RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780382|ref|YP_003064795.1| ATP dependent RNA helicase
protein [Candidatus Liberibacter asiaticus str. psy62]
         (465 letters)



>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 =  395 bits (1015), Expect = e-110
 Identities = 183/464 (39%), Positives = 265/464 (57%), Gaps = 12/464 (2%)

Query: 1   MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60
            +FA LGLSP+++ A+ D G+ +PTPIQ+  IPL+L   DV G AQTGTGKTA+F+LP+L
Sbjct: 29  PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLL 88

Query: 61  TILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKN-YNLTVALLIGGIPFEAQNKKL 119
             + K     +    LIL PTRELA Q+A+   K GKN   L VA++ GG+    Q + L
Sbjct: 89  QKILK-SVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEAL 147

Query: 120 ERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQ 179
           +RG D+++ TPGR+LD   RGKL ++ +E LV+DEADRMLDMGFI  I+ I   +P  RQ
Sbjct: 148 KRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQ 207

Query: 180 TLLFSATMTDELQKVSENFLQNPKRIEVNTP--SSTAETIEHCFVATYAQYSKKCALLQQ 237
           TLLFSATM D++++++  +L +P  IEV+      T + I+  ++   ++  K   LL +
Sbjct: 208 TLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKL-ELLLK 266

Query: 238 LLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQ 297
           LL+ +D     I+F   K+ V  L  SL K+GF V A+HG++ Q  R + L  FK+G ++
Sbjct: 267 LLKDED-EGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELR 325

Query: 298 LMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVA-KEDIKH 356
           ++VA+D+AARGLDIPDV HV N+D+P   E+Y+HRIGRTGRAGR G A + V  +E++K 
Sbjct: 326 VLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKK 385

Query: 357 IDAIEKLIEKKVDWLNGDLSSLNPPLEKIDIAQHNHARKNNPIPQKSTGFDRRKKNYSSQ 416
           +  IEK +E+K+       + L P  E  D       R         +   ++ K+    
Sbjct: 386 LKRIEKRLERKLPS-----AVLLPLDEPEDAKLLKTTRPGLEEESDISDEIKKLKSSKKA 440

Query: 417 KSHIPLKESEKISKLQQDIQENDADSLGFRGNMPAFMLPKNRGK 460
                         L    +E          +        N   
Sbjct: 441 LLRGLGVRFTLSKLLANLGKEIPGAGDAVTIDPELERRSPNSAD 484


>gnl|CDD|35552 KOG0331, KOG0331, KOG0331, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 519

 Score =  334 bits (858), Expect = 3e-92
 Identities = 151/374 (40%), Positives = 219/374 (58%), Gaps = 10/374 (2%)

Query: 2   DFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLT 61
            F +LGLS +++ A+ + G+ KPTPIQ +  P+ L   D+ GIA+TG+GKT +++LP + 
Sbjct: 92  AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIV 151

Query: 62  ILEKGRA---RVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKK 118
            L   +    R   P  L+L PTRELA QV     ++GK+  L    + GG P   Q + 
Sbjct: 152 HLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRD 211

Query: 119 LERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITS-LVPFT 177
           LERG DV+I TPGR++D    G L ++ +  LV+DEADRMLDMGF P I+ I S +    
Sbjct: 212 LERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMGFEPQIRKILSQIPRPD 271

Query: 178 RQTLLFSATMTDELQKVSENFLQNPKRIEV--NTPSSTAETIEHCFVATYAQYSKKCALL 235
           RQTL+FSAT   E+++++E+FL NP +I V           I    +      + K   L
Sbjct: 272 RQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQ--IVEVCDETAKLRKL 329

Query: 236 QQLLQSQDTMKNG--IIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKE 293
            +LL+   +   G  IIFC  K+    L  +L ++G+   AIHG+  Q  R  +L  F+E
Sbjct: 330 GKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFRE 389

Query: 294 GTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKED 353
           G   ++VA+D+AARGLD+PDV  V N+D PN  E+Y+HRIGRTGRAG+ G A T    ++
Sbjct: 390 GKSPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDN 449

Query: 354 IKHIDAIEKLIEKK 367
            K    + K++ + 
Sbjct: 450 AKLARELIKVLREA 463


>gnl|CDD|35551 KOG0330, KOG0330, KOG0330, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 476

 Score =  310 bits (796), Expect = 4e-85
 Identities = 147/392 (37%), Positives = 226/392 (57%), Gaps = 7/392 (1%)

Query: 1   MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60
             FADLG+ P+++ A  + G+ KPT IQ + IP+ L   DV G+A+TG+GKT +F LP+L
Sbjct: 61  KSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPIL 120

Query: 61  TILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLE 120
             L +     ++   L+L PTRELA Q+A+ FE  G    L VA+L+GG+    Q  +L 
Sbjct: 121 QRLLQEP---KLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLS 177

Query: 121 RGADVLICTPGRILDHFNRGKLL-MNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQ 179
           +   +L+ TPGR+ DH    K   +  ++ LV+DEADR+LDM F   +  I  ++P  RQ
Sbjct: 178 KKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDMDFEEELDYILKVIPRERQ 237

Query: 180 TLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLL 239
           T LFSATMT +++K+    L NP ++ V++   T + ++  ++    +  K   L+  L 
Sbjct: 238 TFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKD-KDTYLVYLL- 295

Query: 240 QSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLM 299
            ++    + I+FCN       L   L   GF    +HG + Q  R+  L+ FK G   ++
Sbjct: 296 -NELAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSIL 354

Query: 300 VASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDA 359
           V +D+A+RGLDIP V  V N+D+P  +++YIHR+GRT RAGR GKA TLV + D++ +  
Sbjct: 355 VCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQR 414

Query: 360 IEKLIEKKVDWLNGDLSSLNPPLEKIDIAQHN 391
           IE  + KK+     D + +    E++  AQ  
Sbjct: 415 IEHALGKKLPEYKVDKNEVMSLNERVAEAQKE 446


>gnl|CDD|35559 KOG0338, KOG0338, KOG0338, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 691

 Score =  294 bits (754), Expect = 3e-80
 Identities = 156/436 (35%), Positives = 232/436 (53%), Gaps = 10/436 (2%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
           F  + LS  ++ A    GY KPTPIQ+ TIP+ L   D+C  A TG+GKTA+F LP+L  
Sbjct: 183 FQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILER 242

Query: 63  LEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERG 122
           L     +V   R L+L PTRELA QV    ++  +  ++TV L +GG+  +AQ   L   
Sbjct: 243 LLYRPKKVAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSR 302

Query: 123 ADVLICTPGRILDHF-NRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTL 181
            D++I TPGR++DH  N     +++IE+LV+DEADRML+ GF   +  I  L P  RQT+
Sbjct: 303 PDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEEGFADEMNEIIRLCPKNRQTM 362

Query: 182 LFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSK-KCALLQQLLQ 240
           LFSATMT+E++ ++   L  P RI V+    TA  +   F+    +    + A+L  L+ 
Sbjct: 363 LFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASLIT 422

Query: 241 SQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMV 300
                   I+F   KK    L   L   G     +HG++ Q  R++ L  FK+  I +++
Sbjct: 423 RTFQ-DRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLI 481

Query: 301 ASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAI 360
           A+D+A+RGLDI  V  V N+ +P   E+Y+HR+GRT RAGR G++ TLV + D K    +
Sbjct: 482 ATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRK----L 537

Query: 361 EKLIEKKVDWLNGDLSSLNPPLEKIDIAQHNHARKNNPIPQKSTGFDRRKKNYSSQKSHI 420
            K I K        L + N P E I+        +     Q     +R +K     K+  
Sbjct: 538 LKEIIKSSTKAGSKLKNRNIPPEVIE-KFRKKIEEMEDTIQAVLDEEREEKE--LSKAEA 594

Query: 421 PLKESEKISKLQQDIQ 436
            L++ E + +   +I 
Sbjct: 595 QLEKGENMLEHGDEIY 610


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

 Score =  288 bits (739), Expect = 2e-78
 Identities = 133/380 (35%), Positives = 206/380 (54%), Gaps = 34/380 (8%)

Query: 5   DLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILE 64
           + G   +++  +   GY +PTPIQ + IPL LQ  D  G+A+TG+GKTA+F++P+L  + 
Sbjct: 249 ESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWIS 308

Query: 65  KGRARVRM------PRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKK 118
                 R+      P  +IL PTRELA Q+ +   K+GK   +    +IGG+ FE Q  +
Sbjct: 309 SLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQ 368

Query: 119 LERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFT- 177
           L  G +++I TPGR++D      L++N    +V+DEADRM+DMGF P +Q I   +P + 
Sbjct: 369 LSMGCEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSN 428

Query: 178 ------------------------RQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSST 213
                                   RQT++F+ATM   +++++ ++L+ P  + + +    
Sbjct: 429 AKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSAGKP 488

Query: 214 AETIEHCFVATYAQYSKKCALLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVC 273
              +E           +K   L ++L+S       IIF N KK    L   LEK G+ V 
Sbjct: 489 TPRVEQ--KVEMVSEDEKRKKLIEILESNFD-PPIIIFVNTKKGADALAKILEKAGYKVT 545

Query: 274 AIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRI 333
            +HG   Q  R   L++F+EGT  ++VA+D+A RG+DIP+V  V N+D+    E+Y HRI
Sbjct: 546 TLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRI 605

Query: 334 GRTGRAGRHGKAFTLVAKED 353
           GRTGRAG+ G A + +   D
Sbjct: 606 GRTGRAGKSGTAISFLTPAD 625


>gnl|CDD|35556 KOG0335, KOG0335, KOG0335, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 482

 Score =  266 bits (682), Expect = 9e-72
 Identities = 136/396 (34%), Positives = 214/396 (54%), Gaps = 25/396 (6%)

Query: 2   DFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLT 61
            F +  L   +   +  +GY KPTP+Q  +IP++    D+   AQTG+GKTA+F++P+++
Sbjct: 75  TFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIIS 134

Query: 62  ILEKGR-------ARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEA 114
            L                PR LIL PTREL  Q+ +   K+     +   ++ GG    A
Sbjct: 135 YLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGA 194

Query: 115 QNKKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLD-MGFIPYIQNI--- 170
           Q + ++RG D+L+ TPGR+ D   RGK+ ++N + LV+DEADRMLD MGF P I+ I   
Sbjct: 195 QLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQ 254

Query: 171 -TSLVPFTRQTLLFSATMTDELQKVSENFL-QNPKRIEVNTPSSTAETIEHCFVATYAQY 228
                   RQTLLFSAT   E+Q+++ +FL  N   + V    ST+E I    +    + 
Sbjct: 255 LGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVN-EM 313

Query: 229 SKKCALLQQLLQSQDTMKNG-------IIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQ 281
            K+  LL  L +      +G       ++F   K+    L   L   G+   +IHG+  Q
Sbjct: 314 EKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQ 373

Query: 282 RSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGR 341
             R + L++F+ G   ++VA+++AARGLDIP+V HV N+D+P   ++Y+HRIGRTGR G 
Sbjct: 374 IEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGN 433

Query: 342 HGKAFTLVAKEDIKHIDAIEKLIEK----KVDWLNG 373
            G+A +   +++     A+ +++ +       WL+ 
Sbjct: 434 GGRATSFFNEKNQNIAKALVEILTEANQEVPQWLSE 469


>gnl|CDD|35557 KOG0336, KOG0336, KOG0336, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 629

 Score =  265 bits (678), Expect = 2e-71
 Identities = 132/361 (36%), Positives = 218/361 (60%), Gaps = 7/361 (1%)

Query: 10  PKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILE---KG 66
           P+V+  +   G+ KPTPIQ +  P++LQ  D+ G+AQTGTGKT +F+LP    ++   K 
Sbjct: 229 PEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKR 288

Query: 67  RARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVL 126
           R +   P  L+L PTRELA Q+    +KY  N   +V +  GG   E Q + L+RG +++
Sbjct: 289 REQRNGPGVLVLTPTRELALQIEGEVKKYSYNGLKSVCVYGGGNRNE-QIEDLKRGVEII 347

Query: 127 ICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFSAT 186
           I TPGR+ D      + + +I  LV+DEADRMLDMGF P I+ I   +   RQT++ SAT
Sbjct: 348 IATPGRLNDLQMDNVINLASITYLVLDEADRMLDMGFEPQIRKILLDIRPDRQTVMTSAT 407

Query: 187 MTDELQKVSENFLQNPKRIEVNTPSSTA-ETIEHCFVATYAQYSKKCALLQQLLQSQDTM 245
             + ++++++++L+ P  + V +    A ++++   + T    S+K  ++Q  + +  + 
Sbjct: 408 WPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTD--SEKLEIVQFFVANMSSN 465

Query: 246 KNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLA 305
              IIF ++K    +L      +G S  ++HGN +Q  R   L +FK G ++++VA+DLA
Sbjct: 466 DKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLA 525

Query: 306 ARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEKLIE 365
           +RGLD+PD+ HV+N+D P   E Y+HR+GRTGRAGR G + + + + D    + + +++E
Sbjct: 526 SRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSMAEELIQILE 585

Query: 366 K 366
           +
Sbjct: 586 R 586


>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 =  263 bits (673), Expect = 7e-71
 Identities = 138/376 (36%), Positives = 213/376 (56%), Gaps = 5/376 (1%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
           F D+GL   ++  +   G+ KP+ IQ + IP +L+  DV   AQ+GTGKTA+F + +L  
Sbjct: 29  FDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQS 88

Query: 63  LEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERG 122
           L+     VR  + LIL PTRELA Q+       G   N+     IGG       KKL+ G
Sbjct: 89  LD---ISVRETQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYG 145

Query: 123 ADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLL 182
             V+  TPGR+LD   R  L    +++LV+DEAD ML+ GF   I +I   +P   Q +L
Sbjct: 146 QHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLNKGFKEQIYDIYRYLPPGAQVVL 205

Query: 183 FSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQSQ 242
            SAT+  E+ +++E F+ +P RI V     T E I+  FVA   +  K   L    L   
Sbjct: 206 VSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCD--LYDT 263

Query: 243 DTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVAS 302
            T+   +IFCN K+ V  L   + +  F+V ++HG+++Q+ R KI+++F+ G  ++++ +
Sbjct: 264 LTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITT 323

