RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780619|ref|YP_003065032.1| primosome assembly protein
PriA [Candidatus Liberibacter asiaticus str. psy62]
         (731 letters)



>gnl|CDD|31391 COG1198, PriA, Primosomal protein N' (replication factor Y) -
           superfamily II helicase [DNA replication, recombination,
           and repair].
          Length = 730

 Score =  720 bits (1860), Expect = 0.0
 Identities = 319/720 (44%), Positives = 430/720 (59%), Gaps = 18/720 (2%)

Query: 26  GPYIYSVPSAMKVE-LGSIVRVPLRSRTVLGIVWYNSEEKYKIDSLKLRPIEYVFDC-PP 83
            P+ Y +P  ++ +  GS VRVP   R V+GIV   S E   +D  KL+ IE V D  P 
Sbjct: 14  RPFDYLIPEGLEPDQPGSRVRVPFGGRLVVGIVVELSSES-DVDGRKLKEIERVLDTEPV 72

Query: 84  LSRQMCEFVKWVADYTFSPMGLVARMVVSALSETEKMEEKIQ----------FTGIFPRI 133
           L+ ++   ++W ADY  SP+G V R+ +  L      +  +              +    
Sbjct: 73  LTPELLRLIEWAADYYLSPLGDVLRLALPVLLRQGYAKPSLPVLFYRLTERGRAALPDLK 132

Query: 134 NTVARLRVLDKIKDGKIWEKRDLIRASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLY 193
               + RVL+ +  G  W +  L  A+ VS  V+ GL+ +G+I+ I      VV  P+  
Sbjct: 133 RAKKQARVLEALLQGGEWTRSALAHAAGVSLSVLKGLEKKGLIEIIELEPPLVVAPPDPS 192

Query: 194 FSL-PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLIL 252
            S    L++ QQ  VE ++     GFA  L+ GVTGSGKTEVYLE +A VL  GKQVL+L
Sbjct: 193 LSEWLALNQEQQAAVEAILSS-LGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVL 251

Query: 253 LPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPF 312
           +PEI+LT  +L RF+ RFG K A  HS LS   R ++WR+  RG   V++G RSALFLPF
Sbjct: 252 VPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALFLPF 311

Query: 313 KKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRR 372
           K LGLI++DEEHD SYKQE+G  Y+ARD++++R K E+ PVVL SATPS+ES  N  S +
Sbjct: 312 KNLGLIIVDEEHDSSYKQEDGPRYHARDVAVLRAKKENAPVVLGSATPSLESYANAESGK 371

Query: 373 YHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRG 432
           Y  + L+ R   + LP +++IDMR + +  G+SLSP +++ IR TL R EQ LLFLNRRG
Sbjct: 372 YKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGEQVLLFLNRRG 431

Query: 433 YAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACG 492
           YAPL LC+ CG   +C +C   L  H++  +L CH CG+     QSC  CGS   + A G
Sbjct: 432 YAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE-HLRAVG 490

Query: 493 FGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNF 552
            G ERI EE+   FP ARI  + SD     G L+  L   A GE DI+IGTQ++AKGH+F
Sbjct: 491 PGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDF 550

Query: 553 PRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQA 612
           P ++LVGV+D D GL + D R+SERTFQLL QV GRAGR G     +IQ Y P HP +QA
Sbjct: 551 PNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPAIQA 610

Query: 613 LVSGDADSFYESEIRARESVNLPPFGRLAAVIISGTKYQEVENYAYNLKEHAP--RSSDI 670
           L  GD ++FYE E+  R+ + LPPF RLAAVI S    ++   +A  L+E        D+
Sbjct: 611 LKRGDYEAFYEQELAERKELGLPPFSRLAAVIASAKNEEKALEFARALRELLKEALPVDV 670

Query: 671 VVFGPAESPLFMVRGRYRFRLLIHGKRNSNLQGFFSQMYDNTIKRSNALRVQFDIDPQNF 730
            V GPA +PL  + GRYR+++L+     ++LQ           KRS  +RV  DIDPQ+F
Sbjct: 671 EVLGPAPAPLAKLAGRYRYQILLKSPSRADLQKLLRAWLAVLPKRSGKVRVSIDIDPQSF 730


>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 = 88.5 bits (220), Expect = 6e-18
 Identities = 44/169 (26%), Positives = 72/169 (42%), Gaps = 27/169 (15%)

Query: 208 EQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHL-----GKQVLILLPEISLTSAI 262
            + +P   +G  V L+   TGSGKT  +L  + A+  L     G Q L+L P   L   I
Sbjct: 5   AEAIPAILEGKDV-LVQAPTGSGKTLAFL--LPALQALLKNPDGPQALVLAPTRELAEQI 61

Query: 263 LERFQKRF---GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-------LPF 312
            E  +K     G+K A  +   S   + +  ++       ++VG    L        L  
Sbjct: 62  YEELKKLGKYLGLKVALLYGGDSPKEQLRKLKKGPD----ILVGTPGRLLDLLERGGLLL 117

Query: 313 KKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPS 361
           K L L+V+DE H +    ++G   +  +  I+R       ++L+SAT  
Sbjct: 118 KNLKLLVLDEAHRLL---DQGFGDDLEE--ILRRLPPKRQILLLSATLP 161


>gnl|CDD|31390 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
           helicase) [DNA replication, recombination, and repair /
           Transcription].
          Length = 1139

 Score = 67.6 bits (165), Expect = 1e-11
 Identities = 38/118 (32%), Positives = 59/118 (50%), Gaps = 5/118 (4%)

Query: 222 LISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF---GVKPAEWH 278
           LI G  G GKTEV +      +  GKQV +L+P   L     E F++RF    V+     
Sbjct: 619 LICGDVGFGKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLS 678

Query: 279 SSLSTSMREKIWRQVARGAISVIVGVRSALF--LPFKKLGLIVIDEEHDISYKQEEGI 334
              S   +++I + +A G + +++G    L   + FK LGL++IDEE     K +E +
Sbjct: 679 RFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVKHKEKL 736



 Score = 33.3 bits (76), Expect = 0.27
 Identities = 25/98 (25%), Positives = 42/98 (42%), Gaps = 15/98 (15%)

Query: 495 IERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPR 554
           IE+ AE + E  P ARI++    +      L+  +     GE D+++ T ++  G + P 
Sbjct: 816 IEKKAERLRELVPEARIAVAHGQM--RERELEEVMLDFYNGEYDVLVCTTIIETGIDIPN 873

Query: 555 MSLVGVVDGD-LGLTNADLRSSERTFQLLSQVTGRAGR 591
            + + +   D  GL              L Q+ GR GR
Sbjct: 874 ANTIIIERADKFGLAQ------------LYQLRGRVGR 899



 Score = 30.6 bits (69), Expect = 1.5
 Identities = 13/35 (37%), Positives = 25/35 (71%), Gaps = 2/35 (5%)

Query: 529 LSAIAKGEIDIIIGT-QLVAKGHNFPRMSLVGVVD 562
           L  +A+G++DI+IGT +L++K   F  + L+ ++D
Sbjct: 690 LKGLAEGKVDIVIGTHRLLSKDVKFKDLGLL-IID 723


>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 = 67.4 bits (164), Expect = 1e-11
 Identities = 43/150 (28%), Positives = 67/150 (44%), Gaps = 20/150 (13%)

Query: 222 LISGVTGSGKTEVYLEIVAAVL--HLGKQVLILLPEISLTSAILERFQKRF--GVKPAEW 277
           L++  TGSGKT   L  +  +L    G QVL+L P   L + + ER ++ F  G+K    
Sbjct: 4   LLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYL 63

Query: 278 HSSLSTSMREKIWRQVARGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQ 330
               S   +EK+      G   ++VG    L        L  KKL L+++DE H +  + 
Sbjct: 64  IGGTSIKQQEKL----LSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQG 119

Query: 331 EEGILYNARDMSIVRGKIESFPVVLVSATP 360
                     + I+    +   V+L+SATP
Sbjct: 120 FG-----LLGLKILLKLPKDRQVLLLSATP 144


>gnl|CDD|31393 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
           and repair / Transcription].
          Length = 677

 Score = 64.5 bits (157), Expect = 1e-10
 Identities = 54/179 (30%), Positives = 82/179 (45%), Gaps = 20/179 (11%)

Query: 191 NLYFSLPI-LDKNQQDVVEQVVPLCTKGFAVS-LISGVTGSGKTEVYLEIVAAVLHLGKQ 248
               +LP  L   Q+ V+++++        ++ L+ G  GSGKT V L  + A +  G Q
Sbjct: 254 KFLAALPFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQ 313

