RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780332|ref|YP_003064745.1| replicative DNA helicase
[Candidatus Liberibacter asiaticus str. psy62]
         (504 letters)



>gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional.
          Length = 497

 Score =  817 bits (2113), Expect = 0.0
 Identities = 313/494 (63%), Positives = 391/494 (79%), Gaps = 3/494 (0%)

Query: 8   IILSIPKEDSSQYRESPNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEI 67
           ++   P     + RE P+NIEAEQALLGAIL+NN A  RVSDFLKP HFFE +HQ+I+E 
Sbjct: 6   VLDLAPDAAEPEIRELPHNIEAEQALLGAILINNRALDRVSDFLKPEHFFEPLHQRIYEA 65

Query: 68  MGKLVHMGKTANPVTVKTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLAL 127
           + K++  GK A PVT+KTFL + + LGEL   QYLA+LA+EAV+IIN  DYGRIIY LAL
Sbjct: 66  IAKIIRKGKLATPVTLKTFLENDEALGELGGVQYLAKLATEAVTIINARDYGRIIYDLAL 125

Query: 128 RRTLITIGEEMVNAAYEASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVAID 187
           RR LI IGE++VN AY+A +D +P  QIE+AE+KL+ LAE GRY+GGF +F  A+T A+D
Sbjct: 126 RRELINIGEDVVNNAYDAPVDVAPQEQIEDAEQKLYELAETGRYEGGFQSFGTAITEAVD 185

Query: 188 MAGQAFNRDGRLAGVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAY 247
           MA  AF RDG L+G+STG++ LD ++GGL  SDLII+AGRP MGKT+LATNIA+N A AY
Sbjct: 186 MANAAFKRDGHLSGISTGLRDLDSKLGGLHPSDLIILAGRPSMGKTALATNIAFNAAKAY 245

Query: 248 KAELQTDGSYKTINGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIV 307
           + E Q DGS K +NGG+VGF+SLEMS+EQLATRI+SEQ+E+ SSKIRRG+++  D+EK+V
Sbjct: 246 RREAQPDGSKKAVNGGVVGFFSLEMSAEQLATRILSEQSEISSSKIRRGKISEEDFEKLV 305

Query: 308 ACSQVMQKLPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMT-TSKKIEENRV 366
             SQ +QKLPLYID T  +S+SQL  RARRLKRQ GLDLL+VDY+QL+  +SK+  +NRV
Sbjct: 306 DASQELQKLPLYIDDTPALSISQLRARARRLKRQHGLDLLVVDYLQLIRGSSKRSSDNRV 365

Query: 367 LEITGITMALKALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFV 426
            EI+ IT  LKALAKELNIP+IALSQLSRQVE RD+KRPQLSDLRESGSIEQDADVV+FV
Sbjct: 366 QEISEITQGLKALAKELNIPVIALSQLSRQVEQRDDKRPQLSDLRESGSIEQDADVVMFV 425

Query: 427 IRDEYYIRNKEPTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTR 486
            R+EYY++ KEP        + +WQE +++V   A++IIAKQRHGPTGTV LAF++EFTR
Sbjct: 426 YREEYYLKRKEPREGTP--KHEEWQEKMEKVHNKAEVIIAKQRHGPTGTVKLAFESEFTR 483

Query: 487 FSALSDSSYQTGEH 500
           F  L+D S    E+
Sbjct: 484 FGDLADRSQLPEEY 497


>gnl|CDD|161985 TIGR00665, DnaB, replicative DNA helicase.  This model describes
           the helicase DnaB, a homohexameric protein required for
           DNA replication. The homohexamer can form a ring around
           a single strand of DNA near a replication fork. An
           intein of > 400 residues is found at a conserved
           location in DnaB of Synechocystis PCC6803, Rhodothermus
           marinus (both experimentally confirmed), and
           Mycobacterium tuberculosis. The intein removes itself by
           a self-splicing reaction. The seed alignment contains
           inteins so that the model built from the seed alignment
           will model a low cost at common intein insertion sites.
          Length = 434

 Score =  602 bits (1555), Expect = e-173
 Identities = 220/469 (46%), Positives = 297/469 (63%), Gaps = 37/469 (7%)

Query: 24  PNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTANPVTV 83
           P+NIEAEQA+LGAIL++NEA   V++ LKP  F+   HQ IF+ +  L   G+  + VTV
Sbjct: 3   PHNIEAEQAVLGAILLDNEAIDDVAEILKPEDFYRPAHQLIFQAILDLYEKGEPIDLVTV 62

Query: 84  KTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEMVNAAY 143
           K  L     L E+    YLA LA    S  N E Y  I+   A+ R LI  G E+V  AY
Sbjct: 63  KEELEKDGKLEEVGGLAYLAELADNVPSAANIEYYAEIVKEKAILRRLIEAGTEIVELAY 122

Query: 144 EASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVAIDMAGQAFNRDGRLAGVS 203
           +   D      ++EAE+K+F +AE+ R  GGF +  + +   ++   + + R G + GV 
Sbjct: 123 DPEGD--VEELLDEAEQKIFEIAES-RTSGGFKSIKEILKDTVEEIEELYERGGGITGVP 179

Query: 204 TGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGG 263
           TG   LDK   GLQ SDLII+A RP MGKT+ A NIA N A                 G 
Sbjct: 180 TGFTDLDKLTSGLQPSDLIILAARPSMGKTAFALNIAENAA--------------IKEGK 225

Query: 264 IVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQT 323
            V F+SLEMS+EQLA R++S ++ V S K+R G+L+  D+EK+ + +  + + PLYID T
Sbjct: 226 PVAFFSLEMSAEQLAMRMLSSESRVDSQKLRTGKLSDEDWEKLTSAAGKLSEAPLYIDDT 285

Query: 324 GGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKALAKEL 383
            G+++++L  +ARRLKR+ GL L+++DY+QLM+ S +  ENR  E++ I+ +LKALAKEL
Sbjct: 286 PGLTITELRAKARRLKREHGLGLIVIDYLQLMSGSGR-SENRQQEVSEISRSLKALAKEL 344

Query: 384 NIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKEPTNKDD 443
           N+P+IALSQLSR VE R++KRPQLSDLRESGSIEQDAD+V+F+ RDEYY  N +  +   
Sbjct: 345 NVPVIALSQLSRSVEQREDKRPQLSDLRESGSIEQDADIVMFLYRDEYY--NPDSED--- 399

Query: 444 ILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRFSALSD 492
                         KGIA+IIIAKQR+GPTGTV LAFQ E+TRF  L+ 
Sbjct: 400 --------------KGIAEIIIAKQRNGPTGTVKLAFQGEYTRFENLAR 434


>gnl|CDD|180232 PRK05748, PRK05748, replicative DNA helicase; Provisional.
          Length = 448

 Score =  417 bits (1075), Expect = e-117
 Identities = 197/482 (40%), Positives = 279/482 (57%), Gaps = 37/482 (7%)

Query: 16  DSSQYRESPNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMG 75
           + +  R  P +IEAEQA+LGAI ++ +A   VS++L P  F+   H+ IF  M KL   G
Sbjct: 3   EVAALRVPPQSIEAEQAVLGAIFLDPDALITVSEYLSPDDFYRHAHRLIFRAMLKLSDRG 62

Query: 76  KTANPVTVKTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIG 135
           +  + VTV   L DQ  L E+    YLA LA+   +  N E Y +I+   A+ R LI   
Sbjct: 63  EPIDVVTVTEILDDQGDLEEVGGLSYLAELANSVPTAANIEYYAKIVAEKAMLRRLIRTA 122