Query: 303 DLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEK 362
           D+ ARG+D+  V  V N+D+PN  E YIHRIGR+GR GR G A   V  +D++ +  IE+
Sbjct: 324 DVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRILRDIEQ 383

Query: 363 LIEKKVDWLNGDLSSL 378
               ++D +  +++ L
Sbjct: 384 YYSTQIDEMPMNVADL 399


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

 Score =  262 bits (670), Expect = 2e-70
 Identities = 143/419 (34%), Positives = 224/419 (53%), Gaps = 18/419 (4%)

Query: 2   DFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLT 61
            F+ LGLSP +V  +   G  KPTPIQ   IP +L+  D  G A+TG+GKTA+F LP+L 
Sbjct: 8   PFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILN 67

Query: 62  ILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLER 121
            L +    +     L+L PTRELA Q+A+ F   GK  NL V++++GG     Q   L  
Sbjct: 68  RLSEDPYGIF---ALVLTPTRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSD 124

Query: 122 GADVLICTPGRILDHFNRGKL-----LMNNIEILVIDEADRMLDMGFIPYIQNITSLVPF 176
              V++ TPGR+ DH     L     +   ++ LV+DEADR+L   F   ++ I   +P 
Sbjct: 125 RPHVVVATPGRLADHL-SSNLGVCSWIFQRLKFLVLDEADRVLAGCFPDILEGIEECLPK 183

Query: 177 TRQTLLFSATMTDELQKVSENFLQNP--KRIEVNTPSSTAETIEHCFVATYAQYSKKCAL 234
            RQTLLFSAT+TD ++++    +       +EV    ST ET+   ++   +   K   L
Sbjct: 184 PRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILV-SIDVKDAYL 242

Query: 235 LQQLLQSQDTMK-NGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKE 293
           +  L   ++    + +IF N  +    L  +L+     V ++H  + Q+ R+  LS F+ 
Sbjct: 243 VHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRS 302

Query: 294 GTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKED 353
              ++++A+D+A+RGLDIP V  V N D+P   ++YIHR+GRT RAGR G A ++V + D
Sbjct: 303 NAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRD 362

Query: 354 IKHIDAIEKLIEKKVDWLNGDLSSLNPPLEKIDIAQHNHARKNNPIPQKSTGFDRRKKN 412
           ++ + AIE+ I KK+   N           ++ + Q   A++   +   + GF  R + 
Sbjct: 363 VELLQAIEEEIGKKLTEYNKV-----QRTVELYVTQVTVAKREAEMKMDNNGFGERAQK 416


>gnl|CDD|35560 KOG0339, KOG0339, KOG0339, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 731

 Score =  261 bits (669), Expect = 2e-70
 Identities = 134/355 (37%), Positives = 209/355 (58%), Gaps = 3/355 (0%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
           F   G   +++ A+  + Y KPTPIQ + +P  L   DV GIA+TG+GKTA+F+ PM+  
Sbjct: 225 FEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVH 284

Query: 63  L--EKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLE 120
           +  +        P  +IL PTRELA+Q+    +K+GK Y L V  + GG     Q+K+L+
Sbjct: 285 IMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK 344

Query: 121 RGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQT 180
            GA++++ TPGR++D        ++ +  LV+DEADRM DMGF P +++I   +   RQT
Sbjct: 345 EGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMGFEPQVRSIKQHIRPDRQT 404

Query: 181 LLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQ 240
           LLFSAT   +++K++ + L +P R+         E I        ++  K   LL+ L++
Sbjct: 405 LLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVE 464

Query: 241 SQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMV 300
                K  +IF  +K +   +  +L+ +GF+V  +HG+ DQ  R ++LS FK+    ++V
Sbjct: 465 FSSEGKV-LIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLV 523

Query: 301 ASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIK 355
           A+D+AARGLDIP +  V N+D     + + HRIGRTGRAG  G A+TLV ++D +
Sbjct: 524 ATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAE 578


>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 =  256 bits (656), Expect = 8e-69
 Identities = 132/361 (36%), Positives = 205/361 (56%), Gaps = 9/361 (2%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
           F D+ L   ++  +   G+ KP+ IQ + I   ++ HDV   AQ+GTGKTA+F++    I
Sbjct: 28  FDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLIS---I 84

Query: 63  LEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLER- 121
           L++    V+  + LIL PTRELA Q+       G + +++V   IGG     +++ L + 
Sbjct: 85  LQQIDMSVKETQALILAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKD 144

Query: 122 GADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTL 181
              +++ TPGR+ D  NRG L  + I++ V+DEAD ML  GF   I +I   +P   Q +
Sbjct: 145 KPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLSRGFKDQIYDIFQELPSDVQVV 204

Query: 182 LFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQS 241
           L SATM  ++ +V++ F++ P RI V     T E I+  ++       +K   L  L   
Sbjct: 205 LLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYI-----NVEKEEKLDTLCDL 259

Query: 242 QDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVA 301
              +   +IFCN ++ V NL   L   GF+V AIHG+++Q  R  ++  F+ G+ ++++ 
Sbjct: 260 YRRVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLIT 319

Query: 302 SDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIE 361
           +DL ARG+D+  V  V N+D+P R ENYIHRIGR GR GR G A   V +ED++ +  IE
Sbjct: 320 TDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLKDIE 379

Query: 362 K 362
           K
Sbjct: 380 K 380


>gnl|CDD|35563 KOG0342, KOG0342, KOG0342, ATP-dependent RNA helicase pitchoune
           [RNA processing and modification].
          Length = 543

 Score =  251 bits (643), Expect = 3e-67
 Identities = 139/389 (35%), Positives = 214/389 (55%), Gaps = 8/389 (2%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
           F +  LSP  + A+ + G+   TP+Q KTIP +L+  DV   A+TGTGKT +F+LP + +
Sbjct: 84  FEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIEL 143

Query: 63  LEKGRARVRMP-RTLILEPTRELAAQVADNFEKYGK-NYNLTVALLIGGIPFEAQNKKLE 120
           L K + + R     LI+ PTRELA Q+    ++  K + ++TV ++IGG  F  +  KL 
Sbjct: 144 LRKLKFKPRNGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLV 203

Query: 121 RGADVLICTPGRILDHF-NRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQ 179
           +G ++LI TPGR+LDH  N    L  N++ LV+DEADR+LD+GF   ++ I  ++P  RQ
Sbjct: 204 KGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRLLDIGFEEDVEQIIKILPKQRQ 263

Query: 180 TLLFSATMTDELQKVSENFL-QNPKRIEV--NTPSSTAETIEHCFVATYAQYSKKCALLQ 236
           TLLFSAT   +++ ++   L ++P  + V       T E +E  +V   A    + +LL 
Sbjct: 264 TLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVV--APSDSRFSLLY 321

Query: 237 QLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTI 296
             L+        I+F +   +V      L      V  IHG   Q  R      F +   
Sbjct: 322 TFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAES 381

Query: 297 QLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKH 356
            ++V +D+AARGLDIPDV  V  +D P+  E YIHR+GRT R G+ GKA  L+A  ++  
Sbjct: 382 GILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGF 441

Query: 357 IDAIEKLIEKKVDWLNGDLSSLNPPLEKI 385
           +  ++KL  ++ ++       +   LEK+
Sbjct: 442 LRYLKKLPLEEFEFPPLKPEDVQSQLEKL 470


>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 =  251 bits (643), Expect = 3e-67
 Identities = 100/204 (49%), Positives = 140/204 (68%), Gaps = 1/204 (0%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
           F +LGLSP+++  +   G+ KPTPIQ + IP +L   DV G AQTG+GKTA+F++P+L  
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 63  LEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERG 122
           L+    +   P+ LIL PTRELA Q+A+   K GK+ NL V ++ GG   + Q +KL+RG
Sbjct: 61  LDP-SPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRG 119

Query: 123 ADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLL 182
             +++ TPGR+LD   RGKL ++ ++ LV+DEADRMLDMGF   I+ I  L+P  RQTLL
Sbjct: 120 PHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLL 179

Query: 183 FSATMTDELQKVSENFLQNPKRIE 206
           FSATM  E++ ++  FL+NP RI 
Sbjct: 180 FSATMPKEVRDLARKFLRNPVRIL 203


>gnl|CDD|35555 KOG0334, KOG0334, KOG0334, RNA helicase [RNA processing and
           modification].
          Length = 997

 Score =  248 bits (635), Expect = 2e-66
 Identities = 146/463 (31%), Positives = 235/463 (50%), Gaps = 16/463 (3%)

Query: 4   ADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTIL 63
              GLS K++  +   GY KPTPIQ + IP ++   DV G+A+TG+GKT +F+LPM+  +
Sbjct: 368 TQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHI 427

Query: 64  EKGR--ARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLER 121
           +  R       P  LIL PTRELA Q+     K+ K   + V  + GG     Q  +L+R
Sbjct: 428 KDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKR 487

Query: 122 GADVLICTPGRILDHF--NRGKLL-MNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTR 178
           GA++++CTPGR++D    N G++  +  +  LV+DEADRM DMGF P I  I   +   R
Sbjct: 488 GAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMGFEPQITRILQNLRPDR 547

Query: 179 QTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQL 238
           QT+LFSAT    ++ ++   L+ P  I V   S   + +         +  K   LL+ L
Sbjct: 548 QTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLELL 607

Query: 239 LQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQL 298
            +  +  K  IIF ++++    L   L+K G++  ++HG +DQ  R   + +FK G + L
Sbjct: 608 GERYEDGKT-IIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNL 666

Query: 299 MVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHID 358
           +VA+ + ARGLD+ ++  V N+D PN  E+Y+HR+GRTGRAGR G A T +  + +K+  
Sbjct: 667 LVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAG 726

Query: 359 AIEKLIEKKVDWLNGDLSSLNPPLEKIDIAQH-NHARKNNPIPQKSTGFDRRKKNYSSQK 417
            + K +E              P L +    +     +          GF  +   +   +
Sbjct: 727 DLCKALELS--------KQPVPKLLQALSERFKAKQKAGGSQVHGGGGFGGKGLKFDEVE 778

Query: 418 SHIPLKESEKISKLQQDIQENDADSLGFRGNMPAFMLPKNRGK 460
             +  +E ++  +    ++E D +S     N      P+   +
Sbjct: 779 EEL-RQERKEAQRKDLGLKEGDNESDIEVDNSDKASQPRESIQ 820


>gnl|CDD|35562 KOG0341, KOG0341, KOG0341, DEAD-box protein abstrakt [RNA
           processing and modification].
          Length = 610

 Score =  247 bits (631), Expect = 6e-66
 Identities = 149/412 (36%), Positives = 223/412 (54%), Gaps = 30/412 (7%)

Query: 2   DFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLT 61
            F ++     ++  +   G V PTPIQ++ +P+VL   D+ GIA TG+GKT  FVLP++ 
Sbjct: 171 SFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIM 230

Query: 62  I-LEKGR----ARVRMPRTLILEPTRELAAQVADNFEKYGKNYN------LTVALLIGGI 110
             LE+      AR   P  LI+ P+RELA Q  D  E+Y           L   L IGG+
Sbjct: 231 FALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGV 290

Query: 111 PFEAQNKKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNI 170
           P   Q   + RG  +++ TPGR++D   +  + ++    L +DEADRM+DMGF   I+ I
Sbjct: 291 PVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDMGFEDDIRTI 350

Query: 171 TSLVPFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSK 230
            S     RQTLLFSATM  ++Q  +++ L  P  + VN   + A +++   V    +Y K
Sbjct: 351 FSFFKGQRQTLLFSATMPKKIQNFAKSALVKP--VTVNVGRAGAASLD---VIQEVEYVK 405

Query: 231 KCALLQQLLQS-QDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILS 289
           + A +  LL+  Q T    +IF  +K +V ++   L  +G    AIHG  DQ  R   + 
Sbjct: 406 QEAKIVYLLECLQKTSPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIE 465

Query: 290 NFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLV 349
            F+ G   ++VA+D+A++GLD PD+ HV N+D+P   ENY+HRIGRTGR+G+ G A T +
Sbjct: 466 AFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFI 525

Query: 350 AKE-------DIKHIDAIEKLIEKKVDWLNGDLSSLNPPLEKIDIAQHNHAR 394
            K        D+KH+     L E K + +   L+ L  P+E+  IA     +
Sbjct: 526 NKNQEESVLLDLKHL-----LQEAKQE-VPPVLAELAGPMEEETIADAGGEK 571


>gnl|CDD|35566 KOG0345, KOG0345, KOG0345, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 567

 Score =  245 bits (627), Expect = 2e-65
 Identities = 142/404 (35%), Positives = 216/404 (53%), Gaps = 34/404 (8%)

Query: 1   MDFADLG--LSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLP 58
             F+ L   LSP ++ A+ ++G+ K TP+Q  TIPL+L+  DV   A TG+GKT +F+LP
Sbjct: 4   KSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLP 63

Query: 59  MLTILEKGRARVRMPR--TLILEPTRELAAQ---VADNFEKYGKNYNLTVALLIGGIPFE 113
           ML I+ +  A+    +   LI+ PTRELA Q   VA  F ++  N  L   LL+GG   E
Sbjct: 64  MLEIIYRREAKTPPGQVGALIISPTRELARQIREVAQPFLEHLPN--LNCELLVGGRSVE 121

Query: 114 AQNKKLER-GADVLICTPGRILDHFNRG--KLLMNNIEILVIDEADRMLDMGFIPYIQNI 170
              K  +  G ++L+ TPGR+LD   R   KL   ++EILV+DEADR+LDMGF   +  I
Sbjct: 122 EDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDMGFEASVNTI 181

Query: 171 TSLVPFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSK 230
            S +P  R+T LFSAT T E++ ++   L+NP R+ V   S +A        ++ A    
Sbjct: 182 LSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATP------SSLALEYL 235

Query: 231 KCALLQQLLQ-----SQDTMKNGIIFCNQKKNVVNLCHSLEK--QGFSVCAIHGNIDQRS 283
            C   ++L Q     + +  K  I+F     +V        +  +   + +IHG + Q++
Sbjct: 236 VCEADEKLSQLVHLLNNNKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKA 295

