RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780945|ref|YP_003065358.1| ATP-dependent DNA helicase
RecG [Candidatus Liberibacter asiaticus str. psy62]
         (700 letters)



>gnl|CDD|182836 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
          Length = 681

 Score =  819 bits (2119), Expect = 0.0
 Identities = 303/675 (44%), Positives = 430/675 (63%), Gaps = 12/675 (1%)

Query: 3   PSFLNPLFAPLSTFRGVGKKYSLFLSKIINCGNANETRFIDLLFYHPSSFIDRHYRPKIS 62
           PS L  L APL++ +GVG K +  L+K+            DLL + P  + DR     I+
Sbjct: 1   PSLLLLLDAPLTSLKGVGPKTAEKLAKL------GIHTVQDLLLHLPRRYEDRTRLKPIA 54

Query: 63  EISEERIVTITGYISQHSSFQLQKRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRK 122
           E+     VT+ G +         KRR   + ++DGTG +TL FF      LK     G++
Sbjct: 55  ELRPGEKVTVEGEVLSAEVVF-GKRRRLTVTVSDGTGNLTLRFFNFNQPYLKKQLKVGKR 113

Query: 123 ITVTGKIKKLKNRIIMVHPHYIFHNS-QDVNFPLIEAVYSLPTGLSVDLFKKIIVEALSR 181
           + V GK+K+ K  + MVHP Y             +  VY L  GL     +K+I +AL  
Sbjct: 114 VAVYGKVKRGKYGLEMVHPEYEVLEEESPELEGRLTPVYPLTEGLKQKTLRKLIKQALEL 173

Query: 182 LPVLPEWIEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEWTSPARERLAYDELLAGQIALL 241
           L  LPE + ++LL+K    S+AEA   IH P      E   PAR RL ++EL A Q++LL
Sbjct: 174 LDALPELLPEELLEKYGLLSLAEALRAIHFP---PSDEDLHPARRRLKFEELFALQLSLL 230

Query: 242 LMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGD 301
           L+R   + +   P+  +G++ +K L ++PF  T +Q+  + +IL D++    M R+LQGD
Sbjct: 231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGD 290

Query: 302 VGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQ 361
           VGSGKT+VA +A  AA+EAG QA +MAP  ILA+QHYE +KK  +   I V ++TG++  
Sbjct: 291 VGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKG 350

Query: 362 AHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKATAP 421
             RR+ LE IA G+A I+IGTHAL QD ++++ L LVI+DEQHRFGV+QRL L +K   P
Sbjct: 351 KERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHRFGVEQRLALREKGENP 410

Query: 422 HVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSE 481
           HVL+MTATPIPRTL +T+ GD+D+S I E P GRKPI TV+IP +R DEV ER++  +++
Sbjct: 411 HVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEIAK 470

Query: 482 GKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNG 540
           G++AY +CP IEE ++ + +S  E +  L E F    + ++HGRM   +K++VM +FK G
Sbjct: 471 GRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAG 530

Query: 541 TCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHPPL 600
              +L+ATTVIEVG+DV +A++++IENAE FGLAQLHQLRGRVGRG   S C+LLY  PL
Sbjct: 531 EIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPL 590

Query: 601 SKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILGIKQSGMPKFLIAQPELHDSLLEIAR 660
           S+ +  RL +++ T DGF+IAE+DL+ R  GE+LG +QSG+P+F +A     + LLE AR
Sbjct: 591 SETARERLKIMRETNDGFVIAEKDLELRGPGELLGTRQSGLPEFKVADLVRDEELLEEAR 650

Query: 661 KDAKHILTQDPDLTS 675
           KDA+ +L +DP+L  
Sbjct: 651 KDARELLERDPELAE 665


>gnl|CDD|161975 TIGR00643, recG, ATP-dependent DNA helicase RecG. 
          Length = 630

 Score =  603 bits (1558), Expect = e-173
 Identities = 264/628 (42%), Positives = 385/628 (61%), Gaps = 12/628 (1%)

Query: 43  DLLFYHPSSFIDRHYRPKISEISEERIVTITGYISQHSSFQLQKRRPYKILLND-GTGEI 101
           DLLFY P  + DR     I E+      TI G +  H  F  ++R+  K+ L D G  ++
Sbjct: 8   DLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKL 67

Query: 102 TLLFFYRKTEMLKNVFFEGRKITVTGKIKKLKNRIIMVHPHYIFHNSQDVNFPLIEAVYS 161
            L FF R    LK  F  G K+ V GK+K  K +  ++HP +I           I  VY 
Sbjct: 68  ELRFFNR--AFLKKKFKVGSKVVVYGKVKSSKFKAYLIHPEFISEKDGVEFELKILPVYP 125

Query: 162 LPTGLSVDLFKKIIVEALSRLP-VLPEWIEKDLLQKKSFPSIAEAFNIIHNPRKAKDFEW 220
           L  GL+    +K+I +AL +L   L + + ++L +K    S+ +A   IH P   K    
Sbjct: 126 LTEGLTQKKLRKLIQQALDQLDKSLEDPLPEELREKYGLLSLEDALRAIHFP---KTLSL 182

Query: 221 TSPARERLAYDELLAGQIALL-LMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQES 279
              AR RL +DE    Q+A+L     + ++    P N   ++  K L ++PF  T++Q+ 
Sbjct: 183 LELARRRLIFDEFFYLQLAMLARRLGEKQQFSAPPANPSEELLTKFLASLPFKLTRAQKR 242

Query: 280 AIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYE 339
            +K+ILQD+     M R+LQGDVGSGKTLVA +AM AA+EAG Q  +MAP  ILA+QHY 
Sbjct: 243 VVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYN 302

Query: 340 FIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVI 399
            ++       I V ++TG++    R++ LE IA GQ H+++GTHAL Q+ +++ +L LVI
Sbjct: 303 SLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVI 362

Query: 400 VDEQHRFGVQQRLKLTQKA---TAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRK 456
           +DEQHRFGV+QR KL +K      PHVL+M+ATPIPRTL LT  GD+D S I E P GRK
Sbjct: 363 IDEQHRFGVEQRKKLREKGQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRK 422

Query: 457 PIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS 516
           PI TV+I  +  D V E ++  +++G++AY + P IEE ++ + ++    +  L + F  
Sbjct: 423 PITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPK 482

Query: 517 -SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQ 575
            ++ ++HGRM   +KE+VM+ F+ G   +L+ATTVIEVG+DV +A++++IE+AE FGL+Q
Sbjct: 483 YNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQ 542

Query: 576 LHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQRKEGEILG 635
           LHQLRGRVGRG+  S C+L+Y  P S+++  RL V+ +T DGF+IAEEDL+ R  G++LG
Sbjct: 543 LHQLRGRVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLG 602

Query: 636 IKQSGMPKFLIAQPELHDSLLEIARKDA 663
            KQSG P+F +A       +L  AR+DA
Sbjct: 603 TKQSGYPEFRVADLVRDREILVEAREDA 630


>gnl|CDD|161938 TIGR00580, mfd, transcription-repair coupling factor (mfd).  All
           proteins in this family for which functions are known
           are DNA-dependent ATPases that function in the process
           of transcription-coupled DNA repair in which the repair
           of the transcribed strand of actively transacribed genes
           is repaired at a higher rate than the repair of
           non-transcribed regions of the genome and than the
           non-transcribed strand of the same gene. This family is
           based on the phylogenomic analysis of JA Eisen (1999,
           Ph.D. Thesis, Stanford University). This family is
           closely related to the RecG and UvrB families.
          Length = 926