Query: 249 VLILLPEISLTSAILERFQKRF---GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVR 305
             ++ P   L     E  +K     G++ A    SL    R++I  Q+A G I ++VG  
Sbjct: 314 AALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTH 373

Query: 306 SALF---LPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLV-SATP 360
            AL    + F  LGL++IDE+H     Q             +R K E  P VLV +ATP
Sbjct: 374 -ALIQDKVEFHNLGLVIIDEQHRFGVHQRL----------ALREKGEQNPHVLVMTATP 421



 Score = 34.4 bits (79), Expect = 0.099
 Identities = 30/140 (21%), Positives = 60/140 (42%), Gaps = 28/140 (20%)

Query: 495 IERIAEEVCEYFPLARISILSSDLEGGGGRLQLQ-----LSAIAKGEIDIIIGTQLVAKG 549
            E + EE+  + P  ++ ++        GR++       + A  +GEIDI++ T ++  G
Sbjct: 494 AEELYEELKSFLPELKVGLVH-------GRMKPAEKDAVMEAFKEGEIDILVATTVIEVG 546

Query: 550 HNFPRMSLVGVVDGD-LGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHP 608
            + P  +++ + + +  GL              L Q+ GR GR  L+S  ++    P   
Sbjct: 547 VDVPNATVMVIENAERFGLAQ------------LHQLRGRVGRGDLQSYCVLLYKPPLSE 594

Query: 609 VMQA---LVSGDADSFYESE 625
           V +    ++    D F  +E
Sbjct: 595 VAKQRLKIMRETTDGFVIAE 614



 Score = 32.5 bits (74), Expect = 0.40
 Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 6/67 (8%)

Query: 499 AEEVCEYFPLA--RISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQ-LVAKGHNFPRM 555
            E + ++      R+++L+  L+G   R ++ L  +A GEIDI++GT  L+     F  +
Sbjct: 328 YESLRKWLEPLGIRVALLTGSLKGKA-RKEI-LEQLASGEIDIVVGTHALIQDKVEFHNL 385

Query: 556 SLVGVVD 562
            LV ++D
Sbjct: 386 GLV-IID 391


>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 = 52.3 bits (125), Expect = 5e-07
 Identities = 40/234 (17%), Positives = 82/234 (35%), Gaps = 21/234 (8%)

Query: 199 LDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISL 258
           L   Q+    Q+V    +     L+  VTG+GKTE+  + +   L+ G +V I  P + +
Sbjct: 98  LSPGQKKASNQLVQYIKQKEDT-LVWAVTGAGKTEMIFQGIEQALNQGGRVCIASPRVDV 156

Query: 259 TSAILERFQKRF-GVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGL 317
              +  R ++ F        +    +  R  +           +V     L    +   L
Sbjct: 157 CLELYPRLKQAFSNCDIDLLYGDSDSYFRAPL-----------VVATTHQLLRFKQAFDL 205

Query: 318 IVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVH 377
           ++IDE     +  ++ + Y  +      G       + ++ATP+ +     +      + 
Sbjct: 206 LIIDEVDAFPFSDDQSLQYAVKKARKKEG-----ATIYLTATPTKKLERKILKGNLRILK 260

Query: 378 LSTRYRNSAL--PHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLN 429
           L  R+    L  P    I    + + + K L  ++   +          L+F  
Sbjct: 261 LPARFHGKPLPVPKFVWIGNWNKKLQRNK-LPLKLKRWLEKQRKTGRPVLIFFP 313



 Score = 33.4 bits (76), Expect = 0.20
 Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 14/96 (14%)

Query: 496 ERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRM 555
           E++A  + +  P   I+ + S+ +    R + ++ A   G+I ++I T ++ +G  FP +
Sbjct: 319 EQVAAALKKKLPKETIASVHSEDQH---RKE-KVEAFRDGKITLLITTTILERGVTFPNV 374

Query: 556 SLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGR 591
             V V+  +             T   L Q+ GR GR
Sbjct: 375 D-VFVLGAE---------HRVFTESALVQIAGRVGR 400


>gnl|CDD|31261 COG1061, SSL2, DNA or RNA helicases of superfamily II
           [Transcription / DNA replication, recombination, and
           repair].
          Length = 442

 Score = 44.7 bits (105), Expect = 9e-05
 Identities = 68/428 (15%), Positives = 136/428 (31%), Gaps = 56/428 (13%)

Query: 165 HVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVV-PLCTKGFAVSLI 223
            +   L ++G  +    V+   +    +      L   Q++ ++ +V    T+   V  I
Sbjct: 3   DLKQYLSSKGAEELADYVLDEGLPLKLIVAFEFELRPYQEEALDALVKNRRTERRGV--I 60

Query: 224 SGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLST 283
              TG+GKT V  E +A    L +  L+L+P   L     E  +K       +       
Sbjct: 61  VLPTGAGKTVVAAEAIA---ELKRSTLVLVPTKELLDQWAEALKKFLL--LNDEIGIYGG 115

Query: 284 SMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDMSI 343
             +E    +V    +  +   +        + GLI+ DE H +                I
Sbjct: 116 GEKELEPAKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLP---------APSYRRI 166

Query: 344 VRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQG 403
           +     ++P + ++ATP  E    G                  L    V ++  + +   
Sbjct: 167 LELLSAAYPRLGLTATP--EREDGGRIGDLFD-----------LIGPIVYEVSLKELIDE 213

Query: 404 KSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKK 463
             L+P     I+ TL  +E+   +          L      R +  + +  +     +K 
Sbjct: 214 GYLAPYKYVEIKVTLTEDEER-EYAKESARFRELLRARGTLRAE--NEARRIAIASERKI 270

Query: 464 LYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGG 523
                           ++  S  +          IA+       +  I+  +   E    
Sbjct: 271 AAVRGLLLKHARGDKTLIFASDVE------HAYEIAKLFLAPGIVEAITGETPKEE---- 320

Query: 524 RLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLS 583
           R  + L     G I +++  +++ +G + P   ++ ++             S R F    
Sbjct: 321 REAI-LERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPT---------GSRRLFI--- 367

Query: 584 QVTGRAGR 591
           Q  GR  R
Sbjct: 368 QRLGRGLR 375


>gnl|CDD|30860 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
           recombination, and repair].
          Length = 590

 Score = 44.2 bits (104), Expect = 1e-04
 Identities = 31/108 (28%), Positives = 54/108 (50%), Gaps = 11/108 (10%)

Query: 227 TGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMR 286
           TG GK+  Y   + A+L  G   L++ P ISL    +++ +   G++ A  +S+LS   R
Sbjct: 41  TGGGKSLCYQ--IPALLLEG-LTLVVSPLISLMKDQVDQLE-AAGIRAAYLNSTLSREER 96

Query: 287 EKIWRQVARGAISVIV----GVRSALFLPF---KKLGLIVIDEEHDIS 327
           +++  Q+  G + ++      + S  FL       + L+ IDE H IS
Sbjct: 97  QQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCIS 144


>gnl|CDD|30902 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
           [DNA replication, recombination, and repair].
          Length = 663

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 34/100 (34%), Positives = 54/100 (54%), Gaps = 17/100 (17%)

Query: 497 RIAEEVCEYFPLARISI--LSSD---LEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHN 551
           ++AE++ EY     I +  L SD   LE    R+++ +  +  GE D+++G  L+ +G +
Sbjct: 457 KMAEDLTEYLKELGIKVRYLHSDIDTLE----RVEI-IRDLRLGEFDVLVGINLLREGLD 511

Query: 552 FPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGR 591
            P +SLV ++D D       LR SER+   L Q  GRA R
Sbjct: 512 LPEVSLVAILDAD---KEGFLR-SERS---LIQTIGRAAR 544



 Score = 32.9 bits (75), Expect = 0.37
 Identities = 34/129 (26%), Positives = 59/129 (45%), Gaps = 16/129 (12%)

Query: 199 LDKNQQDVVEQVV-PLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEIS 257
           L+++  +VVEQ++ P    G     I      G+ +  L  +   +   ++VL+     +
Sbjct: 401 LEQSGGNVVEQIIRP---TGLLDPEIEVRPTKGQVDDLLSEIRKRVAKNERVLV----TT 453

Query: 258 LTSAILE---RFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGV---RSALFLP 311
           LT  + E    + K  G+K    HS + T  R +I R +  G   V+VG+   R  L LP
Sbjct: 454 LTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLP 513

Query: 312 FKKLGLIVI 320
             ++ L+ I
Sbjct: 514 --EVSLVAI 520



 Score = 29.8 bits (67), Expect = 2.7
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 202 NQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSA 261
           +Q + + ++V     G     + GVTGSGKT     ++A V    +  L+L    +L + 
Sbjct: 16  DQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANVIAKV---QRPTLVLAHNKTLAAQ 72