Query: 284 RMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHG 343
           R K+L  F++ +  ++  +D+AARGLDIP +  V  FD P    +++HR GRT RAGR G
Sbjct: 296 RAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREG 355

Query: 344 KAFTLVAKE--------DIKHIDAIEKL-IEKKVDWLNGDLSSL 378
            A   +            IK    +E++  EK    +  D+ S+
Sbjct: 356 NAIVFLNPREEAYVEFLRIKGKVELERIDTEKASLSVYQDIRSI 399


>gnl|CDD|35558 KOG0337, KOG0337, KOG0337, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 529

 Score =  241 bits (616), Expect = 3e-64
 Identities = 132/354 (37%), Positives = 205/354 (57%), Gaps = 4/354 (1%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
           F  +GL  KV+ A+   G+  PTPIQ KTIPL+L+  DV G+A+TG+GKTA+F++PM+  
Sbjct: 23  FQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEK 82

Query: 63  LEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERG 122
           L K  ++  + R LIL PTRELA Q     +  G+   L  +LL+GG   E Q   L   
Sbjct: 83  L-KSHSQTGL-RALILSPTRELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNEN 140

Query: 123 ADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLL 182
            D++I TPGR+L       L ++++E +V DEADR+ +MGF   +  I S +P +RQTLL
Sbjct: 141 PDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMGFQEQLHEILSRLPESRQTLL 200

Query: 183 FSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQSQ 242
           FSAT+  +L   ++  L  P  + ++  +  +E ++  F     + ++K A L  +L  +
Sbjct: 201 FSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFF--RVRKAEKEAALLSILGGR 258

Query: 243 DTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVAS 302
              K  I+F   K +V  +   L   G     I+ ++DQ +R     +F+     ++V +
Sbjct: 259 IKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVT 318

Query: 303 DLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKH 356
           D+AARGLDIP + +V N+D P   + ++HR+GR  RAGR G+A++LVA  D  +
Sbjct: 319 DVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPY 372


>gnl|CDD|35564 KOG0343, KOG0343, KOG0343, RNA Helicase [RNA processing and
           modification].
          Length = 758

 Score =  241 bits (615), Expect = 4e-64
 Identities = 134/394 (34%), Positives = 215/394 (54%), Gaps = 13/394 (3%)

Query: 1   MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPML 60
             FADL LS K +  + +A +VK T IQ  TIP+ LQ HDV G A+TG+GKT +F++P+L
Sbjct: 69  KKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVL 128

Query: 61  TIL-EKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKL 119
             L     +       LI+ PTRELA Q  +   K GK+++ +  L+IGG   + + +++
Sbjct: 129 EALYRLKWSPTDGLGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERI 188

Query: 120 ERGADVLICTPGRILDHFNRGKLL-MNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTR 178
            +  ++L+CTPGR+L H +       +N+++LV+DEADRMLDMGF   +  I   +P  R
Sbjct: 189 SQ-MNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMGFKKTLNAIIENLPKKR 247

Query: 179 QTLLFSATMTDELQKVSENFLQNPKRIEV--NTPSSTAETIEHCFVATYAQYSKKCALLQ 236
           QTLLFSAT T  ++ ++   L++P  + V  N  ++T   ++  +V    +   K  +L 
Sbjct: 248 QTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLE--DKIDMLW 305

Query: 237 QLLQSQDTMKNGIIFCNQKKNVVNLCHSLEK--QGFSVCAIHGNIDQRSRMKILSNFKEG 294
             ++S    K  I+F +  K V  L  +  +   G  + A+HG + Q+ R+++   F   
Sbjct: 306 SFIKSHLKKK-SIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRK 364

Query: 295 TIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFT-LVAKED 353
              ++  +D+AARGLD P V  V   D P   + YIHR+GRT R    G++   L   E+
Sbjct: 365 RAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEE 424

Query: 354 IKHIDAIEK-LIE-KKVDWLNGDLSSLNPPLEKI 385
              +  ++K  I  K++      L+S+   LE +
Sbjct: 425 EAMLKKLQKKKIPIKEIKIDPEKLTSIRNKLEAL 458


>gnl|CDD|35547 KOG0326, KOG0326, KOG0326, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 459

 Score =  220 bits (562), Expect = 5e-58
 Identities = 116/367 (31%), Positives = 197/367 (53%), Gaps = 7/367 (1%)

Query: 2   DFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLT 61
           +F D  L  +++  + + G+ KP+PIQ ++IP+ L   D+   A+ GTGKTA++ +P+L 
Sbjct: 86  EFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLE 145

Query: 62  ILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLER 121
            ++  +  ++    +IL PTRELA Q +   ++  K+  + V +  GG        +L +
Sbjct: 146 KIDPKKNVIQ---AIILVPTRELALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQ 202

Query: 122 GADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTL 181
              +++ TPGRILD   +G   +++  ILV+DEAD++L + F P ++ + S +P  RQ L
Sbjct: 203 TVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVDFQPIVEKLISFLPKERQIL 262

Query: 182 LFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQS 241
           L+SAT    ++   +  L+ P  I +    +     ++     + +  +K   L  L  S
Sbjct: 263 LYSATFPLTVKGFMDRHLKKPYEINLMEELTLKGVTQY---YAFVEERQKVHCLNTLF-S 318

Query: 242 QDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVA 301
           +  +   IIFCN    V  L   + + G+S   IH  + Q  R ++  +F+ G  + +V 
Sbjct: 319 KLQINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVC 378

Query: 302 SDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIE 361
           +DL  RG+DI  V  V NFD P  AE Y+HRIGR+GR G  G A  L+  ED  ++  IE
Sbjct: 379 TDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFNLYRIE 438

Query: 362 KLIEKKV 368
           + +  ++
Sbjct: 439 QELGTEI 445


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

 Score =  216 bits (552), Expect = 9e-57
 Identities = 123/387 (31%), Positives = 201/387 (51%), Gaps = 27/387 (6%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQR--HDVCGIAQTGTGKTASFVLPML 60
           F +L L P+++  +    + KP+ IQ   +PL+L     ++   +Q+GTGKTA+FVL ML
Sbjct: 92  FEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTML 151

Query: 61  TILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLE 120
           + ++     V +P+ + L PTRELA Q  +  E+ GK   LT +  I G        K +
Sbjct: 152 SRVD---PDVVVPQCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRG-------SKAK 201

Query: 121 RGAD----VLICTPGRILDHFNRGKLL-MNNIEILVIDEADRMLDM-GFIPYIQNITSLV 174
           RG      ++I TPG +LD   + K + +  I++ V+DEAD M+D  GF      I   +
Sbjct: 202 RGNKLTEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSL 261

Query: 175 PFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCAL 234
           P  +Q LLFSAT  +++   +   + N   I +       + I+  +V    +  K  AL
Sbjct: 262 PRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACRDDKYQAL 321

Query: 235 LQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEG 294
           +   L    T+   IIFC+ K   + L   +  +G  V  +HG++    R  I+  F+EG
Sbjct: 322 VN--LYGLLTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREG 379

Query: 295 TIQLMVASDLAARGLDIPDVGHVFNFDVPNRA------ENYIHRIGRTGRAGRHGKAFTL 348
             ++++ +++ ARG+D+  V  V N+D+P +       E Y+HRIGRTGR G+ G A  L
Sbjct: 380 KEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINL 439

Query: 349 V-AKEDIKHIDAIEKLIEKKVDWLNGD 374
           V  K+ +  ++ I+K    K+  L+ D
Sbjct: 440 VDDKDSMNIMNKIQKHFNMKIKRLDPD 466


>gnl|CDD|35568 KOG0347, KOG0347, KOG0347, RNA helicase [RNA processing and
           modification].
          Length = 731

 Score =  209 bits (533), Expect = 1e-54
 Identities = 120/413 (29%), Positives = 203/413 (49%), Gaps = 54/413 (13%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQ-RHDVCGIAQTGTGKTASFVLPMLT 61
           + +L L  +++ A+ + G+ +PT IQ   +P  ++ + D+ G A+TG+GKT +F +P++ 
Sbjct: 183 WKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVE 242

Query: 62  ILEKGR----------ARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIP 111
            L +            A+   P  L++ PTRELA QV  + +   +   + VA + GG+ 
Sbjct: 243 RLLESSDDSQELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLA 302

Query: 112 FEAQNKKLERGADVLICTPGRILDHFNRGKLLMNNIE---ILVIDEADRMLDMGFIPYIQ 168
            + Q + L +  D+++ TPGR+ +        + N +    LV+DEADRM++ G    + 
Sbjct: 303 VQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNFKKVKCLVLDEADRMVEKGHFEELS 362

Query: 169 NITSLVPFT-----RQTLLFSATMT-----------------DELQKVSEN------FLQ 200
            +   +        RQTL+FSAT+T                 DEL    ++      F  
Sbjct: 363 KLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRG 422

Query: 201 NPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQ--LLQSQDTMKNG--IIFCNQKK 256
            PK I++   S+TA T+    +        +C  L++   L    T   G  ++FCN   
Sbjct: 423 KPKIIDLTPQSATASTLTESLI--------ECPPLEKDLYLYYFLTRYPGRTLVFCNSID 474

Query: 257 NVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGH 316
            V  L   L         +H ++ Q+ R+K L  FK+    +++A+D+AARGLDIP V H
Sbjct: 475 CVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQH 534

Query: 317 VFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEKLIEKKVD 369
           V ++ VP  +E Y+HR GRT RA   G +  L   +++  +  + K ++KK D
Sbjct: 535 VIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKKLCKTLKKKED 587


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

 Score =  204 bits (521), Expect = 3e-53
 Identities = 112/405 (27%), Positives = 191/405 (47%), Gaps = 44/405 (10%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
           F + GL  +++ A+   G+ KPT IQ   IPL L+  DV   A+TG+GKTA++++P+L  
Sbjct: 21  FEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQK 80

Query: 63  L---EKGRARVRMPRTLILEPTRELAAQVADNFEKYGK--NYNLTVALLIGGIPFEAQNK 117
           L   +K     + P  +IL PT+ELA QV    EK  +  + +L    L   +     + 
Sbjct: 81  LLAEKKTNDGEQGPSAVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSV 140

Query: 118 KLERGADVLICTPGRILDHFNRGKLL-MNNIEILVIDEADRMLDMGFIPYIQNITSLVPF 176
            L    D+++ TP ++L H   G L  ++++  LV+DEAD +L  G+   ++ + S +P 
Sbjct: 141 ALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDEADLLLSFGYEEDLKKLRSHLPR 200

Query: 177 TRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPS-STAETIEHCFVATYAQYSKKCALL 235
             Q  L SAT++D++Q + + FL NP  +++        + +    V    +   K  LL
Sbjct: 201 IYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEE--DKFLLL 258

Query: 236 QQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGT 295
             LL+ +      +IF N       L   LE+ G   C ++  +   SR  I+  F +G 
Sbjct: 259 YALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGL 318

Query: 296 IQLMVASDL-----------------------------------AARGLDIPDVGHVFNF 320
             +++A+D                                     +RG+D   V +V NF
Sbjct: 319 YDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNF 378

Query: 321 DVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEKLIE 365
           D P    +YIHR+GRT R    G A + V+ ++    +++E +++
Sbjct: 379 DFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKESLESILK 423


>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 =  202 bits (516), Expect = 2e-52
 Identities = 77/170 (45%), Positives = 108/170 (63%), Gaps = 3/170 (1%)

Query: 25  TPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTREL 84
           TPIQ + IP +L+  DV   A TG+GKT +F+LP L  L K       P+ L+L PTREL
Sbjct: 1   TPIQAEAIPAILEGKDVLVQAPTGSGKTLAFLLPALQALLKNPDG---PQALVLAPTREL 57

Query: 85  AAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICTPGRILDHFNRGKLLM 144
           A Q+ +  +K GK   L VALL GG   + Q +KL++G D+L+ TPGR+LD   RG LL+
Sbjct: 58  AEQIYEELKKLGKYLGLKVALLYGGDSPKEQLRKLKKGPDILVGTPGRLLDLLERGGLLL 117

Query: 145 NNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFSATMTDELQKV 194
            N+++LV+DEA R+LD GF   ++ I   +P  RQ LL SAT+   ++ +
Sbjct: 118 KNLKLLVLDEAHRLLDQGFGDDLEEILRRLPPKRQILLLSATLPRNVEDL 167


>gnl|CDD|35571 KOG0350, KOG0350, KOG0350, DEAD-box ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 620

 Score =  194 bits (495), Expect = 3e-50
 Identities = 118/403 (29%), Positives = 184/403 (45%), Gaps = 65/403 (16%)

Query: 26  PIQIKTIPLVLQRH---------DVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTL 76
           P+Q   +P +L+           D+C  A TG+GKT ++V+P++ +L      V+  R +
Sbjct: 162 PVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLL--SSRPVKRLRAV 219

Query: 77  ILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKL-----ERGADVLICTPG 131
           ++ PTRELA QV D F++      L V  L G    E + ++L     E   D+L+ TPG
Sbjct: 220 VIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPG 279

Query: 132 RILDHFNRGK-LLMNNIEILVIDEADRMLDMGF-----------------------IPYI 167
           R++DH N  K   + ++  LVIDEADR+LD  F                       I   
Sbjct: 280 RLVDHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQR 339

Query: 168 QNITSLV-----------PFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPS----S 212
           Q     V                 L+FSAT++ +  K+ +  L  P+   V+ P     S
Sbjct: 340 QAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYS 399

Query: 213 TAETIEHCFVATYAQYSKKCALLQQLLQSQDTMKNGIIFCNQKKNVVNLCH----SLEKQ 268
              ++ H  V T  ++  K   +  L+ S   +   + F N   +   L H         
Sbjct: 400 LPSSLSHRLVVTEPKF--KPLAVYALITSNK-LNRTLCFVNSVSSANRLAHVLKVEFCSD 456

Query: 269 GFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAEN 328
            F V    G ++ + R K+L  F +G I +++ SD  ARG+D+ DV +V N+D P   + 
Sbjct: 457 NFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKT 516

Query: 329 YIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEKLIEKKVDWL 371
           Y+HR GRT RAG+ G A TL+ K + +      KL++K   W 
Sbjct: 517 YVHRAGRTARAGQDGYAITLLDKHEKRL---FSKLLKKTNLWD 556