 Score =  310 bits (796), Expect = 7e-85
 Identities = 149/410 (36%), Positives = 232/410 (56%), Gaps = 21/410 (5%)

Query: 240 LLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQ 299
           L+ +  + K   G     + +  Q+   + PF  T  Q  AI++I  DM     M R++ 
Sbjct: 419 LIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVC 478

Query: 300 GDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNM 359
           GDVG GKT VA+ A   AV  G Q  ++ P  +LAQQH+E  K+   N  + +E+++   
Sbjct: 479 GDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFR 538

Query: 360 PQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLTQKAT 419
               + + L+ +A G+  I+IGTH L Q  +++  L L+I+DE+ RFGV+Q+ KL +  T
Sbjct: 539 SAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRT 598

Query: 420 APHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINR--IDEVIERLKV 477
           +  VL ++ATPIPRTL ++  G  D+S I   P  R P++T ++  +   + E I R   
Sbjct: 599 SVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEYDPELVREAIRR--- 655

Query: 478 VLSEGKKAYWICPQIE--EKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMD 535
            L  G + +++  +IE  EK  +  R +V           + IAI HG+M++ + E VM 
Sbjct: 656 ELLRGGQVFYVHNRIESIEKLATQLRELVPE---------ARIAIAHGQMTENELEEVML 706

Query: 536 SFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILL 595
            F  G  ++L+ TT+IE GID+ +A+ IIIE A+ FGLAQL+QLRGRVGR ++ +   LL
Sbjct: 707 EFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLL 766

Query: 596 YHP--PLSKNSYTRLSVLKNTED---GFLIAEEDLKQRKEGEILGIKQSG 640
           Y     L++++  RL  ++   +   GF IA  DL+ R  G +LG +QSG
Sbjct: 767 YPHQKALTEDAQKRLEAIQEFSELGAGFKIALHDLEIRGAGNLLGEEQSG 816


>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
           Provisional.
          Length = 1147

 Score =  253 bits (647), Expect = 1e-67
 Identities = 146/379 (38%), Positives = 211/379 (55%), Gaps = 19/379 (5%)

Query: 270 PFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP 329
           PF  T  Q  AI  +L DM Q   M R++ GDVG GKT VA+ A   AVE   Q  ++ P
Sbjct: 598 PFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVP 657

Query: 330 IGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDS 389
             +LAQQHY+  +    N  + +E+++       + + L   A G+  I+IGTH L Q  
Sbjct: 658 TTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSD 717

Query: 390 IQYYKLILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKIT 449
           +++  L L+IVDE+HRFGV+ + ++        +L +TATPIPRTL +   G  D+S I 
Sbjct: 718 VKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIA 777

Query: 450 EKPAGRKPIKTVIIPINRIDEVIER---LKVVLSEGKKAYWICPQIEEKKESNFRSVVER 506
             PA R  +KT    +   D ++ R   L+ +L  G + Y++   +E     N +   ER
Sbjct: 778 TPPARRLAVKTF---VREYDSLVVREAILREIL-RGGQVYYLYNDVE-----NIQKAAER 828

Query: 507 FNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIE 566
              L     + IAI HG+M + + E VM+ F +    +L+ TT+IE GID+  A+ IIIE
Sbjct: 829 LAELVPE--ARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIE 886

Query: 567 NAEHFGLAQLHQLRGRVGRGEEISSCILLYHPP--LSKNSYTRLSVLKNTED---GFLIA 621
            A+HFGLAQLHQLRGRVGR    +   LL   P  ++ ++  RL  + + ED   GF +A
Sbjct: 887 RADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALA 946

Query: 622 EEDLKQRKEGEILGIKQSG 640
             DL+ R  GE+LG +QSG
Sbjct: 947 THDLEIRGAGELLGEEQSG 965


>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. 
          Length = 201

 Score =  104 bits (260), Expect = 1e-22
 Identities = 53/207 (25%), Positives = 84/207 (40%), Gaps = 20/207 (9%)

Query: 265 ILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAV--EAGG 322
           I +         Q+ AI+ +L           IL    GSGKTL AL+    A+    G 
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLS-----GLRDVILAAPTGSGKTLAALLPALEALKRGKGK 55

Query: 323 QAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGT 382
           + +++ P   LA+Q  E +KK   +  + V  + G      +R+ L ++  G+  I++ T
Sbjct: 56  RVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDS---KREQLRKLESGKTDILVTT 112

Query: 383 -----HALFQDSIQYYKLILVIVDEQHRFGVQQRLK-----LTQKATAPHVLLMTATPIP 432
                  L  D ++   + LVI+DE HR             L        +LL++ATP  
Sbjct: 113 PGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPE 172

Query: 433 RTLVLTSLGDIDISKITEKPAGRKPIK 459
               L  L   D   I   P   +PI+
Sbjct: 173 EIENLLELFLNDPVFIDVGPTPLEPIE 199


>gnl|CDD|161946 TIGR00595, priA, primosomal protein N'.  All proteins in this
           family for which functions are known are components of
           the primosome which is involved in replication, repair,
           and recombination.This family is based on the
           phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
           Stanford University).
          Length = 505

 Score = 74.3 bits (183), Expect = 1e-13
 Identities = 92/422 (21%), Positives = 157/422 (37%), Gaps = 105/422 (24%)

Query: 298 LQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP-IGILAQQHYEFIKKYTQNTQIIVEIIT 356
           L G  GSGKT V L A+   +  G   +++ P I +  Q    F  KY   +Q  V ++ 
Sbjct: 2   LFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRF--KYRFGSQ--VAVLH 57

Query: 357 GNMPQAHRRKALERIAHGQAHIIIGTH-ALFQDSIQYYKLILVIVDEQHRFGVQQR---- 411
             +  + + +A  ++ +G+  ++IGT  ALF   + +  L L+IVDE+H    +Q     
Sbjct: 58  SGLSDSEKLQAWRKVKNGEILVVIGTRSALF---LPFKNLGLIIVDEEHDSSYKQEEGPR 114

Query: 412 -------LKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIP 464
                  +   +K   P V+L +ATP   +          +  +T + +GRKP +  +I 
Sbjct: 115 YHARDVAVYRAKKFNCP-VVLGSATPSLESYHNAKQKAYRLLVLTRRVSGRKPPEVKLID 173

Query: 465 INR-------IDEVIERLKVVLSEGKKA------------------YWI----------- 488
           + +         E+I  ++  L+ G+++                   +I           
Sbjct: 174 MRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLT 233

Query: 489 ----------------------CPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRM- 525
                                 CPQ   +         E+             I   R+ 
Sbjct: 234 YHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIA--RID 291

Query: 526 SDIDK-----ESVMDSFKNGTCKLLIATTVIEVGID--------VVDASIIIIEN----A 568
           SD        E++++ F NG   +LI T +I  G          V+DA   +       A
Sbjct: 292 SDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAA 351