Query: 136 EEMVNAAYEASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVAIDMAGQAFNR 195
            E+ N AYE   D +  I ++EAE+K+F ++E  R   GF    D +  A D      N+
Sbjct: 123 TEIANDAYEPE-DDADEI-LDEAEKKIFEVSER-RNKSGFKNIKDVLVKAYDRIEMLHNQ 179

Query: 196 DGRLAGVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDG 255
            G + G+ TG   LDK   GLQ +DLII+A RP +GKT+ A NIA NVA       +TD 
Sbjct: 180 TGDITGIPTGFTDLDKMTSGLQPNDLIIVAARPSVGKTAFALNIAQNVA------TKTDK 233

Query: 256 SYKTINGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQK 315
           +        V  +SLEM +E L  R++  +  + + ++R G+LT  D+ K+      +  
Sbjct: 234 N--------VAIFSLEMGAESLVMRMLCAEGNIDAQRLRTGQLTDDDWPKLTIAMGSLSD 285

Query: 316 LPLYIDQTGGISMSQLATRARRLKRQR-GLDLLIVDYIQLMTTSKKIEENRVLEITGITM 374
            P+YID T GI ++++  R RRL ++  GL L+++DY+QL+  S +  ENR  E++ I+ 
Sbjct: 286 APIYIDDTPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQGSGRSGENRQQEVSEISR 345

Query: 375 ALKALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIR 434
           +LKALAKEL +P+IALSQLSR VE R +KRP +SD+RESGSIEQDAD+V F+ RD+YY  
Sbjct: 346 SLKALAKELKVPVIALSQLSRGVEQRQDKRPVMSDIRESGSIEQDADIVAFLYRDDYY-- 403

Query: 435 NKEPTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRFSALSDSS 494
           ++E  N                 K   +IIIAKQR+GP GTV LAFQ E+ +F  L+   
Sbjct: 404 DEETEN-----------------KNTIEIIIAKQRNGPVGTVELAFQKEYNKFVNLARRE 446

Query: 495 YQ 496
             
Sbjct: 447 ED 448


>gnl|CDD|132639 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family,
           HK022 subfamily.  Members of this family are phage (or
           prophage-region) homologs of the bacterial homohexameric
           replicative helicase DnaB. Some phage may rely on host
           DnaB, while others encode their own verions. This model
           describes the largest phage-specific clade among the
           close homologs of DnaB, but there are, or course, other
           DnaB homologs from phage that fall outside the scope of
           this model.
          Length = 421

 Score =  360 bits (926), Expect = e-100
 Identities = 174/459 (37%), Positives = 262/459 (57%), Gaps = 42/459 (9%)

Query: 26  NIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTANPVTVKT 85
           +IEAEQA+LG +L++N+   RV   LKP HF+   H+ IFE M  +    +  +P+T+  
Sbjct: 1   SIEAEQAVLGGLLLDNDFIERVMAILKPEHFYSQDHRIIFEAMLDMFAENRPVDPLTLAD 60

Query: 86  FLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEMVNAAYEA 145
            L  +    ++    YLA +++   S  N   Y RI+   A  R LI   + +++ A  +
Sbjct: 61  KLEAEGEAEKVGGLAYLAEISNNTPSAANISSYARIVREKAKERKLIAACQRIIDLAC-S 119

Query: 146 SLDKSPSIQIEEAERKLFHLAENGRYDG---GFHTFSDAMTVAIDMAGQAFNRDGRLAGV 202
              ++   ++EEA+  L  L   G  DG   GF TF + +   +    + FN  G L G+
Sbjct: 120 DGGQTAEQKVEEAQAALLAL--TGMSDGQERGFVTFGEVLEDVVRDLDKRFNPKGELTGL 177

Query: 203 STGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTING 262
           STG+  LD+   GL + DLI+I  RP MGKT+LA NIA NVA                 G
Sbjct: 178 STGLPKLDRLTNGLVKGDLIVIGARPSMGKTTLALNIAENVALR--------------EG 223

Query: 263 GIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQ 322
             V F+SLEMS+EQL  R+++ ++ + +  IR G     D+ +++     + +  LYID 
Sbjct: 224 KPVLFFSLEMSAEQLGERLLASKSGINTGNIRTGRFNDSDFNRLLNAVDRLSEKDLYIDD 283

Query: 323 TGGISMSQLATRARRLKRQ-RGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKALAK 381
           TGG++++Q+ + ARR+KR+  GLDL++VDYIQLM  ++    +R  E+ GI+  LKALAK
Sbjct: 284 TGGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMAPTRG--RDRNEELGGISRGLKALAK 341

Query: 382 ELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKEPTNK 441
           EL++P++ L+QL+R  E R +KRP +SDLR+SG+IEQDADV+  + R+ YY   + P   
Sbjct: 342 ELDVPVVLLAQLNRGSEKRTDKRPIMSDLRDSGAIEQDADVIGLIHREGYYDAREPPA-- 399

Query: 442 DDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAF 480
                            G+A++I+AK RHGPTGTV L F
Sbjct: 400 -----------------GVAELILAKNRHGPTGTVELLF 421


>gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated.
          Length = 886

 Score =  323 bits (829), Expect = 7e-89
 Identities = 141/419 (33%), Positives = 221/419 (52%), Gaps = 22/419 (5%)

Query: 10  LSIPKEDSSQY----RESPNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIF 65
           L+   + S       R+ P ++ AEQ++LG +L++ EA  RV + L+P  F+   HQ I+
Sbjct: 7   LAPGMDSSPPSEDYGRQPPQDLAAEQSVLGGMLLSKEAIARVLERLRPGAFYRPAHQNIY 66

Query: 66  EIMGKLVHMGKTANPVTVKTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGL 125
           + +  L   G+ A+ VTV   L  + +L  +    YL  L S   +  N + Y RI+   
Sbjct: 67  DAILDLYGRGEPADLVTVAAELDRRGLLERIGGAPYLHTLISTVPTAANADYYARIVAEK 126

Query: 126 ALRRTLITIGEEMVNAAYEASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVA 185
           AL R LI  G  +V   Y    D    + ++ A+ +++ + +  R    F    D +   
Sbjct: 127 ALLRRLIEAGTRIVQYGYAEGAD-VAEV-VDRAQAEIYDVTDR-RLSEDFVALEDLLQPT 183

Query: 186 IDMAGQAFNRDGRLAGVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVAD 245
            D      +  G   GV TG   LD    GL    LII+A RP MGKT+   + A N A 
Sbjct: 184 FDEIDAIASSGGLARGVPTGFTELDAMTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAI 243

Query: 246 AYKAELQTDGSYKTINGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEK 305
            ++                V  +SLEMS EQL  R++S + ++  S +R G ++  D+ +
Sbjct: 244 RHRLA--------------VAIFSLEMSKEQLVMRLLSAEAKIKLSDMRSGRMSDDDWTR 289

Query: 306 IVACSQVMQKLPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENR 365
           +      + + P++ID T  +++ ++  +ARRL+++  L L++VDY+QLMT+ KK  ENR
Sbjct: 290 LARAMGEISEAPIFIDDTPNLTVMEIRAKARRLRQEANLGLIVVDYLQLMTSGKKY-ENR 348

Query: 366 VLEITGITMALKALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVL 424
             E++ I+  LK LAKEL +P++ALSQLSR VE R +KRP LSDLRESG +  D  ++ 
Sbjct: 349 QQEVSEISRHLKLLAKELEVPVVALSQLSRGVEQRTDKRPMLSDLRESGCLTGDTLILR 407



 Score = 80.6 bits (199), Expect = 1e-15
 Identities = 33/79 (41%), Positives = 44/79 (55%), Gaps = 19/79 (24%)