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

 Score =  193 bits (492), Expect = 8e-50
 Identities = 116/427 (27%), Positives = 198/427 (46%), Gaps = 67/427 (15%)

Query: 3   FADLGLSPKVVCAVLDA-GYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLT 61
           FA LGL P +V  +        PT +Q + IP++L+  D    AQTG+GKT +++LP++ 
Sbjct: 138 FASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQ 197

Query: 62  ILEKGRARVRM---PRTLILEPTRELAAQVADNFEKYGKNYNLTV-ALLIGGIPFEAQNK 117
            L+    +++    P  L++ PTRELA Q+ +  +K  K ++  V  +L+GG   +++  
Sbjct: 198 SLQAMEPKIQRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKA 257

Query: 118 KLERGADVLICTPGRILDHF-NRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLV-- 174
           +L +G ++LI TPGR++DH  N   +  + +  LV+DEADR+L++GF   I  I   V  
Sbjct: 258 RLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLLELGFEKDITQILKAVHS 317

Query: 175 -----------PFTRQTLLFSATMTDELQKVSENFLQNPKRIEV-NTPSSTAETIEHCFV 222
                      P   Q +L SAT+TD + ++++  L++P  I +  + S      +    
Sbjct: 318 IQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQE 377

Query: 223 ATYAQYSKKCALLQ---QLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQG----FSVC-- 273
                   K        QLLQ    +   +        ++N     EKQ     FS    
Sbjct: 378 VDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDS 437

Query: 274 --------------------------------------AIHGNIDQRSRMKILSNFKEGT 295
                                                  +HG+++Q  R  +   F    
Sbjct: 438 VEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSR 497

Query: 296 IQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIK 355
             +++ +D+AARGLD+P VG V  +D P    +Y+HR+GRT RAG  G+A   +   + +
Sbjct: 498 RAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPSEAE 557

Query: 356 HIDAIEK 362
           +++ ++K
Sbjct: 558 YVNYLKK 564


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

 Score =  189 bits (481), Expect = 1e-48
 Identities = 116/467 (24%), Positives = 195/467 (41%), Gaps = 37/467 (7%)

Query: 2   DFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLT 61
            F  L L  +V+  +    +  PT IQ   IP +  + D+   A++GTGKT  F +    
Sbjct: 26  GFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSV---L 82

Query: 62  ILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNY-NLTVALLIGGIPFEAQNKKLE 120
            +E   +R    + +I+ PTRE+A Q+ +   K   ++     ++ IGG      +    
Sbjct: 83  AVESLDSRSSHIQKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAH-KLDLIRL 141

Query: 121 RGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMG-FIPYIQNITSLVPFTRQ 179
           +   ++I TPGRI      G + M+++ + V+DEAD+++D   F   I  I + +P  RQ
Sbjct: 142 KQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTESFQDDINIIINSLPQIRQ 201

Query: 180 TLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVA------TYAQYSKKCA 233
              FSAT    L  +   F+++P  +  N        I+   VA      +  +   K  
Sbjct: 202 VAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQ 261

Query: 234 LLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKE 293
            L  +          ++FC+Q      +   L+  G  V  I G + Q+ R+  +   + 
Sbjct: 262 KLTHVF-KSIPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRA 320

Query: 294 GTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVA-KE 352
             ++++V++DL ARG+D  +V  V N D P   E Y HRIGR GR G HG A TL+  + 
Sbjct: 321 FRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDER 380

Query: 353 DIKHIDAIEKLIEKKVDWLNGDLSSLNPPLEKIDIAQHN--------HARKNNPIPQKST 404
           ++K   A+   I   V  +   +  L   L K      +             N + +   
Sbjct: 381 ELKGFTAMAYRIAVTVKRVVEPVHPLPGDLVKNQEFWKDLDYFIDFETPTGPNDLNKVP- 439

Query: 405 GFDRRKKNYSSQKSHIPLKESEKISKLQQDIQENDADSLGFRGNMPA 451
             +R+              ES K  +     Q+  +     R  M  
Sbjct: 440 --NRQSAV-----------ESLKSEREAS-GQKTSSSKKYTRDEMMV 472


>gnl|CDD|35565 KOG0344, KOG0344, KOG0344, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 593

 Score =  187 bits (475), Expect = 8e-48
 Identities = 127/375 (33%), Positives = 197/375 (52%), Gaps = 20/375 (5%)

Query: 5   DLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILE 64
           D  ++ +++  + + G+ +PTPIQ + IP+ L++ DV   A TG+GKT +F LP+L  L 
Sbjct: 140 DYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHL- 198

Query: 65  KGRARVRMP---RTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKK--- 118
           K  ++ +     R LIL PTRELAAQ+     KY  + +   +L        A   +   
Sbjct: 199 KDLSQEKHKVGLRALILSPTRELAAQIYREMRKY--SIDEGTSLRAAQFSKPAYPSQKPA 256

Query: 119 --LERGADVLICTPGRILDHFNRGKLLMN--NIEILVIDEADRMLD-MGFIPYIQNITSL 173
              +   D+LI TP RI+     GKL ++   +E LV+DEAD + +   F+  + +I S 
Sbjct: 257 FLSDEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSA 316

Query: 174 V--PFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKK 231
              P  R  L FSAT++  +++ +E    + KR+ V   +S  ET++   V   ++  K 
Sbjct: 317 CQSPDIRVAL-FSATISVYVEEWAELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKL 375

Query: 232 CALLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEK-QGFSVCAIHGNIDQRSRMKILSN 290
            AL Q  L +       +IF   K+    L   LE     +V  IHG   Q+ R + +  
Sbjct: 376 LALRQ--LVASGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMER 433

Query: 291 FKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVA 350
           F+ G I +++ +DL ARG+D   V  V N+D P    +YIHRIGRTGRAGR GKA T   
Sbjct: 434 FRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYT 493

Query: 351 KEDIKHIDAIEKLIE 365
            +D+  I +I +++E
Sbjct: 494 DQDMPRIRSIAEVME 508


>gnl|CDD|35550 KOG0329, KOG0329, KOG0329, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 387

 Score =  146 bits (370), Expect = 9e-36
 Identities = 109/373 (29%), Positives = 186/373 (49%), Gaps = 43/373 (11%)

Query: 3   FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
           F D  L P+++ A++D G+  P+ +Q + IP  +   DV   A++G GKTA FVL  L  
Sbjct: 44  FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 103

Query: 63  LEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNY-NLTVALLIGGIPFEAQNKKLER 121
           +E    +V +   L++  TRELA Q++  +E++ K   ++ V++  GG+  +   + L+ 
Sbjct: 104 IEPVDGQVSV---LVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKN 160

Query: 122 GADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRML-DMGFIPYIQNITSLVPFTRQT 180
              +++ TPGRIL       L + N++  V+DE D+ML  +     +Q I  + P  +Q 
Sbjct: 161 CPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQLDMRRDVQEIFRMTPHEKQV 220

Query: 181 LLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQ 240
           ++FSAT++ E++ V   F+Q+P  I V+     A+   H              L Q  ++
Sbjct: 221 MMFSATLSKEIRPVCHKFMQDPMEIFVD---DEAKLTLH-------------GLQQYYVK 264

Query: 241 SQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMV 300
            ++  KN  +         +L   LE   F+   I     QR   +          + +V
Sbjct: 265 LKENEKNRKLN--------DLLDVLE---FNQVVIFVKSVQRLSFQ----------KRLV 303

Query: 301 ASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVA-KEDIKHIDA 359
           A+DL  RG+DI  V  VFN+D+P  ++ Y+HR+ R GR G  G A T V+ + D K ++ 
Sbjct: 304 ATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNP 363

Query: 360 IEKLIEKKVDWLN 372
           ++   E  +  L 
Sbjct: 364 VQDRFEVNIKELP 376


>gnl|CDD|35570 KOG0349, KOG0349, KOG0349, Putative DEAD-box RNA helicase DDX1 [RNA
           processing and modification].
          Length = 725

 Score =  146 bits (369), Expect = 1e-35
 Identities = 93/332 (28%), Positives = 153/332 (46%), Gaps = 49/332 (14%)

Query: 73  PRTLILEPTRELAAQVADN---FEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICT 129
           P  +I+EP+RELA Q  +    F+ +  N  +   L+IGG+    Q K+L+ G  +++ T
Sbjct: 287 PEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGT 346

Query: 130 PGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVP------FTRQTLLF 183
           PGR+L   ++G + + +   LV+DEAD +L  G+   I      +P      F  Q+ + 
Sbjct: 347 PGRLLQPISKGLVTLTHCRFLVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVC 406

Query: 184 SATMTD-ELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQSQ 242
           SAT+   E++KV E  +  P  +++       ET+ H               L+Q +++ 
Sbjct: 407 SATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHHVVKLVCPSVDGSWCDLRQFIETD 466

Query: 243 DT------------------------------------MKNGIIFCNQKKNVVNLCHSLE 266
                                                 M   IIFC  K++  NL   + 
Sbjct: 467 KVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLERMMN 526

Query: 267 KQG---FSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVP 323
           ++G   +S   +HG+     R   L +FK+  ++ ++ +D+AARGLDI  +  + N  +P
Sbjct: 527 QKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLP 586

Query: 324 NRAENYIHRIGRTGRAGRHGKAFTLVAKEDIK 355
           +   NY+HRIGR GRA R G A +LVA    K
Sbjct: 587 DDKTNYVHRIGRVGRAERMGLAISLVATVPEK 618



 Score = 53.5 bits (128), Expect = 1e-07
 Identities = 24/61 (39%), Positives = 38/61 (62%)

Query: 3  FADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTI 62
          F + G+ P++  A  +  +  PT +Q + IPL+L   DV   A+TG+GKT +F LP+L I
Sbjct: 4  FEEFGVLPELGMATDELDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQI 63

Query: 63 L 63
          +
Sbjct: 64 V 64


>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 =  129 bits (326), Expect = 1e-30
 Identities = 58/149 (38%), Positives = 85/149 (57%), Gaps = 5/149 (3%)

Query: 39  HDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKN 98
            DV   A TG+GKT + +LP+L +L+  +      + L+L PTRELA QVA+  ++    
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKG----GQVLVLAPTRELANQVAERLKELFG- 55

Query: 99  YNLTVALLIGGIPFEAQNKKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRM 158
             + V  LIGG   + Q K L    D+++ TPGR+LD   R KL +  +++L++DEA R+
Sbjct: 56  EGIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRL 115

Query: 159 LDMGFIPYIQNITSLVPFTRQTLLFSATM 187
           L+ GF      I   +P  RQ LL SAT 
Sbjct: 116 LNQGFGLLGLKILLKLPKDRQVLLLSATP 144


>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 =  118 bits (296), Expect = 5e-27
 Identities = 50/119 (42%), Positives = 72/119 (60%)

Query: 230 KKCALLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILS 289
           K  ALL+ L +        +IFC  KK +  L   L K G  V A+HG+  Q  R ++L 
Sbjct: 13  KLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLK 72

Query: 290 NFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTL 348
           +F+EG I ++VA+D+ ARG+D+P+V  V N+D+P    +Y+ RIGR GRAG+ G A  L
Sbjct: 73  DFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131


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

 Score =  110 bits (275), Expect = 1e-24
 Identities = 88/354 (24%), Positives = 140/354 (39%), Gaps = 31/354 (8%)

Query: 20  GYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILE 79
           GY    P Q + I  +L   D   +  TG GK+  + +P         A +    TL++ 
Sbjct: 14  GYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIP---------ALLLEGLTLVVS 64

Query: 80  PTRELAA-QVADNFEKYGKNYNLTVALLIGGIPFEAQN---KKLERGA-DVLICTPGRIL 134
           P   L   QV        +   +  A L   +  E +     +L+ G   +L  +P R++
Sbjct: 65  PLISLMKDQVDQL-----EAAGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLM 119

Query: 135 DHFNRGKLLMNNIEILVIDEADRMLDMG--FIPYIQNITSLVP-FTRQTLL-FSATMTDE 190
                  L    I ++ IDEA  +   G  F P  + +  L        +L  +AT T  
Sbjct: 120 SPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTATATPR 179

Query: 191 LQK--VSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQSQDTMKNG 248
           ++     +  LQ+         S     +    V       +   L   L Q     K+G
Sbjct: 180 VRDDIREQLGLQDANIFRG---SFDRPNLALKVVEKGEPSDQLAFLATVLPQLS---KSG 233

Query: 249 IIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARG 308
           II+C  +K V  L   L K G S  A H  +    R ++   F    I++MVA++    G
Sbjct: 234 IIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMG 293

Query: 309 LDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEK 362
           +D PDV  V ++D+P   E+Y    GR GR G   +A  L + EDI+    + +
Sbjct: 294 IDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIE 347


>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 =  104 bits (263), Expect = 4e-23
 Identities = 36/76 (47%), Positives = 51/76 (67%)

Query: 265 LEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPN 324
           L K G  V  +HG + Q  R +IL +F+ G  +++VA+D+A RG+D+PDV  V N+D+P 
Sbjct: 3   LRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNVVINYDLPW 62

Query: 325 RAENYIHRIGRTGRAG 340
              +YI RIGR GRAG
Sbjct: 63  NPASYIQRIGRAGRAG 78


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

 Score = 93.4 bits (232), Expect = 1e-19
 Identities = 92/407 (22%), Positives = 166/407 (40%), Gaps = 45/407 (11%)

Query: 10  PKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLT-ILEKGRA 68
              V       +   TP Q   IP +    +V  IA TG+GKT +  LP++  +L  G+ 
Sbjct: 9   DPRVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKG 68

Query: 69  RVRMP-RTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLI 127
           ++      L + P + L   +    E+  +   + VA+  G  P   + K L+    +LI
Sbjct: 69  KLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILI 128

Query: 128 CTPGRILDHFNRGKL--LMNNIEILVIDEADRMLD----MGFIPYIQNITSLVP-FTRQT 180
            TP  +    N  K   L+ ++  +++DE   + +    +     ++ +  L   F R  
Sbjct: 129 TTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESKRGVQLALSLERLRELAGDFQRIG 188

