: 127 AFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVV 186 Query: 356 TGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLIL-----VIVDEQHR----- 405 G + + ++R I++ T +D I+ K+ L +++DE R Sbjct: 187 YGGTDLGAQLRFIKR----GCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEM 242 Query: 406 -FGVQQRLKLTQKATAPHVLLMTA-------TPIPRTLVLTSLGDIDISKITEKPAGRKP 457 F Q R + Q P T I R + + + + Sbjct: 243 GFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSEN 302 Query: 458 IKTVIIPINR---IDEVIERLKVVLSEGKKA--YW--ICPQIEEKKESNFRSVVERFNSL 510 I I+ +N ++++ L W +E K+ ++ + +S Sbjct: 303 ITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADE--LAAFLSSN 360 Query: 511 HEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEH 570 S IHG + I++E ++ F+NG +L+AT V G+D+ + +I + Sbjct: 361 GYPAKS----IHGDRTQIEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPA 416 Query: 571 FGLAQLHQLRGRVGRG 586 +H++ GR GR Sbjct: 417 DIDDYVHRI-GRTGRV 431 >gnl|CDD|72960 cd04488, RecG_wedge_OBF, RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched chain substrates.. Length = 75 Score = 61.4 bits (149), Expect = 8e-10 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%) Query: 71 TITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKIK 130 T+ G + + RR K+ L+DGTG +TL+FF + LK G ++ V+GK+K Sbjct: 1 TVEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNFQPY-LKKQLPPGTRVRVSGKVK 59 Query: 131 KLKNRIIMVHPHYIF 145 + + + +VHP Y Sbjct: 60 RFRGGLQIVHPEYEL 74 >gnl|CDD|35552 KOG0331, KOG0331, KOG0331, ATP-dependent RNA helicase [RNA processing and modification]. Length = 519 Score = 60.8 bits (147), Expect = 1e-09 Identities = 62/297 (20%), Positives = 116/297 (39%), Gaps = 43/297 (14%) Query: 297 ILQGDVGSGKTLVALIAMAAAVEAGGQ---------AVIMAPIGILAQQHYEFIKKYTQN 347 + GSGKTL L+ + +++AP LA Q +++ ++ Sbjct: 132 VGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKS 191 Query: 348 TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLIL-----VIVDE 402 ++ + G P+ + + LER ++I T D ++ L L +++DE Sbjct: 192 LRLRSTCVYGGAPKGPQLRDLER----GVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDE 247 Query: 403 QHR-----FGVQQRLKLTQKATAPHVLLMTATPIP---RTLVLTSLGD---IDISKITEK 451 R F Q R L+Q LM + P R L L + I++ E Sbjct: 248 ADRMLDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKEL 307 Query: 452 PAGRKPIKTVIIPIN---RIDEVIERLKVVLSE-GKKAYWICPQIEEKKESNFRSVVERF 507 A I+ ++ + ++ ++ + L+ + S+ K C E K+ + Sbjct: 308 KA-NHNIRQIVEVCDETAKLRKLGKLLEDISSDSEGKVIIFC---ETKRTC--DELARNL 361 Query: 508 NSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII 564 + IHG S +++ V+ F+ G +L+AT V G+DV D ++I Sbjct: 362 RRKGWPAVA----IHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDLVI 414 >gnl|CDD|35548 KOG0327, KOG0327, KOG0327, Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]. Length = 397 Score = 60.0 bits (145), Expect = 2e-09 Identities = 69/332 (20%), Positives = 139/332 (41%), Gaps = 40/332 (12%) Query: 273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE---AGGQAVIMAP 329 P+ Q+ AI + K + Q G+GKT LI++ ++ QA+I+AP Sbjct: 49 PSAIQQRAILPCI-----KGHDVIA-QAQSGTGKTAAFLISILQQIDMSVKETQALILAP 102 Query: 330 IGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDS 389 LAQQ + ++ + + V G +AL + HI++GT D Sbjct: 103 TRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDK---PHIVVGTPGRVFDM 159 Query: 390 IQYYKL--------ILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLG 441 + L +L DE G + ++ + V + ++L++ Sbjct: 160 LNRGSLSTDGIKMFVLDEADEMLSRGFKDQIYDIFQELPSDV---------QVVLLSATM 210 Query: 442 DIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKES--- 498 D+ ++T+K R+P++ ++ E I++ + + + +K +C ++ Sbjct: 211 PSDVLEVTKK-FMREPVRILVKKDELTLEGIKQFYINVEKEEKLDTLCDLYRRVTQAVIF 269 Query: 499 -NFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV 557 N R V+ +++ IHG M +++++M F++G+ ++LI T ++ GIDV Sbjct: 270 CNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDV 329 Query: 558 VDASIIII----ENAEHFGLAQLHQLRGRVGR 585 S+++ E++ GR GR Sbjct: 330 QQVSLVVNYDLPARKENYIHRIGRA--GRFGR 359 >gnl|CDD|28928 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.. Length = 203 Score = 58.2 bits (141), Expect = 7e-09 Identities = 51/174 (29%), Positives = 74/174 (42%), Gaps = 29/174 (16%) Query: 273 PTKSQESAIKDILQ--DMSQKNRMLRILQGDVGSGKTLVALIAMAAAV-----EAGGQAV 325 PT Q AI +L D+ I Q GSGKT LI + + + G QA+ Sbjct: 22 PTPIQARAIPPLLSGRDV--------IGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQAL 73 Query: 326 IMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHAL 385 I+AP LA Q E +K ++T + V +I G + + L+R HI++ T Sbjct: 74 ILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKR----GPHIVVATPGR 129 Query: 386 FQDSIQYYKLIL-----VIVDEQHR-----FGVQQRLKLTQKATAPHVLLMTAT 429 D ++ KL L +++DE R F Q R L LL +AT Sbjct: 130 LLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLLFSAT 183 >gnl|CDD|35549 KOG0328, KOG0328, KOG0328, Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]. Length = 400 Score = 58.4 bits (141), Expect = 7e-09 Identities = 74/340 (21%), Positives = 142/340 (41%), Gaps = 57/340 (16%) Query: 273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGG---QAVIMAP 329 P+ Q+ AI IL+ I Q G+GKT I++ +++ QA+I++P Sbjct: 50 PSAIQQRAIPQILKGRDV------IAQAQSGTGKTATFSISVLQSLDISVRETQALILSP 103 Query: 330 IGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQD- 388 LA Q + I + G K L+ +GQ H++ GT D Sbjct: 104 TRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLD---YGQ-HVVSGTPGRVLDM 159 Query: 389 ----SIQYYKLILVIVDEQHRF---GVQQRLKLTQKATAP--HVLLMTATPIPRTLVLTS 439 S++ + ++++DE G ++++ + P V+L++AT L +T Sbjct: 160 IKRRSLRTRAVKMLVLDEADEMLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTE 219 Query: 440 LGDIDISKITEKPAGR--KPIKTVIIPINRIDEVIERLK------------VVLSEGKKA 485 D +I K + IK + + + + + L + + +K Sbjct: 220 KFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKV 279 Query: 486 YWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLL 545 W+ E+ +E+NF +++ +HG M +++ +M+ F++G ++L Sbjct: 280 DWLT---EKMREANF----------------TVSSMHGDMEQKERDKIMNDFRSGKSRVL 320 Query: 546 IATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGR 585 I T V GIDV S++I + + +H++ GR GR Sbjct: 321 ITTDVWARGIDVQQVSLVINYDLPNNRELYIHRI-GRSGR 359 >gnl|CDD|35555 KOG0334, KOG0334, KOG0334, RNA helicase [RNA processing and modification]. Length = 997 Score = 58.1 bits (140), Expect = 8e-09 Identities = 75/347 (21%), Positives = 129/347 (37%), Gaps = 64/347 (18%) Query: 297 ILQGDVGSGKTLVALIAM--------AAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNT 348 I GSGKTL L+ M G A+I+AP LA Q + ++K+ + Sbjct: 406 IGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLL 465 Query: 349 QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQD-------------SIQYYKL 395 I V + G + + L+R A I++ T D + Y L Sbjct: 466 GIRVVCVYGGSGISQQIAELKR----GAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVL 521 Query: 396 ILVIVDEQHRFGVQ----QRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEK 451 DE R Q ++ Q ++ + PR++ + K+ +K Sbjct: 522 -----DEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALAR------KVLKK 570 Query: 452 PA-----GR----KPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRS 502 P GR K + V+ +E +L +L E + E+ K F Sbjct: 571 PVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLELLGE---------RYEDGKTIIFVD 621 Query: 503 VVERFNSLHEHFTSS---IAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVD 559 E+ ++L + +HG + D+ S ++ FKNG LL+AT+V+ G+DV + Sbjct: 622 KQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKE 681 Query: 560 ASIIIIENA-EHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSY 605 +++ + H+ GR GR + + P K + Sbjct: 682 LILVVNYDFPNHY--EDYVHRVGRTGRAGRKGAAVTFITPDQLKYAG 726 >gnl|CDD|39485 KOG4284, KOG4284, KOG4284, DEAD