Query: 415 SIEQDADVVLFVIRDEYYIRNKEPTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTG 474
           SIEQDADVV+ + R +YY    +  +                  G A+ I+AK R+GPTG
Sbjct: 827 SIEQDADVVILLYRPDYY----DRDDPR---------------GGEAEFIVAKHRNGPTG 867

Query: 475 TVTLAFQAEFTRFSALSDS 493
           TVTLAFQ   +RF+ L+ S
Sbjct: 868 TVTLAFQLHLSRFANLARS 886


>gnl|CDD|180791 PRK07004, PRK07004, replicative DNA helicase; Provisional.
          Length = 460

 Score =  322 bits (827), Expect = 1e-88
 Identities = 182/471 (38%), Positives = 267/471 (56%), Gaps = 39/471 (8%)

Query: 21  RESPNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTANP 80
           +  P++IEAEQ++LG +L++N A+ R++DFL    F+   H+ IFE +G+L+   + A+ 
Sbjct: 13  KVPPHSIEAEQSVLGGLLLDNAAWDRIADFLSQSDFYRYDHRIIFEHIGRLIAATRPADV 72

Query: 81  VTVKTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEMVN 140
           +TV   L+      E+    YL  LA    S  N   Y  I+   A+ R L+++ +E+  
Sbjct: 73  ITVYEALTTSGKAEEVGGLAYLNALAQNTPSAANIRRYAEIVRDRAVLRRLVSVADEISA 132

Query: 141 AAYEASLDKSPSIQIEEAERKLFHLAENG-RYDGGFHTFSDAMTVAIDMAGQAFNRDGR- 198
            A+     K     ++EAE K+F +AE G R   GF      +T  ++     ++     
Sbjct: 133 DAFNPQ-GKEVRQLLDEAESKVFSIAEEGARGTQGFLEIGPLLTQVVERIDTLYHTANPS 191

Query: 199 -LAGVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSY 257
            + G  TG   LD+   G+   +LII+AGRP MGKT+ + NI   VA  Y          
Sbjct: 192 DVTGTPTGFVDLDRMTSGMHGGELIIVAGRPSMGKTAFSMNIGEYVAVEY---------- 241

Query: 258 KTINGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLP 317
               G  V  +S+EM   QLA R++     +   ++R G LT  D+ K+    Q M +  
Sbjct: 242 ----GLPVAVFSMEMPGTQLAMRMLGSVGRLDQHRMRTGRLTDEDWPKLTHAVQKMSEAQ 297

Query: 318 LYIDQTGGISMSQLATRARRLKRQRG-LDLLIVDYIQLMTTSKKIEENRVLEITGITMAL 376
           L+ID+TGG++  +L +RARRL RQ G L L+I+DY+QLM+ S +  ENR  EI+ I+ +L
Sbjct: 298 LFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSSQ-GENRATEISEISRSL 356

Query: 377 KALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNK 436
           K+LAKEL++P+IALSQL+R +E R NKRP +SDLRESG+IEQDADV+LF+ RDE Y    
Sbjct: 357 KSLAKELDVPVIALSQLNRGLEQRPNKRPVMSDLRESGAIEQDADVILFIYRDEVY---- 412

Query: 437 EPTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRF 487
            P + D               KG A+III KQR+GP G V L F  ++T+F
Sbjct: 413 NPDSPD---------------KGTAEIIIGKQRNGPIGPVRLTFLGQYTKF 448


>gnl|CDD|181547 PRK08760, PRK08760, replicative DNA helicase; Provisional.
          Length = 476

 Score =  317 bits (813), Expect = 5e-87
 Identities = 177/484 (36%), Positives = 266/484 (54%), Gaps = 39/484 (8%)

Query: 19  QYRESPNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTA 78
           Q R  P+++EAEQA+LG +++  +A  RV+D L    F+   H+ I+  + +L    +  
Sbjct: 29  QLRVPPHSVEAEQAVLGGLMLAPDALDRVNDQLTENDFYRRDHRLIYRAIRELSEKDRPF 88

Query: 79  NPVTVKTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEM 138
           + VT+  +   Q  L ++    YL  LAS   S  N   Y  I+   A+ R LI +G  +
Sbjct: 89  DAVTLGEWFESQGKLEQVGDGAYLIELASTTPSAANIAAYAEIVRDKAVLRQLIEVGTTI 148

Query: 139 VNAAYEASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSD---AMTVAIDMAGQAFNR 195
           VN  ++    +S  + +  AE+ +F +AE G    G   F     A+  A +     F  
Sbjct: 149 VNDGFQPEGRESIEL-LASAEKAVFKIAEAGAR--GRTDFVAMPGALKDAFEELRNRFEN 205

Query: 196 DGRLAGVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDG 255
            G + G+ TG    D    GLQ +DLII+A RP MGKT+ A NIA   A   K       
Sbjct: 206 GGNITGLPTGYNDFDAMTAGLQPTDLIILAARPAMGKTTFALNIAEYAAIKSKKG----- 260

Query: 256 SYKTINGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQK 315
                    V  +S+EMS+ QLA R+IS    + + ++R G L   D+ ++    +++++
Sbjct: 261 ---------VAVFSMEMSASQLAMRLISSNGRINAQRLRTGALEDEDWARVTGAIKMLKE 311

Query: 316 LPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMA 375
             ++ID T G+S   L ++ RRLKR+  L L+++DY+QLM+      ENR  EI+ I+ +
Sbjct: 312 TKIFIDDTPGVSPEVLRSKCRRLKREHDLGLIVIDYLQLMSVPGN-SENRATEISEISRS 370

Query: 376 LKALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRN 435
           LK LAKELN+P+IALSQL+R +E R +KRP ++DLRESG+IEQDAD+++F+ RD+YY  N
Sbjct: 371 LKGLAKELNVPVIALSQLNRSLETRTDKRPVMADLRESGAIEQDADMIVFIYRDDYY--N 428

Query: 436 KEPTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRFSALSDSSY 495
           KE +                  KG+A+III K R GPTG+  L F  E+TRF  L+  S 
Sbjct: 429 KENSPD----------------KGLAEIIIGKHRGGPTGSCKLKFFGEYTRFDNLAHDSV 472

Query: 496 QTGE 499
            + E
Sbjct: 473 GSFE 476


>gnl|CDD|181451 PRK08506, PRK08506, replicative DNA helicase; Provisional.
          Length = 472

 Score =  311 bits (800), Expect = 2e-85
 Identities = 164/480 (34%), Positives = 260/480 (54%), Gaps = 30/480 (6%)

Query: 26  NIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTANPVTVKT 85
           +++ E+A+L +IL + + F  ++  L+P  F+   HQ IFE M KL +  +  +   ++ 
Sbjct: 6   DLDIERAVLSSILFSPDKFEEIASVLEPKDFYLPAHQDIFEAMLKLHNEDEPIDEEFIRK 65

Query: 86  FLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEMVNAAYEA 145
            L     + E  + + LA        I N E Y   I   +++R L+++   +   A E 
Sbjct: 66  KLPKDKKIDEEILLEILA-----TNPIDNIEAYVEEIKEKSIKRELLSLANTIPEQAVEE 120

Query: 146 SLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVAIDMAGQAFNRDGR-LAGVST 204
             D+  S  ++E ER+L+ +  NG     F    + +   ++   +      + + G+ T
Sbjct: 121 --DQKSSDILDEVERELYSIT-NGSNSEDFKDSKEVIESTMEHIKKQKRLGNKDIIGLDT 177

Query: 205 GIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGI 264
           G   L+K   G  + DLIIIA RP MGKT+L  N+A    +  K                
Sbjct: 178 GFVELNKMTKGFNKGDLIIIAARPSMGKTTLCLNMALKALNQDKG--------------- 222