Query: 181 LLFSATMTD--ELQK-----------VSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQ 227
           L  SAT+    E+ K           V  +  +  + I+V +P       E  + A Y +
Sbjct: 189 L--SATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLE-IKVISPVEDLIYDEELWAALYER 245

Query: 228 YSKKCALLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIH-GNIDQRSRMK 286
                 + + + + + T    +IF N +     L   L+K G  +  +H G++ +  R++
Sbjct: 246 ------IAELVKKHRTT----LIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLE 295

Query: 287 ILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTG-RAGRHGKA 345
           +    KEG ++ +VA+     G+DI D+  V     P     ++ RIGR G R G   K 
Sbjct: 296 VEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKG 355

Query: 346 FTLVAK-EDIKHIDAIEKLIEKKVDWLNGDLSSLNPPLEKIDI-AQH 390
             +    +D+     +  L       L G L  +  P   +D+ AQ 
Sbjct: 356 IIIAEDRDDLLECLVLADLA------LEGKLERIKIPKNPLDVLAQQ 396


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

 Score = 80.5 bits (198), Expect = 1e-15
 Identities = 74/415 (17%), Positives = 137/415 (33%), Gaps = 69/415 (16%)

Query: 1   MDFADLGLSPKVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCG----IAQTGTGKTASFV 56
            + AD  L   +   ++ A   +  P Q + +  +++          +  TG GKT    
Sbjct: 14  EELADYVLDEGLPLKLIVAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKT---- 69

Query: 57  LPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQN 116
                ++           TL+L PT+EL  Q A+  +K+         LL   I      
Sbjct: 70  -----VVAAEAIAELKRSTLVLVPTKELLDQWAEALKKFL--------LLNDEIGIYGGG 116

Query: 117 KKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPF 176
           +K    A V + T   +       + L N   +++ DE   +    +   ++ +++  P 
Sbjct: 117 EKELEPAKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILELLSAAYP- 175

Query: 177 TRQTLLFSATMTDELQK---------------------VSENFLQNPKRIEVNTPSSTAE 215
               L  +AT   E                        + E +L   K +E+    +  E
Sbjct: 176 ---RLGLTATPEREDGGRIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDE 232

Query: 216 ---------------------TIEHCFVATYAQYSKKCALLQQLLQSQDTMKNGIIFCNQ 254
                                  E+          +K A ++ LL         +IF + 
Sbjct: 233 EREYAKESARFRELLRARGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASD 292

Query: 255 KKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDV 314
            ++   +       G  V AI G   +  R  IL  F+ G I+++V   +   G+DIPD 
Sbjct: 293 VEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDA 351

Query: 315 GHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEKLIEKKVD 369
             +           +I R+GR  R     +    +    +   D  E+ I ++  
Sbjct: 352 DVLIILRPTGSRRLFIQRLGRGLRPAEGKEDTLALDYSLV-PDDLGEEDIARRRR 405


>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 = 65.8 bits (160), Expect = 2e-11
 Identities = 85/421 (20%), Positives = 159/421 (37%), Gaps = 62/421 (14%)

Query: 11  KVVCAVLDAGYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARV 70
            +  A++ AG  +    Q+  + L+ +  +V     TG+GKT SF+LP+L  L +  +  
Sbjct: 58  SLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA- 116

Query: 71  RMPRTLILEPTRELAAQVADNFEKYGKN--YNLTVALLIGGIPFEAQNKKLERGADVLIC 128
              R L+L PT  LA   A+   +   +    +T     G  P E +   +    D+L+ 
Sbjct: 117 ---RALLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLT 173

Query: 129 TPG----RILDHFNRGKLLMNNIEILVIDEA---------------DRMLDMGFIPYIQN 169
            P      +L + +    L+ N++ LV+DE                 R+L          
Sbjct: 174 NPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRR-------- 225

Query: 170 ITSLVPFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQ-Y 228
                    Q +  SAT+ +  +   E F ++    EV      +      FV       
Sbjct: 226 -LRRYGSPLQIICTSATLANPGEFAEELFGRD---FEVPVDEDGSPRGLRYFVRREPPIR 281

Query: 229 SKKCALLQQLLQSQDTMK-----NGII---FCNQKKNVVNLCHSLEKQ--------GFSV 272
               ++ +  L    T+      NGI    F   +K V  L  S  ++          +V
Sbjct: 282 ELAESIRRSALAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAV 341

Query: 273 CAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAE-NYIH 331
                 + +  R +I + FKEG +  ++A++    G+DI  +  V  +  P  +  ++  
Sbjct: 342 STYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQ 401

Query: 332 RIGRTGRAGRHGKAFTLVAKEDI-----KHIDAIEKLIEKKVDWLNGDLSSLNPPLEKID 386
           R GR GR G+      ++  + +     +H + + +     V+ +  D +  N  L    
Sbjct: 402 RAGRAGRRGQESLVLVVLRSDPLDSYYLRHPEELLETGFGPVESVRVDDN--NEYLLDGH 459

Query: 387 I 387
           +
Sbjct: 460 L 460


>gnl|CDD|35573 KOG0352, KOG0352, KOG0352, ATP-dependent DNA helicase [Replication,
           recombination and repair].
          Length = 641

 Score = 61.7 bits (149), Expect = 4e-10
 Identities = 84/391 (21%), Positives = 146/391 (37%), Gaps = 74/391 (18%)

Query: 25  TPIQIKTIPLVLQRH-DVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRE 83
           + +Q + I  +++R  DV     TG GK+  + LP L  +  G        T+++ P   
Sbjct: 22  SRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPAL--VHGGI-------TIVISP--- 69

Query: 84  LAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKL---ERG------------ADVLIC 128
           L A + D  +           L    +P E+ N KL   ER               +L  
Sbjct: 70  LIALIKDQID----------HLKRLKVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYI 119

Query: 129 TPGRILDHFNRGKLL-----MNNIEILVIDEADRMLDMG--FIPYIQNITSL------VP 175
           TP        + KLL      + +  +V+DEA  +   G  F P    + SL      VP
Sbjct: 120 TPEGAATDGFQ-KLLNGLANRDVLRYIVVDEAHCVSQWGHDFRPDYLTLGSLRSVCPGVP 178

Query: 176 FTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPS---------STAETIEHCFVATYA 226
           +   T   +A + +++    +  L+NP  I   TP+              I  C     A
Sbjct: 179 WVALTATANAKVQEDIAFQLK--LRNPVAI-FKTPTFRDNLFYDNHMKSFITDCL-TVLA 234

Query: 227 QYSKKCALLQQLLQSQDTMKN----GIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQR 282
            +S     L +  ++    K     GI++C  +     +   LE  G    A H  + ++
Sbjct: 235 DFSSSN--LGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKK 292

Query: 283 SRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRH 342
            R ++   +    I ++ A+     G+D PDV  V ++        Y    GR GR G+ 
Sbjct: 293 ERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRDGKR 352

Query: 343 GKAFTLVAKEDIKHIDAIEKLIEKKVDWLNG 373
                  +++D    +A+  L+  ++  L  
Sbjct: 353 SYCRLYYSRQD---KNALNFLVSGELAKLRE 380


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

 Score = 61.4 bits (149), Expect = 5e-10
 Identities = 76/336 (22%), Positives = 137/336 (40%), Gaps = 69/336 (20%)

Query: 48  GTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALLI 107
           G+GKT   +L ML  +E G       +  ++ PT  LA Q  ++  K+ +   + VALL 
Sbjct: 293 GSGKTVVALLAMLAAIEAGY------QAALMAPTEILAEQHYESLRKWLEPLGIRVALLT 346

Query: 108 GGIPFEAQNKKLER----GADVLICTPGRILDHFNRGKLLMNNIEILVIDEADR------ 157
           G +  +A+ + LE+      D+++ T   I D     K+  +N+ +++IDE  R      
Sbjct: 347 GSLKGKARKEILEQLASGEIDIVVGTHALIQD-----KVEFHNLGLVIIDEQHRFGVHQR 401

Query: 158 --MLDMGFIPYIQNITSLVPFTRQTLLFSA------TMTDELQKVSENFLQNPKRIEVNT 209
             + + G       + +  P  R TL  +A      ++ DEL          P R  + T
Sbjct: 402 LALREKGEQNPHVLVMTATPIPR-TLALTAFGDLDVSIIDELP---------PGRKPITT 451

Query: 210 PSSTAETIEHCFVATYAQYSKKCALLQQ------LLQSQDTMKNGIIFCNQKKNVVNLCH 263
                E         Y +  ++ A  +Q      L++  + +        + +    L  
Sbjct: 452 VVIPHERRPE----VYERIREEIAKGRQAYVVCPLIEESEKL--------ELQAAEELYE 499

Query: 264 SLEK--QGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFD 321
            L+       V  +HG +    +  ++  FKEG I ++VA+ +   G+D+P+        
Sbjct: 500 ELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNA----TVM 555

Query: 322 VPNRAENY----IHRI-GRTGRAGRHGKAFTLVAKE 352
           V   AE +    +H++ GR GR G       L+ K 
Sbjct: 556 VIENAERFGLAQLHQLRGRVGR-GDLQSYCVLLYKP 590


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

 Score = 56.1 bits (135), Expect = 2e-08
 Identities = 68/321 (21%), Positives = 120/321 (37%), Gaps = 67/321 (20%)

Query: 44  IAQTGTGKTASFVLPM-LTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLT 102
           IA TG GKT +F L M L + +KG+      R  I+ PT  L  QV +  +K+ ++    
Sbjct: 103 IAPTGVGKT-TFGLLMSLYLAKKGK------RVYIIVPTTTLVRQVYERLKKFAEDAGSL 155

Query: 103 VALLI--GGIPFEAQNKKLER----GADVLICTPGRILDHFNRGKLLMNNIEILVIDEAD 156
             L++    +P + + + LER      D+LI T   +   F   +L     + + +D+ D
Sbjct: 156 DVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFE--ELSKLKFDFIFVDDVD 213

Query: 157 RMLDMGFIPYIQNITSLVPFTRQTLLFSATMTDELQKV--SENFLQNPKRI--EVNTPSS 212
            +L       +  +  L+ F+ + +  SA    +L++    E   +  +    EV     
Sbjct: 214 AILKAS--KNVDRLLRLLGFSEEVIE-SAYELIKLRRKLYGEKRAERVREELREVERERE 270

Query: 213 TAETIEHCFV---ATYAQYSKKCALLQQLL-----QSQDTMKN----------------- 247
                    V   AT      +  L ++LL        + ++N                 
Sbjct: 271 KKRRKLGILVVSSATGKPRGSRLKLFRELLGFEVGSGGEGLRNIVDIYVESESLEKVVEL 330

Query: 248 -------GIIFCNQKKN---VVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQ 297
                  G+IF            L   L   G +   IH       + + L +F+EG + 
Sbjct: 331 VKKLGDGGLIFVPIDYGREKAEELAEYLRSHGINAELIH-----AEKEEALEDFEEGEVD 385

Query: 298 LMVAS----DLAARGLDIPDV 314
           ++V       +  RGLD+P  
Sbjct: 386 VLVGVASYYGVLVRGLDLPHR 406


>gnl|CDD|31308 COG1111, MPH1, ERCC4-like helicases [DNA replication,
           recombination, and repair].
          Length = 542

 Score = 55.7 bits (134), Expect = 3e-08
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 281 QRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAG 340
           Q+ + +I+  F++G   ++VA+ +   GLDIP+V  V  ++        I R GRTGR  
Sbjct: 411 QKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR-K 469

Query: 341 RHGKAFTLVAK 351
           R G+   LV +
Sbjct: 470 RKGRVVVLVTE 480



 Score = 51.0 bits (122), Expect = 7e-07
 Identities = 44/199 (22%), Positives = 85/199 (42%), Gaps = 21/199 (10%)

Query: 21  YVKPTPIQIKTIPL-----VLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRT 75
            +KP  I+ +   L      L ++ +  +  TG GKT    + +   L     +V     
Sbjct: 8   LIKPNTIEPRLYQLNIAAKALFKNTLVVLP-TGLGKTFIAAMVIANRLRWFGGKV----- 61

Query: 76  LILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICTPGRILD 135
           L L PT+ L  Q A+   K        +A L G +  E + +   +   V + TP  + +
Sbjct: 62  LFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVRPEEREELWAKK-KVFVATPQVVEN 120

Query: 136 HFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFSATMT-----DE 190
               G++ ++++ +L+ DEA R   +G   Y+      +   +  L+   T +     ++
Sbjct: 121 DLKAGRIDLDDVSLLIFDEAHRA--VGNYAYVFVAKEYLRSAKNPLILGLTASPGSDLEK 178

Query: 191 LQKVSENFLQNPKRIEVNT 209
           +Q+V EN     +++EV T
Sbjct: 179 IQEVVENL--GIEKVEVRT 195


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

 Score = 55.5 bits (133), Expect = 3e-08
 Identities = 62/361 (17%), Positives = 125/361 (34%), Gaps = 51/361 (14%)

Query: 44  IAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTV 103
            A TG GKT + ++  L +L++        R + + P R +   +    ++    +++  
Sbjct: 220 EAPTGYGKTEASLILALALLDEKIKLK--SRVIYVLPFRTIIEDMYRRAKEIFGLFSVIG 277

Query: 104 ALLIGGIPFEAQNKKLERGAD--------------VLICTPGRIL------DHFNRGKLL 143
             L          +  +                  +++ TP +IL        F    LL
Sbjct: 278 KSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALL 337

Query: 144 MNNIEILVIDEADRMLD---MGFIPYIQNITSLVPFTRQTLLFSATMTDELQKVSENFLQ 200
           + ++  +++DE     D   +  +  +  + +L       LL SAT+   L++  +  L 
Sbjct: 338 LTSL--VILDEVHLYADETMLAAL--LALLEALAEAGVPVLLMSATLPPFLKEKLKKALG 393

Query: 201 NPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQSQDTMKNG--IIFCNQKKNV 258
             + +  N      E                       L S++  +    ++  N     
Sbjct: 394 KGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIELISEEVKEGKKVLVIVNTVDRA 453