Query: 569 EHFGLAQLHQLRGRVGRGEEISSCILLYHPPLSKNSYTRLSVLKNTEDGFLIAEEDLKQR 628
           E  G   L Q+ GR GR E+    I+  + P   N     + L    + F   E++L QR
Sbjct: 352 ER-GFQLLTQVAGRAGRAEDPGQVIIQTYNP---NHPAIQAALTGDYEAFY--EQELAQR 405

Query: 629 KE 630
           + 
Sbjct: 406 RA 407


>gnl|CDD|128766 smart00490, HELICc, helicase superfamily c-terminal domain. 
          Length = 82

 Score = 71.5 bits (176), Expect = 8e-13
 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 517 SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQL 576
            +A +HG +S  ++E +++ F NG  K+L+AT V E G+D+    ++II +   +  A  
Sbjct: 13  KVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASY 71

Query: 577 HQLRGRVGR 585
            Q  GR GR
Sbjct: 72  IQRIGRAGR 80



 Score = 32.6 bits (75), Expect = 0.40
 Identities = 10/47 (21%), Positives = 22/47 (46%)

Query: 339 EFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHAL 385
           E + +  +   I V  + G + Q  R + LE+  +G+  +++ T   
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVA 47


>gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional.
          Length = 773

 Score = 60.7 bits (148), Expect = 1e-09
 Identities = 42/144 (29%), Positives = 70/144 (48%), Gaps = 26/144 (18%)

Query: 303 GSGKTLVALIAMAAAVEA-GGQAVIMAPIGILAQQHYEFIKKYTQ--NTQIIVEIITGNM 359
           G GKT +AL+ +A  +   GG+ +I+AP   L +QH EF +K+      +I+V   TG +
Sbjct: 39  GLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVV--FTGEV 96

Query: 360 PQAHRRKALERIAHGQAHIIIGTHALFQDSI--QYYKL---ILVIVDEQHR--------F 406
               R +  E+     A +I+ T  + ++ +      L    L+I DE HR        +
Sbjct: 97  SPEKRAELWEK-----AKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVY 151

Query: 407 GVQQRLKLTQKATAPHVLLMTATP 430
            + +R    + A  P VL +TA+P
Sbjct: 152 -IAERYH--EDAKNPLVLGLTASP 172



 Score = 34.8 bits (81), Expect = 0.070
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 23/67 (34%)

Query: 533 VMDSFKNGTCKLLIATTVIEVGIDV-----------VDASIIIIENAEHFGLAQLHQLRG 581
           ++D F+ G   +L++T+V E G+D+           V + I  I            Q +G
Sbjct: 415 ILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSI------------QRKG 462

Query: 582 RVGRGEE 588
           R GR EE
Sbjct: 463 RTGRQEE 469


>gnl|CDD|180144 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
          Length = 679

 Score = 59.4 bits (145), Expect = 3e-09
 Identities = 37/133 (27%), Positives = 63/133 (47%), Gaps = 12/133 (9%)

Query: 274 TKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAP-IGI 332
              Q +A+ + ++  +  +  L  L G  GSGKT V L A+A  +  G QA+++ P I  
Sbjct: 146 NPEQAAAV-EAIRAAAGFSPFL--LDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIA- 201

Query: 333 LAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTH-ALFQDSIQ 391
           L  Q    + ++       V ++   +    R     +   G+A ++IG   ALF   + 
Sbjct: 202 LTPQ---MLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF---LP 255

Query: 392 YYKLILVIVDEQH 404
           +  L L+IVDE+H
Sbjct: 256 FKNLGLIIVDEEH 268


>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
          Length = 401

 Score = 47.5 bits (113), Expect = 1e-05
 Identities = 86/343 (25%), Positives = 144/343 (41%), Gaps = 74/343 (21%)

Query: 260 KIAQKILRNIPFS-----PTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAM 314
           K+ + +LR I +S     P+  Q+  IK IL      +    I Q   G+GKT   +IA 
Sbjct: 34  KLNEDLLRGI-YSYGFEKPSAIQQRGIKPIL------DGYDTIGQAQSGTGKTATFVIAA 86

Query: 315 AAAVE---AGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERI 371
              ++      QA+I+AP   LAQQ  + +       ++      G       R  + ++
Sbjct: 87  LQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVV---RDDINKL 143

Query: 372 AHGQAHIIIGTHALFQDSIQYY-----KLILVIVDEQHRF---GVQQRLKLTQKATAP-- 421
             G  H+++GT     D I         L L I+DE       G + ++    K   P  
Sbjct: 144 KAGV-HMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDV 202

Query: 422 HVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERLKVVLSE 481
            V L +AT +P           +I ++T K   R P + ++    + DE+         E
Sbjct: 203 QVALFSAT-MPN----------EILELTTKFM-RDPKRILV----KKDELT-------LE 239

Query: 482 GKKAYWICPQIEEKK--------ES----------NFRSVVERFNS-LHEH-FTSSIAII 521
           G + +++  + EE K        E+          N R  V+     +HE  FT S   +
Sbjct: 240 GIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSC--M 297

Query: 522 HGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII 564
           HG M   D++ +M  F++G+ ++LI T ++  GIDV   S++I
Sbjct: 298 HGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVI 340


>gnl|CDD|162177 TIGR01054, rgy, reverse gyrase.  Generally, these gyrases are
           encoded as a single polypeptide. An exception was found
           in Methanopyrus kandleri, where enzyme is split within
           the topoisomerase domain, yielding a heterodimer of gene
           products designated RgyB and RgyA.
          Length = 1171

 Score = 47.5 bits (113), Expect = 1e-05
 Identities = 29/123 (23%), Positives = 47/123 (38%), Gaps = 14/123 (11%)

Query: 290 QKNRMLRILQGD-------VGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIK 342
           QK    R+L+GD        G GKT   L       + G +  I+ P  +L  Q  E I 
Sbjct: 83  QKMWAKRVLRGDSFAIIAPTGVGKTTFGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKIS 142

Query: 343 KYTQNTQIIVEIIT---GNMPQAHRRKALERIAHGQAHIIIGT----HALFQDSIQYYKL 395
              +   +    I      +P   +++ +ERI +G   I+I T       + +    +  
Sbjct: 143 SLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDF 202

Query: 396 ILV 398
           I V
Sbjct: 203 IFV 205



 Score = 34.4 bits (79), Expect = 0.10
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 14/75 (18%)

Query: 481 EGKKAYWICP------QIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVM 534
           +GK+ Y I P      Q+ EK      S+ E+        T +I   H R+   +K+  M
Sbjct: 120 KGKRCYIILPTTLLVIQVAEK----ISSLAEKAGVG----TVNIGAYHSRLPTKEKKEFM 171

Query: 535 DSFKNGTCKLLIATT 549
           +  +NG   +LI TT
Sbjct: 172 ERIENGDFDILITTT 186


>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family.  This
           family is based on the phylogenomic analysis of JA Eisen
           (1999, Ph.D. Thesis, Stanford University).
          Length = 470

 Score = 47.1 bits (112), Expect = 2e-05
 Identities = 52/236 (22%), Positives = 88/236 (37%), Gaps = 31/236 (13%)

Query: 379 IIGTHALFQDSIQYYKLILVIVDEQH---RFGVQQRLKLTQ----KATAPHVLLM----T 427
              ++ L Q   +   + L+ VDE H   ++G   R         K   P+V +M    T
Sbjct: 112 CSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQKFPNVPIMALTAT 171

Query: 428 ATPIPRTLVLTSLGDIDISKITEKPAGRKPIK-TVIIPINRIDEVIERLKVVLSEGKKAY 486
           A+P  R  +L  L  +   +I      R  +   V     +I E + R      +GK   
Sbjct: 172 ASPSVREDILRQLN-LKNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRKEFKGKSGI 230

Query: 487 WICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLI 546
             CP          R   E+  +  ++   +    H  +    ++ V   F+    ++++
Sbjct: 231 IYCPS---------RKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVV 281

Query: 547 ATTVIEVGIDVVDASIIIIENAEHFGLAQ----LHQLRGRVGRGEEISSCILLYHP 598
           AT    +GI+  D   +I     H+ L +     +Q  GR GR    S C L Y P
Sbjct: 282 ATVAFGMGINKPDVRFVI-----HYSLPKSMESYYQESGRAGRDGLPSECHLFYAP 332


>gnl|CDD|162437 TIGR01587, cas3_core, CRISPR-associated helicase Cas3.  This model
           represents the highly conserved core region of an
           alignment of Cas3, a protein found in association with
           CRISPR repeat elements in a broad range of bacteria and
           archaea. Cas3 appears to be a helicase, with regions
           found by pfam00270 (DEAD/DEAH box helicase) and
           pfam00271 (Helicase conserved C-terminal domain). Some
           but not all members have an N-terminal HD domain region
           (pfam01966) that is not included within this model.
          Length = 358

 Score = 47.1 bits (112), Expect = 2e-05
 Identities = 46/222 (20%), Positives = 81/222 (36%), Gaps = 42/222 (18%)

Query: 380 IGTHALFQDSIQYYK-----LILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRT 434
           I    L  D + +Y      LIL +++      V              +LLM+AT +P+ 
Sbjct: 123 IANSLLIFDEVHFYDEYTLALILAVLEVLKDNDVP-------------ILLMSAT-LPKF 168

Query: 435 LVLTSLG-DIDISKITE--KPAGRKPIKTVIIPINRIDE---VIERLKVVLSEGKKAYWI 488
           L   +              K   R      I   +        +ERL   + +G K   I
Sbjct: 169 LKEYAEKIGYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAII 228

Query: 489 CPQIEEKKESNFRSVVERFNSLHEHF-TSSIAIIHGRMSDIDKES----VMDSFKNGTCK 543
              ++           E +  L E+     I ++H R ++ D+      +++  K     
Sbjct: 229 VNTVDR--------AQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKF 280

Query: 544 LLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGR 585
           +++AT VIE  +D + A ++I    E   +  L Q  GR+ R
Sbjct: 281 VIVATQVIEASLD-ISADVMI---TELAPIDSLIQRLGRLHR 318


>gnl|CDD|177796 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
           Provisional.
          Length = 518

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 99/421 (23%), Positives = 168/421 (39%), Gaps = 105/421 (24%)

Query: 234 LAGQIALLLMRKQFKKEIGIPINVEG-------------KIAQKILRNIPFS----PTKS 276
           L+   A LL RK       + I+V+G              +  K+L N+  +    PT  
Sbjct: 95  LSSSQAELLRRK-------LEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPI 147

Query: 277 QESAIKDILQDMSQKNRMLRILQGDVGSGKT---LVALIAMAAAVEAGGQ-------AVI 326
           Q  AI   L       R L ++  D GSGKT   LV +I+    + +G         A++
Sbjct: 148 QMQAIPAAL-----SGRSL-LVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMV 201

Query: 327 MAPIGILAQQHYEFIKKYTQNTQIIVEIITGN--MPQAHRRKALERIAHGQAHIIIGTHA 384
           + P   L  Q  +  K   +       ++ G   MPQ      L RI  G   +I+GT  
Sbjct: 202 LTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQ-----LYRIQQG-VELIVGTPG 255

Query: 385 -----LFQDSIQYYKLILVIVDE-----QHRFGVQQRLKLTQKATAPHVLLMTATPIPRT 434
                L +  I+   + ++++DE     +  F   Q +++ Q  + P VLL +AT     
Sbjct: 256 RLIDLLSKHDIELDNVSVLVLDEVDCMLERGFR-DQVMQIFQALSQPQVLLFSAT----- 309

Query: 435 LVLTSLGDIDISKITEKPAG---RKPIKTVIIPINRIDEVIERLKVVLSEGKKAYWICPQ 491
                     +S   EK A    +  I   I   NR ++ +++L         A W+  +
Sbjct: 310 ----------VSPEVEKFASSLAKDIILISIGNPNRPNKAVKQL---------AIWVETK 350

Query: 492 IEEKK-------ESNFRS-VVERFNS------LHEHFTSSIAI----IHGRMSDIDKESV 533
            +++K       + +F+   V   +S      L    T    +    IHG  S  ++  V
Sbjct: 351 QKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREV 410

Query: 534 MDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCI 593
           M SF  G   +++AT V+  G+D++    +II +  +     +HQ+ GR  R  E  + I
Sbjct: 411 MKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQI-GRASRMGEKGTAI 469

Query: 594 L 594
           +
Sbjct: 470 V 470


>gnl|CDD|179415 PRK02362, PRK02362, ski2-like helicase; Provisional.
          Length = 737

 Score = 41.1 bits (97), Expect = 0.001
 Identities = 20/55 (36%), Positives = 35/55 (63%), Gaps = 1/55 (1%)

Query: 304 SGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGN 358
           SGKTL+A +AM  A+  GG+A+ + P+  LA + +E  +++ +   + V I TG+
Sbjct: 50  SGKTLIAELAMLKAIARGGKALYIVPLRALASEKFEEFERFEE-LGVRVGISTGD 103


>gnl|CDD|181823 PRK09401, PRK09401, reverse gyrase; Reviewed.
          Length = 1176

 Score = 37.6 bits (88), Expect = 0.010
 Identities = 29/120 (24%), Positives = 54/120 (45%), Gaps = 16/120 (13%)

Query: 296 RILQGD-------VGSGKTLVALIAMAA--AVEAGGQAVIMAPIGILAQQHYEFIKKYTQ 346
           R+L G+        G GKT    + M+   A + G ++ I+ P  +L +Q  E ++K+ +
Sbjct: 91  RLLLGESFAIIAPTGVGKT-TFGLVMSLYLAKK-GKKSYIIFPTRLLVEQVVEKLEKFGE 148

Query: 347 NTQIIVEII--TGNMPQAHRRKALERIAHGQAHIIIGTHALFQ---DSIQYYKLILVIVD 401
                V+I+    ++ +  + + LER+  G   I++ T        D +   K   V VD
Sbjct: 149 KVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDELPKKKFDFVFVD 208



 Score = 31.4 bits (72), Expect = 0.80
 Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 7/72 (9%)

Query: 480 SEGKKAYWICPQIEEKKESNFRSVVERFNSLHE--HFTSSIAIIHGRMSDIDKESVMDSF 537
            +GKK+Y I P            VVE+     E       I   H  +   +KE  ++  
Sbjct: 121 KKGKKSYIIFP-----TRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERL 175

Query: 538 KNGTCKLLIATT 549
           K G   +L+ T+
Sbjct: 176 KEGDFDILVTTS 187


>gnl|CDD|166873 PRK00254, PRK00254, ski2-like helicase; Provisional.
          Length = 720