Query: 265 VGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQTG 324
           V F+SLEM +EQL  R++S +T +P   +R G+L   ++E++      + K  L++  +G
Sbjct: 223 VAFFSLEMPAEQLMLRMLSAKTSIPLQNLRTGDLDDDEWERLSDACDELSKKKLFVYDSG 282

Query: 325 GISMSQLATRARRLKRQ-RGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKALAKEL 383
            +++ Q+  + R+LK Q   + L ++DY+QLM+ S   ++ R L+I+ I+  LK LA+EL
Sbjct: 283 YVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMSGSGNFKD-RHLQISEISRGLKLLAREL 341

Query: 384 NIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKEPTNKDD 443
           +IPIIALSQL+R +E+R +KRP LSDLRESG+IEQDAD++LFV RD+ Y   +E   +  
Sbjct: 342 DIPIIALSQLNRSLESRADKRPMLSDLRESGAIEQDADIILFVYRDDVYKEREEKEKEKK 401

Query: 444 ILAYTKWQEDLKRVKGI---ADIIIAKQRHGPTGTVTLAFQAEFTRF-SALSDSSYQTGE 499
                K +  +         A+III K R+GPTGTV L FQ EFTRF     +S Y+ GE
Sbjct: 402 AKKEGKEERRIHFQNKSIEEAEIIIGKNRNGPTGTVKLRFQKEFTRFVDKPIESHYEEGE 461


>gnl|CDD|180157 PRK05595, PRK05595, replicative DNA helicase; Provisional.
          Length = 444

 Score =  305 bits (783), Expect = 2e-83
 Identities = 173/473 (36%), Positives = 262/473 (55%), Gaps = 37/473 (7%)

Query: 18  SQYRESPNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKT 77
           +  R  P +IEAEQ++LGA++++  +    ++ LK   F+   H+ IF  + +L      
Sbjct: 3   APIRSLPQSIEAEQSVLGAMIIDKTSIAEAAEVLKSEDFYRDSHKVIFSAIIELYQKDIA 62

Query: 78  ANPVTVKTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEE 137
            + +T+   L   D L       Y+  L++  VS  N + Y +I+   +  R LI    E
Sbjct: 63  VDMLTLTENLKSTDKLEAAGGVTYITELSNSIVSTANIQSYIKIVKDKSTLRRLIKSSTE 122

Query: 138 MVNAAYEASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVAIDMAGQAFNRDG 197
           ++  +Y    D    + I+ AE+K+F ++E  R    F   S+ +    +     FN  G
Sbjct: 123 IIENSYNNQ-DDVEKV-IDSAEKKIFDISEK-RTTSDFEPLSNVLERGFEQIENLFNNKG 179

Query: 198 RLAGVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSY 257
              GV++G + LD +  G Q+ D+I+IA RP MGKT+ A NIA   A             
Sbjct: 180 ETTGVASGFRELDAKTSGFQKGDMILIAARPSMGKTTFALNIAEYAA------------- 226

Query: 258 KTINGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLP 317
               G  V  +SLEMS EQLA +++  +  V   ++R G L   D+E I   S  +    
Sbjct: 227 -LREGKSVAIFSLEMSKEQLAYKLLCSEANVDMLRLRTGNLEDKDWENIARASGPLAAAK 285

Query: 318 LYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALK 377
           ++ID T G+S+ ++ ++ RRLK + G+D++++DY+QLM+  K   E+R  E++ I+ ++K
Sbjct: 286 IFIDDTAGVSVMEMRSKCRRLKIEHGIDMILIDYLQLMSGGKG-SESRQQEVSEISRSIK 344

Query: 378 ALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKE 437
           ALAKE+  P+IALSQLSR  E R + RP LSDLRESGSIEQDADVV+F+ RDEYY  NKE
Sbjct: 345 ALAKEMECPVIALSQLSRAPEQRADHRPMLSDLRESGSIEQDADVVMFLYRDEYY--NKE 402

Query: 438 PTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRFSAL 490
                         ED    K +A+ IIAKQR+GPTGTV LA+  ++++F  L
Sbjct: 403 -------------TED----KNVAECIIAKQRNGPTGTVKLAWLGQYSKFGNL 438


>gnl|CDD|181193 PRK08006, PRK08006, replicative DNA helicase; Provisional.
          Length = 471

 Score =  291 bits (747), Expect = 2e-79
 Identities = 173/477 (36%), Positives = 270/477 (56%), Gaps = 41/477 (8%)

Query: 24  PNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTANPVTV 83
           P++IEAEQ++LG ++++NE +  V++ +    F+   H+ IF  M +L   G   + +T+
Sbjct: 28  PHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGSPIDLITL 87

Query: 84  KTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEMVNAAY 143
              L  Q  L  +    YLA L+    S  N   Y  I+   A+ R +I++  E+ +A Y
Sbjct: 88  AESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRERAVVREMISVANEIADAGY 147

Query: 144 EASLDKSPSIQIEEAERKLFHLAEN-GRYDGGFHTFSDAMTVAIDMAGQAFNR--DGRLA 200
           +     S  + ++ AE ++F +AE+    D G    +D +   +    Q F +  DG + 
Sbjct: 148 DPQGRTSEDL-LDLAESRVFQIAESRANKDEGPKNIADILDATVARIEQLFQQPHDG-VT 205

Query: 201 GVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI 260
           GV+TG   L+K+  GLQ SDLII+A RP MGKT+ A N+  N A               +
Sbjct: 206 GVNTGYDDLNKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAA--------------ML 251

Query: 261 NGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQV-MQKLPLY 319
               V  +SLEM  EQ+  R+++  + V  ++IR G+L   D+ +I     + ++K  +Y
Sbjct: 252 QDKPVLIFSLEMPGEQIMMRMLASLSRVDQTRIRTGQLDDEDWARISGTMGILLEKRNMY 311

Query: 320 IDQTGGISMSQLATRARRLKRQR-GLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKA 378
           ID + G++ +++ +RARR+ R+  GL L+++DY+QLM     + +NR LEI  I+ +LKA
Sbjct: 312 IDDSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMRVPS-LSDNRTLEIAEISRSLKA 370

Query: 379 LAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKEP 438
           LAKEL +P++ALSQL+R +E R +KRP  SDLRESGSIEQDAD+++F+ RDE Y  N + 
Sbjct: 371 LAKELQVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRDEVYHENSD- 429

Query: 439 TNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRFSALSDSSY 495
                             +KGIA+III KQR+GP GTV L F  +++RF   +   Y
Sbjct: 430 ------------------LKGIAEIIIGKQRNGPIGTVRLTFNGQWSRFDNYAGPQY 468


>gnl|CDD|136106 PRK06904, PRK06904, replicative DNA helicase; Validated.
          Length = 472

 Score =  287 bits (735), Expect = 5e-78
 Identities = 181/477 (37%), Positives = 269/477 (56%), Gaps = 42/477 (8%)

Query: 24  PNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTANPVTV 83
           P++IEAEQA+LG I+++N  +  V++ +    F+   H+ IF+ M  L       + +T+
Sbjct: 24  PHSIEAEQAVLGGIMLDNRHWDSVAERVIADDFYTFEHRIIFQEMELLFRQNTPIDLLTL 83

Query: 84  KTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEMVNAAY 143
              L  +    E+    YLA L++   S  N   Y  I+   A+ R LI++G  +   AY
Sbjct: 84  DQALKTKGKSDEVGGFAYLAELSNNTPSAANILAYADIVREKAILRELISVGNNIAKNAY 143