box protein [Transcription]. Length = 980 Score = 56.7 bits (136), Expect = 2e-08 Identities = 73/341 (21%), Positives = 128/341 (37%), Gaps = 51/341 (14%) Query: 273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGG---QAVIMAP 329 PTK Q +AI I M I+Q G+GKTLV + ++++ Q VI+ P Sbjct: 48 PTKIQAAAIPAIFSKMDL------IVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTP 101 Query: 330 IGILAQQHYEFIKKYTQN-TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-----H 383 +A Q E ++K + T + G L+ Q I+IGT Sbjct: 102 TREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLK-----QTRIVIGTPGRIAQ 156 Query: 384 ALFQDSIQYYKLILVIVDE----------QHRFGV------QQRLKLTQKATAPHVLLMT 427 + ++ + L ++DE Q + Q R AT P L Sbjct: 157 LVELGAMNMSHVRLFVLDEADKLMDTESFQDDINIIINSLPQIRQVAAFSATYPRNLDNL 216 Query: 428 ATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYW 487 + R L D+ ++ + P N ++E+ +L+ L+ Sbjct: 217 LSKFMRDPALVRFNADDVQLF----GIKQYVVAKCSPNNSVEEMRLKLQK-LTH------ 265 Query: 488 ICPQIEEKKESNFRSVVERFNSLHEHFTSS---IAIIHGRMSDIDKESVMDSFKNGTCKL 544 + I + F + R + H SS + I G MS D+ +D + ++ Sbjct: 266 VFKSIPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRI 325 Query: 545 LIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGR 585 L++T + GID + ++++ +A H++ GR GR Sbjct: 326 LVSTDLTARGIDADNVNLVVNIDAPADEETYFHRI-GRAGR 365 >gnl|CDD|31308 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]. Length = 542 Score = 54.5 bits (131), Expect = 1e-07 Identities = 48/201 (23%), Positives = 82/201 (40%), Gaps = 27/201 (13%) Query: 303 GSGKTLVALIAMAAA-VEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQ 361 G GKT +A + +A GG+ + +AP L QH EF +K T + + +TG + Sbjct: 39 GLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVRP 98 Query: 362 AHRRKALERIAHGQAHIIIGT-HALFQD----SIQYYKLILVIVDEQHRFG-----VQQR 411 R + + + + T + D I + L+I DE HR V Sbjct: 99 EEREELWAK-----KKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVA 153 Query: 412 LKLTQKATAPHVLLMTATP-IPRTLVLTSLGDIDISKI---TEKPAGRKP----IKTVII 463 + + A P +L +TA+P + + ++ I K+ TE+ +P IK I Sbjct: 154 KEYLRSAKNPLILGLTASPGSDLEKIQEVVENLGIEKVEVRTEEDPDVRPYVKKIKVEWI 213 Query: 464 PI---NRIDEVIERLKVVLSE 481 + I E+ + L+ L Sbjct: 214 KVDLPEEIKEIRDLLRDALKP 234 Score = 42.2 bits (99), Expect = 5e-04 Identities = 24/108 (22%), Positives = 49/108 (45%), Gaps = 10/108 (9%) Query: 498 SNFRSVVERF-NSLHEHFTSSIAIIHGR--------MSDIDKESVMDSFKNGTCKLLIAT 548 + +R E N L + + G+ MS +++ ++D F+ G +L+AT Sbjct: 373 TEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVAT 432 Query: 549 TVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLY 596 +V E G+D+ + ++I + + Q +GR GR + +L+ Sbjct: 433 SVGEEGLDIPEVDLVIFYEPVPSEIRSI-QRKGRTGRKRKGRVVVLVT 479 >gnl|CDD|35551 KOG0330, KOG0330, KOG0330, ATP-dependent RNA helicase [RNA processing and modification]. Length = 476 Score = 53.8 bits (129), Expect = 2e-07 Identities = 74/412 (17%), Positives = 149/412 (36%), Gaps = 42/412 (10%) Query: 273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQ---AVIMAP 329 PTK Q AI L R + L + GSGKT + + + + A+++ P Sbjct: 84 PTKIQSEAIPVALG-----GRDVIGL-AETGSGKTGAFALPILQRLLQEPKLFFALVLTP 137 Query: 330 IGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT------H 383 LAQQ E + + V ++ G M + L + + HI++ T H Sbjct: 138 TRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSK----KPHILVATPGRLWDH 193 Query: 384 ALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDI 443 +L +++DE R + ++ P R L S Sbjct: 194 LENTKGFSLEQLKFLVLDEADRLLDMDFEEELDY-------ILKVIPRERQTFLFSATMT 246 Query: 444 DISKITEKPAGRKPIKTVIIPINRI-DEVIERLKVVLSEGKKAYWICPQIEEKKESNF-- 500 + ++ + P+K + + D + + V + K Y + + E ++ Sbjct: 247 KKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDKDTYLV-YLLNELAGNSVIV 305 Query: 501 ---RSVVERFNS--LHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGI 555 RF + L +I +HG+MS + ++ FK G +L+ T V G+ Sbjct: 306 FCNTCNTTRFLALLLRNLGFQAIP-LHGQMSQSKRLGALNKFKAGARSILVCTDVASRGL 364 Query: 556 DVVDASIIIIENAEHFGLAQLHQL--RGRVGRGEEISSCILLYHPPL----SKNSYTRLS 609 D+ +++ + +H++ R GR + + + Y L +L Sbjct: 365 DIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQRIEHALGKKLP 424 Query: 610 VLKNTEDGFLIAEEDLKQRKEGEILGIKQSGMPKFLIAQPELHDSLLEIARK 661 K ++ + E + + ++ + +K+ G K Q + D ++ + Sbjct: 425 EYKVDKNEVMSLNERVAEAQKEAGMEMKELGKRKGKRPQGDAFDEEMDGGER 476 >gnl|CDD|30860 COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair]. Length = 590 Score = 53.0 bits (127), Expect = 3e-07 Identities = 71/347 (20%), Positives = 132/347 (38%), Gaps = 57/347 (16%) Query: 277 QESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQ 336 Q+ I +L L ++ G GK+L I A+ G ++++P+ L + Sbjct: 22 QQEIIDALLS----GKDTLVVMP--TGGGKSLCYQIP---ALLLEGLTLVVSPLISLMKD 72 Query: 337 HYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT-----HALFQDSIQ 391 + ++ I + + + R++ L ++ GQ ++ + F + ++ Sbjct: 73 QVDQLEAA----GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLK 128 Query: 392 YYKLILVIVDEQH---------RFGVQQRLKLTQKATAPHVLLMTATPIPRTL--VLTSL 440 + LV +DE H R ++ +L P VL +TAT PR + L Sbjct: 129 RLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTATATPRVRDDIREQL 188 Query: 441 GDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKES-- 498 G D + + P + +V+E+ + + ++ + + +S Sbjct: 189 GLQDANIF---------RGSFDRPNLAL-KVVEKGEPSD----QLAFLATVLPQLSKSGI 234 Query: 499 ---NFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGI 555 R VE S H +S+ ++E V +F N K+++AT +GI Sbjct: 235 IYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGI 294 Query: 556 DVVDASIIIIENAEHFGLAQ----LHQLRGRVGRGEEISSCILLYHP 598 D D +I H+ L +Q GR GR + ILLY P Sbjct: 295 DKPDVRFVI-----HYDLPGSIESYYQETGRAGRDGLPAEAILLYSP 336 >gnl|CDD|35572 KOG0351, KOG0351, KOG0351, ATP-dependent DNA helicase [Replication, recombination and repair]. Length = 941 Score = 51.6 bits (123), Expect = 6e-07 Identities = 59/277 (21%), Positives = 100/277 (36%), Gaps = 56/277 (20%) Query: 355 ITGNMPQAHRRKALERIAHGQAHIII------------GTHALFQDSIQYYKLILVIVDE 402 ++ A R L+++A+G I I G D L L ++DE Sbjct: 334 LSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDE 393 Query: 403 QH---RFGVQ-----QRLKLTQKATAPH-VLLMTATPIPRTL--VLTSLGDIDISKITEK 451 H ++G +RL L + + +TAT R V+ SLG + Sbjct: 394 AHCVSQWGHDFRPSYKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKSS 453 Query: 452 PAGRKPIKTVIIPINRIDEVIERLKVVLSEGKK-AYWICPQIEEKKES-------NFRSV 503 NR + E V K I + + + R Sbjct: 454 F-------------NRPNLKYE---VSPKTDKDALLDILEESKLRHPDQSGIIYCLSRKE 497 Query: 504 VERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASII 563 E+ +++ S A H + ++E+V ++ + ++++AT +GID D + Sbjct: 498 CEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFV 557 Query: 564 IIENAEHFGLAQL----HQLRGRVGRGEEISSCILLY 596 I H+ L + +Q GR GR SSC+LLY Sbjct: 558 I-----HYSLPKSFEGYYQEAGRAGRDGLPSSCVLLY 589 >gnl|CDD|35571 KOG0350, KOG0350, KOG0350, DEAD-box ATP-dependent RNA helicase [RNA processing and modification]. Length = 620 Score = 51.6 bits (123), Expect = 8e-07 Identities = 59/350 (16%), Positives = 109/350 (31%), Gaps = 63/350 (18%) Query: 303 GSGKTLVALIAMAAAVEAGG----QAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGN 358 GSGKTL +I + + + +AV++ P LA Q Y+ K+ T + V ++G Sbjct: 193 GSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQ 252 Query: 359 MPQAHRRKALERIAHG-QAHIIIGTHALFQD------SIQYYKLILVIVDEQHRFGVQQR 411 + L + I++ T D S L +++DE R Sbjct: 253 NSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRL----- 307 Query: 412 LKLTQKATAPHVLLMTATPIPRTL-----------VLTSLGDIDISKITEKPAGRKPIKT 460 L + + V+ + T T L ++ P K + + Sbjct: 308 LDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFS 367 Query: 461 VII-----PINRIDEVIERLKVVLSEGKKAYWICPQIEEKK------------------- 496 + + + I RL V Y + + + Sbjct: 368 ATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEPKFKPLAVYALITSN 427 Query: 497 -------ESNFRSVVER----FNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLL 545 N S R ++ G+++ + +++ F G +L Sbjct: 428 KLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVL 487 Query: 546 IATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILL 595 I + + GIDV D +I + +H+ GR R + I L Sbjct: 488 ICSDALARGIDVNDVDNVINYDPPASDKTYVHRA-GRTARAGQDGYAITL 536 >gnl|CDD|31396 COG1203, COG1203, Predicted helicases [General function prediction only]. Length = 733 Score = 50.9 bits (121), Expect = 1e-06 Identities = 87/425 (20%), Positives = 154/425 (36%), Gaps = 65/425 (15%) Query: 269 IPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQA---V 325 I + QE A++ IL+ +K +L +L+ G GKT +LI A ++ + V Sbjct: 192 IEHEGYELQEKALELILR--LEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRV 249 Query: 326 IMA-PIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQ----AHRRKALERIAHGQAHIII 380 I P + + Y K+ +I + + + + + L + ++ + Sbjct: 250 IYVLPFRTIIEDMYRRAKEIFGLFSVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKL 309 Query: 381 GTHALFQDSIQYYKLI---------------LVIVDEQHRFG-------VQQRLKLTQKA 418 + IQ LVI+DE H + + L+ +A Sbjct: 310 LLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADETMLAALLALLEALAEA 369 Query: 419 TAPHVLLMTATPIPRTLV-----LTSLGDIDISKITEKPAGRKPIKTVIIPINRID---- 469 P VLLM+AT +P L G + P +P ++ D Sbjct: 370 GVP-VLLMSAT-LPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQE 427 Query: 470 EVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDID 529 E+IE + + EGKK I N + + ++H R + D Sbjct: 428 ELIELISEEVKEGKKVLVIV---------NTVDRAIELYEKLKEKGPKVLLLHSRFTLKD 478 Query: 530 KE----SVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGR 585 +E + FK +++AT VIE G+D +D ++I E A + L Q GRV R Sbjct: 479 REEKERELKKLFKQNEGFIVVATQVIEAGVD-IDFDVLITELA---PIDSLIQRAGRVNR 534 Query: 586 -GEEISSCILLY----HPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSG 640 G++ + I +Y P K SY +L + + + + E+ Sbjct: 535 HGKKENGKIYVYNDEERGPYLKYSYEKLEKKLKSLEELPLEIINGDSLLSDEVDEKINQD 594 Query: 641 MPKFL 645 + + Sbjct: 595 ILRIQ 599 >gnl|CDD|35560 KOG0339, KOG0339, KOG0339, ATP-dependent RNA helicase [RNA processing and modification]. Length = 731 Score = 49.7 bits (118), Expect = 3e-06 Identities = 64/312 (20%), Positives = 122/312 (39%), Gaps = 41/312 (13%) Query: 302 VGSGKTLVALIAMAAAVE--------AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVE 353 GSGKT + M + G VI+ P LA Q + KK+ + + V Sbjct: 269 TGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVV 328 Query: 354 IITGNMPQAHRRKALERIAHGQAHIIIGTHALFQD-----SIQYYKLILVIVDEQHRF-- 406 + G + + K L+ A I++ T D + ++ +++DE R Sbjct: 329 AVYGGGSKWEQSKELKE----GAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFD 384 Query: 407 -GVQQRLKLTQKATAP--HVLLMTATPIPRT--LVLTSLGD-IDISKITEKPAGRKPIKT 460 G + +++ ++ P LL +AT + L L D + + + A +T Sbjct: 385 MGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQT 444 Query: 461 VII---PINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSS 517 V + +++ ++ L SEGK ++ K+++ + L + Sbjct: 445 VSVCPSEEKKLNWLLRHLVEFSSEGKVLIFV------TKKADAEEIAANL-KLKGF---N 494 Query: 518 IAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLH 577 ++++HG ++ V+ FK +L+AT V G+D+ ++ N + H Sbjct: 495 VSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVV--NYDFARDIDTH 552 Query: 578 QLR-GRVGRGEE 588 R GR GR E Sbjct: 553 THRIGRTGRAGE 564 >gnl|CDD|31307 COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and repair]. Length = 1187 Score = 48.4 bits (115), Expect = 6e-06 Identities = 30/125 (24%), Positives = 54/125 (43%), Gaps = 12/125 (9%) Query: 290 QKNRMLRILQGD-------VGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIK 342 Q+ R+++G G GKT L+ + G + I+ P L +Q YE +K Sbjct: 87 QRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLK 146 Query: 343 KYTQNTQI--IVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQ---DSIQYYKLIL 397 K+ ++ ++ + +P + +ALERI G I+I T + + K Sbjct: 147 KFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELSKLKFDF 206 Query: 398 VIVDE 402 + VD+ Sbjct: 207 IFVDD 211 Score = 31.4 bits (71), Expect = 0.82 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 15/74 (20%) Query: 482 GKKAYWICP------QIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMD 535 GK+ Y I P Q+ E+ + E SL + + H + +KE ++ Sbjct: 125 GKRVYIIVPTTTLVRQVYER----LKKFAEDAGSL-----DVLVVYHSALPTKEKEEALE 175 Query: 536 SFKNGTCKLLIATT 549 ++G +LI T+ Sbjct: 176 RIESGDFDILITTS 189 >gnl|CDD|35554 KOG0333, KOG0333, KOG0333, U5 snRNP-like RNA helicase subunit [RNA processing and modification]. Length = 673 Score = 47.7 bits (113), Expect = 1e-05 Identities = 82/374 (21%), Positives = 148/374 (39%), Gaps = 64/374 (17%) Query: 272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA----------- 320 PT Q AI LQ+ I + GSGKT LI + + + Sbjct: 267 EPTPIQRQAIPLGLQNRDP------IGVAETGSGKTAAFLIPLLIWISSLPPMARLENNI 320 Query: 321 -GGQAVIMAPIGILAQQHYEFIKKYTQNTQI-IVEIITGNMPQAHRRKALERIAHGQAHI 378 G A+I+AP LAQQ E K+ + I V +I G + +++ G I Sbjct: 321 EGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGG----LSFEEQGFQLSMG-CEI 375 Query: 379 IIGTHALFQDSIQYYKLIL-----VIVDEQHRF-------GVQQRL---------KLTQK 417 +I T DS++ L+L V++DE R VQ+ L T + Sbjct: 376 VIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDE 435 Query: 418 ATAPHVLLM---TATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIER 474 + ++ +T++ T+ + ++ + R+P+ I + +E+ Sbjct: 436 KEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLA-RSYLRRPVVVTIGSAGKPTPRVEQ 494 Query: 475 LKVVLSEGKKAYWICPQIEEKKES------NFRSVVERFNSLHEHFTSSIAIIHGRMSDI 528 ++SE +K + +E + N + + + E + +HG S Sbjct: 495 KVEMVSEDEKRKKLIEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQE 554 Query: 529 DKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII----IENAEHFGLAQLHQLRGRVG 584 +E+ + F+ GT +L+AT V GID+ + S++I ++ E + H++ GR G Sbjct: 555 QRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDY----THRI-GRTG 609 Query: 585 RGEEISSCILLYHP 598 R + + I P Sbjct: 610 RAGKSGTAISFLTP 623 >gnl|CDD|35567 KOG0346, KOG0346, KOG0346, RNA helicase [RNA processing and modification]. Length = 569 Score = 46.5 bits (110), Expect = 2e-05 Identities = 48/179 (26%), Positives = 71/179 (39%), Gaps = 32/179 (17%) Query: 273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAM---------AAAVEAGGQ 323 PT Q SAI L+ K+ + R GSGKT LI + E G Sbjct: 42 PTLIQSSAIPLALE---GKDVVAR---ARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPS 95 Query: 324 AVIMAPIGILAQQHYEFIKKYTQNTQIIVEI--ITGNMPQAHRRKALERIAHGQAHIIIG 381 AVI+ P LAQQ Y+ I+K + + + +M + AL I++ Sbjct: 96 AVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALM----DLPDIVVA 151 Query: 382 THA-----LFQDSIQYYKLI-LVIVDEQH---RFGVQQRLKLTQKATAP--HVLLMTAT 429 T A L ++Y + ++VDE FG ++ LK + LM+AT Sbjct: 152 TPAKLLRHLAAGVLEYLDSLSFLVVDEADLLLSFGYEEDLKKLRSHLPRIYQCFLMSAT 210 >gnl|CDD|34219 COG4581, COG4581, Superfamily II RNA helicase [DNA replication, recombination, and repair]. Length = 1041 Score = 45.0 bits (106), Expect = 7e-05 Identities = 49/256 (19%), Positives = 94/256 (36%), Gaps = 40/256 (15%) Query: 267 RNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVI 326 R PF Q+ AI + + S ++ SGKT+VA A+A A+ G + + Sbjct: 114 REYPFELDPFQQEAIAILERGES------VLVCAPTSSGKTVVAEYAIALALRDGQRVIY 167 Query: 327 MAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHAL- 385 +PI L+ Q Y + + +V ++TG+ I +++ T L Sbjct: 168 TSPIKALSNQKYRDLLAKFGDVADMVGLMTGD----------VSINPDAPCLVMTTEILR 217 Query: 386 ---FQDSIQYYKLILVIVDEQHRFGVQQR-----LKLTQKATAPHVLLMTATPIPRTLVL 437 ++ S + V+ DE H G ++R + + ++AT +P Sbjct: 218 NMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDHVRFVFLSAT-VPNAEEF 276 Query: 438 TSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKE 497 I ++ +P V+ +R L+ + GK + + + ++ Sbjct: 277 ----AEWIQRVHSQP------IHVVSTEHRPVP----LEHFVYVGKGLFDLVDEKKKFNA 322 Query: 498 SNFRSVVERFNSLHEH 513 NF S + E Sbjct: 323 ENFPSANRSLSCFSEK 338 Score = 30.3 bits (68), Expect = 1.6 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 7/75 (9%) Query: 518 IAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLA--- 574 IA+ H + KE V + F+ G K++ AT +GI++ +++ ++ G Sbjct: 447 IAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRW 506 Query: 575 ----QLHQLRGRVGR 585 + Q+ GR GR Sbjct: 507 LSPGEYTQMSGRAGR 521 >gnl|CDD|35562 KOG0341, KOG0341, KOG0341, DEAD-box protein abstrakt [RNA processing and modification]. Length = 610 Score = 44.6 bits (105), Expect = 9e-05 Identities = 77/329 (23%), Positives = 130/329 (39%), Gaps = 77/329 (23%) Query: 303 GSGKTLVAL-----------IAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQ-- 349 GSGKTLV + + + A G +I+ P LA+Q ++ I++Y Q Sbjct: 217 GSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEA 276 Query: 350 ----IIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLIL-----VIV 400 + + G +P R+ L+ + G HI++ T D + + L + + Sbjct: 277 GYPELRSLLCIGGVPV---REQLDVVRRG-VHIVVATPGRLMDMLAKKIMSLDACRYLTL 332 Query: 401 DEQHRF---GVQQRLKL------TQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEK 451 DE R G + ++ Q+ T LL +AT +P+ + + K Sbjct: 333 DEADRMIDMGFEDDIRTIFSFFKGQRQT----LLFSAT-MPKKI-----------QNFAK 376 Query: 452 PAGRKPIKTVIIPINRID----EVIERLKVVLSEGKKAYWI-CPQIEEKKESNFRSVVER 506 A KP V + + R +VI+ ++ V E K Y + C Q F Sbjct: 377 SALVKP---VTVNVGRAGAASLDVIQEVEYVKQEAKIVYLLECLQKTSPPVLIFAEKKAD 433 Query: 507 FNSLHEHFT---SSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASII 563 + +HE+ IHG D+ +++F+ G +L+AT V G+D D + Sbjct: 434 VDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHV 493 Query: 564 I-------IENAEHFGLAQLHQLRGRVGR 585 I IEN +H++ GR GR Sbjct: 494 INYDMPEEIEN-------YVHRI-GRTGR 514 >gnl|CDD|35557 KOG0336, KOG0336, KOG0336, ATP-dependent RNA helicase [RNA processing and modification]. Length = 629 Score = 44.2 bits (104), Expect = 1e-04 Identities = 70/330 (21%), Positives = 124/330 (37%), Gaps = 71/330 (21%) Query: 303 GSGKTLVALIAMAAAVEA---------GGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVE 353 G+GKTL L+ ++A G +++ P LA Q +KKY+ N V Sbjct: 267 GTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYSYNGLKSVC 326 Query: 354 IITGNMPQAHRRKALERIAHGQAHIIIGTHALFQD-----SIQYYKLILVIVDEQHR--- 405 + G +R + +E + G III T D I + +++DE R Sbjct: 327 VYGG----GNRNEQIEDLKRG-VEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLD 381 Query: 406 --FGVQ----------QRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPA 453 F Q R + AT P + A + ++ +G +D+ + Sbjct: 382 MGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAV----- 436 Query: 454 GRKPIKTVIIPINRID--EVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLH 511 K +K II + E+++ +S K + + Sbjct: 437 --KSVKQNIIVTTDSEKLEIVQFFVANMSSNDKVIIFVSR----------------KVMA 478 Query: 512 EHFTSSIAI-------IHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII 564 +H +S + +HG D+E ++ FK+G ++L+AT + G+DV D + + Sbjct: 479 DHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVY 538 Query: 565 IENAEHFGLAQLHQLRGRVGR----GEEIS 590 + +H++ GR GR G IS Sbjct: 539 NYDFPRNIEEYVHRV-GRTGRAGRTGTSIS 567 >gnl|CDD|31397 COG1204, COG1204, Superfamily II helicase [General function prediction only]. Length = 766 Score = 43.8 bits (103), Expect = 2e-04 Identities = 33/108 (30%), Positives = 56/108 (51%), Gaps = 14/108 (12%) Query: 303 GSGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQ 361 GSGKTL+AL+A+ + + E GG+ V + P+ LA++ YE + + I V I TG+ Sbjct: 57 GSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRLEE-LGIRVGISTGDYDL 115 Query: 362 AHRRKALERIAHGQAHIIIGTH----ALFQDSIQYYKLI-LVIVDEQH 404 R A + +I+ T +L + + + + LV++DE H Sbjct: 116 DDERLA-------RYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIH 156 >gnl|CDD|35575 KOG0354, KOG0354, KOG0354, DEAD-box like helicase [General function prediction only]. Length = 746 Score = 43.8 bits (103), Expect = 2e-04 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 3/73 (4%) Query: 525 MSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVG 584 M+ +++ V+D F++G +L+AT+V E G+D+ + +++I + + + Q RGR G Sbjct: 458 MTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMV-QRRGR-G 515 Query: 585 RGEEISSCILLYH 597 R S C+LL Sbjct: 516 RARN-SKCVLLTT 527 Score = 38.4 bits (89), Expect = 0.007 Identities = 32/146 (21%), Positives = 54/146 (36%), Gaps = 28/146 (19%) Query: 303 GSGKTLVALIAMAAAVE--AGGQAVIMAP-IGILAQQHYEFIK---KYTQNTQIIVEIIT 356 GSGKT +A + M E G+ V +AP ++ QQ F Y+ Q+ + Sbjct: 86 GSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFSIYLIPYSVTGQLGDTVPR 145 Query: 357 GNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQ------YYKLILVIVDEQHR----- 405 N + K + T + ++ ++ L++ DE HR Sbjct: 146 SNRGEIVASK----------RVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNH 195 Query: 406 -FGVQQRLKLTQKATAPHVLLMTATP 430 + R L K +L +TA+P Sbjct: 196 PYNNIMREYLDLKNQGNQILGLTASP 221 >gnl|CDD|35568 KOG0347, KOG0347, KOG0347, RNA helicase [RNA processing and modification]. Length = 731 Score = 43.1 bits (101), Expect = 3e-04 Identities = 83/417 (19%), Positives = 140/417 (33%), Gaps = 83/417 (19%) Query: 266 LRNIPFS-PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQ- 323 L N+ FS PT+ Q + ++ ++ + + GSGKTL I + + Sbjct: 196 LSNLGFSRPTEIQSLVLPAAIRG-----KVDILGAAETGSGKTLAFGIPIVERLLESSDD 250 Query: 324 ---------------AVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKAL 368 A+++ P LA Q + +K + TQI V ITG + + Sbjct: 251 SQELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQ---- 306 Query: 369 ERIAHGQAHIIIGTHALFQDSIQ--------YYKLILVIVDEQHRF----------GVQQ 410 +R+ + + I++ T + I+ + K+ +++DE R + + Sbjct: 307 QRLLNQRPDIVVATPGRLWELIEEDNTHLGNFKKVKCLVLDEADRMVEKGHFEELSKLLK 366 Query: 411 RLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPI-----------K 459 L QK L+ +AT TLVL K ++ I K Sbjct: 367 HLNEEQKNRQRQTLVFSAT---LTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRGK 423 Query: 460 TVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKE---------------SNFRSVV 504 II + L L E CP +E+ N V Sbjct: 424 PKIIDLTPQSATASTLTESLIE-------CPPLEKDLYLYYFLTRYPGRTLVFCNSIDCV 476 Query: 505 ERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII 564 +R L + +H M + ++ FK +LIAT V G+D+ +I Sbjct: 477 KRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVI 536 Query: 565 IENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRL-SVLKNTEDGFLI 620 +H+ GR R ++L P +L LK ED + Sbjct: 537 HYQVPRTSEIYVHR-SGRTARANSEGVSVMLCGPQ-EVGPLKKLCKTLKKKEDLPIF 591 >gnl|CDD|35569 KOG0348, KOG0348, KOG0348, ATP-dependent RNA helicase [RNA processing and modification]. Length = 708 Score = 43.1 bits (101), Expect = 3e-04 Identities = 41/150 (27%), Positives = 74/150 (49%), Gaps = 26/150 (17%) Query: 272 SPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEA---------GG 322 +PT Q+ AI +L+ ++ ++R GSGKTL L+ + +++A G Sbjct: 159 APTSVQKQAIPVLLEG---RDALVR---AQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGP 212 Query: 323 QAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALE-RIAHGQAHIIIG 381 A+++ P LA Q YE ++K + IV G + ++K+ + R+ G +I+IG Sbjct: 213 YALVIVPTRELALQIYETVQKLLKPFHWIV---PGVLMGGEKKKSEKARLRKG-INILIG 268 Query: 382 T------HALFQDSIQYYKLILVIVDEQHR 405 T H SI++ +L +++DE R Sbjct: 269 TPGRLVDHLKNTKSIKFSRLRWLVLDEADR 298 Score = 33.8 bits (77), Expect = 0.16 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 1/78 (1%) Query: 521 IHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLR 580 +HG M ++ SV F + +L+ T V G+D+ +++ + LH++ Sbjct: 477 LHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRV- 535 Query: 581 GRVGRGEEISSCILLYHP 598 GR R E +L P Sbjct: 536 GRTARAGEKGEALLFLLP 553 >gnl|CDD|35558 KOG0337, KOG0337, KOG0337, ATP-dependent RNA helicase [RNA processing and modification]. Length = 529 Score = 42.7 bits (100), Expect = 3e-04 Identities = 70/326 (21%), Positives = 124/326 (38%), Gaps = 47/326 (14%) Query: 255 INVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAM 314 + ++ K+ + I + +PT Q I IL + M R GSGKT LI M Sbjct: 26 MGLDYKVLRAIHKKGFNTPTPIQRKTIPLIL-EGRDVVGMAR-----TGSGKTAAFLIPM 79 Query: 315 AAA----VEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALER 370 + G +A+I++P LA Q + +K + T++ ++ G + L Sbjct: 80 IEKLKSHSQTGLRALILSPTRELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILL-- 137 Query: 371 IAHGQAHIIIGTHALFQDSIQYYKLIL-----VIVDEQHRF---GVQQRL--KLTQKATA 420 + III T L L V+ DE R G Q++L L++ + Sbjct: 138 --NENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMGFQEQLHEILSRLPES 195 Query: 421 PHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKV-VL 479 LL +AT +PR LV + K P+ + +I E+++ V Sbjct: 196 RQTLLFSAT-LPRDLVDFA-----------KAGLVPPVLVRLDVETKISELLKVRFFRVR 243 Query: 480 SEGKKAYWICPQIEEKKESNFRSV--------VERFNSLHEHFTSSIAIIHGRMSDIDKE 531 K+A + I + + +++ VE L F + I+ + ++ Sbjct: 244 KAEKEAALLS--ILGGRIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARK 301 Query: 532 SVMDSFKNGTCKLLIATTVIEVGIDV 557 F+ +L+ T V G+D+ Sbjct: 302 INGRDFRGRKTSILVVTDVAARGLDI 327 >gnl|CDD|35547 KOG0326, KOG0326, KOG0326, ATP-dependent RNA helicase [RNA processing and modification]. Length = 459 Score = 42.3 bits (99), Expect = 4e-04 Identities = 68/332 (20%), Positives = 138/332 (41%), Gaps = 43/332 (12%) Query: 273 PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGI 332 P+ QE +I L + ++ + R G + + ++ + QA+I+ P Sbjct: 108 PSPIQEESIPIAL---TGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRE 164 Query: 333 LAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQ- 391 LA Q + K+ +++ I V + TG R + R+ + H+++GT D + Sbjct: 165 LALQTSQVCKELSKHLGIKVMVTTGG---TSLRDDIMRL-NQTVHLVVGTPGRILDLAKK 220 Query: 392 ----YYKLILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISK 447 +++++DE + L + + ++ P R ++L S K Sbjct: 221 GVADLSDCVILVMDEADKL-----LSVDFQPIVEKLISFL--PKERQILLYSATFPLTVK 273 Query: 448 ITEKPAGRKPIKTVIIPINRIDEV----IERLKVVLSEGKKAYWICP---QIEEKKESNF 500 +KP + IN ++E+ + + + E +K + + +++ + F Sbjct: 274 GFMDRHLKKPYE-----INLMEELTLKGVTQYYAFVEERQKVHCLNTLFSKLQINQSIIF 328 Query: 501 RSVVERFNSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV 557 + R L + T S IH +M+ + V F+NG C+ L+ T + GID+ Sbjct: 329 CNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDI 388 Query: 558 VDASIII----IENAEHFGLAQLHQLRGRVGR 585 +++I +NAE + LH++ GR GR Sbjct: 389 QAVNVVINFDFPKNAETY----LHRI-GRSGR 415 >gnl|CDD|144799 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain. This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain. Length = 75 Score = 40.7 bits (96), Expect = 0.001 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 3/75 (4%) Query: 70 VTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRKITVTGKI 129 VT+ G ++ + + L DGTG I ++ F + E L EG + VTGK+ Sbjct: 1 VTVAGRVTSVRR---SGGKVAFLTLRDGTGSIQVVLFKEEAEKLAKKLKEGDVVLVTGKV 57 Query: 130 KKLKNRIIMVHPHYI 144 KK + + I Sbjct: 58 KKRPGGELELVVEEI 72 >gnl|CDD|30902 COG0556, UvrB, Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]. Length = 663 Score = 39.0 bits (91), Expect = 0.005 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 6/76 (7%) Query: 270 PFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQ-AVIMA 328 PF P Q AI ++++ + + + L G GSGKT MA + + +++A Sbjct: 10 PFKPAGDQPEAIAELVEGIENGLKH-QTLLGVTGSGKTF----TMANVIAKVQRPTLVLA 64 Query: 329 PIGILAQQHYEFIKKY 344 LA Q Y K++ Sbjct: 65 HNKTLAAQLYSEFKEF 80 >gnl|CDD|36165 KOG0947, KOG0947, KOG0947, Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]. Length = 1248 Score = 38.8 bits (90), Expect = 0.006 Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 12/93 (12%) Query: 267 RNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVI 326 PF Q+ AI + + S + +GKT+VA A+A A + + + Sbjct: 292 LIYPFELDTFQKEAIYHLERGDSV------FVAAHTSAGKTVVAEYAIALAQKHMTRTIY 345 Query: 327 MAPIGILAQQHY-EFIKKYTQNTQIIVEIITGN 358 +PI L+ Q + +F + + V ++TG+ Sbjct: 346 TSPIKALSNQKFRDFKETFGD-----VGLLTGD 373 Score = 30.3 bits (68), Expect = 1.8 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 7/75 (9%) Query: 518 IAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGL---- 573 IA+ HG + I KE V F+ G K+L AT +G+++ +++ +H G Sbjct: 633 IAVHHGGLLPIVKEVVELLFQRGLVKVLFATETFAMGVNMPARTVVFSSLRKHDGNEFRE 692 Query: 574 ---AQLHQLRGRVGR 585 + Q+ GR GR Sbjct: 693 LLPGEYTQMAGRAGR 707 >gnl|CDD|36170 KOG0952, KOG0952, KOG0952, DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]. Length = 1230 Score = 38.0 bits (88), Expect = 0.009 Identities = 73/351 (20%), Positives = 122/351 (34%), Gaps = 79/351 (22%) Query: 303 GSGKTLVALIAMAAAV-EAGGQAVIM---------APIGILAQQHYEFIKKYTQNTQIIV 352 GSGKT++A + + + E Q I AP+ LA + + K I V Sbjct: 136 GSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFSKKLAPLGISV 195 Query: 353 EIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQ-------DSIQYYKLI-LVIVDEQH 404 +TG+ Q + + + II+ T + + L+ LVI+DE H Sbjct: 196 RELTGDT-QLTKTEIAD------TQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVH 248 Query: 405 RFG-------------VQQRLKLTQK--------ATAPHVL-LMTATPIPRTLVLTSLGD 442 + ++ +Q AT P+ + + L S Sbjct: 249 LLHDDRGPVLETIVARTLRLVESSQSMIRIVGLSATLPNYEDVARFLRVNPYAGLFSF-- 306 Query: 443 IDIS----KITEKPAGRKPIKTVIIPINRIDEV-IERLKVVLSEGKKAYWICPQIEE--- 494 D +T+ G K K N IDEV +++ L EG + E Sbjct: 307 -DQRYRPVPLTQGFIGIKGKKNRQQKKN-IDEVCYDKVVEFLQEGHQVLVFVHSRNETIR 364 Query: 495 -----KKESNFRSVVERFNS------LHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCK 543 ++ + + F L E F + I H M D++ V FK G K Sbjct: 365 TAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHIK 424 Query: 544 LLIATTVIEVGIDVVDASIII----IENAEHFGLAQLH-----QLRGRVGR 585 +L T + G+++ ++II + ++ L Q+ GR GR Sbjct: 425 VLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGR 475 >gnl|CDD|35564 KOG0343, KOG0343, KOG0343, RNA Helicase [RNA processing and modification]. Length = 758 Score = 37.7 bits (87), Expect = 0.012 Identities = 59/282 (20%), Positives = 103/282 (36%), Gaps = 45/282 (15%) Query: 303 GSGKTLVALIAMAAAV-------EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEII 355 GSGKTL L+ + A+ G A+I++P LA Q +E + K ++ +I Sbjct: 116 GSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTRELALQTFEVLNKVGKHHDFSAGLI 175 Query: 356 TGNMPQAHRRKALERIAHGQAHIIIGT------HALFQDSIQYYKLILVIVDEQHR---F 406 G + + ++ +I++ T H + L ++++DE R Sbjct: 176 IGGKDVKFELERISQM-----NILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDM 230 Query: 407 GVQQRLKLTQKATAPH--VLLMTATPIPRT--LVLTSLGDIDISKITEKPAGRKPIKTVI 462 G ++ L + LL +AT L SL D + E P Sbjct: 231 GFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATP----- 285 Query: 463 IPINRIDEVIERLKVVLSEGKKAYWICPQIE---EKKESNFRSVVERFNSLHEHFT---- 515 +++ V++ K + I+ +KK F S ++ L+E F Sbjct: 286 -------SNLQQSYVIVPLEDKIDMLWSFIKSHLKKKSIVFLSSCKQVKFLYEAFCRLRP 338 Query: 516 -SSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGID 556 + +HG MS + V F +L T V G+D Sbjct: 339 GIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLD 380 >gnl|CDD|35566 KOG0345, KOG0345, KOG0345, ATP-dependent RNA helicase [RNA processing and modification]. Length = 567 Score = 37.2 bits (86), Expect = 0.014 Identities = 66/330 (20%), Positives = 123/330 (37%), Gaps = 53/330 (16%) Query: 303 GSGKTLVALIAMAAAV------EAGGQ--AVIMAPIGILAQQHYEFIKKYTQNT-QIIVE 353 GSGKTL L+ M + GQ A+I++P LA+Q E + + ++ + E Sbjct: 53 GSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQIREVAQPFLEHLPNLNCE 112 Query: 354 IITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYK-------LILVIVDEQHRF 406 ++ G + ++ +I++GT D +Q L ++++DE R Sbjct: 113 LLVGGR---SVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRL 169 Query: 407 GVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPIN 466 L + +A+ +L + P R L S T+ + + Sbjct: 170 -----LDMGFEASVNTIL--SFLPKQRRTGLFS--------ATQTQEVEDLARAGLRNPV 214 Query: 467 RIDEVIERLKVVLSEGKKAYWICPQIE--------------EKKESNFRS--VVERFNSL 510 R+ + S Y +C E +K F + VE F L Sbjct: 215 RVSVKEKSKSATPSSLALEYLVCEADEKLSQLVHLLNNNKDKKCIVFFPTCASVEYFGKL 274 Query: 511 HEHFTSSIAI--IHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENA 568 I IHG+MS + V+++F+ + +L T V G+D+ +++ + Sbjct: 275 FSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDP 334 Query: 569 EHFGLAQLHQLRGRVGRGEEISSCILLYHP 598 + +H+ GR R + I+ +P Sbjct: 335 PKDPSSFVHRC-GRTARAGREGNAIVFLNP 363 >gnl|CDD|37014 KOG1803, KOG1803, KOG1803, DNA helicase [Replication, recombination and repair]. Length = 649 Score = 36.9 bits (85), Expect = 0.020 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 5/70 (7%) Query: 260 KIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE 319 I K + + SQ++A+ + N+ L I+ G G+GKT + ++ V+ Sbjct: 173 NIEIKKITFFNKNLNSSQKAAVS-----FAINNKDLLIIHGPPGTGKTRTLVEIISQLVK 227 Query: 320 AGGQAVIMAP 329 + ++ AP Sbjct: 228 QKKRVLVCAP 237 >gnl|CDD|143942 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). Length = 295 Score = 36.5 bits (85), Expect = 0.022 Identities = 37/161 (22%), Positives = 66/161 (40%), Gaps = 16/161 (9%) Query: 282 KDILQDM-SQKNRMLR-ILQGDVGSGKTL--VALIA-MAAAVEAGGQAVIMAPIGILAQQ 336 + + + S N L IL ++G GKTL ++L+A + G +++ P+ L Sbjct: 3 LEGVNWLISLYNNGLGGILADEMGLGKTLQTISLLAYLKELKPLAGPHLVVCPLSTLDNW 62 Query: 337 HYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH----ALFQDSIQY 392 EF +K+ + I+V G+ R + L + ++ T +D + Sbjct: 63 LNEF-EKWAPDLNIVVYYGDGD----SRSELLRNVLRTGKFDVLITSYEYIRRDKDELHK 117 Query: 393 YKLILVIVDEQHRF--GVQQRLKLTQKATAPHVLLMTATPI 431 VI+DE HR + + + LL+T TPI Sbjct: 118 ANWRYVILDEGHRIKNAKSKLSLALKSLKTNNRLLLTGTPI 158 >gnl|CDD|35563 KOG0342, KOG0342, KOG0342, ATP-dependent RNA helicase pitchoune [RNA processing and modification]. Length = 543 Score = 36.5 bits (84), Expect = 0.028 Identities = 57/328 (17%), Positives = 106/328 (32%), Gaps = 67/328 (20%) Query: 274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV-------EAGGQAVI 326 T Q+ I +L+ + G+GKTL L+ + G +I Sbjct: 106 TPVQQKTIPPLLEGKDV------LAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLI 159 Query: 327 MAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALF 386 + P LA Q + K+ + + I I + + +++ G +I+I T Sbjct: 160 ICPTRELAMQIFAEAKELLKYHESITVGIV--IGGNNFSVEADKLVKG-CNILIATPGRL 216 Query: 387 QDSIQYYK------LILVIVDEQHRF-------GVQQRLKLTQKATAPHVLLMTATPIPR 433 D +Q L +++DE R V+Q +K+ K + T + Sbjct: 217 LDHLQNTSGFLFRNLKCLVLDEADRLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVK 276 Query: 434 TLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICP--- 490 L +L R P+ ++ + ++ Y + P Sbjct: 277 DLARGALK-------------RDPV--------FVNVDDGGERETHERLEQGYVVAPSDS 315 Query: 491 -----------QIEEKKESNFRS---VVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDS 536 I+ K F S V+ L + + IHG+ + S Sbjct: 316 RFSLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFE 375 Query: 537 FKNGTCKLLIATTVIEVGIDVVDASIII 564 F +L+ T V G+D+ D ++ Sbjct: 376 FCKAESGILVCTDVAARGLDIPDVDWVV 403 >gnl|CDD|35570 KOG0349, KOG0349, KOG0349, Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]. Length = 725 Score = 35.4 bits (81), Expect = 0.057 Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 1/92 (1%) Query: 504 VERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASII 563 +ER + S +HG ++++ ++SFK K LI T V G+D+ + Sbjct: 521 LERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFM 580 Query: 564 IIENAEHFGLAQLHQLRGRVGRGEEISSCILL 595 I +H++ GRVGR E + I L Sbjct: 581 INVTLPDDKTNYVHRI-GRVGRAERMGLAISL 611 >gnl|CDD|36169 KOG0951, KOG0951, KOG0951, RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]. Length = 1674 Score = 34.9 bits (80), Expect = 0.080 Identities = 31/107 (28%), Positives = 54/107 (50%), Gaps = 11/107 (10%) Query: 303 GSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHY-EFIKKYTQNTQIIVEIITGNMPQ 361 GSGKT A +A+ G +AV +AP+ +A + Y ++ KK+++ + + +TG Sbjct: 1169 GSGKTACAELALLRPDTIG-RAVYIAPLEEIADEQYRDWEKKFSKLLGLRIVKLTGE--- 1224 Query: 362 AHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLI-LVIVDEQHRFG 407 +L+ + +II T + D +Q + + L IVDE H G Sbjct: 1225 ----TSLDLKLLQKGQVIISTPEQW-DLLQSIQQVDLFIVDELHLIG 1266 Score = 32.6 bits (74), Expect = 0.35 Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 9/87 (10%) Query: 508 NSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII--- 564 L + AI H ++ D+E V D F +G ++L++T + G+++ ++II Sbjct: 600 PDLKDLLPYGFAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGT 659 Query: 565 -IENAEHFGLAQLH-----QLRGRVGR 585 + + E +L Q+ GR GR Sbjct: 660 QVYDPEKGRWTELSPLDVMQMLGRAGR 686 >gnl|CDD|39353 KOG4150, KOG4150, KOG4150, Predicted ATP-dependent RNA helicase [RNA processing and modification]. Length = 1034 Score = 34.7 bits (79), Expect = 0.084 Identities = 28/122 (22%), Positives = 46/122 (37%), Gaps = 6/122 (4%) Query: 466 NRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRM 525 +++ EV ++ G + CP + E E H +I G Sbjct: 509 SKVVEVSHLFAEMVQHGLRCIAFCP-SRKLCELVLCLTREILAETAPHLVEAITSYRGGY 567 Query: 526 SDIDKESVMDSFKNGTCKLLIATTVIEVGIDV--VDASIIIIENAEHFGLAQLHQLRGRV 583 D+ + G +IAT +E+GID+ +DA + + +A L Q GR Sbjct: 568 IAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLDAVLHL---GFPGSIANLWQQAGRA 624 Query: 584 GR 585 GR Sbjct: 625 GR 626 >gnl|CDD|35561 KOG0340, KOG0340, KOG0340, ATP-dependent RNA helicase [RNA processing and modification]. Length = 442 Score = 34.2 bits (78), Expect = 0.12 Identities = 46/278 (16%), Positives = 105/278 (37%), Gaps = 20/278 (7%) Query: 303 GSGKTLVALIAMAAAVE---AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNM 359 GSGKT + + + G A+++ P LA Q E + + V +I G Sbjct: 54 GSGKTAAFALPILNRLSEDPYGIFALVLTPTRELALQIAEQFIALGKLLNLKVSVIVGGT 113 Query: 360 PQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKAT 419 + L + H+++ T D + + + ++ +F V Sbjct: 114 DMIMQAAILSD----RPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVLAGC 169 Query: 420 APHVLLMTATPIP---RTLVLTSLGDIDISKITEKPAGRKPIKTV-IIPINRIDEVIERL 475 P +L +P +TL+ ++ I ++ P + + +I E + + Sbjct: 170 FPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQG 229 Query: 476 KVVLSE-GKKAYWI----CPQIEEKKE----SNFRSVVERFNSLHEHFTSSIAIIHGRMS 526 +++S K AY + + +E N + + ++ + +H +M Sbjct: 230 YILVSIDVKDAYLVHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMP 289 Query: 527 DIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII 564 ++ + + F++ ++LIAT V G+D+ +++ Sbjct: 290 QKERLAALSRFRSNAARILIATDVASRGLDIPTVELVV 327 >gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]. Length = 935 Score = 33.8 bits (77), Expect = 0.15 Identities = 41/139 (29%), Positives = 64/139 (46%), Gaps = 26/139 (18%) Query: 217 DFEWTSPARERLAYDELLAGQIALLLMRKQ------FKKEIGIPINVEGKIAQKIL---R 267 DF W S + +R+ + LL + ++ + K +G P VE +K+L Sbjct: 352 DFVWKSTSFDRMQ------LALKLLAVDEKKVSGYLYHKLLGHP--VEDSSLKKLLPRRF 403 Query: 268 NIPFSP--TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLV-ALIAMAAAVEAGGQA 324 ++P P SQ +A+K +LQ R L ++QG G+GKT+ A I A + G Sbjct: 404 SVPNLPKLNASQSNAVKHVLQ------RPLSLIQGPPGTGKTVTSATIVYHLARQHAGPV 457 Query: 325 VIMAPIGILAQQHYEFIKK 343 ++ AP I Q E I K Sbjct: 458 LVCAPSNIAVDQLAEKIHK 476 >gnl|CDD|33842 COG4085, COG4085, Predicted RNA-binding protein, contains TRAM domain [General