 Score = 37.1 bits (86), Expect = 0.015
 Identities = 36/115 (31%), Positives = 52/115 (45%), Gaps = 16/115 (13%)

Query: 304 SGKTLVALIAMAAAV-EAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQA 362
           SGKTLVA I M   +   GG+AV + P+  LA++ Y   K + +   + V + TG+    
Sbjct: 50  SGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYREFKDW-EKLGLRVAMTTGDYDST 108

Query: 363 HRRKALERIAHGQAHIIIGTHALFQDSIQYYK------LILVIVDEQHRFGVQQR 411
                      G+  III T   F DS+  +       + LV+ DE H  G   R
Sbjct: 109 DEWL-------GKYDIIIATAEKF-DSLLRHGSSWIKDVKLVVADEIHLIGSYDR 155



 Score = 34.4 bits (79), Expect = 0.11
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 510 LHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII--IEN 567
           L +     +A  H  +   ++  + D+F+ G  K++ AT  +  GI++    +II   + 
Sbjct: 290 LKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKR 349

Query: 568 AEHFGLA-----QLHQLRGRVGR 585
             +FG       ++ Q+ GR GR
Sbjct: 350 YSNFGWEDIPVLEIQQMMGRAGR 372


>gnl|CDD|183308 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
          Length = 460

 Score = 36.7 bits (86), Expect = 0.022
 Identities = 30/102 (29%), Positives = 50/102 (49%), Gaps = 10/102 (9%)

Query: 501 RSVVERFNSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDA 560
           +   E  ++L+    S++A+ HG +   D++ V+  F N +C +L+AT V   G+D+   
Sbjct: 253 KECQEVADALNAQGFSALAL-HGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKAL 311

Query: 561 SIIIIENAEHFGLA---QLHQLR-GRVGRGEEISSCILLYHP 598
             +I  N E   LA   ++H  R GR GR       + L  P
Sbjct: 312 EAVI--NYE---LARDPEVHVHRIGRTGRAGSKGLALSLVAP 348



 Score = 34.4 bits (80), Expect = 0.098
 Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 12/92 (13%)

Query: 297 ILQGDVGSGKTLVALIAMAAAVEA---GGQAVIMAPIGILAQQHYEFIKK---YTQNTQI 350
           I Q   GSGKT    + +   ++      QA+++ P   LA Q  + I++   +  N ++
Sbjct: 45  IAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKV 104

Query: 351 IVEIITGNMPQAHRRKALERIAHGQAHIIIGT 382
           +   + G +P   +  +LE   HG AHII+GT
Sbjct: 105 LT--LCGGVPMGPQIDSLE---HG-AHIIVGT 130


>gnl|CDD|185453 PTZ00110, PTZ00110, helicase; Provisional.
          Length = 545

 Score = 35.9 bits (83), Expect = 0.039
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 15/73 (20%)

Query: 521 IHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII-------IENAEHFGL 573
           IHG     ++  V++ FK G   ++IAT V   G+DV D   +I       IE+      
Sbjct: 407 IHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIED------ 460

Query: 574 AQLHQLRGRVGRG 586
             +H++ GR GR 
Sbjct: 461 -YVHRI-GRTGRA 471


>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ.  The
           ATP-dependent DNA helicase RecQ of E. coli is about 600
           residues long. This model represents bacterial proteins
           with a high degree of similarity in domain architecture
           and in primary sequence to E. coli RecQ. The model
           excludes eukaryotic and archaeal proteins with RecQ-like
           regions, as well as more distantly related bacterial
           helicases related to RecQ.
          Length = 591

 Score = 34.7 bits (80), Expect = 0.081
 Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 9/86 (10%)

Query: 517 SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIII----IENAEHFG 572
           S    H  +S+  +    + F     K+++AT    +GID  +   +I      N E + 
Sbjct: 250 SALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESY- 308

Query: 573 LAQLHQLRGRVGRGEEISSCILLYHP 598
               +Q  GR GR    +  ILLY P
Sbjct: 309 ----YQEAGRAGRDGLPAEAILLYSP 330


>gnl|CDD|183029 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
          Length = 434

 Score = 34.5 bits (80), Expect = 0.091
 Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 8/78 (10%)

Query: 495 KKESNFRSVV-----ERFNSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGTCKLLI 546
           K+    RS+V     ER + L         +   + G M    +   +    +G   +L+
Sbjct: 241 KQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLV 300

Query: 547 ATTVIEVGIDVVDASIII 564
           AT V   GID+ D S +I
Sbjct: 301 ATDVAARGIDIDDVSHVI 318


>gnl|CDD|179861 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
          Length = 572

 Score = 34.2 bits (78), Expect = 0.13
 Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 352 VEIITGNMPQAHRRKALERIAHGQAHIIIGT----HALFQDSIQY---YKLILVIVDEQH 404
           V +++G++PQ  R   L R   GQ  I++ T      L  D ++Y   Y L     D  H
Sbjct: 284 VGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVH 343

Query: 405 RFGVQQRL 412
           R G   RL
Sbjct: 344 RIGRTARL 351



 Score = 33.4 bits (76), Expect = 0.21
 Identities = 61/287 (21%), Positives = 118/287 (41%), Gaps = 43/287 (14%)

Query: 299 QGDVGSGKTLVALI----------AMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNT 348
           Q   G+GKTL  L+          A+A       +A+I+AP   LA Q ++   K+  + 
Sbjct: 52  QAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADL 111

Query: 349 QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKLI------LVIVDE 402
            +   ++ G +    +R+ L++       +II T     D ++ +K++      + ++DE
Sbjct: 112 GLRFALVYGGVDYDKQRELLQQ----GVDVIIATPGRLIDYVKQHKVVSLHACEICVLDE 167

Query: 403 QHRF-------GVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKI---TEKP 452
             R         ++  L+   +      LL +AT   R L L      +  K+   TE  
Sbjct: 168 ADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETI 227

Query: 453 AGRKPIKTVIIPINRIDEVIERLKVVL--SEGKKAYWICPQIEEKKESNFRSVVERFNSL 510
              +  + +  P +  +E    L  +L  SEG +              N ++ VER    
Sbjct: 228 TAARVRQRIYFPAD--EEKQTLLLGLLSRSEGARTMVFV---------NTKAFVERVART 276

Query: 511 HEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV 557
            E     + ++ G +    +ES+++ F+ G  ++L+AT V   G+ +
Sbjct: 277 LERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHI 323


>gnl|CDD|183441 PRK12326, PRK12326, preprotein translocase subunit SecA; Reviewed.
          Length = 764

 Score = 33.0 bits (76), Expect = 0.25
 Identities = 18/38 (47%), Positives = 21/38 (55%), Gaps = 8/38 (21%)

Query: 294 MLRILQGDV-----GSGKTLVALIAMAAAVEA-GGQAV 325
            LR+L GDV     G GKTL    A+AAA  A  G+ V
Sbjct: 87  ALRLLAGDVIEMATGEGKTLAG--AIAAAGYALQGRRV 122


>gnl|CDD|184873 PRK14873, PRK14873, primosome assembly protein PriA; Provisional.
          Length = 665