Query: 262 ILERFQKRF 270
           +   F++ F
Sbjct: 73  LYSEFKEFF 81


>gnl|CDD|31397 COG1204, COG1204, Superfamily II helicase [General function
           prediction only].
          Length = 766

 Score = 42.7 bits (100), Expect = 4e-04
 Identities = 51/230 (22%), Positives = 91/230 (39%), Gaps = 31/230 (13%)

Query: 222 LISGVTGSGKTEV-YLEIVAAVLHLGKQVLILLPEISLTSAILERFQK--RFGVKPAEWH 278
           LIS  TGSGKT +  L I++ +L  G +V+ ++P  +L     E F +    G++     
Sbjct: 51  LISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRLEELGIRVGIST 110

Query: 279 SSLSTSMREKIWRQVARGAISVIVGVRSALF-------LPFKKLGLIVIDEEHDISYKQE 331
                   E++ R        VIV     L           +++ L+VIDE H +  +  
Sbjct: 111 GDYDLD-DERLARY------DVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTR 163

Query: 332 EGILYNARDMSIVRGKIESFPVVLVSAT-PSIES-----RVNGISRRYHSVHLSTRYRNS 385
             +L     ++ +R   E   +V +SAT P+ E          +   +  V L       
Sbjct: 164 GPVL--ESIVARMRRLNELIRIVGLSATLPNAEEVADWLNAKLVESDWRPVPLRRG---- 217

Query: 386 ALPHLQVIDMRGQTIAQGKSLSPEM-IDGIRHTLARNEQTLLFLNRRGYA 434
            +P++               L   + ++ +  +LA   Q L+F++ R  A
Sbjct: 218 -VPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVFVHSRKEA 266


>gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit. 
          Length = 103

 Score = 42.6 bits (101), Expect = 4e-04
 Identities = 19/45 (42%), Positives = 25/45 (55%)

Query: 222 LISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERF 266
           LI   TGSGKT    +++A +L   K+VL L+P   L    LE F
Sbjct: 22  LIVMATGSGKTLTAAKLIARLLKGKKKVLFLVPRKDLLEQALEEF 66


>gnl|CDD|31307 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
           and repair].
          Length = 1187

 Score = 39.5 bits (92), Expect = 0.003
 Identities = 28/111 (25%), Positives = 46/111 (41%), Gaps = 12/111 (10%)

Query: 223 ISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEW----- 277
           I   TG GKT   L +   +   GK+V I++P  +L   + ER +K F            
Sbjct: 102 IIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKK-FAEDAGSLDVLVV 160

Query: 278 -HSSLSTSMREKIWRQVARGAISVIVGVRSALF-----LPFKKLGLIVIDE 322
            HS+L T  +E+   ++  G   +++     L      L   K   I +D+
Sbjct: 161 YHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELSKLKFDFIFVDD 211


>gnl|CDD|36170 KOG0952, KOG0952, KOG0952, DNA/RNA helicase MER3/SLH1, DEAD-box
           superfamily [RNA processing and modification].
          Length = 1230

 Score = 39.5 bits (92), Expect = 0.004
 Identities = 59/257 (22%), Positives = 100/257 (38%), Gaps = 48/257 (18%)

Query: 210 VVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQ-------------VLILLPEI 256
           V P+  K     LI   TGSGKT +       +L   K+             ++ + P  
Sbjct: 118 VFPVAYKSNENMLICAPTGSGKTVLAE---LCILRTIKEHEEQGDIAKDDFKIVYIAPMK 174

Query: 257 SLTSAILERFQKRF---GVKPAEWHSSLSTS----MREKI-------WRQVARGAISVIV 302
           +L + ++++F K+    G+   E       +       +I       W  V R ++    
Sbjct: 175 ALAAEMVDKFSKKLAPLGISVRELTGDTQLTKTEIADTQIIVTTPEKWDVVTRKSVG--- 231

Query: 303 GVRSALFLPFKKLGLIVIDEEHDISYKQE---EGILYNARDMSIVRGKIESFPVVLVSAT 359
              SAL   F  + L++IDE H +   +    E I+  AR + +V        +V +SAT
Sbjct: 232 --DSAL---FSLVRLVIIDEVHLLHDDRGPVLETIV--ARTLRLVESSQSMIRIVGLSAT 284

Query: 360 -PSIE--SRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEM-IDGIR 415
            P+ E  +R   ++          RYR   L     I ++G+   Q K    E+  D + 
Sbjct: 285 LPNYEDVARFLRVNPYAGLFSFDQRYRPVPL-TQGFIGIKGKKNRQQKKNIDEVCYDKVV 343

Query: 416 HTLARNEQTLLFLNRRG 432
             L    Q L+F++ R 
Sbjct: 344 EFLQEGHQVLVFVHSRN 360


>gnl|CDD|114433 pfam05707, Zot, Zonular occludens toxin (Zot).  This family
           consists of bacterial and viral proteins which are very
           similar to the Zonular occludens toxin (Zot). Zot is
           elaborated by bacteriophages present in toxigenic
           strains of Vibrio cholerae. Zot is a single polypeptide
           chain of 44.8 kDa, with the ability to reversibly alter
           intestinal epithelial tight junctions, allowing the
           passage of macromolecules through mucosal barriers.
          Length = 183

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 30/108 (27%), Positives = 43/108 (39%), Gaps = 30/108 (27%)

Query: 219 AVSLISGVTGSGKT--EVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAE 276
            + LI+G  GSGKT   V   I+ A+   G++V+  +  ++L     ERF K FG    +
Sbjct: 1   MIYLITGKPGSGKTLEAVSYHILPALKK-GRKVITNIDGLNL-----ERFPKVFG---ED 51

Query: 277 WHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEH 324
               L        WR   +GA                   L+VIDE  
Sbjct: 52  VRERLEDIGYMDPWRTYPKGA-------------------LLVIDEAQ 80


>gnl|CDD|37016 KOG1805, KOG1805, KOG1805, DNA replication helicase [Replication,
           recombination and repair].
          Length = 1100

 Score = 35.3 bits (81), Expect = 0.057
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 178 QIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLE 237
           +  + +S V+        L  L+ +Q+  + +   L  + +A  LI G+ G+GKT     
Sbjct: 649 KFVDALSKVLIPKIKKIILLRLNNDQRQALLKA--LAAEDYA--LILGMPGTGKTTTISL 704

Query: 238 IVAAVLHLGKQVLI 251
           ++  ++ LGK+VL+
Sbjct: 705 LIKILVALGKKVLL 718


>gnl|CDD|37014 KOG1803, KOG1803, KOG1803, DNA helicase [Replication, recombination
           and repair].
          Length = 649

 Score = 35.3 bits (81), Expect = 0.059
 Identities = 36/211 (17%), Positives = 69/211 (32%), Gaps = 19/211 (9%)

Query: 135 TVARLRVLDKIKDGKIWEKRDLIRASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYF 194
           T++ LR+L           +D +      S+      +  V++ +F    P+        
Sbjct: 121 TLSSLRLLKLENKVTYRRMKDTMICLSKFSNPG---PSSDVVETLFGDRKPIPSPNIEIK 177

Query: 195 SLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLP 254
            +   +KN     +  V        + +I G  G+GKT   +EI++ ++   K+VL+  P
Sbjct: 178 KITFFNKNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKKRVLVCAP 237

Query: 255 EISLTSAILERFQ------KRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSAL 308
                  I+ER         R G       S    S+      +        I       
Sbjct: 238 SNVAVDNIVERLTHLKLNLVRVGHPARLLESVADHSLDLLSNTKDNSQNAKDIS------ 291

Query: 309 FLPFKKLGLIVIDEEHDISYKQEEGILYNAR 339
               K + ++        + K  +GI    +
Sbjct: 292 ----KDIDILFQKNTKTKNDKLRKGIRKEIK 318


>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 = 34.9 bits (80), Expect = 0.080
 Identities = 23/104 (22%), Positives = 45/104 (43%), Gaps = 12/104 (11%)

Query: 497 RIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMS 556
           ++ +E+ E      I + +   +G     +  L    +GEI +++ T ++A+G + P +S
Sbjct: 39  KMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVS 98

Query: 557 LVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLI 600
           +V   D     ++              Q  GRAGR G K   ++
Sbjct: 99  VVINYDLPWSPSS------------YLQRIGRAGRAGQKGTAIL 130



 Score = 33.4 bits (76), Expect = 0.24
 Identities = 23/77 (29%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSM 285
                K E  LE++   L  G +VLI  P   +   + E  +K  G+K A  H   S   
Sbjct: 8   PVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKP-GIKVAALHGDGSQEE 66