Query: 259 VNLCHSLEKQGFSVCAIHGNIDQRSR----MKILSNFKEGTIQLMVASDLAARGLDIPDV 314
           + L   L+++G  V  +H     + R     ++   FK+    ++VA+ +   G+DI   
Sbjct: 454 IELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI--- 510

Query: 315 GHVFNFDV----PNRAENYIHRIGRTGRAGRHGKAFTLVAK--EDIKHIDAIEKLIEKKV 368
               +FDV        ++ I R GR     RHGK          D +    ++   EK  
Sbjct: 511 ----DFDVLITELAPIDSLIQRAGR---VNRHGKKENGKIYVYNDEERGPYLKYSYEKLE 563

Query: 369 D 369
            
Sbjct: 564 K 564


>gnl|CDD|35574 KOG0353, KOG0353, KOG0353, ATP-dependent DNA helicase [General
           function prediction only].
          Length = 695

 Score = 53.7 bits (128), Expect = 1e-07
 Identities = 71/337 (21%), Positives = 123/337 (36%), Gaps = 53/337 (15%)

Query: 26  PIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELA 85
           P+Q+  I   +   D   I  TG GK+  + LP L     G A V  P   ++E      
Sbjct: 97  PLQLAAINATMAGEDAFLILPTGGGKSLCYQLPAL--CADGFALVICPLISLMEDQILQL 154

Query: 86  AQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICTPGRILDHFNRGKLLMN 145
            Q+  +      N +   A  +        NK  E    ++  TP +I     + K  MN
Sbjct: 155 KQLGIDASMLNANSSKEEAKRVEA---AITNKDSE--FKLIYVTPEKIA----KSKKFMN 205

Query: 146 NIE---------ILVIDEA--------DRMLDMGFIPYIQNITSLVPFTRQTLLFSATMT 188
            +E         ++ IDE         D   D   +  ++      P    T   +  + 
Sbjct: 206 KLEKALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVL 265

Query: 189 DELQKV---------SENFLQNPKRIEV-NTPSSTAETIEHCFVATYAQYSKKCALLQQL 238
           D+ + +            F +   + EV   P +  + IE                + +L
Sbjct: 266 DDAKDILCIEAAFTFRAGFNRPNLKYEVRQKPGNEDDCIED---------------IAKL 310

Query: 239 LQSQDTMKNGIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQL 298
           ++     ++GII+C  +K+   +  +L+  G    A H N++   +      +  G IQ+
Sbjct: 311 IKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQV 370

Query: 299 MVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGR 335
           +VA+     G+D PDV  V +  +P   ENY     R
Sbjct: 371 IVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQASAR 407


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

 Score = 51.9 bits (124), Expect = 3e-07
 Identities = 29/130 (22%), Positives = 58/130 (44%), Gaps = 9/130 (6%)

Query: 26  PIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELA 85
           P Q      +L   +V   A TG+GKT   +L +L+ L +G  +V     + + P + LA
Sbjct: 35  PQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKV-----VYIVPLKALA 89

Query: 86  AQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICTPGRILDHFNRGKLLMN 145
            +  + F +  +   + V +  G       + +     DV++ TP ++     +    + 
Sbjct: 90  EEKYEEFSRL-EELGIRVGISTGDYDL---DDERLARYDVIVTTPEKLDSLTRKRPSWIE 145

Query: 146 NIEILVIDEA 155
            ++++VIDE 
Sbjct: 146 EVDLVVIDEI 155


>gnl|CDD|35575 KOG0354, KOG0354, KOG0354, DEAD-box like helicase [General function
           prediction only].
          Length = 746

 Score = 51.9 bits (124), Expect = 4e-07
 Identities = 48/232 (20%), Positives = 86/232 (37%), Gaps = 44/232 (18%)

Query: 143 LMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFS----ATMTDELQKVSENF 198
           L      L+I +  R +D   + Y+++    V   +   L           E     E+ 
Sbjct: 329 LRKYNLALLISDGIRFVD--ALDYLEDFYEEVALKKYLKLELEARLIRNFTENMNELEHL 386

Query: 199 LQNPKRIEVNTPSSTAETIEHCFVATYAQYSKKCALLQQLLQSQDTMKNGIIFCNQKKNV 258
             +P               E+       +  K   +L +  + Q+     IIF   +++ 
Sbjct: 387 SLDPP-------------KEN------PKLEKLVEILVEQFE-QNPDSRTIIFVETRESA 426

Query: 259 VNLCHSLEK-------------QGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLA 305
           + L   L +             QG S  +      Q+ + ++L  F++G I ++VA+ +A
Sbjct: 427 LALKKWLLQLHELGIKAEIFIGQGKSTQSTGMT--QKEQKEVLDKFRDGEINVLVATSVA 484

Query: 306 ARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAK-EDIKH 356
             GLDI +   V  +D  +     + R GR GRA R+ K   L    E I+ 
Sbjct: 485 EEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRA-RNSKCVLLTTGSEVIEF 534


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

 Score = 49.6 bits (118), Expect = 2e-06
 Identities = 82/383 (21%), Positives = 154/383 (40%), Gaps = 52/383 (13%)

Query: 35  VLQRHDVCGI-AQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNF- 92
            ++++ V  I  +TG+GKT    LP   +LE+G            +P R LAA+      
Sbjct: 61  AIEQNQVVIIVGETGSGKTTQ--LP-QFLLEEGLGIAGK--IGCTQP-RRLAARSVAERV 114

Query: 93  -EKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICTPGRILDHFNRGKLLMNNIEILV 151
            E+ G+    TV   I    FE++     R   + + T G +L       LL +   +++
Sbjct: 115 AEELGEKLGETVGYSI---RFESKVSPRTR---IKVMTDGILLREIQNDPLL-SGYSVVI 167

Query: 152 IDEA-DRMLDMGFI-PYIQNITSLVPFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNT 209
           IDEA +R L+   +   ++++ +      + ++ SAT+    ++ S  F   P  IE+  
Sbjct: 168 IDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLDA--ERFSAYFGNAP-VIEIEG 224

Query: 210 PSSTAETI-EHCFVATYAQYSKKCALLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQ 268
            +   E        A Y       A +   L+      + ++F   ++ +      LEK 
Sbjct: 225 RTYPVEIRYLPEAEADYILLDAIVAAVDIHLREGS--GSILVFLPGQREIERTAEWLEKA 282

Query: 269 ----GFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPN 324
                  +  ++G +    ++++      G  ++++A+++A   L IP + +V +  +  
Sbjct: 283 ELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGL-A 341

Query: 325 RAENYIHRIG----------------RTGRAGR--HGKAFTLVAKEDIKHIDAIEKLIEK 366
           + + Y  R G                R GRAGR   G  + L ++ED             
Sbjct: 342 KEKRYDPRTGLTRLETEPISKASADQRAGRAGRTGPGICYRLYSEEDFLAFPE-----FT 396

Query: 367 KVDWLNGDLSSLNPPLEKIDIAQ 389
             + L  DLS L   L+ + I Q
Sbjct: 397 LPEILRTDLSGLVLQLKSLGIGQ 419


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

 Score = 49.0 bits (117), Expect = 3e-06
 Identities = 50/200 (25%), Positives = 84/200 (42%), Gaps = 37/200 (18%)

Query: 255 KKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDV 314
           KK   +L   L++ G  V  +H +ID   R++I+ + + G   ++V  +L   GLD+P+V
Sbjct: 456 KKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEV 515

Query: 315 GHVFNFDVPN----RAE-NYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEKLIEKKVD 369
             V   D       R+E + I  IGR  R   +GK         I + D I   ++K +D
Sbjct: 516 SLVAILDADKEGFLRSERSLIQTIGRAAR-NVNGKV--------ILYADKITDSMQKAID 566

Query: 370 WLNGDLSSLNPPLEKIDIAQHNHARKNNPIPQ-----------KSTGFDRRKKNYSSQKS 418
                         + +I Q  +  ++   PQ                D  K     + S
Sbjct: 567 ETE----------RRREI-QMAYNEEHGITPQTIKKKIRDILDGEYEEDEYKAKIEKKAS 615

Query: 419 HIPLKESEK-ISKLQQDIQE 437
            +  KE EK I KL+++++E
Sbjct: 616 KMSKKELEKLIKKLEKEMKE 635



 Score = 28.6 bits (64), Expect = 4.2
 Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 9/49 (18%)

Query: 47 TGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKY 95
          TG+GKT +    M  ++    A+V+ P TL+L   + LAAQ+   F+++
Sbjct: 41 TGSGKTFT----MANVI----AKVQRP-TLVLAHNKTLAAQLYSEFKEF 80


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

 Score = 48.5 bits (115), Expect = 4e-06
 Identities = 30/108 (27%), Positives = 45/108 (41%)

Query: 248 GIIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAAR 307
           GII+C  +K    +   L   G S    H  +  + R  +   +    I+++VA+     
Sbjct: 488 GIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGM 547

Query: 308 GLDIPDVGHVFNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIK 355
           G+D PDV  V ++ +P   E Y    GR GR G       L    DI 
Sbjct: 548 GIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYADIS 595


>gnl|CDD|36138 KOG0920, KOG0920, KOG0920, ATP-dependent RNA helicase A [RNA
           processing and modification].
          Length = 924

 Score = 44.5 bits (105), Expect = 7e-05
 Identities = 73/386 (18%), Positives = 141/386 (36%), Gaps = 69/386 (17%)

Query: 24  PTPIQIKTIPLVLQRHDVCGIA-QTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTR 82
           P      TI   ++ + V  I+ +TG GKT    +P   IL++          +  +P R
Sbjct: 173 PAYKMRDTILDAIEENQVVVISGETGCGKTTQ--VPQF-ILDEAIESGAACNIICTQPRR 229

Query: 83  ELAAQVADNFEK-YGKNYNLTVALLIGGIPFEAQNKKLERGADVLICTPGRILDHFNRGK 141
             A  VA+   K  G++    V   +          K  R   +L CT G +L    +  
Sbjct: 230 ISAISVAERVAKERGESLGEEVGYQVRL------ESKRSRETRLLFCTTGVLLRRL-QSD 282

Query: 142 LLMNNIEILVIDEA-DRMLDMGFIPYIQNITSLVPFTR--QTLLFSATMTDELQK----- 193
             ++ +  +++DE  +R ++  F+  +  +  L+P     + +L SAT+  EL       
Sbjct: 283 PTLSGVTHIIVDEVHERSINTDFLLIL--LKDLLPRNPDLKVILMSATLDAELFSDYFGG 340

Query: 194 ------------VSENFLQN-----PKRIEVNTPSSTAETIEHCFVATYAQYSK-KCALL 235
                       V E FL++         E ++  S  E  +           +    L+
Sbjct: 341 CPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDLI 400

Query: 236 QQLLQS-QDTMKNGIIFC---------NQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRM 285
           + L++   +    G I             K+ +       +   F++  +H +I    + 
Sbjct: 401 EDLIEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQ 460

Query: 286 KILSNFKEGTIQLMVASDLAARGLDIPDVGHVFN--------FDVPNRAE---------- 327
            +     +GT ++++A+++A   + I DV +V +        +D   +            
Sbjct: 461 AVFKRPPKGTRKIILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKA 520

Query: 328 NYIHRIGRTGRAGRHGKAFTLVAKED 353
           N   R GR GR  R G  + L  +  
Sbjct: 521 NAKQRRGRAGRV-RPGICYHLYTRSR 545


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

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 22/98 (22%), Positives = 48/98 (48%), Gaps = 9/98 (9%)

Query: 271 SVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENY- 329
            +   HG + +R   +++ +F  G   ++V + +   G+DIP+     N  +  RA+ + 
Sbjct: 831 RIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNA----NTIIIERADKFG 886

Query: 330 ---IHRI-GRTGRAGRHGKAFTLVAKEDIKHIDAIEKL 363
              ++++ GR GR+ +   A+ L   +     DA ++L
Sbjct: 887 LAQLYQLRGRVGRSNKQAYAYFLYPPQKALTEDAEKRL 924


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

 Score = 40.7 bits (95), Expect = 8e-04
 Identities = 26/118 (22%), Positives = 51/118 (43%), Gaps = 12/118 (10%)

Query: 45  AQTGTGKTASFVLPMLTILEKGRARVRMPR----TLILEPTRELAAQVADNFEKYGKNYN 100
           A TG+GKT    L +L  +++   +  + +     + + P + LAA++ D F K      
Sbjct: 133 APTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFSKKLAPLG 192

Query: 101 LTVALLIGGIPFEAQNKKLERGADVLICTPGRILDHFNRGKL----LMNNIEILVIDE 154
           ++V  L G                +++ TP +  D   R  +    L + + +++IDE
Sbjct: 193 ISVRELTGDTQLTKTEIA---DTQIIVTTPEK-WDVVTRKSVGDSALFSLVRLVIIDE 246


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

 Score = 39.2 bits (91), Expect = 0.003
 Identities = 54/277 (19%), Positives = 102/277 (36%), Gaps = 35/277 (12%)

Query: 117 KKLERGADVLICTPGRILDHFNRGKLLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPF 176
           ++L+     + C P R+L H    +L    I   ++   +R   +      Q+++  V  
Sbjct: 210 QRLKSAKSGVYCGPLRLLAHEVYDRLNALGIPCDLLTGEERRFVLDNGNPAQHVSCTVEM 269

Query: 177 TRQTLLFSATMTDELQKVSE--------NFLQNPKRIEVN---TPS------STAETIEH 219
                 +   + DE+Q + +          L      E++    PS         +    
Sbjct: 270 VSVNTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAADEIHLCGEPSVLDLVRKILKMTGD 329

Query: 220 CFVATYAQYSKKCALLQQLLQSQDTMKNG-IIFCNQKKNVVNLCHSLEKQGFSVCA-IHG 277
                  +      + +  L S   +K G  +    KK++  +   +EK G   CA I+G
Sbjct: 330 DVEVREYERLSPLVVEETALGSLSNLKPGDCVVAFSKKDIFTVKKKIEKAGNHKCAVIYG 389

Query: 278 NIDQRSRMKILSNF--KEGTIQLMVASDLAARGLDIPDVGHVFN-FDVPNRAE------N 328
           ++   +R+   + F        ++VASD    GL++     +F      +  E      +
Sbjct: 390 SLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNLNIRRIIFYSLIKYSGRETEDITVS 449