 Score = 33.0 bits (76), Expect = 0.29
 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 313 AMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIA 372
           A AA + AG  A+++ P      +    ++       + V  ++  +  A R +    + 
Sbjct: 180 AAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAV--LSAGLGPADRYRRWLAVL 237

Query: 373 HGQAHIIIGTHA 384
            GQA +++GT +
Sbjct: 238 RGQARVVVGTRS 249


>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
          Length = 674

 Score = 32.9 bits (75), Expect = 0.29
 Identities = 20/86 (23%), Positives = 44/86 (51%), Gaps = 9/86 (10%)

Query: 508 NSLHEHFTSSIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIEN 567
           +SL+E     +A  H  +S+  +  + + F+N   K+++AT  +  G++ + A ++I+ +
Sbjct: 278 DSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVN-LPARLVIVRD 336

Query: 568 AEHFGLA--------QLHQLRGRVGR 585
              +G          ++ Q+ GR GR
Sbjct: 337 ITRYGNGGIRYLSNMEIKQMIGRAGR 362


>gnl|CDD|162952 TIGR02621, cas3_GSU0051, CRISPR-associated helicase Cas3,
           Anaes-subtype.  This model describes a CRISPR-associated
           putative DEAH-box helicase, or Cas3, of a subtype found
           in Actinomyces naeslundii MG1, Geobacter sulfurreducens
           PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea
           psychrophila. This protein includes both DEAH and HD
           motifs.
          Length = 844

 Score = 32.7 bits (74), Expect = 0.30
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 545 LIATTVIEVGIDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSC-ILLYHPPLSKN 603
           L+ T+  EVG++ + A  ++ + A    + Q     GRV R  E+ +C I + H  L K+
Sbjct: 340 LVCTSAGEVGVN-ISADHLVCDLAPFESMQQRF---GRVNRFGELQACQIAVVHLDLGKD 395

Query: 604 S 604
            
Sbjct: 396 Q 396


>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
           activities.  AAA - ATPases associated with a variety of
           cellular activities. This profile/alignment only detects
           a fraction of this vast family. The poorly conserved
           N-terminal helix is missing from the alignment.
          Length = 148

 Score = 32.7 bits (74), Expect = 0.32
 Identities = 34/174 (19%), Positives = 57/174 (32%), Gaps = 32/174 (18%)

Query: 297 ILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIIT 356
           ++ G  GSGKT +A          GG  + +    IL +          Q   IIV    
Sbjct: 6   LIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEV-------LDQLLLIIVGGKK 58

Query: 357 GNMPQAHR-RKALERIAHGQAHIIIGTHALFQDSIQYYKLILVIVDEQHRFGVQQRLKLT 415
            +     R R AL                      +  K  ++I+DE       ++  L 
Sbjct: 59  ASGSGELRLRLALAL-------------------ARKLKPDVLILDEITSLLDAEQEALL 99

Query: 416 QKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRID 469
                  +LL+  +    T++LT+  + D+      PA  +      I +  I 
Sbjct: 100 LLLEELRLLLLLKSEKNLTVILTTNDEKDL-----GPALLRRRFDRRIVLLLIL 148


>gnl|CDD|162382 TIGR01479, GMP_PMI, mannose-1-phosphate
           guanylyltransferase/mannose-6-phosphate isomerase.  This
           enzyme is known to be bifunctional, as both
           mannose-6-phosphate isomerase (EC 5.3.1.8) (PMI) and
           mannose-1-phosphate guanylyltransferase (EC 2.7.7.22) in
           Pseudomonas aeruginosa, Xanthomonas campestris, and
           Gluconacetobacter xylinus. The literature on the enzyme
           from E. coli attributes mannose-6-phosphate isomerase
           activity to an adjacent gene, but the present sequence
           has not been shown to lack the activity. The PMI domain
           is C-terminal.
          Length = 468

 Score = 32.7 bits (75), Expect = 0.36
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 9/64 (14%)

Query: 375 QAHIIIGTHALFQDSIQY-----YKLILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTAT 429
           Q   ++G   + Q +++          LVI +E+HRF V ++L+      A +++L    
Sbjct: 25  QFLALVGDLTMLQQTLKRLAGLPCSSPLVICNEEHRFIVAEQLR-EIGKLASNIIL---E 80

Query: 430 PIPR 433
           P+ R
Sbjct: 81  PVGR 84


>gnl|CDD|183247 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
          Length = 629

 Score = 32.5 bits (74), Expect = 0.37
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 9/71 (12%)

Query: 519 AIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASII----IIENAEHFGLA 574
           A ++G M+   +E  ++  K+G   +LIAT V   G+DV   S++    I  ++E +   
Sbjct: 273 AALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESY--- 329

Query: 575 QLHQLRGRVGR 585
            +H++ GR GR
Sbjct: 330 -VHRI-GRTGR 338



 Score = 28.7 bits (64), Expect = 5.1
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 355 ITGNMPQAHRRKALERIAHGQAHIIIGT 382
           + G+M QA R + LER+  G+  I+I T
Sbjct: 275 LNGDMNQALREQTLERLKDGRLDILIAT 302


>gnl|CDD|178682 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
           Provisional.
          Length = 1195

 Score = 32.2 bits (73), Expect = 0.45
 Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 9/82 (10%)

Query: 519 AIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDVVDASIIIIENAEHFGLAQ--- 575
           A  HG M    +  V   +      ++ AT    +GI+  D   +I     H  L +   
Sbjct: 708 AFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVI-----HHSLPKSIE 762

Query: 576 -LHQLRGRVGRGEEISSCILLY 596
             HQ  GR GR  + SSC+L Y
Sbjct: 763 GYHQECGRAGRDGQRSSCVLYY 784


>gnl|CDD|162351 TIGR01420, pilT_fam, pilus retraction protein PilT.  This model
           represents the PilT subfamily of proteins related to
           GspE, a protein involved in type II secretion (also
           called the General Secretion Pathway). PilT is an
           apparent cytosolic ATPase associated with type IV pilus
           systems. It is not required for pilin biogenesis, but is
           required for twitching motility and social gliding
           behaviors, shown in some species, powered by pilus
           retraction. Members of this family may be found in some
           species that type IV pili but have related structures
           for DNA uptake and natural transformation.
          Length = 343

 Score = 31.9 bits (73), Expect = 0.57
 Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 12/98 (12%)

Query: 226 ERLAYDELLAGQIALLLMRKQFKKEIGIP------INV---EGKIAQKILRNIPFSPTKS 276
           ++L  + L   Q        +      +P      +N     G +A  +LR IP      
Sbjct: 47  QKLLREILSEKQREEFEENGELDFSYSLPGVSRFRVNAFKQRGGVAL-VLRLIPSKIPTF 105

Query: 277 QESAIKDILQDMSQKNRMLRILQGDVGSGK--TLVALI 312
           +E  +  +L++++++ R L ++ G  GSGK  TL ++I
Sbjct: 106 EELGLPPVLRELAERPRGLILVTGPTGSGKSTTLASMI 143


>gnl|CDD|163066 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
           Members of this protein family resemble the widely
           distributed ATP-dependent protease La, also called Lon
           and LonA. It resembles even more closely LonB, which is
           a LonA paralog found in genomes if and only if the
           species is capable of endospore formation (as in
           Bacillus subtilis, Clostridium tetani, and select other
           members of the Firmicutes) and expressed specifically in
           the forespore compartment. Members of this family are
           restricted to a subset of spore-forming species, and are
           very likely to participate in the program of endospore
           formation. We propose the designation LonC.
          Length = 615