Query: 144 EASLDKSPSIQIEEAERKLFHLAE--NGRYDGGFHTFS--DAMTVAIDMAGQAFNRDGRL 199
                    I ++EAER +F +AE      +G  +  +  +     I+        +G +
Sbjct: 144 SPKGQDIKDI-LDEAERDVFSIAEKRTTANEGPQNVINLLENTIDKIENLAATPTNNG-V 201

Query: 200 AGVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKT 259
            GV+TG   LDK+  GLQ SDLII+A RP MGKT+ A N+  N A A +           
Sbjct: 202 TGVTTGFTDLDKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMASEKP--------- 252

Query: 260 INGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGE-LTRPDYEKIVACSQVM-QKLP 317
                V  +SLEM +EQ+  R+++  + V  +KIR G+ L + D+ KI +   +  QK  
Sbjct: 253 -----VLVFSLEMPAEQIMMRMLASLSRVDQTKIRTGQNLDQQDWAKISSTVGMFKQKPN 307

Query: 318 LYIDQTGGISMSQLATRARRLKRQRG-LDLLIVDYIQLMTTSKKIEENRVLEITGITMAL 376
           LYID + G++ ++L +RARR+ R+ G L L++VDY+QLM  +   E+NR LEI  I+ +L
Sbjct: 308 LYIDDSSGLTPTELRSRARRVYRENGGLSLIMVDYLQLMR-APGFEDNRTLEIAEISRSL 366

Query: 377 KALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNK 436
           KALAKEL +P++ALSQL+R +ENR +KRP  SDLRESGSIEQDAD+++F+ RDE Y    
Sbjct: 367 KALAKELKVPVVALSQLNRTLENRGDKRPVNSDLRESGSIEQDADLIMFIYRDEVYNETT 426

Query: 437 EPTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRFSALSDS 493
           E                    KG+A+III KQR+GP G V LAFQ +++RF  L++ 
Sbjct: 427 EDN------------------KGVAEIIIGKQRNGPIGRVRLAFQGQYSRFDNLANI 465


>gnl|CDD|181562 PRK08840, PRK08840, replicative DNA helicase; Provisional.
          Length = 464

 Score =  284 bits (727), Expect = 4e-77
 Identities = 176/469 (37%), Positives = 271/469 (57%), Gaps = 41/469 (8%)

Query: 24  PNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTANPVTV 83
           P+++EAEQ+++G +L++NE +  V++ +    F+   H+ IFE +  ++  GK  + +T+
Sbjct: 21  PHSLEAEQSVIGGLLLDNERWDTVAEKVVASDFYSRPHRLIFEGVKSILEAGKPLDLITL 80

Query: 84  KTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEMVNAAY 143
              L  ++ L ++    YLA LA    S  N   Y  I+   AL R LI +  E+ +A Y
Sbjct: 81  SEHLERREQLEDVGGFAYLADLAKNTPSAANINAYADIVAERALVRNLIGVANEIADAGY 140

Query: 144 EASLDKSPSIQIEEAERKLFHLAENGRYDG-GFHTFSDAMTVAIDMAGQAFN--RDGRLA 200
           +     S  + ++ AE K+F +AE    +  G       +   ++     +   +DG + 
Sbjct: 141 DPQGRTSEDL-LDMAESKVFAIAEARTSENEGPQNVDSILEKTLERIELLYKTPQDG-VT 198

Query: 201 GVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI 260
           GV TG   L+K+  GLQ SDLII+A RP MGKT+ A N+  N A      +  D      
Sbjct: 199 GVDTGFTDLNKKTAGLQGSDLIIVAARPSMGKTTFAMNLCENAA------MDQDKP---- 248

Query: 261 NGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQV-MQKLPLY 319
               V  +SLEM +EQL  R+++  + V  +KIR G+L   D+ +I +   + M+K  +Y
Sbjct: 249 ----VLIFSLEMPAEQLMMRMLASLSRVDQTKIRTGQLDDEDWARISSTMGILMEKKNMY 304

Query: 320 IDQTGGISMSQLATRARRLKRQR-GLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKA 378
           ID + G++ +++ +RARR+ R+  GL +++VDY+QLM     + +NR LEI  I+ +LKA
Sbjct: 305 IDDSSGLTPTEVRSRARRIAREHGGLSMIMVDYLQLMRVPA-LSDNRTLEIAEISRSLKA 363

Query: 379 LAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKEP 438
           LAKELN+P++ALSQL+R +E R +KRP  SDLRESGSIEQDAD+++F+ RDE Y      
Sbjct: 364 LAKELNVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRDEVY------ 417

Query: 439 TNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRF 487
            N D  L            KG A+III KQR+GP G+V L FQ +++RF
Sbjct: 418 -NPDSPL------------KGTAEIIIGKQRNGPIGSVRLTFQGQYSRF 453


>gnl|CDD|180528 PRK06321, PRK06321, replicative DNA helicase; Provisional.
          Length = 472

 Score =  280 bits (718), Expect = 5e-76
 Identities = 169/501 (33%), Positives = 257/501 (51%), Gaps = 68/501 (13%)

Query: 12  IPKEDSSQYRESPNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKL 71
             K   +Q    PN+ E+E  +LG +L +       ++ L+   F+   H+ IF ++   
Sbjct: 5   TKKPQPTQLLSPPNSKESEMIVLGCMLTSVNYLNLAANQLQEDDFYFLEHKIIFRVLQDA 64

Query: 72  VHMGKTANPVTVKTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTL 131
               K  +       L  ++ L  +  P YL  LA  A +    E+Y  II   ++ R +
Sbjct: 65  FKSDKPIDVHLAGEELKRRNQLNVIGGPSYLITLAEFAGTSAYIEEYAEIIRSKSILRKM 124

Query: 132 ITIGEEMVNAAYEASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVAIDMAG- 190
           I   +E+   A E   D   +  ++EA+  LF +++           +  + VA  + G 
Sbjct: 125 IQTAKEIEKKALEEPKDV--ATALDEAQNLLFKISQTT-------NLAQYVLVADKLKGL 175

Query: 191 ----------------QAFNRDGR------LAGVSTGIQTLDKQMGGLQRSDLIIIAGRP 228
                           +AF +  +      ++G+ T    LDK + G   S+L+I+A RP
Sbjct: 176 TSSKDKPFLLQLQERQEAFQQSAQGDSSPMISGIPTHFIDLDKMINGFSPSNLMILAARP 235

Query: 229 GMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMSSEQLATRIISEQTEV 288
            MGKT+LA NIA N    ++  L             VG +SLEM+ +QL  RII  ++EV
Sbjct: 236 AMGKTALALNIAENF--CFQNRLP------------VGIFSLEMTVDQLIHRIICSRSEV 281

Query: 289 PSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQTGGISMSQLATRARRLKRQRGLDLLI 348
            S KI  G+L+  D+++IV+    MQ+  L ID   G+ ++ L  RARR+K    +  LI
Sbjct: 282 ESKKISVGDLSGRDFQRIVSVVNEMQEHTLLIDDQPGLKITDLRARARRMKESYDIQFLI 341

Query: 349 VDYIQLMTTS--KKIEENRVLEITGITMALKALAKELNIPIIALSQLSRQVENRDNKRPQ 406
           +DY+QL++ S   +  E+R  EI+ I+  LK LA+ELNIPI+ LSQLSR+VE+R N RP 
Sbjct: 342 IDYLQLLSGSGNLRNSESRQTEISEISRMLKNLARELNIPILCLSQLSRKVEDRANHRPM 401

Query: 407 LSDLRESGSIEQDADVVLFVIRDEYYIRNKEPTNKDDILAYTKWQEDLKRVKGIADIIIA 466
           +SDLRESGSIEQD+D+V+F++R EYY  N +P                    G A++I+A
Sbjct: 402 MSDLRESGSIEQDSDLVMFLLRREYYDPNDKP--------------------GTAELIVA 441