Query: 329 YIHRIGRTGRAGRHGKAF-----TLVAKEDIKHIDAI 360
            I +I   GRAGR G  +     T +  ED+K +  I
Sbjct: 450 QIKQIA--GRAGRFGSKYPQGEVTTLHSEDLKLLKRI 484


>gnl|CDD|36141 KOG0923, KOG0923, KOG0923, mRNA splicing factor ATP-dependent RNA
           helicase [RNA processing and modification].
          Length = 902

 Score = 38.0 bits (88), Expect = 0.006
 Identities = 31/124 (25%), Positives = 48/124 (38%), Gaps = 25/124 (20%)

Query: 255 KKNVVNLCHSLEKQG--FSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIP 312
           K+N+   C  L  +     V  I+ N+    + KI      G  ++++A+++A   L I 
Sbjct: 490 KENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTID 549

Query: 313 DVGHVFN--FDVPNRAENYIHRIG----------------RTGRAGRH--GKAFTLVAKE 352
            + +V +  F   N    Y  R G                R GRAGR   GK F L    
Sbjct: 550 GIKYVIDPGFVKQNS---YNPRTGMESLLVTPISKASANQRAGRAGRTGPGKCFRLYTAW 606

Query: 353 DIKH 356
             +H
Sbjct: 607 AYEH 610


>gnl|CDD|30899 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
           [Transcription / DNA replication, recombination, and
           repair].
          Length = 866

 Score = 37.8 bits (86), Expect = 0.006
 Identities = 32/149 (21%), Positives = 56/149 (37%), Gaps = 14/149 (9%)

Query: 249 IIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARG 308
           +IF      +  L   L+  G     + G+   + R +++  F     + +    L A G
Sbjct: 715 LIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGG 774

Query: 309 LDIPDVG--HVFNFD------VPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDI--KHID 358
           L +   G   V  FD      V  +A +  HRIG+     R  K + L+ +  I  K ++
Sbjct: 775 LGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQK----RPVKVYRLITRGTIEEKILE 830

Query: 359 AIEKLIEKKVDWLNGDLSSLNPPLEKIDI 387
             EK  E     ++ +       L   D+
Sbjct: 831 LQEKKQELLDSLIDAEGEKELSKLSIEDL 859


>gnl|CDD|36220 KOG1002, KOG1002, KOG1002, Nucleotide excision repair protein RAD16
           [Replication, recombination and repair].
          Length = 791

 Score = 35.8 bits (82), Expect = 0.026
 Identities = 40/154 (25%), Positives = 72/154 (46%), Gaps = 18/154 (11%)

Query: 233 ALLQQL--LQSQDTMKNGIIFCNQKKNVVNLCH-SLEKQGFSVCAIHGNIDQRSRMKILS 289
           AL+++L  L+ +D     I+F +Q  ++++L    L K GFS   + G++   +R   + 
Sbjct: 624 ALVEELYFLRERDRTAKSIVF-SQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIK 682

Query: 290 NFKEGTIQLMVASDLAARG--LDIPDVGHVFNFD------VPNRAENYIHRIGRTGRAGR 341
            FK      +    L A G  L++ +   VF  D      V  +A++ IHRIG+     R
Sbjct: 683 YFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQY----R 738

Query: 342 HGKAFTLVAKEDIKHIDAIEKLIEKKVDWLNGDL 375
             K      +  I+  + I +L EKK + ++  +
Sbjct: 739 PVKVVRFCIENSIE--EKIIELQEKKANMIHATI 770


>gnl|CDD|36169 KOG0951, KOG0951, KOG0951, RNA helicase BRR2, DEAD-box superfamily
           [RNA processing and modification].
          Length = 1674

 Score = 35.7 bits (82), Expect = 0.026
 Identities = 29/120 (24%), Positives = 47/120 (39%), Gaps = 15/120 (12%)

Query: 20  GYVKPTPIQIKTIPLVLQRHD-VCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLIL 78
           G      IQ K     L+  + +   A TG GKT    + +LTIL++    +R   ++ L
Sbjct: 306 GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKT---NVAVLTILQELGNHLREDGSVNL 362

Query: 79  E--------PTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICTP 130
                    P + L  ++  +F K      +TV  L G        K+      V++ TP
Sbjct: 363 APFKIVYIAPMKALVQEMVGSFSKRLAPLGITVLELTGD---SQLGKEQIEETQVIVTTP 419



 Score = 32.6 bits (74), Expect = 0.21
 Identities = 30/108 (27%), Positives = 45/108 (41%), Gaps = 10/108 (9%)

Query: 26   PIQIKTIPLVLQRHDVCGI-AQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTREL 84
            PIQ +    +   +D   + A  G+GKTA   L +L     GRA    P   I +     
Sbjct: 1146 PIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLRPDTIGRAVYIAPLEEIAD----- 1200

Query: 85   AAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICTPGR 132
              Q  D  +K+ K   L +  L G     + + KL +   V+I TP +
Sbjct: 1201 -EQYRDWEKKFSKLLGLRIVKLTGE---TSLDLKLLQKGQVIISTPEQ 1244


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

 Score = 35.3 bits (81), Expect = 0.038
 Identities = 36/171 (21%), Positives = 66/171 (38%), Gaps = 15/171 (8%)

Query: 23  KPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTR 82
           +  P Q + I ++ +   V   A T +GKT      ++       A     R +   P +
Sbjct: 119 ELDPFQQEAIAILERGESVLVCAPTSSGKT------VVAEYAIALALRDGQRVIYTSPIK 172

Query: 83  ELAAQV-ADNFEKYGKNYNLTVALLIGGIPFEAQNKKLERGADVLICTPGRILDHFNRGK 141
            L+ Q   D   K+G      V L+ G +        +   A  L+ T   + +   RG 
Sbjct: 173 ALSNQKYRDLLAKFGD-VADMVGLMTGDV-------SINPDAPCLVMTTEILRNMLYRGS 224

Query: 142 LLMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFSATMTDELQ 192
             + +IE +V DE   + D       + +  L+P   + +  SAT+ +  +
Sbjct: 225 ESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDHVRFVFLSATVPNAEE 275


>gnl|CDD|36340 KOG1125, KOG1125, KOG1125, TPR repeat-containing protein [General
           function prediction only].
          Length = 579

 Score = 34.2 bits (78), Expect = 0.080
 Identities = 22/131 (16%), Positives = 37/131 (28%), Gaps = 6/131 (4%)

Query: 332 RIGRTGRAGRHGKAFTLVAKEDIKHIDAIEKLIEKKVDWLNGDLSSLNPPLEKIDIAQHN 391
                    R   A   VA      +   ++LI + +   N    S  PP  K+D     
Sbjct: 27  DNNNLQEQLRAHLAKASVAFYIPLQLAEGDELINEFLQQNNQPNVSRGPPSFKMDNLLAE 86

Query: 392 HARKN----NPIPQKSTGFDRRKKNYSSQKSHIPLKESEKISKLQQDIQENDADSLGFRG 447
            A  +        ++  G       +S + S   L   +    + Q +  N   S     
Sbjct: 87  TADISIKGVRNASKEFQGLQ--NSQWSEEFSQFFLNALKSDRDVTQPLSRNQHGSEFINE 144

Query: 448 NMPAFMLPKNR 458
           +        NR
Sbjct: 145 SSDPLASSHNR 155


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

 Score = 33.0 bits (76), Expect = 0.18
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 6/70 (8%)

Query: 23 KPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTR 82
          +  P QI+ I  +L++     +  TG+GKT    L    ++ +     +  + L L P +
Sbjct: 3  ELRPYQIEAIRNLLEKKRGLIVMATGSGKT----LTAAKLIARLLKGKK--KVLFLVPRK 56

Query: 83 ELAAQVADNF 92
          +L  Q  + F
Sbjct: 57 DLLEQALEEF 66


>gnl|CDD|36168 KOG0950, KOG0950, KOG0950, DNA polymerase theta/eta, DEAD-box
           superfamily [General function prediction only].
          Length = 1008

 Score = 32.3 bits (73), Expect = 0.33
 Identities = 24/122 (19%), Positives = 48/122 (39%), Gaps = 8/122 (6%)

Query: 270 FSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDV----PNR 325
           + V   H  +    R  I + F+EG I ++VA+   A G+++P    +            
Sbjct: 523 YGVAYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLT 582

Query: 326 AENYIHRIGRTGRAGRH--GKAFTLVAKEDIKHIDAIEKLIEKKVDWLNGDLSSLNPPLE 383
              Y   +GR GR G    G +  ++   + K +  +     K ++  +   + +N P+ 
Sbjct: 583 RLEYKQMVGRAGRTGIDTLGDSILIIKSSEKKRVRELVNSPLKPLN--SCLSNEVNGPIL 640

Query: 384 KI 385
             
Sbjct: 641 MA 642


>gnl|CDD|36218 KOG1000, KOG1000, KOG1000, Chromatin remodeling protein
           HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure
           and dynamics].
          Length = 689

 Score = 31.5 bits (71), Expect = 0.48
 Identities = 35/197 (17%), Positives = 70/197 (35%), Gaps = 23/197 (11%)

Query: 249 IIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGT-IQLMVASDLAAR 307
           ++F + +  +  +   + K+      I G+     R  +  +F+    +++ V S  AA 
Sbjct: 496 LVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAG 555

Query: 308 -GLDIPDVGHV------FNFDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAI 360
            GL +     V      +N  V  +AE+  HRIG+            LVAK      D +
Sbjct: 556 VGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQKSSVFVQ----YLVAKGTAD--DYM 609

Query: 361 EKLIEKKVDWLNGDLSSLNPPLEKIDIAQHNHARKNNPIPQKSTGFDRRKKNYSSQKSHI 420
             ++++K+D L G +   +      +         N+        +        +  + I
Sbjct: 610 WPMLQQKLDVL-GSVGLSSDTFRTAEKM---GLSFNDAAQPGIAEY-----LKKTPDTTI 660

Query: 421 PLKESEKISKLQQDIQE 437
              E     K   D++ 
Sbjct: 661 DEWEDPVEEKEDDDLEI 677


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

 Score = 31.5 bits (71), Expect = 0.55
 Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 16/75 (21%)

Query: 286 KILSNFKEGTIQLMVASDLAARGLDIPDVGHV---------FNFDVPNRAENYIHRI--- 333
            +L  F  G   +++ + + A+G D P+V  V          + D   RA     ++   
Sbjct: 525 DLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDF--RASERTFQLLMQ 582

Query: 334 --GRTGRAGRHGKAF 346
             GR GRAG+ G+  
Sbjct: 583 VAGRAGRAGKPGEVV 597


>gnl|CDD|36339 KOG1123, KOG1123, KOG1123, RNA polymerase II transcription
           initiation/nucleotide excision repair factor TFIIH,
           3'-5' helicase subunit SSL2 [Transcription, Replication,
           recombination and repair].
          Length = 776

 Score = 31.1 bits (70), Expect = 0.71
 Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 12/88 (13%)

Query: 275 IHGNIDQRSRMKILSNFKEG-TIQLMVASDLAARGLDIPDVGHVFNFDV---PNRAENYI 330
           I+G   Q  RMKIL NF+    +  +  S +    +D+P+   +          R E   
Sbjct: 568 IYGPTSQNERMKILQNFQTNPKVNTIFLSKVGDTSIDLPEANVLIQISSHGGSRRQE--A 625

Query: 331 HRIGRTGRAGRHG----KAF--TLVAKE 352
            R+GR  RA +       AF  +LV+K+
Sbjct: 626 QRLGRILRAKKRNDEEFNAFFYSLVSKD 653


>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 = 31.1 bits (70), Expect = 0.72
 Identities = 67/319 (21%), Positives = 122/319 (38%), Gaps = 58/319 (18%)

Query: 45  AQTGTGKTASFVLPMLTILEKG-RARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTV 103
           A TG GKT      +   L +G R  +  PR  +     EL  ++   F       N  +
Sbjct: 123 AVTGAGKTEMIFQGIEQALNQGGRVCIASPRVDVC---LELYPRLKQAFS------NCDI 173

Query: 104 ALLIGGIP--FEAQNKKLERGADVLICTPGRIL---DHFNRGKLLMNNIEILVIDEADRM 158
            LL G     F A          +++ T  ++L     F          ++L+IDE D  
Sbjct: 174 DLLYGDSDSYFRAP---------LVVATTHQLLRFKQAF----------DLLIIDEVDAF 214

Query: 159 LDMGFIPYIQNITSLVPFTRQ------TLLFSATMTDELQKV----SENFLQNPKRIEVN 208
                 P+  + +      +       T+  +AT T +L++     +   L+ P R    
Sbjct: 215 ------PFSDDQSLQYAVKKARKKEGATIYLTATPTKKLERKILKGNLRILKLPARFH-G 267

Query: 209 TPSSTAETIEHCFVATYAQYSKKCALLQQLLQSQ-DTMKNGIIFCNQKKNVVNLCHSLEK 267
            P    + +         Q +K    L++ L+ Q  T +  +IF  + + +  +  +L+K
Sbjct: 268 KPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKK 327

Query: 268 Q-GFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNR- 325
           +      A   + DQ  R + +  F++G I L++ + +  RG+  P+V  VF     +R 
Sbjct: 328 KLPKETIASVHSEDQ-HRKEKVEAFRDGKITLLITTTILERGVTFPNV-DVFVLGAEHRV 385

Query: 326 --AENYIHRIGRTGRAGRH 342
                 +   GR GR+   
Sbjct: 386 FTESALVQIAGRVGRSLER 404


>gnl|CDD|35920 KOG0701, KOG0701, KOG0701, dsRNA-specific nuclease Dicer and
           related ribonucleases [RNA processing and modification].
          Length = 1606

 Score = 30.4 bits (68), Expect = 1.1
 Identities = 27/122 (22%), Positives = 47/122 (38%), Gaps = 12/122 (9%)

Query: 231 KCALLQQLLQSQDTMKNGIIFCNQKKNVVNLCHSLEKQG----FSVCAIHGNIDQRSRM- 285
            C L+ +    +    +GIIF +Q+     L   L +        V    G    +S   
Sbjct: 278 VCPLVDKEYLEKIETLSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKN 337