 Score = 31.7 bits (72), Expect = 0.65
 Identities = 23/58 (39%), Positives = 29/58 (50%)

Query: 260 KIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAA 317
           K AQ +LR   FS    QE AIK +L  ++       IL G  G GKT  A +A+  A
Sbjct: 142 KSAQSLLRPRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEA 199


>gnl|CDD|114722 pfam06016, Reovirus_L2, Reovirus core-spike protein lambda-2 (L2). 
           This family consists of several Reovirus core-spike
           protein lambda-2 (L2) sequences. The reovirus L2 genome
           segment encodes the core spike protein lambda-2, which
           mediates enzymatic reactions in 5' capping of the viral
           plus-strand transcripts.
          Length = 1289

 Score = 31.7 bits (72), Expect = 0.72
 Identities = 12/38 (31%), Positives = 17/38 (44%)

Query: 407 GVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDID 444
           GVQQ +     A+   + L    P+P    L  L +ID
Sbjct: 907 GVQQLISQIVDASVKTLWLQLNCPLPSVGSLPGLLEID 944


>gnl|CDD|183476 PRK12366, PRK12366, replication factor A; Reviewed.
          Length = 637

 Score = 30.8 bits (70), Expect = 1.2
 Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 9/96 (9%)

Query: 49  PSSFIDRHYRPKISEISEERI-VTITGY---ISQHSSFQLQKRRPYK---ILLNDGTGEI 101
                +     KIS+I E +I V ITG    IS   +F  +     K   I + D TG I
Sbjct: 54  EYGQEEEEEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTGTI 113

Query: 102 TLLFFYRKTEMLKNVFFEGRKITVTG-KIKKLKNRI 136
            L  +    ++LK    EG  I +   + +K  N +
Sbjct: 114 RLTLWNDNAKLLKG-LKEGDVIKIENARSRKWNNDV 148



 Score = 30.0 bits (68), Expect = 1.9
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 7/83 (8%)

Query: 60  KISEISEERIVTITGY---ISQHSSFQLQKRRPY--KILLNDGTGEITLLFFYRKTEMLK 114
           +++E  +   V + G    IS     +   R      I L DGTG + + F+  K ++L+
Sbjct: 284 ELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGTGRVRVSFWGEKAKILE 343

Query: 115 NVFFEGRKITVTG-KIKKLKNRI 136
           N+  EG  + +   K++   +  
Sbjct: 344 NL-KEGDAVKIENCKVRTYYDNE 365


>gnl|CDD|181223 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
           polymerase III subunit epsilon; Validated.
          Length = 928

 Score = 30.7 bits (70), Expect = 1.3
 Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 11/48 (22%)

Query: 364 RRKALERIAHGQAHIIIGTHA-LFQDSIQYYKLI----LVIVDEQHRF 406
           + +A        A ++I  HA L  D      L+     +I+DE H F
Sbjct: 426 KNRAKF------ADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHF 467


>gnl|CDD|179884 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
          Length = 423

 Score = 30.3 bits (69), Expect = 1.9
 Identities = 28/106 (26%), Positives = 41/106 (38%), Gaps = 17/106 (16%)

Query: 299 QGDVGSGKTLVALIA-----MAAAVEAGGQ-----AVIMAPIGILAQQHYEFIKKYTQNT 348
           Q   G+GKT+  L A     ++       +     A+IMAP   LA Q +   +   Q T
Sbjct: 51  QAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQAT 110

Query: 349 QIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYK 394
            + + +  G      + K LE        I+IGT       I Y K
Sbjct: 111 GLKLGLAYGGDGYDKQLKVLES----GVDILIGTTGRL---IDYAK 149


>gnl|CDD|183820 PRK12898, secA, preprotein translocase subunit SecA; Reviewed.
          Length = 656

 Score = 30.0 bits (68), Expect = 1.9
 Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 6/87 (6%)

Query: 296 RILQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEII 355
           R+ +   G GKTL A +    A  AG    ++     LA++  E ++   +   + V  +
Sbjct: 119 RLAEMQTGEGKTLTATLPAGTAALAGLPVHVITVNDYLAERDAELMRPLYEALGLTVGCV 178

Query: 356 TGNMPQAHRRKALERIAHGQAHIIIGT 382
             +     RR A        A I   T
Sbjct: 179 VEDQSPDERRAAY------GADITYCT 199


>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
           Provisional.
          Length = 1490

 Score = 29.9 bits (67), Expect = 2.5
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 522 HGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV--VDASIIIIENAEHFGLAQLHQL 579
           HG +S   +     + K+G  + ++AT+ +E+GID+  VD   ++I+ A    +A   Q 
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVD---LVIQVATPLSVASGLQR 364

Query: 580 RGRVG 584
            GR G
Sbjct: 365 IGRAG 369


>gnl|CDD|150847 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
           3.  This is a family of conserved proteins which were
           originally described as death-associated-protein-3
           (DAP-3). The proteins carry a P-loop DNA-binding motif,
           and induce apoptosis. DAP3 has been shown to be a
           pro-apoptotic factor in the mitochondrial matrix and to
           be crucial for mitochondrial biogenesis and so has also
           been designated as MRP-S29 (mitochondrial ribosomal
           protein subunit 29).
          Length = 274

 Score = 29.1 bits (66), Expect = 3.7
 Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 286 QDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVEAG 321
            D S+K     +L G+ GSGK+++   AMA A+  G
Sbjct: 17  ADASKKVVR-FVLTGERGSGKSVLLAQAMAYALTQG 51


>gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated.
          Length = 233

 Score = 29.0 bits (65), Expect = 3.8
 Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 298 LQGDVGSGKTLVALIAMAAAVEAGGQAVIMAPI 330
           L G  G+GKT +AL A+ AA E  G++    P+
Sbjct: 46  LSGPAGTGKTHLAL-ALCAAAEQAGRSSAYLPL 77


>gnl|CDD|184957 PRK14995, PRK14995, methyl viologen resistance protein SmvA;
           Provisional.
          Length = 495

 Score = 29.3 bits (66), Expect = 3.9
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 160 YSLPTGLSVDLFKKIIVEALSRLPVLPEWIEKDLLQKKSFPSIAEAFNIIHN 211
           Y L  GL + +F  ++  + S    LP  +   L++K S  SI EA  + ++
Sbjct: 396 YELGAGLGIAIFGLLLSRSYSASIRLPAGLPAQLIEKAS-SSIGEAVQLANS 446


>gnl|CDD|162340 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
           Gram-positive type.  The N-terminal region of about 200
           amino acids is rich in low-complexity sequence, poorly
           alignable, and not included n this model.
          Length = 1213

 Score = 28.9 bits (65), Expect = 4.3
 Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 7/75 (9%)

Query: 64  ISEERIVTITGYISQHSSFQLQ-KRRPYKILLNDGTGEITLLFFYRKTEMLKNVFFEGRK 122
             EE  V I GYI +    +L+  R   KI + D T  + L  F +  E  +   F+G K
Sbjct: 4   NEEENRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPE--KFDGIK 61

Query: 123 IT----VTGKIKKLK 133
           I       GKI+   
Sbjct: 62  IGKWVRARGKIELDN 76


