RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780947|ref|YP_003065360.1| transcription-repair coupling factor [Candidatus Liberibacter asiaticus str. psy62] (1187 letters) >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 = 894 bits (2312), Expect = 0.0 Identities = 383/962 (39%), Positives = 551/962 (57%), Gaps = 46/962 (4%) Query: 150 LETNGFQRVNAVYKVGEYAVRGGILDVYEPTKKYPVRLDFFGNTIDSLRLFDSSTQRTIR 209 L G++RV+ V + GE++VRG ILD++ P + PVR++FFG+ I+S+R FD +QR++ Sbjct: 1 LVELGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLE 60 Query: 210 EISIFEINTLSE-VMLTSQNISRFRENYLANFGTTTQEDPLYVAISQGRRYPGMEHWLPF 268 E+ I E ++L + I+R ++N A+S+G G E +LP Sbjct: 61 ELLEITILPAKEFILLEEETIARLKDNAARVEDAKHL--ETIEALSEGTLPAGEEMFLPL 118 Query: 269 FYQSMETIFPYLSEFCIITDPLVKETARKRSQLIQDYYEARLQYSSDKKQYSVYKPIAPE 328 F++ + ++F YL + I + L ++ E KK I P Sbjct: 119 FFEDLSSLFDYLPDNTPILLDDPERFHSAARFLQRELEEFYNALEEAKK------LINPP 172 Query: 329 KLYLNYQQFDALIQTTHKLVQMTAFNQQETAHNRVV--HLNAFPGKSWVPSAVQKIESQD 386 +L L+ AF + +RV + + S QK + Sbjct: 173 RLDLD--------------PSELAFEASAISLSRVQLENEHLSLKASEAIEGAQKHSRLE 218 Query: 387 NWESGGRFDKFLSHVAQQAQKGIKTIISASSQGALQHLIHLIESHGFKKIKKINTLTEIN 446 E ++ + G K ++A S+ + L L+ H + E Sbjct: 219 FGEILAFKEELFRWLKA----GFKITVAAESESQAERLKSLLAEHDIA----AQVIDESC 270 Query: 447 SLLKEEIAAVI---LPINQGFETKHMILVTETDLLGKKIARR--VVRKKNVHAQSFFDSS 501 ++ + V+ L T + ++TE++L G ++ RR R K+ +S + Sbjct: 271 -IIIPAVRYVMIGALSSGFILPTAGLAVITESELFGSRVLRRPKKSRLKSKPIESL---N 326 Query: 502 NIEEGAIIVHAEHGIGRFVRLYSIEVSGTFHDCLELHYADNAKLFVPVENIDLISRYS-T 560 + G +VH +HGIGRF+ L ++EV G D L L YA KL+VPVE + LISRY Sbjct: 327 ELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGG 386 Query: 561 EITTVTLDKLGGSAWKTRKANLKKRLEDLAQKLVDIAAKRAIHSVPPLMVSQDLYSQFIK 620 LDKLGG +W+ KA +KK + ++A KL+++ AKR + +F Sbjct: 387 SGKNPALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFED 446 Query: 621 RFPHVETEDQEKAIDAVIQDLSSGRLMDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVI 680 FP ET DQ KAI+ + D+ S R MDRL+CGDVGFGKTE+A+RAAF AV++G QVAV+ Sbjct: 447 SFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVL 506 Query: 681 APTTLLVRQHFRLFSERFQGFSVRIASISRFVQTKEAALHKKSITEGQVDIVIGTHALLN 740 PTTLL +QHF F ERF F V I +SRF KE K + G++DI+IGTH LL Sbjct: 507 VPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQ 566 Query: 741 PKITFANLGLIIIDEEQHFGVKHKEALKETHTGVHVLTLSATPIPRTLQLAITGVRELSL 800 + F +LGL+IIDEEQ FGVK KE LKE T V VLTLSATPIPRTL ++++G+R+LS+ Sbjct: 567 KDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSI 626 Query: 801 ISMPPINRIACRTSISIFDPLVVRETLMREYYRGGQSFYVCPRLSDLEKCYTFLQSEVPE 860 I+ PP +R+ RT + +DP +VRE + RE RGGQ FYV R+ +EK T L+ VPE Sbjct: 627 IATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPE 686 Query: 861 LKIAMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQ 920 +IA+AHGQM+ LE+ M FY+G++ VL+ T+I+E+G+D+P ANT+I++RAD FGLAQ Sbjct: 687 ARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQ 746 Query: 921 LYQLRGRVGRSKIASFALFLLPENRPLTAAAQKRLRILQSLNTLGAGFQLASYDLDIRGT 980 LYQLRGRVGRSK ++A L P + LT AQKRL +Q + LGAGF++A +DL+IRG Sbjct: 747 LYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGAGFKIALHDLEIRGA 806 Query: 981 GNLLGEEQSGHIREIGFELYQKMLEETVASIKGQK-DLVESDWSPQVLIEASVMIPESYV 1039 GNLLGEEQSGHI IGF+LY ++LEE + +KG K +E + + + S IP+ Y+ Sbjct: 807 GNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLEEE--TDIELPYSAFIPDDYI 864 Query: 1040 SDINLRLSLYRRLGNITDHADISHFKEEMVDRFGPLPIEVIHLLKVVFLKLLCRIANIDK 1099 +D +LRL Y+R+ + ++ ++E++DRFGPLP E LL V LKLL R I K Sbjct: 865 ADDSLRLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRK 924 Query: 1100 MD 1101 + Sbjct: 925 LK 926 >gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor; Provisional. Length = 1147 Score = 706 bits (1823), Expect = 0.0 Identities = 388/1088 (35%), Positives = 600/1088 (55%), Gaps = 67/1088 (6%) Query: 65 DIRVIIFPAWDCLPYDRVSPSPYVVTRRLSCISNLVSFNSSKETIIVLTTVSAVMCRSVN 124 D V+ W+ LPYD SP +++ RLS + L + +++ V+ +M R Sbjct: 64 DQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRG----VLILPVNTLMQRVCP 119 Query: 125 IMSIKDYKLSIQSKDQIDMAKVIEKLETNGFQRVNAVYKVGEYAVRGGILDVYEPTKKYP 184 + + L ++ ++ + +LE G++ V+ V + GEYA RG +LD++ + P Sbjct: 120 HSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRGALLDLFPMGSEEP 179 Query: 185 VRLDFFGNTIDSLRLFDSSTQRTIREISIFEINTL-SEVMLTSQN-ISRFRENYLANFGT 242 R+DFF + IDSLR+FD +QRT+ E+ IN L + T + I FR + F Sbjct: 180 YRIDFFDDEIDSLRVFDVDSQRTLEEVE--AINLLPAHEFPTDKAAIELFRSQWRDTFEV 237 Query: 243 TTQEDPLYVAISQGRRYPGMEHWLP-FFYQSMETIFPYLSE--FCIITDPLVKETARKRS 299 + +Y +S+G G+E+W P FF + + +F Y + T L + +A + Sbjct: 238 KRDAEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDL-ETSAERFW 296 Query: 300 QLIQDYYEARLQYSSDKKQYSVYKPI-APEKLYLNYQQFDALIQTTHKL--VQMTAFNQQ 356 +E R +P+ PE L+L D L VQ+ + Sbjct: 297 ADTLARFENR--------GVDPMRPLLPPESLWLR---VDELFSELKNWPRVQLKTEHLP 345 Query: 357 ETAHNRVVHLNAFPGKSWVPSAVQKIESQDNWESGGRFDKFLSHVAQQAQKGIKTIISAS 416 A N + P + +++Q D L + + + S Sbjct: 346 TKAANTNLGYQKLPDLA--------VQAQ----QKAPLDA-LRRFLESFDGPV--VFSVE 390 Query: 417 SQG---ALQHLIHLIESHGFKKI--KKINTLTEINSLLKEEIAAVILPINQGF--ETKHM 469 S+G AL L+ I KI K+I L E + +I GF +++ Sbjct: 391 SEGRREALGELLARI------KIAPKRIMRLDEASD---RGRYLMIGAAEHGFIDTVRNL 441 Query: 470 ILVTETDLLGKKIARRVVRKKN---VHAQSFFDS-SNIEEGAIIVHAEHGIGRFVRLYSI 525 L+ E+DLLG+++ARR R+ + ++ + + + + G +VH EHG+GR+ + ++ Sbjct: 442 ALICESDLLGERVARR--RQDSRRTINPDTLIRNLAELHPGQPVVHLEHGVGRYAGMTTL 499 Query: 526 EVSGTFHDCLELHYADNAKLFVPVENIDLISRYSTEI-TTVTLDKLGGSAWKTRKANLKK 584 E G + L L YA++AKL+VPV ++ LISRY+ L KLGG AW + + Sbjct: 500 EAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAE 559 Query: 585 RLEDLAQKLVDIAAKRAIHSVPPLMVSQDLYSQFIKRFPHVETEDQEKAIDAVIQDLSSG 644 ++ D+A +L+DI A+RA ++ Y F FP T DQ +AI+AV+ D+ Sbjct: 560 KVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQP 619 Query: 645 RLMDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVR 704 MDRL+CGDVGFGKTE+A+RAAF+AV N QVAV+ PTTLL +QH+ F +RF + VR Sbjct: 620 LAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVR 679 Query: 705 IASISRFVQTKEAALHKKSITEGQVDIVIGTHALLNPKITFANLGLIIIDEEQHFGVKHK 764 I +SRF KE EG++DI+IGTH LL + + +LGL+I+DEE FGV+HK Sbjct: 680 IEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHK 739 Query: 765 EALKETHTGVHVLTLSATPIPRTLQLAITGVRELSLISMPPINRIACRTSISIFDPLVVR 824 E +K V +LTL+ATPIPRTL +A++G+R+LS+I+ PP R+A +T + +D LVVR Sbjct: 740 ERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVR 799 Query: 825 ETLMREYYRGGQSFYVCPRLSDLEKCYTFLQSEVPELKIAMAHGQMSPKNLEDKMNAFYE 884 E ++RE RGGQ +Y+ + +++K L VPE +IA+ HGQM + LE MN F+ Sbjct: 800 EAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHH 859 Query: 885 GQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQLYQLRGRVGRSKIASFALFLLPEN 944 +++VL+ T+I+E+G+D+P ANT+I++RAD FGLAQL+QLRGRVGRS ++A L P Sbjct: 860 QRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP 919 Query: 945 RPLTAAAQKRLRILQSLNTLGAGFQLASYDLDIRGTGNLLGEEQSGHIREIGFELYQKML 1004 + +T AQKRL + SL LGAGF LA++DL+IRG G LLGEEQSG + IGF LY ++L Sbjct: 920 KAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFSLYMELL 979 Query: 1005 EETVASIK-GQKDLVESDWSPQVLIE--ASVMIPESYVSDINLRLSLYRRLGNITDHADI 1061 E V ++K G++ +E S Q +E ++P+ ++ D+N RLS Y+R+ + + ++ Sbjct: 980 ENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENEL 1039 Query: 1062 SHFKEEMVDRFGPLPIEVIHLLKVVFLKLLCRIANIDKMDIGLKGIIIQFRHKTFSNPEA 1121 K E++DRFG LP +LL + L+ + I K++ KG I+F K +P Sbjct: 