Query: 286 REKIWRQVARGAISVIV 302
           RE++ +    G I V+V
Sbjct: 67  REEVLKDFREGEIVVLV 83


>gnl|CDD|31392 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
           replication, recombination, and repair].
          Length = 654

 Score = 34.7 bits (79), Expect = 0.089
 Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 191 NLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAV-LHLGKQV 249
            + F        Q+++ E V      G  + LI   TG+GKT  YL    A     GK+V
Sbjct: 8   AVAFPGFEPRPEQREMAEAVAEALKGGEGL-LIEAPTGTGKTLAYLLPALAYAREEGKKV 66

Query: 250 LILLPEISLTSAILERF 266
           +I     +L   +LE  
Sbjct: 67  IISTRTKALQEQLLEED 83


>gnl|CDD|31396 COG1203, COG1203, Predicted helicases [General function prediction
           only].
          Length = 733

 Score = 34.3 bits (78), Expect = 0.13
 Identities = 33/171 (19%), Positives = 62/171 (36%), Gaps = 40/171 (23%)

Query: 223 ISGVTGSGKTEVYLEIVAAVLH----LGKQVLILLPEISLTSAILERFQKRFGVKPAEWH 278
           +   TG GKTE  L +  A+L     L  +V+ +LP  ++   +  R ++ FG+      
Sbjct: 219 LEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFSVIGK 278

Query: 279 SSLSTSM---------REKIWRQVARGAISVIVGVR----------SALFLPFKKLGLI- 318
           S  S+S             +          +++ +           S     F+ L L+ 
Sbjct: 279 SLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLL 338

Query: 319 ----VIDEEHDISYKQE----EGILYNARDMSIVRGKIESFPVVLVSATPS 361
               ++DE H  + +        +L    +  +        PV+L+SAT  
Sbjct: 339 TSLVILDEVHLYADETMLAALLALLEALAEAGV--------PVLLMSATLP 381


>gnl|CDD|31395 COG1202, COG1202, Superfamily II helicase, archaea-specific
           [General function prediction only].
          Length = 830

 Score = 34.2 bits (78), Expect = 0.14
 Identities = 32/121 (26%), Positives = 53/121 (43%), Gaps = 26/121 (21%)

Query: 222 LISGVTGSGKTEV-YLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSS 280
           L+   T SGKT +  L  +  +L  GK++L L+P ++L +   E F++R+          
Sbjct: 236 LVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERYS------KLG 289

Query: 281 LSTSMREKIWRQVARG---------AISVIVG--------VRSALFLPFKKLGLIVIDEE 323
           L  ++R  + R   R             +IVG        +R+   L    +G +VIDE 
Sbjct: 290 LKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTGKDL--GDIGTVVIDEI 347

Query: 324 H 324
           H
Sbjct: 348 H 348



 Score = 30.3 bits (68), Expect = 2.0
 Identities = 10/40 (25%), Positives = 18/40 (45%)

Query: 263 LERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV 302
           L       G+K A +H+ L    R+ + R  A   ++ +V
Sbjct: 456 LADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVV 495


>gnl|CDD|34219 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
           recombination, and repair].
          Length = 1041

 Score = 33.8 bits (77), Expect = 0.17
 Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 8/85 (9%)

Query: 534 KGEIDIIIGTQLVAKGHNFPRMSLV--GVVDGDLGLTNADLRSSERTFQLLSQVTGRAGR 591
           +G + ++  T+  A G N P  ++V   +   D G  +  L   E T     Q++GRAGR
Sbjct: 468 EGLVKVVFATETFAIGINMPARTVVFTSLSKFD-GNGHRWLSPGEYT-----QMSGRAGR 521

Query: 592 FGLKSLGLIQAYQPTHPVMQALVSG 616
            GL  LG +   +P      +  +G
Sbjct: 522 RGLDVLGTVIVIEPPFESEPSEAAG 546


>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 = 33.2 bits (75), Expect = 0.26
 Identities = 44/209 (21%), Positives = 75/209 (35%), Gaps = 42/209 (20%)

Query: 208 EQVVPLCTKGFAVSLISGVTGSGKTEVY-LEIVAAVLHLGK----QVLILLPEISLTSAI 262
              +PL   G  V L    TG+GKT  + L ++  +L   +      LIL P   L   I
Sbjct: 57  LAAIPLILAGRDV-LGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQI 115

Query: 263 LERFQK----RFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-------LP 311
            E  +K      G++ A  +     S+R++I   + RG   ++V     L        L 
Sbjct: 116 AEELRKLGKNLGGLRVAVVYG--GVSIRKQI-EALKRGV-DIVVATPGRLLDLIKRGKLD 171

Query: 312 FKKLGLIVIDEEHDISYKQEEGILYNARDMSI---VRGKIESFP----VVLVSAT--PSI 362
              +  +V+DE         + +L    DM     +   +++ P     +L SAT    I
Sbjct: 172 LSGVETLVLDE--------ADRML----DMGFIDDIEKILKALPPDRQTLLFSATMPDDI 219

Query: 363 ESRVNGISRRYHSVHLSTRYRNSALPHLQ 391
                        + +S       L  ++
Sbjct: 220 RELARRYLNDPVEIEVSVEKLERTLKKIK 248



 Score = 29.7 bits (66), Expect = 2.9
 Identities = 40/180 (22%), Positives = 69/180 (38%), Gaps = 26/180 (14%)

Query: 139 LRVLDKIKDGKIWEKRDLIRASQVSSHVI---DGLKAQGVIKQIFEVISPV-VDSPNLYF 194
            R+LD IK GK+         S V + V+   D +   G I  I +++  +  D   L F
Sbjct: 159 GRLLDLIKRGKL-------DLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQTLLF 211

Query: 195 S-------LPILDKNQQDVVEQVVPLCTKGFAVSLISGV-----TGSGKTEVYLEIVAAV 242
           S         +  +   D VE  V +      +  I        +   K E+ L+++   
Sbjct: 212 SATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLK-- 269

Query: 243 LHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV 302
                +V++ +    L   + E  +KR G K A  H  L    R++   +   G + V+V
Sbjct: 270 DEDEGRVIVFVRTKRLVEELAESLRKR-GFKVAALHGDLPQEERDRALEKFKDGELRVLV 328


>gnl|CDD|33853 COG4096, HsdR, Type I site-specific restriction-modification
           system, R (restriction) subunit and related helicases
           [Defense mechanisms].
          Length = 875

 Score = 33.0 bits (75), Expect = 0.26
 Identities = 38/184 (20%), Positives = 65/184 (35%), Gaps = 40/184 (21%)

Query: 173 QGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKT 232
           +G++ +    I  +        S       Q   + +V+   +KG   +L+   TG+GKT
Sbjct: 142 EGLLYRRQLRIQQLAYIDI--DSAIGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKT 199

Query: 233 EVYLEIVAAVLHLG--KQVLILLPEISLTSAILERFQK-------------RFGVKPAEW 277
              + I+  ++  G  K+VL L    +L       F+              + G   +E 
Sbjct: 200 RTAIAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFGTKMNKIEDKKGDTSSEI 259

Query: 278 HSSLSTSM------REKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQE 331
           + S   +M      +E  +R+   G                    LIVIDE H   Y + 
Sbjct: 260 YLSTYQTMTGRIEQKEDEYRRFGPGFFD-----------------LIVIDEAHRGIYSEW 302

Query: 332 EGIL 335
             IL
Sbjct: 303 SSIL 306


>gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing
           factor (pNORF1) [RNA processing and modification].
          Length = 935

 Score = 33.1 bits (75), Expect = 0.27
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 6/62 (9%)

Query: 194 FSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGK-QVLIL 252
            +LP L+ +Q + V+ V+        +SLI G  G+GKT     IV  +       VL+ 
Sbjct: 406 PNLPKLNASQSNAVKHVL-----QRPLSLIQGPPGTGKTVTSATIVYHLARQHAGPVLVC 460

Query: 253 LP 254
            P
Sbjct: 461 AP 462


>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 = 33.1 bits (75), Expect = 0.27
 Identities = 46/254 (18%), Positives = 81/254 (31%), Gaps = 44/254 (17%)

Query: 222 LISGVTGSGKTEVY-LEIVAAVLHLGK-QVLILLPEISLTSAILERFQK-----RFGVKP 274
           +++  TGSGKTE + L I+  +L     + L+L P  +L +   ER ++        V  
Sbjct: 89  VVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELISDLPGKVTF 148