function prediction only]. Length = 204 Score = 33.1 bits (75), Expect = 0.27 Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 8/84 (9%) Query: 60 KISEISEERIVTITGYISQHSSFQLQKRRPYKIL---LNDGTGEITLLFFYRKTEMLKN- 115 +I+ I+E + Q I LNDGTG IT++ E L+ Sbjct: 39 QIATINEGDGRLNEEVTVKGEVTADQNAIGGGIESLVLNDGTGTITVVASRSTEETLELN 98 Query: 116 ----VFFEGRKITVTGKIKKLKNR 135 V EG + VTG++++ + Sbjct: 99 EGMPVTVEGEIVEVTGRVEEYRGS 122 >gnl|CDD|36168 KOG0950, KOG0950, KOG0950, DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]. Length = 1008 Score = 32.7 bits (74), Expect = 0.31 Identities = 56/284 (19%), Positives = 96/284 (33%), Gaps = 48/284 (16%) Query: 303 GSGKTLVALIAMAA-AVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQ 361 +GKTLVA I M + +++ P + Q+ + ++ + VE G P Sbjct: 250 SAGKTLVAEILMLREVLCRRRNVLLILPYVSIVQEKISALSPFSIDLGFPVEEYAGRFPP 309 Query: 362 AHRRKALERIAHGQAHIIIGT----HALFQDSIQYYKLI---LVIVDEQHRFGVQQR--- 411 RRK + I T ++L I+ +L +V+VDE H G + R Sbjct: 310 EKRRKRE--------SVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAI 361 Query: 412 -------LKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIP 464 + T+ ++ M+AT IP +L D + +P P+K I P Sbjct: 362 LELLLAKILYENLETSVQIIGMSAT-IPNNSLLQDWLDAFVYTTRFRPV---PLKEYIKP 417 Query: 465 INRIDEV--------IERLKVVLSEGKKAYWICPQIEEKKESNFRSVV--------ERFN 508 + I E I L + + E +V E Sbjct: 418 GSLIYESSRNKVLREIANLYSSNLGDEDPDHLVGLCTETAPEGSSVLVFCPSKKNCENVA 477 Query: 509 SLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKL--LIATTV 550 SL R+ + S+ + + L ++A T+ Sbjct: 478 SLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTI 521 >gnl|CDD|30899 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]. Length = 866 Score = 32.4 bits (72), Expect = 0.48 Identities = 39/166 (23%), Positives = 70/166 (42%), Gaps = 15/166 (9%) Query: 285 LQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG----GQAVIMAPIGILAQQHYEF 340 L ++ + N + IL D+G GKT+ + + + +E+ G A+I+ P +L+ EF Sbjct: 350 LSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPASLLSNWKREF 409 Query: 341 IKKYTQNTQIIVEIITGNMPQAHR---RKALERIAHGQAHIIIGTHALFQDSIQYYKLI- 396 K ++V + R R L+ ++I T+ L + + + + Sbjct: 410 EKFAPDLRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLK 469 Query: 397 -----LVIVDEQHRFGVQQRL--KLTQKATAPHVLLMTATPIPRTL 435 V++DE HR Q K Q A + L +T TP+ L Sbjct: 470 KIEWDRVVLDEAHRIKNDQSSEGKALQFLKALNRLDLTGTPLENRL 515 >gnl|CDD|31930 COG1744, Med, Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]. Length = 345 Score = 32.3 bits (73), Expect = 0.53 Identities = 32/127 (25%), Positives = 50/127 (39%), Gaps = 16/127 (12%) Query: 291 KNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMA-----PIGILA--QQHYEFIKK 343 K R + L+ +G+ L A A A A G+ +A I + Q YE + K Sbjct: 2 KFRRILGLKLALGAALLLAACGASLAGAAAAGKKKKVAVIDVGGIDDKSFNQSAYEGLLK 61 Query: 344 YTQNTQIIVEIITGNMPQ----AHRRKALERIAHGQAHIIIGTHALFQDSI-----QYYK 394 + + VE Q A +AL +A +I GT F D++ +Y Sbjct: 62 AKKELGLKVETYYWEYVQSDSEADYERALRALAEDGYDLIFGTGFAFSDALEKVAAEYPD 121 Query: 395 LILVIVD 401 + VI+D Sbjct: 122 VKFVIID 128 >gnl|CDD|32636 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 353 Score = 32.1 bits (73), Expect = 0.56 Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 2/50 (4%) Query: 265 ILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGK--TLVALI 312 +LR IP +E + I++++++ R L ++ G GSGK TL A+I Sbjct: 97 VLRLIPSKIPTLEELGLPPIVRELAESPRGLILVTGPTGSGKSTTLAAMI 146 >gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit. Length = 103 Score = 31.8 bits (73), Expect = 0.59 Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 1/42 (2%) Query: 391 QYYKLILVIVDEQHRFGVQQR-LKLTQKATAPHVLLMTATPI 431 Q + ++I+DE H + + K+ + +L +TATP Sbjct: 61 QALEEFVIIIDEAHHSSAKTKYRKILEYFKPAFLLGLTATPE 102 >gnl|CDD|35559 KOG0338, KOG0338, KOG0338, ATP-dependent RNA helicase [RNA processing and modification]. Length = 691 Score = 31.9 bits (72), Expect = 0.60 Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 4/65 (6%) Query: 521 IHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLR 580 +HG ++ + ++ FK +LIAT V G+D+ +I LH Sbjct: 456 LHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLH--- 512 Query: 581 GRVGR 585 RVGR Sbjct: 513 -RVGR 516 >gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 509 Score = 31.7 bits (72), Expect = 0.63 Identities = 34/184 (18%), Positives = 69/184 (37%), Gaps = 18/184 (9%) Query: 189 IEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIALLLMRKQFK 248 ++L P+ + F ++ + +KA+ + R L + LA + L + Sbjct: 241 KPVEILGLSEVPAAGDVFIVVKDEKKARAI---AELRVVLLREAELASKKKGELEELIAE 297 Query: 249 KEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSG-KT 307 +I + I + + T+ A+K L+ + +RI+ VG ++ Sbjct: 298 IKIRGELKELNVILK--------ADTQGSLEALKGSLKKLGVDEVKVRIIHAGVGGITES 349 Query: 308 LVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKA 367 V L A + AV G + LA+ I+ Y ++I ++ +A + Sbjct: 350 DVMLAAASDAVIIGFNVRVDPEARRLAESEGVKIRYYDVIYKLIEDV------EAAMKGM 403 Query: 368 LERI 371 LE Sbjct: 404 LEPE 407 >gnl|CDD|31392 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]. Length = 654 Score = 31.7 bits (71), Expect = 0.80 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 3/71 (4%) Query: 270 PFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALI-AMAAAVEAGGQAVIMA 328 F P Q + + + + + +++ G+GKTL L+ A+A A E G + +I Sbjct: 13 GFEPRPEQREMAEAVAEALKGGEGL--LIEAPTGTGKTLAYLLPALAYAREEGKKVIIST 70 Query: 329 PIGILAQQHYE 339 L +Q E Sbjct: 71 RTKALQEQLLE 81 >gnl|CDD|35573 KOG0352, KOG0352, KOG0352, ATP-dependent DNA helicase [Replication, recombination and repair]. Length = 641 Score = 31.2 bits (70), Expect = 0.93 Identities = 27/111 (24%), Positives = 47/111 (42%), Gaps = 13/111 (11%) Query: 522 HGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRG 581 H + ++ V + + N ++ AT +G+D D +I + LA +Q G Sbjct: 286 HAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQ-NLAGYYQESG 344 Query: 582 RVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGE 632 R GR + S C L Y S+ L+ FL++ E K R++ + Sbjct: 345 RAGRDGKRSYCRLYY----SRQDKNALN--------FLVSGELAKLREKAK 383 >gnl|CDD|32671 COG2843, PgsA, Putative enzyme of poly-gamma-glutamate biosynthesis (capsule formation) [Cell envelope biogenesis, outer membrane]. Length = 372 Score = 30.8 bits (69), Expect = 1.4 Identities = 14/65 (21%), Positives = 23/65 (35%), Gaps = 1/65 (1%) Query: 421 PHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLS 480 PHVL I +L SLG+ + EK + V+ +N + + + Sbjct: 265 PHVLQPIEIYIQGKPILYSLGNFLFDQDYEKIWDIAVEREVLGELNYLVR-FDPTPGNIY 323 Query: 481 EGKKA 485 E Sbjct: 324 EVSPG 328 >gnl|CDD|33078 COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]. Length = 269 Score = 30.7 bits (69), Expect = 1.6 Identities = 21/129 (16%), Positives = 52/129 (40%), Gaps = 9/129 (6%) Query: 280 AIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIM--APIGILAQQH 337 A+ + ++ +L + G+VGSGKT++ A+ A++ AV++ P A Sbjct: 39 ALLMLHAAIADGQGILAVT-GEVGSGKTVLRR-ALLASLNEDQVAVVVIDKPTLSDATLL 96 Query: 338 YEFIKKYTQNTQIIVEIITGNMPQAHRR--KALERIAHGQAHIIIGTHALFQDSIQYYKL 395 + ++ V + Q R +++ ++ H L +++ +L Sbjct: 97 EAIVADLESQPKVNVNAVL---EQIDRELAALVKKGKRPVVLMVDEAHDLNDSALEALRL 153 Query: 396 ILVIVDEQH 404 + + ++ Sbjct: 154 LTNLEEDSS 162 >gnl|CDD|34587 COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein]. Length = 866 Score = 30.4 bits (68), Expect = 1.6 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 14/79 (17%) Query: 613 NTEDGFLIAEEDLKQRKEGEIL---GIKQSGMPKFLIAQPELHDSLLEI----------- 658 +T+ G + E+D+K R E+L GI++ F E L E+ Sbjct: 774 DTKSGEPVDEKDVKARYHDEVLERCGIREIVDELFAGYNDEKKPLLQEVFLDKDLEFFVA 833 Query: 659 ARKDAKHILTQDPDLTSVR 677 ++++A+ + DP+ T + Sbjct: 834 SKEEARAFVDFDPEHTVIF 852 >gnl|CDD|36167 KOG0949, KOG0949, KOG0949, Predicted