1040 EEIKVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEGNEKGGFIEFAEKNHVDPAW 1099 Query: 1122 LLQYIAQQ 1129 L+ + +Q Sbjct: 1100 LIGLLQKQ 1107 >gnl|CDD|182836 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional. Length = 681 Score = 339 bits (873), Expect = 2e-93 Identities = 159/432 (36%), Positives = 246/432 (56%), Gaps = 39/432 (9%) Query: 583 KKRL---EDLAQKLVDIAAKRAIHSV--PPLMVSQDLYSQFIKRFPHVETEDQEKAIDAV 637 ++RL E A +L + + S PL +L +F+ P T Q++ + + Sbjct: 214 RRRLKFEELFALQLSLLLLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEI 273 Query: 638 IQDLSSGRLMDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSER 697 + DL+S + M+RL+ GDVG GKT +A AA A+ G Q A++APT +L QH+ + Sbjct: 274 LADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKL 333 Query: 698 FQGFSVRIASISRFVQTKEAALHKKSITEGQVDIVIGTHALLNPKITFANLGLIIIDEEQ 757 + +R+A ++ ++ KE ++I G+ DIVIGTHAL+ + F NLGL+IIDE Q Sbjct: 334 LEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDE-Q 392 Query: 758 H-FGVKHKEALKETHTGVHVLTLSATPIPRTLQLAITGVRELSLI-SMPPINRIACRTSI 815 H FGV+ + AL+E HVL ++ATPIPRTL + G ++S+I +PP R I Sbjct: 393 HRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPP-----GRKPI 447 Query: 816 SIFDPLVVRETLMREYYR--------GGQSFYVCPR--------LSDLEKCYTFLQSEVP 859 +V+ ++ E Y G Q++ VCP L E+ Y LQ P Sbjct: 448 ---TTVVIPDSRRDEVYERIREEIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFP 504 Query: 860 ELKIAMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLA 919 EL++ + HG+M P + M AF G+ D+L++T+++E G+D+P A M+++ A+ FGLA Sbjct: 505 ELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLA 564 Query: 920 QLYQLRGRVGRSKIASFALFLLPENRPLTAAAQKRLRIL-QSLNTLGAGFQLASYDLDIR 978 QL+QLRGRVGR S+ + L + PL+ A++RL+I+ ++ + GF +A DL++R Sbjct: 565 QLHQLRGRVGRGAAQSYCVLLYKD--PLSETARERLKIMRETND----GFVIAEKDLELR 618 Query: 979 GTGNLLGEEQSG 990 G G LLG QSG Sbjct: 619 GPGELLGTRQSG 630 >gnl|CDD|161975 TIGR00643, recG, ATP-dependent DNA helicase RecG. Length = 630 Score = 326 bits (838), Expect = 2e-89 Identities = 152/419 (36%), Positives = 241/419 (57%), Gaps = 23/419 (5%) Query: 604 SVPPLMVSQDLYSQFIKRFPHVETEDQEKAIDAVIQDLSSGRLMDRLICGDVGFGKTEIA 663 S PP S++L ++F+ P T Q++ + ++QDL S M+RL+ GDVG GKT +A Sbjct: 214 SAPPANPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVA 273 Query: 664 LRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASISRFVQTKEAALHKKS 723 A A+ G QVA++APT +L QH+ + +A ++ ++ K ++ Sbjct: 274 ALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLET 333 Query: 724 ITEGQVDIVIGTHALLNPKITFANLGLIIIDEEQHFGVKHKEALKETHTG---VHVLTLS 780 I GQ+ +V+GTHAL+ K+ F L L+IIDE+ FGV+ ++ L+E G HVL +S Sbjct: 334 IASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGGFTPHVLVMS 393 Query: 781 ATPIPRTLQLAITGVRELSLI-SMPPINRIACRTSISIFDPL-VVRETLMREYYRGGQSF 838 ATPIPRTL L + G + S+I +PP R T + D +V E + E +G Q++ Sbjct: 394 ATPIPRTLALTVYGDLDTSIIDELPP-GRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAY 452 Query: 839 YVCPRLSDLEKC--------YTFLQSEVPELKIAMAHGQMSPKNLEDKMNAFYEGQYDVL 890 V P + + EK Y L+ P+ + + HG+M E M F EG+ D+L Sbjct: 453 VVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDIL 512 Query: 891 LSTSIVESGLDLPKANTMIVQRADMFGLAQLYQLRGRVGRSKIASFALFLLPENRPLTAA 950 ++T+++E G+D+P A M+++ A+ FGL+QL+QLRGRVGR S+ L+ +N P + + Sbjct: 513 VATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYC-LLVYKN-PKSES 570 Query: 951 AQKRLRIL-QSLNTLGAGFQLASYDLDIRGTGNLLGEEQSGHI--REIGFELYQKMLEE 1006 A+KRLR++ +L+ GF +A DL++RG G+LLG +QSG+ R +++L E Sbjct: 571 AKKRLRVMADTLD----GFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVE 625 >gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. Length = 201 Score = 94.9 bits (236), Expect = 1e-19 Identities = 49/206 (23%), Positives = 83/206 (40%), Gaps = 23/206 (11%) Query: 618 FIKRFPHVETEDQEKAIDAVIQDLSSGRLMDRLICGDVGFGKTEIALRAAFIAVMNGL-- 675 K Q++AI+A++ L D ++ G GKT AL A A+ G Sbjct: 1 IEKFGFEPLRPYQKEAIEALLS-----GLRDVILAAPTGSGKTLAALLPALEALKRGKGK 55 Query: 676 QVAVIAPTTLLVRQHFRLFSERFQGFSVRIASISRFVQTKEAALHKKSITEGQVDIVIGT 735 +V V+ PT L Q + +++ + +E + + G+ DI++ T Sbjct: 56 RVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQ---LRKLESGKTDILVTT 112 Query: 736 -----HALLNPKITFANLGLIIIDEEQH-----FGVKHKEALKETHTGVHVLTLSATP-- 783 L N + +N+ L+I+DE FG + ++ LK V +L LSATP Sbjct: 113 PGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPE 172 Query: 784 -IPRTLQLAITGVRELSLISMPPINR 808 I L+L + + + P Sbjct: 173 EIENLLELFLNDPVFIDVGPTPLEPI 198 >gnl|CDD|128766 smart00490, HELICc, helicase superfamily c-terminal domain. Length = 82 Score = 66.5 bits (163), Expect = 4e-11 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%) Query: 860 ELKIAMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLA 919 +K+A HG +S + E+ + F G+ VL++T + E GLDLP + +I+ + A Sbjct: 11 GIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPA 69 Query: 920 QLYQLRGRVGR 930 Q GR GR Sbjct: 70 SYIQRIGRAGR 80 >gnl|CDD|180144 PRK05580, PRK05580, primosome assembly protein PriA; Validated. Length = 679 Score = 59.8 bits (146), Expect = 4e-09 Identities = 44/142 (30%), Positives = 61/142 (42%), Gaps = 32/142 (22%) Query: 627 TEDQEKAIDAVIQDLSSGRLMDRLICGDVGFGKTEIALRAAFIA-VMN-GLQVAV----I 680 +Q A++A+ L+ G G GKTE+ L+A IA V+ G Q V I Sbjct: 146 NPEQAAAVEAIRAAAGFSPF---LLDGVTGSGKTEVYLQA--IAEVLAQGKQALVLVPEI 200 Query: 681 APTTLLVRQHFRLFSERFQG-FSVRIA----SISRFVQTKEAALHKKSITEGQVDIVIGT 735 A T ++ RF+ F +A +S + K G+ +VIG Sbjct: 201 ALTPQML--------ARFRARFGAPVAVLHSGLS--DGERLDEWRK--AKRGEAKVVIGA 248 Query: 736 H-ALLNPKITFANLGLIIIDEE 756 AL P F NLGLII+DEE Sbjct: 249 RSALFLP---FKNLGLIIVDEE 267 Score = 30.9 bits (71), Expect = 1.9 Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 23/97 (23%) Query: 854 LQSEVPELKIAMAHGQMS------PKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANT 907 L PE +I ++ LE + F G+ D+L+ T ++ G D P Sbjct: 446 LAELFPEARIL----RIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTL 501 Query: 908 MIVQRADMFGL-----------AQLY-QLRGRVGRSK 932 + V AD+ GL QL Q+ GR GR++ Sbjct: 502 VGVLDADL-GLFSPDFRASERTFQLLTQVAGRAGRAE 537 >gnl|CDD|180000 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional. Length = 652 Score = 55.1 bits (134), Expect = 1e-07 Identities = 30/130 (23%), Positives = 67/130 (51%), Gaps = 14/130 (10%) Query: 92 RLSCISNLVSFNSSKETIIVLTTVSAVMCRSVNIMSIKDYK---LSIQSKDQIDMAKVIE 148 R S +L+ + I+V +VS + + S ++Y LS++ +ID +++ Sbjct: 123 RHSATKSLLERR---DVIVV-ASVSCIY----GLGSPEEYLKMVLSLRVGQEIDRRELLR 174 Query: 149 KLETNGFQRVNAVYKVGEYAVRGGILDVYEP--TKKYPVRLDFFGNTIDSLRLFDSSTQR 206 +L ++R + ++ G + VRG +++++ P ++ +R++FFG+ I+ + FD T Sbjct: 175 RLVDLQYERNDIDFQRGTFRVRGDVIEIF-PAYYEERAIRIEFFGDEIERISEFDPLTGE 233 Query: 207 TIREISIFEI 216 + E+ I Sbjct: 234 VLGELDRVTI 243 >gnl|CDD|161969 TIGR00631, uvrb, excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 655 Score = 52.3 bits (126), Expect = 8e-07 Identities = 29/127 (22%), Positives = 63/127 (49%), Gaps = 8/127 (6%) Query: 92 RLSCISNLVSFNSSKETIIVLTTVSAVMCRSVNIMSIKDYKLSIQSKDQIDMAKVIEKLE 151 R S +L + +IV+ +VS + + L ++ +ID +++ +L Sbjct: 120 RHSATRSL----LERRDVIVVASVSCIYGLG-SPEEYLKMVLHLEVGKEIDRRELLRRLV 174 Query: 152 TNGFQRVNAVYKVGEYAVRGGILDVYEP--TKKYPVRLDFFGNTIDSLRLFDSSTQRTIR 209 ++R + ++ G + VRG +++++ P ++ VR++FFG+ I+ + D T +R Sbjct: 175 ELQYERNDVDFQRGTFRVRGDVVEIF-PAYEDEFAVRIEFFGDEIERISRVDPLTGEVLR 233 Query: 210 EISIFEI 216 E+ F I Sbjct: 234 ELDSFTI 240 >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 = 50.1 bits (120), Expect = 3e-06 Identities = 49/145 (33%), Positives = 64/145 (44%), Gaps = 17/145 (11%) Query: 650 LICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASIS 709 L+ G G GKTE+ L+A + G V V+ P L Q + F RF G V + Sbjct: 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRF-GSQVAVLHSG 59 Query: 710 RFVQTKEAALHKKSITEGQVDIVIGTH-ALLNPKITFANLGLIIIDEEQHFGVKHKE--- 765 K A K + G++ +VIGT AL P F NLGLII+DEE K +E Sbjct: 60 LSDSEKLQAWRK--VKNGEILVVIGTRSALFLP---FKNLGLIIVDEEHDSSYKQEEGPR 114 Query: 766 ------ALKETH-TGVHVLTLSATP 783 A+ V+ SATP Sbjct: 115 YHARDVAVYRAKKFNCPVVLGSATP 139 Score = 45.5 bits (108), Expect = 8e-05 Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 13/111 (11%) Query: 836 QSFYVCPRLSDLEKCYTFLQSEVPELKIAMAHGQM--SPKNLEDKMNAFYEGQYDVLLST 893 S + + E+ L P +IA E +N F G+ D+L+ T Sbjct: 260 GSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGT 319 Query: 894 SIVESGLDLPKANTMIVQRAD--MF---------GLAQLYQLRGRVGRSKI 933 ++ G P + V AD + G L Q+ GR GR++ Sbjct: 320 QMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAED 370 >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 = 44.4 bits (105), Expect = 2e-04 Identities = 71/317 (22%), Positives = 123/317 (38%), Gaps = 49/317 (15%) Query: 656 GFGKTEIALRAAFIAVMNGLQVAVI--APTTLLVRQHFRLFSERFQGFSVRIASISRFVQ 713 G+GKTE AL A ++ + VI PT + +R E F + S S F + Sbjct: 9 GYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGSNLGLLHSSSSFKR 68 Query: 714 TKE------------------AALHKKSITEGQVDIVIG--THALLNPKITFANLG--LI 751 KE L IT +D V+ + + T A++ L+ Sbjct: 69 IKEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLL 128 Query: 752 IIDEEQHFG-------VKHKEALKETHTGVHVLTLSATPIP---RTLQLAITGVRELSLI 801 I DE + + E LK+ V +L +SAT +P + I V + Sbjct: 129 IFDEVHFYDEYTLALILAVLEVLKDN--DVPILLMSAT-LPKFLKEYAEKIGYVEFNEPL 185 Query: 802 SMPPINRIACRTSISIFDPLVVRET----LMREYYRGGQSFYVCPRLSDLEKCYTFLQSE 857 + R I I V + L+ +GG+ + + ++ Y L+ Sbjct: 186 DLKEERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKEN 245 Query: 858 VPELKIAMAHGQMSPKNLEDK----MNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRA 913 PE +I + H + + K+ K + + + V+++T ++E+ LD+ A+ MI + A Sbjct: 246 APEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDI-SADVMITELA 304 Query: 914 DMFGLAQLYQLRGRVGR 930 + L Q GR+ R Sbjct: 305 P---IDSLIQRLGRLHR 318 >gnl|CDD|181823 PRK09401, PRK09401, reverse gyrase; Reviewed. Length = 1176 Score = 41.5 bits (98), Expect = 0.001 Identities = 31/109 (28%), Positives = 47/109 (43%), Gaps = 15/109 (13%) Query: 656 GFGKTEIALRAA-FIAVMNGLQVAVIAPTTLLVRQ---HFRLFSERFQGFSVRIASISRF 711 G GKT L + ++A G + +I PT LLV Q F E+ G V+I Sbjct: 105 GVGKTTFGLVMSLYLAK-KGKKSYIIFPTRLLVEQVVEKLEKFGEKV-GCGVKILYYHSS 162 Query: 712 VQTKEAALHKKSITEGQVDIVIGTHALLN------PKITFANLGLIIID 754 ++ KE + + EG DI++ T L+ PK F + +D Sbjct: 163 LKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDELPKKKF---DFVFVD 208 Score = 31.4 bits (72), Expect = 1.5 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 16/72 (22%) Query: 833 RGGQSFYVCP----------RLSDLEKCYTFLQSEVPELKIAMAHGQMSPKNLEDKMNAF 882 +G +S+ + P +L + +KI H + K E+ + Sbjct: 122 KGKKSYIIFPTRLLVEQVVEKLEKFGEKVGC------GVKILYYHSSLKKKEKEEFLERL 175 Query: 883 YEGQYDVLLSTS 894 EG +D+L++TS Sbjct: 176 KEGDFDILVTTS 187 >gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional. Length = 773 Score = 41.0 bits (97), Expect = 0.002 Identities = 31/113 (27%), Positives = 52/113 (46%), Gaps = 13/113 (11%) Query: 650 LICGDVGFGKTEIA-LRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASI 708 L+ G GKT IA L A G +V ++APT LV QH F + +I Sbjct: 33 LVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVF 92 Query: 709 SRFVQTKE-AALHKKSITEGQVDIVIGT-----HALLNPKITFANLGLIIIDE 755 + V ++ A L +K+ +++ T + L+ +I+ ++ L+I DE Sbjct: 93 TGEVSPEKRAELWEKA------KVIVATPQVIENDLIAGRISLEDVSLLIFDE 139 Score = 38.3 bits (90), Expect = 0.011 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 23/74 (31%) Query: 870 MSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMI-----------VQRADMFGL 918 MS K + ++ F G+++VL+STS+ E GLD+P + +I +QR Sbjct: 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQR------ 460 Query: 919 AQLYQLRGRVGRSK 932 +GR GR + Sbjct: 461 ------KGRTGRQE 468 >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 = 38.3 bits (89), Expect = 0.011 Identities = 30/105 (28%), Positives = 42/105 (40%), Gaps = 5/105 (4%) Query: 656 GFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQ---HFRLFSERFQGFSVRIASISRFV 712 G GKT L + G + +I PTTLLV Q +E+ +V I + + Sbjct: 103 GVGKTTFGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRL 162 Query: 713 QTKEAALHKKSITEGQVDIVIGTHALL--NPKITFANLGLIIIDE 755 TKE + I G DI+I T L N I +D+ Sbjct: 163 PTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDFIFVDD 207 >gnl|CDD|184796 PRK14701, PRK14701, reverse gyrase; Provisional. Length = 1638 Score = 35.6 bits (82), Expect = 0.071 Identities = 26/105 (24%), Positives = 42/105 (40%), Gaps = 5/105 (4%) Query: 656 GFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQ--GFSVRIASISRFVQ 713 G GK+ A + G + +I PTTLLV+Q + VR+ ++ Sbjct: 104 GMGKSTFGAFIALFLALKGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLR 163 Query: 714 TKEAALHKKSITEGQVDIVIGTHALLN---PKITFANLGLIIIDE 755 KE + I G DI++ T L P++ I +D+ Sbjct: 164 KKEKEEFLERIENGDFDILVTTAQFLARNFPEMKHLKFDFIFVDD 208 >gnl|CDD|162365 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. Length = 586 Score = 35.1 bits (81), Expect = 0.095 Identities = 36/183 (19%), Positives = 60/183 (32%), Gaps = 44/183 (24%) Query: 587 EDLAQKLVDIAAKRAIHS-VPPLMVSQDLYSQFIKRFPHVETEDQEKAIDAVIQDLSSGR 645 E LA KL + R + L FP + ++ +K A+ L S Sbjct: 115 EKLAAKLRTLLEARKRTAPSAILENL----------FPLLNEQNWQKVAVALA--LKSNF 162 Query: 646 LMDRLICGDVGFGKTE-----IALRAAFIAVMNGLQVAVIAPT--------TLLVRQHFR 692 LI G G GKT + L++A+ APT L + Sbjct: 163 S---LITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKN 219 Query: 693 LFSERFQGFSVRIASISRFVQTKEAALHKKSITEGQVDIVIGTHALLNPKITFANLGLII 752 L + IA++ T +H+ + I T + + L +++ Sbjct: 220 LAAAE-----ALIAALPSEAVT----IHR------LLGIKPDTKRFRHHERNPLPLDVLV 264 Query: 753 IDE 755 +DE Sbjct: 265 VDE 267 Score = 29.4 bits (66), Expect = 5.3 Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 1/45 (2%) Query: 404 QAQKGIKTIISASSQGALQHLIHLIESHGFKKIKKINTLTE-INS 447 QA K I S + ++ L SH F K I L + INS Sbjct: 324 QAYALCKKINSKTRNPLSDNVCFLKTSHRFGKDSGIGQLAKAINS 368 >gnl|CDD|177796 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional. Length = 518 Score = 34.8 bits (80), Expect = 0.13 Identities = 27/90 (30%), Positives = 45/90 (50%), Gaps = 6/90 (6%) Query: 861 LKIAMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQ 920 LK HG+ S K + M +F G+ V+++T ++ G+DL + +I+ DM + Sbjct: 393 LKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVII--FDMPNTIK 450 Query: 921 LY--QLRGRVGRSKIASFA-LFLLPENRPL 947 Y Q+ GR R A +F+ E+R L Sbjct: 451 EYIHQI-GRASRMGEKGTAIVFVNEEDRNL 479 >gnl|CDD|132282 TIGR03238, dnd_assoc_3, dnd system-associated protein 3. cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A. Length = 504 Score = 33.7 bits (77), Expect = 0.31 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 5/47 (10%) Query: 619 IKRFPHVETE---DQEKAIDAVIQDLSSGRLMDRLICGDVGFGKTEI 662 K++ +V+ + D E+ + ++L S L+ +CG G GK+EI Sbjct: 4 FKKYLYVKRKIQTDLERILVKFNKELPSSSLL--FLCGSSGDGKSEI 48 >gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated. Length = 319 Score = 33.8 bits (77), Expect = 0.31 Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 1/59 (1%) Query: 630 QEKAIDAVIQDLSSGRL-MDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLV 687 Q++A D + L +GRL LICG G GK +AL A + +G A T L+ Sbjct: 9 QQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLI 67 >gnl|CDD|181738 PRK09265, PRK09265, aminotransferase AlaT; Validated. Length = 404 Score = 31.3 bits (72), Expect = 1.4 Identities = 25/71 (35%), Positives = 30/71 (42%), Gaps = 17/71 (23%) Query: 335 QQF--DALIQTTHKLVQMTAFNQQETAHNRVVHLNAFPGKSWVPSAVQKIESQDNWESGG 392 +QF D L+Q LVQ T FN E H R+V L P D E+ G Sbjct: 349 EQFVLDLLLQEKVLLVQGTGFNWPEPDHFRIVTL---------PRV------DDLEEAIG 393 Query: 393 RFDKFLSHVAQ 403 R +FLS Q Sbjct: 394 RIGRFLSGYRQ 404 >gnl|CDD|152839 pfam12404, DUF3663, Peptidase. This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with pfam00883. There is a conserved WAF sequence motif. Length = 77 Score = 31.4 bits (72), Expect = 1.4 Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 3/42 (7%) Query: 397 FLSHVAQQAQKGIKTIISASSQGALQHLIHLIESHGFKKIKK 438 LS A A G K ++S + GA IHL E + I++ Sbjct: 4 TLSQEAAAAHWGEKALLSFNEDGA---TIHLTEDDDLRLIQR 42 >gnl|CDD|179051 PRK00509, PRK00509, argininosuccinate synthase; Provisional. Length = 399 Score = 30.8 bits (71), Expect = 2.2 Identities = 8/18 (44%), Positives = 12/18 (66%), Gaps = 2/18 (11%) Query: 878 KMNAFYEGQYDVLLSTSI 895 + NA YEG+Y L T++ Sbjct: 77 RANALYEGKY--PLGTAL 92 >gnl|CDD|181223 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated. Length = 928 Score = 30.7 bits (70), Expect = 2.3 Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 5/37 (13%) Query: 728 QVDIVIGTHALL-----NPKITFANLGLIIIDEEQHF 759 D+VI HALL + + + IIIDE HF Sbjct: 431 FADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHF 467 >gnl|CDD|177899 PLN02257, PLN02257, phosphoribosylamine--glycine ligase. Length = 434 Score = 30.5 bits (69), Expect = 2.6 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 11/52 (21%) Query: 1087 FLKLLCRIANIDKMDIGLKGIIIQFRHKTFSNPEALLQYIAQQKGKIIIRPD 1138 F+K LC DK I +++TF++P A +YI +Q I+++ D Sbjct: 105 FMKDLC-----DKYKIPTA------KYETFTDPAAAKKYIKEQGAPIVVKAD 145 >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 = 30.4 bits (68), Expect = 2.9 Identities = 18/73 (24%), Positives = 22/73 (30%) Query: 650 LICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASIS 709 LI G G GKT +A A G V I +L +L G + Sbjct: 6 LIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGEL 65 Query: 710 RFVQTKEAALHKK 722 R A K Sbjct: 66 RLRLALALARKLK 78 >gnl|CDD|114848 pfam06153, DUF970, Protein of unknown function (DUF970). Family of uncharacterized bacterial proteins. Length = 109 Score = 30.4 bits (69), Expect = 3.1 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 11/56 (19%) Query: 632 KAIDAVIQDLSSGRLMDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLV 687 K + A++QD + RL D L + GF T++A F+ N TTLL+ Sbjct: 2 KLVIAIVQDQDANRLSDAL--TEKGFRATKLASTGGFLKAGN---------TTLLI 46 >gnl|CDD|183247 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional. Length = 629 Score = 30.2 bits (68), Expect = 3.5 Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 4/83 (4%) Query: 864 AMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQLYQ 923 A +G M+ E + +G+ D+L++T + GLD+ + + +V D+ ++ Y Sbjct: 273 AALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERIS--LVVNYDIPMDSESYV 330 Query: 924 LR-GRVGRSKIASFALFLLPENR 945 R GR GR+ A AL L ENR Sbjct: 331 HRIGRTGRAGRAGRAL-LFVENR 352 >gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional. Length = 401 Score = 29.4 bits (66), Expect = 5.4 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 6/72 (8%) Query: 867 HGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQLYQLR- 925 