Query: 467 KQRHGPTGTVTLAFQAEFTRF 487
           K RHG  G+V L F+ EF RF
Sbjct: 442 KNRHGSIGSVPLVFEKEFARF 462


>gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional.
          Length = 505

 Score =  277 bits (711), Expect = 3e-75
 Identities = 152/473 (32%), Positives = 256/473 (54%), Gaps = 35/473 (7%)

Query: 16  DSSQYRESPNNIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMG 75
           +   +R+ P + EAEQ +LGA+L++ +    + + L P  F+   HQ IF+ +  L    
Sbjct: 63  EYRDFRQPPYDNEAEQGVLGAMLLSPDTVIDIVEVLTPEDFYRPAHQLIFQAIIDLFSDN 122

Query: 76  KTANPVTVKTFLSDQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIG 135
           K  +PV V   L   + L  +    YL  L     +  N   Y  I+   A+ R L+  G
Sbjct: 123 KEIDPVIVAGRLDRTNDLERVGGAPYLHTLIQSVPTAANARYYAEIVSEKAVLRRLVDAG 182

Query: 136 EEMVNAAYEASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVAIDMAGQAFNR 195
             +V   YE          I+ A++++F +++  + +  +   +D +   +D      ++
Sbjct: 183 TRVVQLGYEGDEGAEIDSVIDRAQQEVFAVSQKNQSED-YAVLADILDPTMDELEMLSSQ 241

Query: 196 DGRLAGVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDG 255
            G   G+ TG + LD    GL+   +II+A RPG+GK++LA +   +      A ++   
Sbjct: 242 GGIATGIPTGFKDLDDLTNGLRGGQMIIVAARPGVGKSTLALDFMRS------ASIK--- 292

Query: 256 SYKTINGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQK 315
                +      +SLEMS  ++  R++S + EV  S +R G++    +EK+V     + +
Sbjct: 293 -----HNKASVIFSLEMSKSEIVMRLLSAEAEVRLSDMRGGKMDEDAWEKLVQRLGKIAQ 347

Query: 316 LPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMA 375
            P++ID +  ++M ++ ++ARRLK++  L L++VDY+QLM++ K++E +R  E++  +  
Sbjct: 348 APIFIDDSANLTMMEIRSKARRLKQKHDLKLIVVDYLQLMSSGKRVE-SRQQEVSEFSRQ 406

Query: 376 LKALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRN 435
           LK LAKEL++P+IA+SQL+R  E+R +KRPQL+DLRESGS+EQDAD+V+ + R       
Sbjct: 407 LKLLAKELDVPLIAISQLNRGPESRTDKRPQLADLRESGSLEQDADMVMLLYR------- 459

Query: 436 KEPTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRFS 488
            +  +KDD  A            G ADII+AK R GP  TV +A Q  ++RF 
Sbjct: 460 PDSQDKDDERA------------GEADIILAKHRGGPIDTVQVAHQLHYSRFV 500


>gnl|CDD|168658 PRK06749, PRK06749, replicative DNA helicase; Provisional.
          Length = 428

 Score =  233 bits (596), Expect = 7e-62
 Identities = 153/468 (32%), Positives = 236/468 (50%), Gaps = 54/468 (11%)

Query: 26  NIEAEQALLGAILVNNEAFYRVSDFLKPLHFFEAIHQKIFEIMGKLVHMGKTANPVTVKT 85
           N+EAE+ +LG++L++ E        L   +F   +H+ IF++M K+   G+   P+ + T
Sbjct: 5   NVEAEKTVLGSLLLDGELIKECR--LTEQYFSMPVHKSIFQLMRKMEDEGQ---PIDLVT 59

Query: 86  FLS--DQDMLGELTVPQYLARLASEAVSIINTEDYGRIIYGLALRRTLITIGEEMVNAAY 143
           F S  D + L  +   +Y   L     +  N   Y  ++ G         +G +M     
Sbjct: 60  FTSRVDPNFLKGIGGMEYFIGLMDGVPTTSNFSYYEGLVRGAWKMYQAGVLGHKMGERLI 119

Query: 144 EASLDKSPSIQIEEAERKLFHLAENGRYDGGFHTFSDAMTVAIDMAGQAFNRDGRLAGVS 203
               +KS  I I E    L  L E            DA+   +D+  +       + G+ 
Sbjct: 120 A---EKSEKI-IGETITALCELEEKDCVCE--FDLKDAL---VDLYEELHQDAKEITGIE 170

Query: 204 TGIQTLDKQMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGG 263
           TG  +L+K   GLQ  D +++  RP MGKT+ A N+  + A +  A              
Sbjct: 171 TGYTSLNKMTCGLQEGDFVVLGARPSMGKTAFALNVGLHAAKSGAA-------------- 216

Query: 264 IVGFYSLEMSSEQLATRIISEQTEVPSSKIR--RGELTRPDYEKIVACSQVMQKLPLYID 321
            VG +SLEMSS+QL  R+ S   EV   +++  +      D+EK+      + +LPL I 
Sbjct: 217 -VGLFSLEMSSKQLLKRMASCVGEVSGGRLKNPKHRFAMEDWEKVSKAFAEIGELPLEIY 275

Query: 322 QTGGISMSQLATRARRLKRQRGLD--LLIVDYIQLMTTSKKIEENRVLEITGITMALKAL 379
              G+++  +  + R+LKR+ G    L+IVDY+QL+T   K + NR  EI+ I+  LK L
Sbjct: 276 DNAGVTVQDIWMQTRKLKRKHGDKKILIIVDYLQLITGDPKHKGNRFQEISEISRKLKLL 335

Query: 380 AKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKEPT 439
           A+ELN+ ++ALSQLSR VE+R +KRP LSDLRE+G IEQDADV++ + R++YY  +KE  
Sbjct: 336 ARELNVCVVALSQLSRSVESRQDKRPLLSDLRETGQIEQDADVIMLMYREDYY--DKETM 393

Query: 440 NKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRF 487
            K+                 + +I +AK R+GP G+  L F  EF RF
Sbjct: 394 QKE-----------------MTEIHVAKHRNGPVGSFKLRFLKEFGRF 424


>gnl|CDD|177377 PHA02542, 41, 41 helicase; Provisional.
          Length = 473

 Score = 56.6 bits (137), Expect = 1e-08
 Identities = 59/228 (25%), Positives = 102/228 (44%), Gaps = 35/228 (15%)

Query: 214 GGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMS 273
           GG +R  L ++     +GK+    ++A   AD     LQ         G  V + S+EM+
Sbjct: 185 GGAERKTLNVLLAGVNVGKSLGLCSLA---ADY----LQQ--------GYNVLYISMEMA 229

Query: 274 SEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQ--TGGIS---- 327
            E +A RI +   +V    I   +L++ +Y+  +   +   +  L I Q  TGG      
Sbjct: 230 EEVIAKRIDANLLDVSLDDID--DLSKAEYKAKMEKLRSKTQGKLIIKQYPTGGAHAGHF 287

Query: 328 ---MSQLATRARRLKRQRGLDLLIVDYIQLMTTS--KKIEENRVLEITGITMALKALAKE 382
              +++L     +LK+    D++IVDY+ +  +S  +   EN    +  I   L+ LA E
Sbjct: 288 RALLNEL-----KLKKNFKPDVIIVDYLGICASSRLRVSSENSYTYVKAIAEELRGLAVE 342

Query: 383 LNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDE 430
            ++ +   +Q +R     D+    +SD  ES  +   AD +L VI  E
Sbjct: 343 HDVVVWTAAQTTR--SGWDSSDVDMSDTAESAGLPATADFMLAVIETE 388


>gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional.
          Length = 237

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 40/200 (20%), Positives = 75/200 (37%), Gaps = 48/200 (24%)

Query: 213 MGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEM 272
              L+  DL+++  RPG GKT L   +A    +A K      G           F++LE 
Sbjct: 58  FSQLKPGDLVLLGARPGHGKTLLGLELA---VEAMK-----SGRTGV-------FFTLEY 102

Query: 273 SSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQTGGISMSQLA 332
           + + +  R+         ++                            D +  I    + 
Sbjct: 103 TEQDVRDRL--RALGADRAQFAD---------------------LFEFDTSDAICADYI- 138

Query: 333 TRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVL-EITGITMALKALAKELNIPIIALS 391
               RL       L+++DY+QL+      ++ R   +++    ALK+ A+E  + I+ +S
Sbjct: 139 --IARLASAPRGTLVVIDYLQLL------DQRREKPDLSVQVRALKSFARERGLIIVFIS 190

Query: 392 QLSRQVENRDNKRPQLSDLR 411
           Q+ R  +      P + D+R
Sbjct: 191 QIDRSFDPSAKPLPDIRDVR 210


>gnl|CDD|181771 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
          Length = 509

 Score = 42.6 bits (101), Expect = 3e-04
 Identities = 16/41 (39%), Positives = 26/41 (63%), Gaps = 1/41 (2%)

Query: 202 VSTGIQTLDKQMG-GLQRSDLIIIAGRPGMGKTSLATNIAY 241
           +S+G+  LD+ +G G  R  +I+++G  G GKT LA+  A 
Sbjct: 255 ISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKFAE 295


>gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
          Length = 446

 Score = 38.5 bits (91), Expect = 0.004
 Identities = 46/198 (23%), Positives = 77/198 (38%), Gaps = 68/198 (34%)

Query: 202 VSTGIQTLDKQMG-GLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI 260
           +STGI  LD+ +G GL    +++I G PG+GK++L   +A  +A A    L     Y  +
Sbjct: 62  ISTGIGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVL-----Y--V 114

Query: 261 NGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYI 320
           +G        E S+ Q+  R  +E+  +PS  +    L   + E I+A   + ++ P   
Sbjct: 115 SG--------EESASQIKLR--AERLGLPSDNLYL--LAETNLEAILA--TIEEEKP--- 157

Query: 321 DQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGI-------- 372
                                   DL+++D IQ M +          E+           
Sbjct: 158 ------------------------DLVVIDSIQTMYSP---------ELESAPGSVSQVR 184

Query: 373 --TMALKALAKELNIPII 388
                L  LAK+  I + 
Sbjct: 185 ECAAELMRLAKQRGIAVF 202


>gnl|CDD|161868 TIGR00416, sms, DNA repair protein RadA.  The gene protuct codes
           for a probable ATP-dependent protease involved in both
           DNA repair and degradation of proteins, peptides,
           glycopeptides. Also known as sms. Residues 11-28 of the
           SEED alignment contain a putative Zn binding domain.
           Residues 110-117 of the seed contain a putative ATP
           binding site both documented in Haemophilus and in
           Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
           178:5045-5048(1996)).
          Length = 454

 Score = 34.8 bits (80), Expect = 0.054
 Identities = 45/181 (24%), Positives = 73/181 (40%), Gaps = 36/181 (19%)

Query: 202 VSTGIQTLDKQMGG-LQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTI 260
            S+G   LD+ +GG +    LI+I G PG+GK++L   +A  +A      L   G     
Sbjct: 76  FSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSG----- 130

Query: 261 NGGIVGFYSLEMSSEQLATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYI 320
                     E S +Q+  R I      P+  +    L+  ++E+I A  +        I
Sbjct: 131 ----------EESLQQIKMRAIRLGLPEPNLYV----LSETNWEQICANIEEENPQACVI 176

Query: 321 D----------QTGGISMSQL---ATRARRLKRQRGLDLLIVDYIQLMTTSKKIEENRVL 367
           D           +   S+SQ+        RL + RG+ + IV ++   T    I   +VL
Sbjct: 177 DSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHV---TKEGSIAGPKVL 233

Query: 368 E 368
           E
Sbjct: 234 E 234


>gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family.
           Members of this protein family are archaeal
           single-domain KaiC_related proteins, homologous to the
           Cyanobacterial circadian clock cycle protein KaiC, an
           autokinase/autophosphorylase that has two copies of the
           domain.
          Length = 229

 Score = 34.3 bits (79), Expect = 0.078
 Identities = 17/41 (41%), Positives = 25/41 (60%), Gaps = 1/41 (2%)

Query: 202 VSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAY 241
           +STG++ LDK + GG+ R   + + G PG GKT    + AY
Sbjct: 2   LSTGVEGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAY 42


>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus.  This family consists of the
           C-terminal region of several eukaryotic and archaeal
           RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
           or TIP49b) proteins. The N-terminal domain contains the
           pfam00004 domain. In zebrafish, the liebeskummer (lik)
           mutation, causes development of hyperplastic embryonic
           hearts. lik encodes Reptin, a component of a
           DNA-stimulated ATPase complex. Beta-catenin and Pontin,
           a DNA-stimulated ATPase that is often part of complexes
           with Reptin, are in the same genetic pathways. The
           Reptin/Pontin ratio serves to regulate heart growth
           during development, at least in part via the
           beta-catenin pathway. TBP-interacting protein 49 (TIP49)
           was originally identified as a TBP-binding protein, and
           two related proteins are encoded by individual genes,
           tip49a and b. Although the function of this gene family
           has not been elucidated, they are supposed to play a
           critical role in nuclear events because they interact
           with various kinds of nuclear factors and have DNA
           helicase activities.TIP49a has been suggested to act as
           an autoantigen in some patients with autoimmune
           diseases.
          Length = 395

 Score = 34.2 bits (79), Expect = 0.086
 Identities = 22/52 (42%), Positives = 28/52 (53%), Gaps = 10/52 (19%)

Query: 222 IIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMS 273
           ++IAG PG GKT+LA  I+         EL  D  +  I+G  V  YSLEM 
Sbjct: 53  VLIAGPPGTGKTALAIAIS--------KELGEDTPFCPISGSEV--YSLEMK 94


>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
          Length = 602

 Score = 34.0 bits (79), Expect = 0.099
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 222 IIIAGRPGMGKTSLATNIA 240
           I+IAG PG GK++ A  +A
Sbjct: 260 ILIAGAPGAGKSTFAQALA 278


>gnl|CDD|148381 pfam06745, KaiC, KaiC.  This family represents a conserved region
           within bacterial and archaeal proteins, most of which
           are hypothetical. More than one copy is sometimes found
           in each protein. This family includes KaiC, which is one
           of the Kai proteins among which direct protein-protein
           association may be a critical process in the generation
           of circadian rhythms in cyanobacteria.
          Length = 231

 Score = 33.4 bits (77), Expect = 0.15
 Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 202 VSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYN 242
           V TGI  LD+ + GG+    +++I G PG GKT       YN
Sbjct: 1   VKTGIPGLDEILKGGIPEGRVVLITGGPGTGKTIFGLQFLYN 42


>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
           Members of this family contain a single copy of the KaiC
           domain (pfam06745) that occurs in two copies of the
           circadian clock protein kinase KaiC itself. Members
           occur primarily in thermophilic archaea and in
           Thermotoga.
          Length = 237

 Score = 32.8 bits (75), Expect = 0.22
 Identities = 13/42 (30%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 202 VSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYN 242
           V TGI  +D+ + GG+   ++++++G PG GK+  +    +N
Sbjct: 3   VKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWN 44