Query: 275 AEWHSSLSTSMREKIWRQVARGAI--------SVIVGVRSALFLPFKKLGLIVIDEEHDI 326
             +        R  I R      +         ++    + L+L  + L  +V+DE H  
Sbjct: 149 GRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWL-LRNLKYLVVDELH-- 205

Query: 327 SYKQEEG---ILYNARDMSIVRGKIESFPVVLVSATPS-------------IESRVNGIS 370
           +Y+  +G    L   R +  +R       ++  SAT +              E  V+   
Sbjct: 206 TYRGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPGEFAEELFGRDFEVPVDEDG 265

Query: 371 RRYHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNR 430
                 +   R          +       +A   +L                QTL+F   
Sbjct: 266 SPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVR----------NGIQTLVFFRS 315

Query: 431 RGYAPLTLCQVCGN 444
           R    L        
Sbjct: 316 RKQVELLYLSPRRR 329


>gnl|CDD|30782 COG0433, COG0433, Predicted ATPase [General function prediction
           only].
          Length = 520

 Score = 32.6 bits (73), Expect = 0.39
 Identities = 41/306 (13%), Positives = 84/306 (27%), Gaps = 23/306 (7%)

Query: 105 LVARMVVSALSETEKME--EKIQFTGIFPRINTVARLRVLDKIKDGKIWEKRDLIRASQV 162
           L  R+    L     +E         +      +A+ RVL ++ + ++   R  +R    
Sbjct: 65  LADRITSIDLEALADLEAFIISSVLDLEGSYVGIAKRRVLGEL-EPELLPPRSPVR---- 119

Query: 163 SSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILD-KNQQDVVEQVVPLCTKGFAVS 221
                       V +   EV+  ++        L +    +  +V   +           
Sbjct: 120 --------PGSPVYRASDEVLEKILGFDVDGRGLLLGALLDGGEVPVYLDLNKLVLARHI 171

Query: 222 LISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSL 281
            I G TGSGK+ +   ++  +L      +++         +        G +     +  
Sbjct: 172 AILGSTGSGKSNLAKVLLEELLGKDGATVVIFDPHGEYDLLRLDRADGEGYRIRILEAGG 231

Query: 282 STSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIV--IDEEHDISYKQEEGI----- 334
                 K +       +   +    A  L        V  + E   + +     I     
Sbjct: 232 LVPEGPKPYEIADLLGVLRELIESLAEVLDLGLYPKDVVALAEARLLLFALAPKILLLDK 291

Query: 335 LYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVID 394
           L        +R K     + +             +S +  S         +    L VID
Sbjct: 292 LEELVLEDEIRLKSLKGVIFVSIEDLERPLERLDVSLQLGSRVSPAIRALTEPGRLAVID 351

Query: 395 MRGQTI 400
           + G  I
Sbjct: 352 LSGLDI 357


>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 = 32.5 bits (75), Expect = 0.39
 Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 12/60 (20%)

Query: 534 KGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFG 593
            G+  +++ T +  +G + P +++  V++ DL    A             Q  GRAGR G
Sbjct: 31  NGKSKVLVATDVAGRGIDLPDVNV--VINYDLPWNPASYI----------QRIGRAGRAG 78


>gnl|CDD|35561 KOG0340, KOG0340, KOG0340, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 442

 Score = 32.2 bits (73), Expect = 0.55
 Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 9/66 (13%)

Query: 529 LSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGR 588
           LS        I+I T + ++G + P + LV          N D+    + +      T R
Sbjct: 297 LSRFRSNAARILIATDVASRGLDIPTVELV---------VNHDIPRDPKDYIHRVGRTAR 347

Query: 589 AGRFGL 594
           AGR G+
Sbjct: 348 AGRKGM 353


>gnl|CDD|35572 KOG0351, KOG0351, KOG0351, ATP-dependent DNA helicase [Replication,
           recombination and repair].
          Length = 941

 Score = 32.0 bits (72), Expect = 0.57
 Identities = 37/187 (19%), Positives = 67/187 (35%), Gaps = 32/187 (17%)

Query: 191 NLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVL 250
              F       NQ + +   +           +   TG GK+  Y   + A+L LG   +
Sbjct: 257 KEVFGHKGFRPNQLEAINATLSGKDC-----FVLMPTGGGKSLCYQ--LPALL-LGGVTV 308

Query: 251 ILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISV---------I 301
           ++ P ISL    +     + G+      S  + + R  I +++A G   +         +
Sbjct: 309 VISPLISLMQDQVTHL-SKKGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKV 367

Query: 302 VGVRSALFLPF-----KKLGLIVIDEEHDISYKQEEGILYNARD----MSIVRGKIESFP 352
           V     L           L L VIDE H +S        ++ R     + ++R +    P
Sbjct: 368 VASEGLLESLADLYARGLLALFVIDEAHCVS-----QWGHDFRPSYKRLGLLRIRFPGVP 422

Query: 353 VVLVSAT 359
            + ++AT
Sbjct: 423 FIALTAT 429


>gnl|CDD|36171 KOG0953, KOG0953, KOG0953, Mitochondrial RNA helicase SUV3,
           DEAD-box superfamily [RNA processing and modification].
          Length = 700

 Score = 31.9 bits (72), Expect = 0.68
 Identities = 35/197 (17%), Positives = 70/197 (35%), Gaps = 32/197 (16%)

Query: 472 SAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSA 531
           S +    CVV  S   +      IE+     C        +++   L       Q  L  
Sbjct: 353 SNLKPGDCVVAFSKKDIFTVKKKIEKAGNHKC--------AVIYGSLPPETRLAQAALFN 404

Query: 532 IAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGR 591
               E D+++ +  +  G N   +++  ++   L   +          Q+  Q+ GRAGR
Sbjct: 405 DPSNECDVLVASDAIGMGLN---LNIRRIIFYSLIKYSGRETEDITVSQIK-QIAGRAGR 460

Query: 592 FGLKSLGLIQAYQPTHPVMQALVSGDADSFYESEIRA-RESVNLPPFGRLAAVIISGTKY 650
           FG K         P          G+  + +  +++  +  +  P      A +      
Sbjct: 461 FGSK--------YP---------QGEVTTLHSEDLKLLKRILKRPVEPIKNAGL--WPTD 501

Query: 651 QEVENYAYNLKEHAPRS 667
           +++E +AY+L +  P +
Sbjct: 502 EQIELFAYHLPDATPSN 518


>gnl|CDD|35554 KOG0333, KOG0333, KOG0333, U5 snRNP-like RNA helicase subunit [RNA
           processing and modification].
          Length = 673

 Score = 31.5 bits (71), Expect = 0.75
 Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 11/88 (12%)

Query: 508 LARISILSSDLEGGGGRLQLQ--LSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDL 565
           L +     + L GG  + Q +  L+   +G  DI++ T +  +G + P +SLV       
Sbjct: 537 LEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLV------- 589

Query: 566 GLTNADLRSSERTFQLLSQVTGRAGRFG 593
              N D+  S   +      TGRAG+ G
Sbjct: 590 --INYDMAKSIEDYTHRIGRTGRAGKSG 615


>gnl|CDD|31394 COG1201, Lhr, Lhr-like helicases [General function prediction
           only].
          Length = 814

 Score = 31.8 bits (72), Expect = 0.79
 Identities = 13/60 (21%), Positives = 23/60 (38%)

Query: 247 KQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRS 306
           +  LI     S    +  R +K         H SLS  +R ++  ++  G +  +V   S
Sbjct: 254 RTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSS 313



 Score = 30.2 bits (68), Expect = 1.9
 Identities = 31/139 (22%), Positives = 59/139 (42%), Gaps = 19/139 (13%)

Query: 205 DVVEQVVPLCTKGFAVSLISGVTGSGKTEV-YLEIVAAVLHLGK-------QVLILLPEI 256
                 +P    G  V LI   TGSGKTE  +L ++  +L LGK         L + P  
Sbjct: 25  PPQRYAIPEIHSGENV-LIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLK 83

Query: 257 SLTSAILERFQ---KRFGVKPAEWHSSLSTSMREKIWRQ------VARGAISVIVGVRSA 307
           +L + I  R +   +  G++ A  H     S ++K+ +           ++++++     
Sbjct: 84  ALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKF 143

Query: 308 LFLPFKKLGLIVIDEEHDI 326
             L  + +  +++DE H +
Sbjct: 144 REL-LRDVRYVIVDEIHAL 161


>gnl|CDD|35569 KOG0348, KOG0348, KOG0348, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 708

 Score = 31.1 bits (70), Expect = 1.1
 Identities = 43/181 (23%), Positives = 80/181 (44%), Gaps = 30/181 (16%)