Query: 286 -------KILSNFKEGTIQLMVASDLAARGLDIPDVGHVFNFDVPNRAENYIHRIGRTGR 338
                  ++L  F    + L++A+ +   G+D+P    V  FD P    +Y+ + GR   
Sbjct: 338 ELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPKCNLVVLFDAPTYYRSYVQKKGRARA 397

Query: 339 AG 340
           A 
Sbjct: 398 AD 399


>gnl|CDD|36219 KOG1001, KOG1001, KOG1001, Helicase-like transcription factor
           HLTF/DNA helicase RAD5, DEAD-box superfamily
           [Transcription, Replication, recombination and repair].
          Length = 674

 Score = 30.0 bits (67), Expect = 1.6
 Identities = 31/127 (24%), Positives = 53/127 (41%), Gaps = 14/127 (11%)

Query: 249 IIFCNQKKNVVNLCHSLEKQGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAAR- 307
           +IF      +  +C  L  +GF      G +  + R K  ++F    +   +   L A  
Sbjct: 543 VIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGK 602

Query: 308 -GLDIPDVGHVFNFD------VPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAI 360
            GL++    HV   D      V  +A +  HRIG+T    +  K    + K+ ++  + I
Sbjct: 603 VGLNLTAASHVLLMDPWWNPAVEEQAIDRAHRIGQT----KPVKVSRFIIKDTVE--ERI 656

Query: 361 EKLIEKK 367
            K+ EKK
Sbjct: 657 LKIQEKK 663


>gnl|CDD|176220 cd08259, Zn_ADH5, Alcohol dehydrogenases of the MDR family.
           NAD(P)(H)-dependent oxidoreductases are the major
           enzymes in the interconversion of alcohols and
           aldehydes, or ketones. This group contains proteins that
           share the characteristic catalytic and structural
           zinc-binding sites of the zinc-dependent alcohol
           dehydrogenase family.  Alcohol dehydrogenase in the
           liver converts ethanol and NAD+ to acetaldehyde and
           NADH, while in yeast and some other microorganisms ADH
           catalyzes the conversion acetaldehyde to ethanol in
           alcoholic fermentation. ADH is a member of the medium
           chain alcohol dehydrogenase family (MDR), which have a
           NAD(P)(H)-binding domain in a Rossmann fold of a
           beta-alpha form.  The NAD(H)-binding region is comprised
           of 2 structurally similar halves, each of which contacts
           a mononucleotide. A GxGxxG motif after the first
           mononucleotide contact half allows the close contact of
           the coenzyme with the ADH backbone. The N-terminal
           catalytic domain has a distant homology to GroES. These
           proteins typically form dimers (typically higher plants,
           mammals) or tetramers (yeast, bacteria), and have 2
           tightly bound zinc atoms per subunit, a catalytic zinc
           at the active site and a structural zinc in a lobe of
           the catalytic domain. NAD(H)-binding occurs in the cleft
           between the catalytic and coenzyme-binding domains at
           the active site, and coenzyme binding induces a
           conformational closing of this cleft. Coenzyme binding
           typically precedes and contributes to substrate binding.
           In human ADH catalysis, the zinc ion helps coordinate
           the alcohol, followed by deprotonation of  a histidine
           (His-51), the ribose of NAD, a serine (Ser-48), then the
           alcohol, which allows the transfer of a hydride to NAD+,
           creating NADH and a zinc-bound aldehyde or ketone. In
           yeast and some bacteria, the active site zinc binds an
           aldehyde, polarizing it, and leading to the reverse
           reaction.
          Length = 332

 Score = 29.6 bits (67), Expect = 1.8
 Identities = 7/24 (29%), Positives = 12/24 (50%)

Query: 20  GYVKPTPIQIKTIPLVLQRHDVCG 43
           G V P P  ++   L+L+   + G
Sbjct: 256 GNVTPDPAPLRPGLLILKEIRIIG 279


>gnl|CDD|30955 COG0610, COG0610, Type I site-specific restriction-modification
           system, R (restriction) subunit and related helicases
           [Defense mechanisms].
          Length = 962

 Score = 29.6 bits (66), Expect = 1.9
 Identities = 26/114 (22%), Positives = 43/114 (37%), Gaps = 11/114 (9%)

Query: 47  TGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNYNLTVALL 106
            G+GKT +    M  +        + P+ L +   ++L  Q +D F+ +GK         
Sbjct: 282 QGSGKTLT----MFKLARLLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDPKAE 337

Query: 107 IGGIPFEAQNKKLERGADVLICTPGRILDHFN--RGKLLMNNIEILVI-DEADR 157
                 E     LE G   +I T  +  +         L+    ++VI DEA R
Sbjct: 338 STSELKEL----LEDGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHR 387


>gnl|CDD|33260 COG3457, COG3457, Predicted amino acid racemase [Amino acid
           transport and metabolism].
          Length = 353

 Score = 29.1 bits (65), Expect = 2.4
 Identities = 5/41 (12%), Positives = 15/41 (36%)

Query: 354 IKHIDAIEKLIEKKVDWLNGDLSSLNPPLEKIDIAQHNHAR 394
           ++    +E     ++  ++   ++    L    +   NH R
Sbjct: 181 LQGKKKLEASSGIQLKQVSAGNATSLTLLPMGSLPGINHLR 221


>gnl|CDD|173823 cd00314, plant_peroxidase_like, Heme-dependent peroxidases similar
           to plant peroxidases.  Along with animal peroxidases,
           these enzymes belong to a group of peroxidases
           containing a heme prosthetic group (ferriprotoporphyrin
           IX), which catalyzes a multistep oxidative reaction
           involving hydrogen peroxide as the electron acceptor.
           The plant peroxidase-like superfamily is found in all
           three kingdoms of life and carries out a variety of
           biosynthetic and degradative functions. Several
           sub-families can be identified. Class I includes
           intracellular peroxidases present in fungi, plants,
           archaea and bacteria, called catalase-peroxidases, that
           can exhibit both catalase and broad-spectrum peroxidase
           activities depending on the steady-state concentration
           of hydrogen peroxide. Catalase-peroxidases are typically
           comprised of two homologous domains that probably arose
           via a single gene duplication event. Class II includes
           ligninase and other extracellular fungal peroxidases,
           while class III is comprised of classic extracellular
           plant peroxidases, like horseradish peroxidase.
          Length = 255

 Score = 28.7 bits (64), Expect = 3.3
 Identities = 16/69 (23%), Positives = 23/69 (33%), Gaps = 9/69 (13%)

Query: 50  GKTASFVLPMLTILEK---GR-----ARVRMPRTLILEPTRELAAQVA-DNFEKYGKNYN 100
           G  A         L     GR       + +P    L P    +A    D F++ G + +
Sbjct: 90  GAVAVESTFGGGPLIPFRFGRLDATEPDLGVPDPEGLLPNETSSATELRDKFKRMGLSPS 149

Query: 101 LTVALLIGG 109
             VAL  G 
Sbjct: 150 ELVALSAGA 158


>gnl|CDD|73027 cd03268, ABC_BcrA_bacitracin_resist, The BcrA subfamily represents
           ABC transporters involved in peptide antibiotic
           resistance.  Bacitracin is a dodecapeptide antibiotic
           produced by B. licheniformis and B. subtilis.  The
           synthesis of bacitracin is non-ribosomally catalyzed by
           a multienzyme complex BcrABC.  Bacitracin has potent
           antibiotic activity against gram-positive bacteria.  The
           inhibition of peptidoglycan biosynthesis is the best
           characterized bacterial effect of bacitracin.  The
           bacitracin resistance of B. licheniformis is mediated by
           the ABC transporter Bcr which is composed of two
           identical BcrA ATP-binding subunits and one each of the
           integral membrane proteins, BcrB and BcrC.  B. subtilis
           cells carrying bcr genes on high-copy number plasmids
           develop collateral detergent sensitivity, a similar
           phenomenon in human cells with overexpressed multi-drug
           resistance P-glycoprotein..
          Length = 208

 Score = 28.6 bits (64), Expect = 3.5
 Identities = 15/56 (26%), Positives = 30/56 (53%)

Query: 143 LMNNIEILVIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFSATMTDELQKVSENF 198
           L+ N ++L++DE    LD   I  ++ +   +     T+L S+ +  E+QKV++  
Sbjct: 141 LLGNPDLLILDEPTNGLDPDGIKELRELILSLRDQGITVLISSHLLSEIQKVADRI 196


>gnl|CDD|38880 KOG3676, KOG3676, KOG3676, Ca2+-permeable cation channel OSM-9 and
           related channels (OTRPC family) [Inorganic ion transport
           and metabolism, Signal transduction mechanisms].
          Length = 782

 Score = 28.0 bits (62), Expect = 5.6
 Identities = 14/42 (33%), Positives = 17/42 (40%)

Query: 345 AFTLVAKEDIKHIDAIEKLIEKKVDWLNGDLSSLNPPLEKID 386
             TL AK   K +        K  DW  G ++S   PL  ID
Sbjct: 311 PLTLAAKLGKKEMFQHILERRKFTDWAYGPVTSSLYPLNSID 352


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

 Score = 27.8 bits (61), Expect = 6.1
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 9/72 (12%)

Query: 21 YVKPTPIQIKTIPLV---LQRHDVCGI-AQTGTGKTASFVLPMLTILEKGRARVRMPRTL 76
            +P P Q +    V   L+  +   I A TGTGKT +++LP L       AR    + +
Sbjct: 13 GFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAY-----AREEGKKVI 67

Query: 77 ILEPTRELAAQV 88
          I   T+ L  Q+
Sbjct: 68 ISTRTKALQEQL 79


>gnl|CDD|111435 pfam02534, TraG, TraG/TraD family.  These proteins contain a
          P-loop and walker-B site for nucleotide binding. TraG
          is essential for DNA transfer in bacterial conjugation.
          These proteins are thought to mediate interactions
          between the DNA-processing (Dtr) and the mating pair
          formation (Mpf) systems.
          Length = 468

 Score = 27.8 bits (62), Expect = 6.3
 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 8/53 (15%)

Query: 44 IAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYG 96
           A TG+GK    V+P   +L    + V      +L+P  EL    +   EK G
Sbjct: 50 FAGTGSGKGVGVVIP--NLLVWKGSIV------VLDPKGELWELTSGIREKQG 94


>gnl|CDD|36040 KOG0822, KOG0822, KOG0822, Protein kinase inhibitor [Cell cycle
           control, cell division, chromosome partitioning].
          Length = 649

 Score = 27.6 bits (61), Expect = 7.4
 Identities = 12/63 (19%), Positives = 19/63 (30%), Gaps = 21/63 (33%)

Query: 365 EKKVDWLNGDLSSLNPPLEKIDI---------------------AQHNHARKNNPIPQKS 403
           + +V  ++ D+   N P E+ DI                     AQ         IP   
Sbjct: 420 DNRVTIISSDMRKWNAPREQADIIVSELLGSFGDNELSPECLDGAQKFLKPDGISIPSSY 479

Query: 404 TGF 406
           T +
Sbjct: 480 TSY 482


>gnl|CDD|32062 COG1878, COG1878, Predicted metal-dependent hydrolase [General
           function prediction only].
          Length = 218

 Score = 27.5 bits (61), Expect = 8.6
 Identities = 23/108 (21%), Positives = 33/108 (30%), Gaps = 5/108 (4%)

Query: 306 ARGLDIPDVGHVFNFDVPNRAENYIHRIG-----RTGRAGRHGKAFTLVAKEDIKHIDAI 360
              +DI            +         G     RTG + R G             I+A 
Sbjct: 79  GVVIDISGKDPDEVITEDDIEAWDAEHPGDIVLIRTGWSKRWGDEPAFQYHFPGISIEAA 138

Query: 361 EKLIEKKVDWLNGDLSSLNPPLEKIDIAQHNHARKNNPIPQKSTGFDR 408
           E LIE+ V  +  D  S +P L +   A          I +  T  D+
Sbjct: 139 EYLIERGVKAVGIDTPSTDPGLSEDFPAHRLLLSAGILIVENLTNLDK 186


>gnl|CDD|37551 KOG2340, KOG2340, KOG2340, Uncharacterized conserved protein
           [Function unknown].
          Length = 698

 Score = 27.3 bits (60), Expect = 8.7
 Identities = 29/127 (22%), Positives = 49/127 (38%), Gaps = 31/127 (24%)

Query: 123 ADVLICTP-GRILDHFNRGKL-----LMNNIEILVIDEADRMLDMGFIPYIQNITS---L 173
           +D+L+ +P G  +   N G        +++IE+L+ID+AD ML M    ++ +I     L
Sbjct: 386 SDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIML-MQNWEHLLHIFDHLNL 444

Query: 174 VP---------------------FTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSS 212
            P                     + RQTLLFS         +   + QN           
Sbjct: 445 QPSKQHDVDFSRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMAGKVKARNLQ 504

Query: 213 TAETIEH 219
           +  +I +
Sbjct: 505 SGGSISN 511


>gnl|CDD|31237 COG1034, NuoG, NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75
           kD subunit (chain G) [Energy production and conversion].
          Length = 693

 Score = 27.3 bits (60), Expect = 8.9
 Identities = 16/78 (20%), Positives = 26/78 (33%), Gaps = 4/78 (5%)

Query: 328 NYIHRIGRTGRAGRHGKAFTLVAKEDIKHIDAIEKLIEKKVDWLNGDLSSLNPPLEKIDI 387
           N   R+ R  +A R         +ED + + A+   +  K+D+   D             
Sbjct: 569 NLEGRVQRFNQALR----PGGDEREDWRVLHALASELGLKLDFDQLDAVRAALAAAHPGF 624

Query: 388 AQHNHARKNNPIPQKSTG 405
           A  + A K    P    G
Sbjct: 625 ALIDSAAKGEREPPAGEG 642


  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
   0.320    0.136    0.394 

Gapped
Lambda     K      H
   0.267   0.0775    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,500,963
Number of extensions: 291117
Number of successful extensions: 1027
Number of sequences better than 10.0: 1
Number of HSP's gapped: 908
Number of HSP's successfully gapped: 102
Length of query: 465
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 368
Effective length of database: 4,167,664
Effective search space: 1533700352
Effective search space used: 1533700352
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 (21.8 bits)
S2: 59 (26.4 bits)