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)