Query: 206 VVEQVVPLCTKGFAVSLISGVTGSGKTEVY-LEIVAAVLHLGKQV--------LILLPEI 256
           V +Q +P+  +G    L+   TGSGKT  Y L IV ++  +  ++        L+++P  
Sbjct: 163 VQKQAIPVLLEGRDA-LVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTR 221

Query: 257 SLTSAILERFQKRFGVKPAEW--HSSLSTSMREKIWRQVARGAISVIVG--------VRS 306
            L   I E  QK   +KP  W     L    ++K  +   R  I++++G        +++
Sbjct: 222 ELALQIYETVQKL--LKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKN 279

Query: 307 ALFLPFKKLGLIVIDEEH---DISYKQE-EGILYNARDMSIVRGKIESFPV----VLVSA 358
              + F +L  +V+DE     ++ ++++   IL     +     K    P     +L+SA
Sbjct: 280 TKSIKFSRLRWLVLDEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSA 339

Query: 359 T 359
           T
Sbjct: 340 T 340


>gnl|CDD|31829 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
           and repair].
          Length = 845

 Score = 31.1 bits (70), Expect = 1.1
 Identities = 33/151 (21%), Positives = 63/151 (41%), Gaps = 22/151 (14%)

Query: 219 AVSLISGVTGSGK-TEVYLEIVAAVLHLGKQVLILLP-EISLTSAILERFQKRFGVKPAE 276
            V +I G TGSGK T++   ++   L +  ++    P  ++  S   ER  +  G K  E
Sbjct: 66  QVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSVA-ERVAEELGEKLGE 124

Query: 277 -------WHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPF-KKLGLIVIDEEHDISY 328
                  + S +S   R K+   +  G     + +R     P      +++IDE H+ S 
Sbjct: 125 TVGYSIRFESKVSPRTRIKV---MTDG-----ILLREIQNDPLLSGYSVVIIDEAHERSL 176

Query: 329 KQEEGILYNARDMSIVRGKIESFPVVLVSAT 359
             +  +      ++  R   +   ++++SAT
Sbjct: 177 NTDILLGLLKDLLARRR---DDLKLIIMSAT 204


>gnl|CDD|143980 pfam00225, Kinesin, Kinesin motor domain. 
          Length = 321

 Score = 30.6 bits (70), Expect = 1.6
 Identities = 10/30 (33%), Positives = 19/30 (63%), Gaps = 1/30 (3%)

Query: 204 QDVVEQVVPLCTKGFAVSLIS-GVTGSGKT 232
           ++  + +V    +G+ V++ + G TGSGKT
Sbjct: 59  EETAKPLVESVLEGYNVTIFAYGQTGSGKT 88


>gnl|CDD|39485 KOG4284, KOG4284, KOG4284, DEAD box protein [Transcription].
          Length = 980

 Score = 30.5 bits (68), Expect = 1.7
 Identities = 25/128 (19%), Positives = 39/128 (30%), Gaps = 24/128 (18%)

Query: 539 IIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLG 598
           I++ T L A+G +   ++LV          N D  + E T+       GRAGRFG  + G
Sbjct: 325 ILVSTDLTARGIDADNVNLV---------VNIDAPADEETYF---HRIGRAGRFG--AHG 370

Query: 599 LIQAYQPTHPVMQALVSGDA-DSFYESEIRARESVNLPPFGRLAAVIISGTKYQEVENYA 657
                         L        F     R   +V                  +  ++  
Sbjct: 371 AAVTL---------LEDERELKGFTAMAYRIAVTVKRVVEPVHPLPGDLVKNQEFWKDLD 421

Query: 658 YNLKEHAP 665
           Y +    P
Sbjct: 422 YFIDFETP 429


>gnl|CDD|30088 cd01366, KISc_C_terminal, Kinesin motor domain,
           KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a
           spindle motor protein necessary for chromosome
           segregation in meiosis. KIFC2/KIFC3-like kinesins have
           been implicated in motility of the Golgi apparatus as
           well as dentritic and axonal transport in neurons. This
           catalytic (head) domain has ATPase activity and belongs
           to the larger group of P-loop NTPases. Kinesins are
           microtubule-dependent molecular motors that play
           important roles in intracellular transport and in cell
           division. In this subgroup the motor domain is found at
           the C-terminus (C-type). C-type kinesins are (-)
           end-directed motors, i.e. they transport cargo towards
           the (-) end of the microtubule. Kinesin motor domains
           hydrolyze ATP at a rate of about 80 per second, and move
           along the microtubule at a speed of about 6400 Angstroms
           per second. To achieve that, kinesin head groups work in
           pairs. Upon replacing ADP with ATP, a kinesin motor
           domain increases its affinity for microtubule binding
           and locks in place. Also, the neck linker binds to the
           motor domain, which repositions the other head domain
           through the coiled-coil domain close to a second tubulin
           dimer, about 80 Angstroms along the microtubule.
           Meanwhile, ATP hydrolysis takes place, and when the
           second head domain binds to the microtubule, the first
           domain again replaces ADP with ATP, triggering a
           conformational change that pulls the first domain
           forward..
          Length = 329

 Score = 30.2 bits (68), Expect = 2.1
 Identities = 17/37 (45%), Positives = 23/37 (62%), Gaps = 4/37 (10%)

Query: 200 DKNQQDVVEQVVPL---CTKGFAVSLIS-GVTGSGKT 232
           D +Q+DV E+V PL      G+ V + + G TGSGKT
Sbjct: 56  DASQEDVFEEVSPLVQSALDGYNVCIFAYGQTGSGKT 92


>gnl|CDD|36167 KOG0949, KOG0949, KOG0949, Predicted helicase, DEAD-box superfamily
            [General function prediction only].
          Length = 1330

 Score = 30.0 bits (67), Expect = 2.1
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 12/82 (14%)

Query: 535  GEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGL 594
            G + ++  T+ ++ G N P  ++V   D  L L   + +          Q+ GRAGR G 
Sbjct: 987  GHLQVLFATETLSLGINMPCRTVVFAGD-SLQLDPLNYK----------QMAGRAGRRGF 1035

Query: 595  KSLG-LIQAYQPTHPVMQALVS 615
             +LG ++    P   V + L S
Sbjct: 1036 DTLGNVVFMGIPRQKVQRLLTS 1057


>gnl|CDD|30100 cd01378, MYSc_type_I, Myosin motor domain, type I myosins. Myosin I
           generates movement at the leading edge in cell motility,
           and class I myosins have been implicated in phagocytosis
           and vesicle transport. Myosin I, an unconventional
           myosin, does not form dimers. This catalytic (head)
           domain has ATPase activity and belongs to the larger
           group of P-loop NTPases. Myosins are actin-dependent
           molecular motors that play important roles in muscle
           contraction, cell motility, and organelle transport. The
           head domain is a molecular motor, which utilizes ATP
           hydrolysis to generate directed movement toward the plus
           end along actin filaments. A cyclical interaction
           between myosin and actin provides the driving force.
           Rates of ATP hydrolysis and consequently the speed of
           movement along actin filaments vary widely, from about
           0.04 micrometer per second for myosin I to 4.5
           micrometer per second for myosin II in skeletal muscle.
           Myosin II moves in discrete steps about 5-10 nm long and
           generates 1-5 piconewtons of force. Upon ATP binding,
           the myosin head dissociates from an actin filament. ATP
           hydrolysis causes the head to pivot and associate with a
           new actin subunit. The release of Pi causes the head to
           pivot and move the filament (power stroke). Release of
           ADP completes the cycle..
          Length = 674

 Score = 30.2 bits (68), Expect = 2.1
 Identities = 35/141 (24%), Positives = 64/141 (45%), Gaps = 36/141 (25%)

Query: 155 DLIRASQVS-SHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPIL---------DKNQQ 204
           DL+  S++S   +++ LK +     I+  I PV+ S N +  LPI           K++ 
Sbjct: 4   DLVLLSKISEEAIVENLKKRFQNDLIYTYIGPVLISVNPFKQLPIYTDETIELYKGKSRY 63

Query: 205 DVVEQVVPLCTKGFAVS----------------LISGVTGSGKTEVYLEI---VAAVLHL 245
           ++   +       +A++                +ISG +G+GKTE   +I   +AAV   
Sbjct: 64  ELPPHI-------YALADNAYRSMKSENENQCVIISGESGAGKTEAAKKIMQYIAAVSGG 116

Query: 246 GKQVLILLPEISLTSAILERF 266
           G++V  +   I  ++ +LE F
Sbjct: 117 GQKVERVKDVILQSNPLLEAF 137


>gnl|CDD|36165 KOG0947, KOG0947, KOG0947, Cytoplasmic exosomal RNA helicase SKI2,
           DEAD-box superfamily [RNA processing and modification].
          Length = 1248