helicase, DEAD-box superfamily [General function prediction only]. Length = 1330 Score = 30.0 bits (67), Expect = 2.4 Identities = 18/90 (20%), Positives = 38/90 (42%), Gaps = 1/90 (1%) Query: 514 FTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGL 573 I + H ++ + V F+ G ++L AT + +GI++ +++ ++ Sbjct: 961 LYRGIGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDP 1020 Query: 574 AQLHQLRGRVG-RGEEISSCILLYHPPLSK 602 Q+ GR G RG + ++ P K Sbjct: 1021 LNYKQMAGRAGRRGFDTLGNVVFMGIPRQK 1050 >gnl|CDD|146464 pfam03843, Slp, Outer membrane lipoprotein Slp family. Length = 160 Score = 29.9 bits (68), Expect = 2.5 Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 9/43 (20%) Query: 116 VFFEGRKITVTGKIKKLKNRIIMVHPHYIFHNSQDVNFPLIEA 158 ++ +GR +TV G IK ++ I D +P++ A Sbjct: 90 IYKKGRLVTVVGTIKGVEEGKI---------GEYDYTYPVVAA 123 >gnl|CDD|73319 cd02750, MopB_Nitrate-R-NarG-like, Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. Members of the MopB_Nitrate-R-NarG-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.. Length = 461 Score = 29.4 bits (66), Expect = 3.3 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 7/57 (12%) Query: 332 ILAQQHY--EFIKKYTQ-----NTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIG 381 I+ ++ Y +++K+YT T E ITG + R A E +G++ II+G Sbjct: 238 IIKEKLYDEDYLKEYTDLPFLVYTPAWQEAITGVPRETVIRLAREFATNGRSMIIVG 294 >gnl|CDD|34328 COG4712, COG4712, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 234 Score = 29.3 bits (65), Expect = 3.5 Identities = 24/141 (17%), Positives = 45/141 (31%), Gaps = 14/141 (9%) Query: 151 VNFPLIEAVYSLPTGLSVDLFKKIIVEALSRLPVLPEWIEKDLLQKKSFPSIAEAFNIIH 210 V F + +Y LP L+ + E R+P+LP+W K + N + Sbjct: 108 VQFGIGRYLYDLPFIW-AGLWPDEVTENKKRVPLLPKWAFPV---KSINYNQEREINQLE 163 Query: 211 NPRKAKDFEWTSPARERLAYDELLAGQIALLLMRKQFKKEIGIPINVEGKIAQKILRNIP 270 ++ ++ D A + + L +K K +++P Sbjct: 164 IVDNNVRYK----LGTDISTDIDKA-TVVIPLDKKATGKPNSNTYK-----CAVCGKSVP 213 Query: 271 FSPTKSQESAIKDILQDMSQK 291 +S +L QK Sbjct: 214 EKVASYSKSKFGKVLCMEHQK 234 >gnl|CDD|145001 pfam01628, HrcA, HrcA protein C terminal domain. HrcA is found to negatively regulate the transcription of heat shock genes. HrcA contains an amino terminal helix-turn-helix domain, however this corresponds to the carboxy terminal domain. Length = 224 Score = 29.0 bits (66), Expect = 4.3 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 6/76 (7%) Query: 224 ARERLAYDELLAGQIALLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKD 283 +E YDELL + LL F +E + V G +L FS + +++ Sbjct: 100 PQELQEYDELLDEVLDLLEAVLSFLEEDEERLYVGGTS--NLLNQPEFSDVEK----LRE 153 Query: 284 ILQDMSQKNRMLRILQ 299 +L+ + +K+ +L +L Sbjct: 154 LLELLEEKSVLLELLD 169 >gnl|CDD|34613 COG5008, PilU, Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 375 Score = 29.1 bits (65), Expect = 4.5 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 2/75 (2%) Query: 265 ILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGK--TLVALIAMAAAVEAGG 322 +LR I +E + ++L+D++ R L I+ G GSGK T+ A+I G Sbjct: 99 VLRRIETKIPTFEELKLPEVLKDLALAKRGLVIIVGATGSGKSTTMAAMIGYRNKNSTGH 158 Query: 323 QAVIMAPIGILAQQH 337 I PI + + Sbjct: 159 IITIEDPIEFIHKHK 173 >gnl|CDD|33754 COG3973, COG3973, Superfamily I DNA and RNA helicases [General function prediction only]. Length = 747 Score = 28.8 bits (64), Expect = 4.5 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 13/70 (18%) Query: 266 LRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMA------AAVE 319 +R+I + K Q I+ +KN++L ++QG GSGKT +AL +A Sbjct: 206 MRDIVETIQKEQNEIIRF------EKNKIL-VVQGAAGSGKTTIALHRVAYLLYGYRGPL 258 Query: 320 AGGQAVIMAP 329 +++ P Sbjct: 259 QAKPVLVLGP 268 >gnl|CDD|36345 KOG1130, KOG1130, KOG1130, Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]. Length = 639 Score = 28.5 bits (63), Expect = 6.7 Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 6/40 (15%) Query: 366 KALERIAH---GQAHIIIGTHALFQDSIQYYKLILVIVDE 402 +A ER AH G HI +G F+ +I++YKL L + E Sbjct: 231 RAAERRAHSNLGNCHIFLGN---FELAIEHYKLTLNLAIE 267 >gnl|CDD|30955 COG0610, COG0610, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]. Length = 962 Score = 28.5 bits (63), Expect = 6.7 Identities = 30/157 (19%), Positives = 61/157 (38%), Gaps = 19/157 (12%) Query: 258 EGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAA 317 +G + +K R + ++ + AIK IL+ + + + GSGKTL Sbjct: 241 DGLVKKKYQRYAQY---RAVQKAIKRILKASNPGDGKGGYIWHTQGSGKTLTMFKLARLL 297 Query: 318 VEAGGQA--VIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQ 375 +E + + L Q + + + + + + + ++ LE Sbjct: 298 LELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDPKAESTS----ELKELLEDGKGK- 352 Query: 376 AHIIIGTHALFQDSIQYYKL-------ILVIVDEQHR 405 II+ T F +++ +L ++VI+DE HR Sbjct: 353 --IIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHR 387 >gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.. Length = 165 Score = 28.2 bits (62), Expect = 8.2 Identities = 23/86 (26%), Positives = 34/86 (39%), Gaps = 6/86 (6%) Query: 300 GDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQ---NTQIIVEIIT 356 G GSGKT +AL GG+ V+ I ++ E + + +I+ T Sbjct: 6 GPTGSGKTTLALQLALNIATKGGK-VVYVDIEEEIEELTERLIGESLKGALDNLIIVFAT 64 Query: 357 GNMPQAHR--RKALERIAHGQAHIII 380 + P A R KA G +II Sbjct: 65 ADDPAAARLLSKAERLRERGGDDLII 90 >gnl|CDD|36166 KOG0948, KOG0948, KOG0948, Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]. Length = 1041 Score = 28.0 bits (62), Expect = 9.1 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 6/72 (8%) Query: 267 RNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVI 326 + PF+ Q +AIK I + S ++ +GKT+VA A+A ++ + + Sbjct: 124 KTYPFTLDPFQSTAIKCIDRGESV------LVSAHTSAGKTVVAEYAIAMSLREKQRVIY 177 Query: 327 MAPIGILAQQHY 338 +PI L+ Q Y Sbjct: 178 TSPIKALSNQKY 189 >gnl|CDD|143922 pfam00154, RecA, recA bacterial DNA recombination protein. RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyses an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination. Length = 322 Score = 28.0 bits (63), Expect = 9.3 Identities = 13/21 (61%), Positives = 16/21 (76%) Query: 304 SGKTLVALIAMAAAVEAGGQA 324 SGKT +AL A+A A +AGG A Sbjct: 63 SGKTTLALHAIAEAQKAGGTA 83 >gnl|CDD|176254 cd08294, leukotriene_B4_DH_like, 13-PGR is a bifunctional enzyme with delta-13 15-prostaglandin reductase and leukotriene B4 12 hydroxydehydrogenase activity. Prostaglandins and related eicosanoids are metabolized by the oxidation of the 15(S)-hydroxyl group of the NAD+-dependent (type I 15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH) followed by reduction by NADPH/NADH-dependent (type II 15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to 15-keto- 13,14,-dihydroprostaglandins. 13-PGR is a bifunctional enzyme, since it also has leukotriene B(4) 12-hydroxydehydrogenase activity. These 15-PGDH and related enzymes are members of the medium chain dehydrogenase/reductase family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. Length = 329 Score = 28.0 bits (63), Expect = 9.6 Identities = 9/21 (42%), Positives = 13/21 (61%) Query: 614 TEDGFLIAEEDLKQRKEGEIL 634 E F + EE+L K+GE+L Sbjct: 17 KESDFELVEEELPPLKDGEVL 37 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.322 0.138 0.393 Gapped Lambda K H 0.267 0.0724 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 8,518,338 Number of extensions: 474314 Number of successful extensions: 1541 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1488 Number of HSP's successfully gapped: 129 Length of query: 700 Length of database: 6,263,737 Length adjustment: 101 Effective length of query: 599 Effective length of database: 4,081,228 Effective search space: 2444655572 Effective search space used: 2444655572 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)