>gnl|CDD|149617 pfam08623, TIP120, TATA-binding protein interacting (TIP20).
           TIP120 (also known as cullin-associated and
           neddylation-dissociated protein 1) is a TATA binding
           protein interacting protein that enhances transcription.
          Length = 169

 Score = 28.7 bits (65), Expect = 5.3
 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 467 RIDEVIERLKVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAIIH 522
           R+D + E L+  LS+  K   +  +IE+++E   RSV+    SL+     +    H
Sbjct: 103 RLDSLAEPLRKTLSKKVKEKAVKQEIEKQQELI-RSVLRLVVSLNLKLPEAEDSPH 157


>gnl|CDD|149922 pfam09015, NgoMIV_restric, NgoMIV restriction enzyme.  Members of
           this family are prokaryotic DNA restriction enzymes,
           exhibiting an alpha/beta structure, with a central
           region comprising a mixed six-stranded beta-sheet with
           alpha-helices on each side. A long 'arm' protrudes out
           of the core of the domain between strands beta2 and
           beta3 and is mainly involved in the tetramerisation
           interface of the protein. These restriction enzymes
           recognize the double-stranded sequence GCCGGC and cleave
           after G-1.
          Length = 277

 Score = 28.6 bits (64), Expect = 5.8
 Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 2/31 (6%)

Query: 416 QKATAPHVLLMTATPIPRTLVLTSL--GDID 444
           +K   PH++++TA P+P  +   +L  GDID
Sbjct: 200 RKGRLPHIVVVTAEPLPSRIASLALGTGDID 230


>gnl|CDD|173333 PTZ00036, PTZ00036, glycogen synthase kinase; Provisional.
          Length = 440

 Score = 28.5 bits (63), Expect = 6.3
 Identities = 12/24 (50%), Positives = 17/24 (70%)

Query: 276 SQESAIKDILQDMSQKNRMLRILQ 299
           S++ AIK +LQD   KNR L I++
Sbjct: 91  SEKVAIKKVLQDPQYKNRELLIMK 114


>gnl|CDD|179031 PRK00448, polC, DNA polymerase III PolC; Validated.
          Length = 1437

 Score = 28.3 bits (64), Expect = 7.0
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 8/76 (10%)

Query: 60  KISEIS-EERIVTITGYISQHSSFQLQKRRP-YKILLNDGTGEITLLFFYRKTEMLKNVF 117
            + EI+ EER V + GY+ +    +L+  R      + D T  I +  F R  E LK   
Sbjct: 228 PMKEINEEERRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLK--K 285

Query: 118 FEGRK----ITVTGKI 129
           F+  K    + V G +
Sbjct: 286 FDEIKKGDWVKVRGSV 301


>gnl|CDD|148880 pfam07517, SecA_DEAD, SecA DEAD-like domain.  SecA protein binds to
           the plasma membrane where it interacts with proOmpA to
           support translocation of proOmpA through the membrane.
           SecA protein achieves this translocation, in association
           with SecY protein, in an ATP dependent manner. This
           domain represents the N-terminal ATP-dependent helicase
           domain, which is related to the pfam00270.
          Length = 381

 Score = 28.3 bits (64), Expect = 7.8
 Identities = 32/127 (25%), Positives = 53/127 (41%), Gaps = 27/127 (21%)

Query: 295 LRILQGDV-----GSGKTLVALIAMAAAVEA-GGQAVIMAPIG-ILAQQHYEFIKKYTQN 347
           L + +G +     G GKTL A   + A + A  G+ V +  +   LA++  E++    + 
Sbjct: 87  LVLHEGKIAEMKTGEGKTLTA--TLPAYLNALSGKGVHVVTVNDYLAKRDAEWMGPLYEF 144

Query: 348 TQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQ-----DSIQYYK-------L 395
             + V +IT +M    RR+A          I  GT++        D++   K       L
Sbjct: 145 LGLSVGVITSDMSPEERREAY------NCDITYGTNSELGFDYLRDNMALSKEDKVQRGL 198

Query: 396 ILVIVDE 402
              IVDE
Sbjct: 199 NFAIVDE 205


>gnl|CDD|184796 PRK14701, PRK14701, reverse gyrase; Provisional.
          Length = 1638

 Score = 28.3 bits (63), Expect = 7.9
 Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 7/71 (9%)

Query: 481 EGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTSSIAII--HGRMSDIDKESVMDSFK 538
           +GKK Y I P     K+      VE+  S  E     + ++  H  +   +KE  ++  +
Sbjct: 121 KGKKCYIILPTTLLVKQ-----TVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIE 175

Query: 539 NGTCKLLIATT 549
           NG   +L+ T 
Sbjct: 176 NGDFDILVTTA 186


>gnl|CDD|135660 PRK05927, PRK05927, hypothetical protein; Provisional.
          Length = 350

 Score = 27.9 bits (62), Expect = 8.5
 Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 1/39 (2%)

Query: 497 ESNFRSVVERFNSLHEHFTSSIAIIHG-RMSDIDKESVM 534
           E   R  V+ F SLH HF S++ I H  ++S I  E  +
Sbjct: 112 EELVRITVKEFPSLHPHFFSAVEIAHAAQVSGISTEQAL 150


>gnl|CDD|182572 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
          Length = 456

 Score = 27.8 bits (62), Expect = 9.3
 Identities = 13/39 (33%), Positives = 22/39 (56%)

Query: 519 AIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVGIDV 557
           A IHG  S   +   +  FK+G  ++L+AT +   G+D+
Sbjct: 273 AAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDI 311


>gnl|CDD|132559 TIGR03520, GldE, gliding motility-associated protein GldE.  Members
           of this protein family are exclusive to the
           Bacteroidetes phylum (previously
           Cytophaga-Flavobacteria-Bacteroides). GldC is a protein
           linked to a type of rapid surface gliding motility found
           in certain Bacteroidetes, such as Flavobacterium
           johnsoniae and Cytophaga hutchinsonii. GldE was
           discovered because of its adjacency to GldD in F.
           johnsonii. Overexpression of GldE partially supresses
           the effects of a GldB point mutant suggesting that GldB
           and GldE interact. Gliding motility appears closely
           linked to chitin utilization in the model species
           Flavobacterium johnsoniae. Not all Bacteroidetes with
           members of this protein family appear to have all of the
           genes associated with gliding motility and in fact some
           do not appear to express the gliding phenotype.
          Length = 408

 Score = 27.7 bits (62), Expect = 9.4
 Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 24/66 (36%)

Query: 169 DLFKKIIVEALSRLPVLPEWIE--------KDLLQKKSFPSIAEAFNIIHNPRKAKDFEW 220
           ++  KII    SR+PV  E I+        KDLL     P +             K+F+W
Sbjct: 214 EIIPKIIENGYSRIPVYKETIDNITGVLYIKDLL-----PHL-----------NKKNFDW 257

Query: 221 TSPARE 226
            S  RE
Sbjct: 258 QSLLRE 263


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.322    0.138    0.393 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 11,728,270
Number of extensions: 804150
Number of successful extensions: 1968
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1927
Number of HSP's successfully gapped: 92
Length of query: 700
Length of database: 5,994,473
Length adjustment: 100
Effective length of query: 600
Effective length of database: 3,833,673
Effective search space: 2300203800
Effective search space used: 2300203800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.3 bits)