 Score = 30.0 bits (67), Expect = 2.2
 Identities = 27/101 (26%), Positives = 44/101 (43%), Gaps = 13/101 (12%)

Query: 534 KGEIDIIIGTQLVAKGHNFPRMSLV--GVVDGDLGLTNADLRSSERTFQLLSQVTGRAGR 591
           +G + ++  T+  A G N P  ++V   +   D G    +L   E T     Q+ GRAGR
Sbjct: 654 RGLVKVLFATETFAMGVNMPARTVVFSSLRKHD-GNEFRELLPGEYT-----QMAGRAGR 707

Query: 592 FGLKSLG----LIQAYQPTHPVMQALVSGDADSFYESEIRA 628
            GL   G    + +   P+   ++ L+ G      ES+ R 
Sbjct: 708 RGLDETGTVIIMCKDSVPSAATLKRLIMGGPTRL-ESQFRL 747


>gnl|CDD|100116 cd06008, NF-X1-zinc-finger, Presumably a zinc binding domain, which
           has been shown to bind to DNA in the human nuclear
           transcriptional repressor NF-X1. The zinc finger can be
           characterized by the pattern
           C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The
           NF-X1 zinc finger co-occurs with atypical RING-finger
           and R3H domains. Human NF-X1 is involved in the
           transcriptional repression of major histocompatibility
           complex class II genes. The drosophila homolog encoded
           by stc (shuttle craft) plays a role in embryonic
           development, and the Arabidopsis homologue AtNFXL1 has
           been shown to function in the response to trichothecene
           and other defense mechanisms..
          Length = 49

 Score = 30.0 bits (68), Expect = 2.4
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 17/58 (29%)

Query: 440 QVCGNRLKCLHCSCWLVEHRSKKKLYCH-----QCGHSAIYSQSCVVCGSSGKMIACG 492
           +VCG  L C +       H+ ++   CH      C       + C  CG + K + CG
Sbjct: 3   EVCGKPLPCGN-------HKCEQL--CHEGPCPPC--PETVKKKC-RCGKTTKEVPCG 48


>gnl|CDD|39644 KOG4443, KOG4443, KOG4443, Putative transcription factor HALR/MLL3,
           involved in embryonic development [General function
           prediction only].
          Length = 694

 Score = 30.1 bits (67), Expect = 2.5
 Identities = 13/81 (16%), Positives = 21/81 (25%), Gaps = 5/81 (6%)

Query: 389 HLQVIDMRGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKC 448
           H          +  G  L  +          + + TL  L+         C  C +   C
Sbjct: 94  HCYCQKPPNDKVPSGPWLCKKCTR-----CRQCDSTLPGLSLDLQEGYLQCAPCASLSYC 148

Query: 449 LHCSCWLVEHRSKKKLYCHQC 469
             C     +  S   + C  C
Sbjct: 149 PVCLIVYQDSESLPMVCCSIC 169


>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 = 29.3 bits (66), Expect = 3.5
 Identities = 33/132 (25%), Positives = 57/132 (43%), Gaps = 24/132 (18%)

Query: 208 EQVVPLCTKGFAVSLISGVTGSGKTEVY-LEIVAAVLHLGK----QVLILLP--EISL-T 259
            + +P    G  V +    TGSGKT  + + I+  +    K    Q LIL P  E++L  
Sbjct: 27  ARAIPPLLSGRDV-IGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQI 85

Query: 260 SAILERFQKRFGVKPAEWHSSL--STSMREKIWRQVARGAISVIVGVRSALF-------L 310
           + +  +  K   +K       +   TS+ ++I R++ RG   ++V     L        L
Sbjct: 86  AEVARKLGKHTNLKVV----VIYGGTSIDKQI-RKLKRGP-HIVVATPGRLLDLLERGKL 139

Query: 311 PFKKLGLIVIDE 322
              K+  +V+DE
Sbjct: 140 DLSKVKYLVLDE 151


>gnl|CDD|33387 COG3587, COG3587, Restriction endonuclease [Defense mechanisms].
          Length = 985

 Score = 29.5 bits (66), Expect = 3.5
 Identities = 20/92 (21%), Positives = 34/92 (36%), Gaps = 15/92 (16%)

Query: 227 TGSGKTEVYLEIVAAV---LHLGKQVLILLPEIS------LTSAILER--FQKRFGVKPA 275
           TG+GKT  YL  +  +     L K  +I++P ++      LTS       F+  +     
Sbjct: 83  TGTGKTYTYLRTMFELHKKYGLFK-FIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRL 141

Query: 276 EWHSSLSTSMREKIWRQVARGAISVIVGVRSA 307
           E +       + K           V++   SA
Sbjct: 142 ESYIYDEDIEKFKFKSN---NKPCVLLIFVSA 170


>gnl|CDD|29474 cd01062, RNase_T2_prok, Ribonuclease T2 (RNase T2) is a widespread
           family of secreted RNases found in every organism
           examined thus far.  This family includes RNase Rh, RNase
           MC1, RNase LE, and self-incompatibility RNases
           (S-RNases).  Plant T2 RNases are expressed during leaf
           senescence in order to scavenge phosphate from
           ribonucleotides. They are also expressed in response to
           wounding or pathogen invasion. S-RNases are thought to
           prevent self-fertilization by acting as selective
           cytotoxins of "self" pollen. Generally, RNases have two
           distinct binding sites: the primary site (B1 site) and
           the subsite (B2 site), for nucleotides located at the
           5'- and 3'- terminal ends of the sessil bond,
           respectively. This CD includes the prokaryotic RNase T2
           family members..
          Length = 184

 Score = 29.2 bits (65), Expect = 4.3
 Identities = 11/33 (33%), Positives = 17/33 (51%)

Query: 617 DADSFYESEIRARESVNLPPFGRLAAVIISGTK 649
           D D+++      RE++ +PP  RL A  I  T 
Sbjct: 93  DPDAYFAKARNLREALKIPPELRLLAGNIGVTA 125


>gnl|CDD|36166 KOG0948, KOG0948, KOG0948, Nuclear exosomal RNA helicase MTR4,
           DEAD-box superfamily [RNA processing and modification].
          Length = 1041

 Score = 28.7 bits (64), Expect = 5.1
 Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 17/95 (17%)

Query: 534 KGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLS-----QVTGR 588
           +G + ++  T+  + G N P  ++V         T    +   + F+ +S     Q++GR
Sbjct: 470 EGLVKVLFATETFSIGLNMPAKTVV--------FTAVR-KFDGKKFRWISSGEYIQMSGR 520

Query: 589 AGRFGLKSLG---LIQAYQPTHPVMQALVSGDADS 620
           AGR G+   G   L+   +    V + ++ G AD 
Sbjct: 521 AGRRGIDDRGIVILMIDEKMEPQVAKDMLKGSADP 555


>gnl|CDD|35567 KOG0346, KOG0346, KOG0346, RNA helicase [RNA processing and
           modification].
          Length = 569

 Score = 28.8 bits (64), Expect = 5.8
 Identities = 37/174 (21%), Positives = 69/174 (39%), Gaps = 28/174 (16%)

Query: 206 VVEQVVPLCTKGFAVSLISGVTGSGKTEVYL-EIVAAVLH--------LGKQVLILLPEI 256
           +    +PL  +G  V +    TGSGKT  YL  ++  +L          G   +IL+P  
Sbjct: 45  IQSSAIPLALEGKDV-VARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTK 103

Query: 257 SLTSAILERFQKRFGVKPAEWHS-SLSTSMREKIWRQVARGAISVIVGVRSAL------- 308
            L   + +  +K       +  + +L++SM + +          ++V   + L       
Sbjct: 104 ELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAG 163

Query: 309 -FLPFKKLGLIVIDE-EHDISYKQEEGILYNARDMSIVRGKI-ESFPVVLVSAT 359
                  L  +V+DE +  +S+  EE       D+  +R  +   +   L+SAT
Sbjct: 164 VLEYLDSLSFLVVDEADLLLSFGYEE-------DLKKLRSHLPRIYQCFLMSAT 210


>gnl|CDD|30084 cd00124, MYSc, Myosin motor domain. This catalytic (head) domain
           has ATPase activity and belongs to the larger group of
           P-loop NTPases. Myosins are actin-dependent molecular
           motors that play important roles in muscle contraction,
           cell motility, and organelle transport. The head domain
           is a molecular motor, which utilizes ATP hydrolysis to
           generate directed movement toward the plus end along
           actin filaments. A cyclical interaction between myosin
           and actin provides the driving force. Rates of ATP
           hydrolysis and consequently the speed of movement along
           actin filaments vary widely, from about 0.04 micrometer
           per second for myosin I to 4.5 micrometer per second for
           myosin II in skeletal muscle. Myosin II moves in
           discrete steps about 5-10 nm long and generates 1-5
           piconewtons of force. Upon ATP binding, the myosin head
           dissociates from an actin filament. ATP hydrolysis
           causes the head to pivot and associate with a new actin
           subunit. The release of Pi causes the head to pivot and
           move the filament (power stroke). Release of ADP
           completes the cycle..
          Length = 679