HG M K+ + M F G VL++T ++ G+D+ + + +I D+ + Y R Sbjct: 298 HGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVI--NYDLPASPENYIHRI 355 Query: 926 ---GRVGRSKIA 934 GR GR +A Sbjct: 356 GRSGRFGRKGVA 367 >gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional. Length = 259 Score = 29.3 bits (66), Expect = 5.5 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 10/75 (13%) Query: 622 FPHVETEDQ------EKAIDAVIQDLSSGRLMDR----LICGDVGFGKTEIALRAAFIAV 671 FP V+T ++ A +Q L S ++R ++ G G GKT +A+ + AV Sbjct: 68 FPAVKTFEEYDFTFATGAPQKQLQSLRSLSFIERNENIVLLGPSGVGKTHLAIALGYEAV 127 Query: 672 MNGLQVAVIAPTTLL 686 G++V LL Sbjct: 128 RAGIKVRFTTAADLL 142 >gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional. Length = 675 Score = 29.2 bits (66), Expect = 6.1 Identities = 20/90 (22%), Positives = 43/90 (47%), Gaps = 14/90 (15%) Query: 853 FLQSEVPELKIAMAHGQMSPKNLEDKMNAFYEGQY-DVLLSTSIVESGLDLPKANTMI-- 909 +L+ +P + HG++ N+++ + Y + +++ST +ES + + A + Sbjct: 414 YLEKRLPIYDFYIIHGKV--PNIDEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDT 471 Query: 910 --VQRADMFGLAQLY-------QLRGRVGR 930 V + FG +++ Q +GRVGR Sbjct: 472 GRVYVPEPFGGKEMFISKSMRTQRKGRVGR 501 >gnl|CDD|168145 PRK05639, PRK05639, 4-aminobutyrate aminotransferase; Provisional. Length = 457 Score = 29.1 bits (65), Expect = 7.4 Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 18/89 (20%) Query: 917 GLAQLYQLRGRVGRSKI---ASFALFLLPENRP-LTAAAQKRLRILQSLNTLGAGFQLAS 972 G+A L G +GR ++ S + L P P ++AAA+ L I++ N L ++ Sbjct: 292 GVASGMGLSGVIGRKELMDLTSGSALLTPAANPVISAAAEATLEIIEEENLLKNALKVGE 351 Query: 973 ------------YDL--DIRGTGNLLGEE 987 +++ D+RG G ++G E Sbjct: 352 FIKKRLLEMKESFEVIGDVRGKGLMIGVE 380 >gnl|CDD|179915 PRK05015, PRK05015, aminopeptidase B; Provisional. Length = 424 Score = 29.1 bits (66), Expect = 8.1 Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 3/42 (7%) Query: 397 FLSHVAQQAQKGIKTIISASSQGALQHLIHLIESHGFKKIKK 438 LS A+ G K ++S + GA IHL I++ Sbjct: 4 TLSTQPADARWGEKALLSFNEDGA---TIHLNGKDDLGLIQR 42 >gnl|CDD|131494 TIGR02441, fa_ox_alpha_mit, fatty acid oxidation complex, alpha subunit, mitochondrial. Members represent alpha subunit of mitochondrial multifunctional fatty acid degradation enzyme complex. Subunit activities include: enoyl-CoA hydratase (EC 4.2.1.17) & 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35). Some characterization in human, pig, and rat. The beta subunit has activity: acetyl-CoA C-acyltransferase (EC 2.3.1.16). Length = 737 Score = 28.6 bits (64), Expect = 9.2 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 6/67 (8%) Query: 407 KGIKTIISASSQGALQHLIHLIESHGFKKIKKINTLTEINSLLKEEIAAVILPI--NQGF 464 KG+KT++ ++ L + KK+K+ +I SL ++ I + + P GF Sbjct: 357 KGLKTVLKDATPAGLDRGQQQVFKGLNKKVKR----KKITSLERDSILSNLTPTLDYSGF 412 Query: 465 ETKHMIL 471 + M++ Sbjct: 413 KNADMVI 419 >gnl|CDD|184617 PRK14317, glmM, phosphoglucosamine mutase; Provisional. Length = 465 Score = 28.8 bits (65), Expect = 9.6 Identities = 10/13 (76%), Positives = 11/13 (84%) Query: 980 TGNLLGEEQSGHI 992 TG +LG EQSGHI Sbjct: 333 TGAMLGGEQSGHI 345 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 0.137 0.390 Gapped Lambda K H 0.267 0.0598 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 19,330,782 Number of extensions: 1301927 Number of successful extensions: 2686 Number of sequences better than 10.0: 1 Number of HSP's gapped: 2645 Number of HSP's successfully gapped: 50 Length of query: 1187 Length of database: 5,994,473 Length adjustment: 104 Effective length of query: 1083 Effective length of database: 3,747,241 Effective search space: 4058262003 Effective search space used: 4058262003 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: 63 (28.3 bits)