 Score = 28.7 bits (64), Expect = 6.4
 Identities = 28/135 (20%), Positives = 51/135 (37%), Gaps = 26/135 (19%)

Query: 155 DLIRASQVS-SHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPL 213
           DL     ++ + V++ L+ +     I+    P++ + N Y  LP       + + +    
Sbjct: 4   DLASLPHLNEATVLNNLRQRYKKDLIYTYAGPILIAVNPYKDLPNYG---PETIRKYRGK 60

Query: 214 CTKG-----FAVS----------------LISGVTGSGKTEVYLEIVAAVLHLGKQVLIL 252
                    FA++                +ISG +G+GKTE    I+  +  L       
Sbjct: 61  SRSELPPHVFAIADRAYRNMLRDRRNQSIIISGESGAGKTENTKLIMKYLASLAGSNDTG 120

Query: 253 LPEISLTS-AILERF 266
           + E  L +  ILE F
Sbjct: 121 IEEKILAANPILEAF 135


>gnl|CDD|39444 KOG4243, KOG4243, KOG4243, Macrophage maturation-associated protein
           [Defense mechanisms].
          Length = 298

 Score = 28.4 bits (63), Expect = 6.5
 Identities = 8/29 (27%), Positives = 12/29 (41%), Gaps = 3/29 (10%)

Query: 450 HCSCWLVEHRSKKKL---YCHQCGHSAIY 475
           H   W   H++K +      H C  + IY
Sbjct: 138 HIVSWKKSHQNKLRTLEHCLHMCDRAVIY 166


>gnl|CDD|35553 KOG0332, KOG0332, KOG0332, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 477

 Score = 28.4 bits (63), Expect = 7.8
 Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 16/91 (17%)

Query: 511 ISILSSDLEGGGGRLQLQLSAIAK----GEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLG 566
           +S+L  DL         Q +AI      G+  ++I T + A+G +  ++S+V  V+ DL 
Sbjct: 357 VSLLHGDLTVE------QRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVV--VNYDLP 408

Query: 567 LTNADLRSSERTFQLLSQVTGRAGRFGLKSL 597
           +        E  ++      GR GRFG K L
Sbjct: 409 VKYTG----EPDYETYLHRIGRTGRFGKKGL 435


>gnl|CDD|73041 cd03282, ABC_MSH4_euk, MutS4 homolog in eukaryotes.  The MutS
           protein initiates DNA mismatch repair by recognizing
           mispaired and unpaired bases embedded in duplex DNA and
           activating endo- and exonucleases to remove the
           mismatch.  Members of the MutS family possess C-terminal
           domain with a conserved ATPase activity that belongs to
           the ATP binding cassette (ABC) superfamily.  MutS
           homologs (MSH) have been identified in most prokaryotic
           and all eukaryotic organisms examined.  Prokaryotes have
           two homologs (MutS1 and MutS2), whereas seven MSH
           proteins (MSH1 to MSH7) have been identified in
           eukaryotes.  The homodimer MutS1 and heterodimers
           MSH2-MSH3 and MSH2-MSH6 are primarily involved in
           mitotic mismatch repair, whereas MSH4-MSH5 is involved
           in resolution of Holliday junctions during meiosis.  All
           members of the MutS family contain the highly conserved
           Walker A/B ATPase domain, and many share a common
           mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and
           MSH4-MSH5 dimerize to form sliding clamps, and
           recognition of specific DNA structures or lesions
           results in ADP/ATP exchange..
          Length = 204

 Score = 28.4 bits (63), Expect = 8.1
 Identities = 13/44 (29%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 197 PILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVA 240
           PILD+++++ +   + L        +I+G   SGK+  YL+ +A
Sbjct: 8   PILDRDKKNFIPNDIYLTRGSSRFHIITGPNMSGKS-TYLKQIA 50


>gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
           trafficking and secretion].
          Length = 340

 Score = 28.3 bits (63), Expect = 8.5
 Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 12/96 (12%)

Query: 161 QVSSHVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLP-----ILDKNQQDVVEQVVPLCT 215
           + +  +I+ L+ +   K+       + D   +  +L      IL    +  +   +P   
Sbjct: 84  ETAEEIIEELRKREGKKK------KIKDEETVKEALREALIEILRPVDKVDLPLEIPKEK 137

Query: 216 KGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLI 251
           K F V L  GV G GKT    ++   +   GK VL+
Sbjct: 138 KPF-VILFVGVNGVGKTTTIAKLAKYLKQQGKSVLL 172


>gnl|CDD|73263 cd01379, MYSc_type_III, Myosin motor domain, type III myosins.
           Myosin III has been shown to play a role in  the vision
           process in insects and in hearing in mammals. Myosin
           III, an unconventional myosin, does not form dimers.
           This catalytic (head) domain has ATPase activity and
           belongs to the larger group of P-loop NTPases. Myosins
           are actin-dependent molecular motors that play important
           roles in muscle contraction, cell motility, and
           organelle transport. The head domain is a molecular
           motor, which utilizes ATP hydrolysis to generate
           directed movement toward the plus end along actin
           filaments. A cyclical interaction between myosin and
           actin provides the driving force. Rates of ATP
           hydrolysis and consequently the speed of movement along
           actin filaments vary widely, from about 0.04 micrometer
           per second for myosin I to 4.5 micrometer per second for
           myosin II in skeletal muscle. Myosin II moves in
           discrete steps about 5-10 nm long and generates 1-5
           piconewtons of force. Upon ATP binding, the myosin head
           dissociates from an actin filament. ATP hydrolysis
           causes the head to pivot and associate with a new actin
           subunit. The release of Pi causes the head to pivot and
           move the filament (power stroke). Release of ADP
           completes the cycle..
          Length = 653

 Score = 28.1 bits (62), Expect = 8.6
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 222 LISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPE-ISLTSAILERF 266
           +ISG +GSGKTE    +V  +  LGK     L E I   ++++E F
Sbjct: 90  VISGESGSGKTESAHLLVQQLTVLGKANNRTLQEKILQVNSLVEAF 135


>gnl|CDD|38946 KOG3742, KOG3742, KOG3742, Glycogen synthase [Carbohydrate
           transport and metabolism].
          Length = 692

 Score = 28.0 bits (62), Expect = 9.0
 Identities = 16/57 (28%), Positives = 30/57 (52%)

Query: 133 INTVARLRVLDKIKDGKIWEKRDLIRASQVSSHVIDGLKAQGVIKQIFEVISPVVDS 189
           I ++ARL  L K+          LI  ++ +S  ++ LK Q V KQ+++ ++ V + 
Sbjct: 344 IESLARLNYLLKVSGSPKTVVAFLIMPAKTNSFNVESLKGQAVRKQLWDTVNEVKEK 400


>gnl|CDD|39924 KOG4726, KOG4726, KOG4726, Ultrahigh sulfur keratin-associated
           protein [Extracellular structures].
          Length = 146

 Score = 28.1 bits (62), Expect = 9.5
 Identities = 10/50 (20%), Positives = 14/50 (28%)

Query: 439 CQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKM 488
           CQ    +  C   +C+     S     C + G        C  C  S   
Sbjct: 41  CQPACCQSSCCQPTCYCSLAPSCCSSGCCRSGCCGSSCCRCGCCRPSCCC 90


>gnl|CDD|37954 KOG2743, KOG2743, KOG2743, Cobalamin synthesis protein [Coenzyme
           transport and metabolism].
          Length = 391

 Score = 28.0 bits (62), Expect = 9.5
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 4/60 (6%)

Query: 203 QQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAI 262
           ++DVV +          V++I+G  G+GKT + L  +    H GK++ ++L E   +S I
Sbjct: 44  EEDVVTKSSL--GARIPVTIITGYLGAGKTTL-LNYILTGQH-GKRIAVILNEFGESSDI 99


  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    0.137    0.401 

Gapped
Lambda     K      H
   0.267   0.0704    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 8,732,036
Number of extensions: 474478
Number of successful extensions: 1474
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1451
Number of HSP's successfully gapped: 89
Length of query: 731
Length of database: 6,263,737
Length adjustment: 101
Effective length of query: 630
Effective length of database: 4,081,228
Effective search space: 2571173640
Effective search space used: 2571173640
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)