>gnl|CDD|179826 PRK04328, PRK04328, hypothetical protein; Provisional.
          Length = 249

 Score = 32.4 bits (74), Expect = 0.31
 Identities = 13/42 (30%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 202 VSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYN 242
           V TGI  +D+ + GG+   ++++++G PG GK+  +    +N
Sbjct: 5   VKTGIPGMDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWN 46


>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 = 31.6 bits (71), Expect = 0.43
 Identities = 34/178 (19%), Positives = 54/178 (30%), Gaps = 51/178 (28%)

Query: 218 RSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMSSEQL 277
             ++I+I G PG GKT+LA  +A  +           G    I+G       +       
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELG-------PPGGGVIYIDGED-----ILEEVLDQ 48

Query: 278 ATRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQTGGISMSQLATRARR 337
              II    +   S   R  L                                    A  
Sbjct: 49  LLLIIVGGKKASGSGELRLRL------------------------------------ALA 72

Query: 338 LKRQRGLDLLIVDYIQLMTTSKKIEENRVLEITGITMALKALAKELNIPIIALSQLSR 395
           L R+   D+LI+D I  +      E+  +L +      L  L  E N+ +I  +   +
Sbjct: 73  LARKLKPDVLILDEITSLL---DAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEK 127


>gnl|CDD|181799 PRK09361, radB, DNA repair and recombination protein RadB;
           Provisional.
          Length = 225

 Score = 31.0 bits (71), Expect = 0.78
 Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 202 VSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYNVA 244
           + TG + LD+ + GG +R  +  I G PG GKT++   +A   A
Sbjct: 5   LPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAA 48


>gnl|CDD|178594 PLN03023, PLN03023, Expansin-like B1; Provisional.
          Length = 247

 Score = 30.9 bits (70), Expect = 0.87
 Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 2/42 (4%)

Query: 442 DDILAYTKWQEDLKRVKGIADIIIA--KQRHGPTGTVTLAFQ 481
           +DILA   WQED K  +G+     A     + P G +TL FQ
Sbjct: 173 NDILAVEIWQEDCKEWRGMRKAYGAVWDMPNPPKGPITLRFQ 214


>gnl|CDD|131703 TIGR02655, circ_KaiC, circadian clock protein KaiC.  Members of
           this family are the circadian clock protein KaiC, part
           of the kaiABC operon that controls circadian rhythm. It
           may be universal in Cyanobacteria. Each member has two
           copies of the KaiC domain (Pfam model pfam06745), which
           is also found in other proteins. KaiC performs
           autophosphorylation and acts as its own transcriptional
           repressor.
          Length = 484

 Score = 30.7 bits (69), Expect = 0.99
 Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 202 VSTGIQTLDKQMGGLQRSDLIIIA-GRPGMGKTSLATNIAYN 242
           VS+G+  LD+  GG    D II+A G  G GKT L +    N
Sbjct: 245 VSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLEN 286


>gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase
           domain-containing protein; Reviewed.
          Length = 229

 Score = 29.9 bits (68), Expect = 1.5
 Identities = 14/68 (20%), Positives = 22/68 (32%), Gaps = 14/68 (20%)

Query: 175 FHTFSDAMTVAID-MAGQAFNRDGRLAGVSTGIQTLDKQMGGLQRSDLIIIAGRPGMGKT 233
               +      I+ +      R   L                 QR  ++ IAG PG GK+
Sbjct: 1   LKVQAQYRDEEIEAVHKPLLRRLAALQAEP-------------QRRTIVGIAGPPGAGKS 47

Query: 234 SLATNIAY 241
           +LA  +  
Sbjct: 48  TLAEFLEA 55


>gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
          Length = 328

 Score = 29.7 bits (68), Expect = 1.8
 Identities = 11/21 (52%), Positives = 16/21 (76%)

Query: 220 DLIIIAGRPGMGKTSLATNIA 240
           D +++ G PG+GKT+LA  IA
Sbjct: 52  DHVLLYGPPGLGKTTLANIIA 72


>gnl|CDD|180192 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
          Length = 1135

 Score = 29.7 bits (68), Expect = 1.9
 Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 7/39 (17%)

Query: 351 YIQLMTTSKKIEENRVLEITGITMALKALAKELNIPIIA 389
           Y++LM     IE  RV        AL  LAKEL +P++A
Sbjct: 168 YLELMRHGLPIER-RVEH------ALLELAKELGLPLVA 199


>gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional.
          Length = 174

 Score = 29.5 bits (67), Expect = 2.2
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 222 IIIAGRPGMGKTSLATNIA 240
           I I G PG+GKT+L   IA
Sbjct: 3   IGITGPPGVGKTTLVLKIA 21


>gnl|CDD|180750 PRK06921, PRK06921, hypothetical protein; Provisional.
          Length = 266

 Score = 29.4 bits (66), Expect = 2.3
 Identities = 11/27 (40%), Positives = 15/27 (55%)

Query: 217 QRSDLIIIAGRPGMGKTSLATNIAYNV 243
            R + I + G+PG GKT L T  A  +
Sbjct: 115 SRKNSIALLGQPGSGKTHLLTAAANEL 141


>gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated.
          Length = 234

 Score = 29.2 bits (66), Expect = 2.6
 Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 1/41 (2%)

Query: 202 VSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAY 241
           +STG + LD+++ GG+    LI+I G  G GK+ L+    Y
Sbjct: 7   ISTGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVY 47


>gnl|CDD|181679 PRK09181, PRK09181, aspartate kinase; Validated.
          Length = 475

 Score = 29.1 bits (66), Expect = 3.0
 Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 2/33 (6%)

Query: 367 LEITGITM-ALKALAKELNIPIIALSQLSRQVE 398
           + + G+   A++ALA+   I ++AL Q  RQV 
Sbjct: 412 IAVPGVLAKAVQALAEA-GINVLALHQSMRQVN 443


>gnl|CDD|149035 pfam07744, SPOC, SPOC domain.  The SPOC (Spen paralogue and
           orthologue C-terminal) domain is involved in
           developmental signalling.
          Length = 108

 Score = 28.8 bits (65), Expect = 3.0
 Identities = 8/39 (20%), Positives = 23/39 (58%)

Query: 311 QVMQKLPLYIDQTGGISMSQLATRARRLKRQRGLDLLIV 349
           +++  LPL ++  G + +SQ+    R+L++     ++++
Sbjct: 25  KLVSLLPLKLEIRGRLDLSQVEKYLRKLRKSSTKAVVVL 63


>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
           Provisional.
          Length = 482

 Score = 29.1 bits (66), Expect = 3.0
 Identities = 10/19 (52%), Positives = 15/19 (78%)

Query: 222 IIIAGRPGMGKTSLATNIA 240
           +++ G PG+GKTSLA  +A
Sbjct: 42  LLLYGPPGVGKTSLAHALA 60


>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
           RuvA specifically binds Holliday junctions as a sandwich
           of two tetramers and maintains the configuration of the
           junction. It forms a complex with two hexameric rings of
           RuvB, the subunit that contains helicase activity. The
           complex drives ATP-dependent branch migration of the
           Holliday junction recombination intermediate. The
           endonuclease RuvC resolves junctions.
          Length = 305

 Score = 28.8 bits (65), Expect = 3.7
 Identities = 11/21 (52%), Positives = 16/21 (76%)

Query: 220 DLIIIAGRPGMGKTSLATNIA 240
           D +++ G PG+GKT+LA  IA
Sbjct: 31  DHLLLYGPPGLGKTTLAHIIA 51


>gnl|CDD|131290 TIGR02236, recomb_radA, DNA repair and recombination protein RadA. 
           This family consists exclusively of archaeal RadA
           protein, a homolog of bacterial RecA (TIGR02012),
           eukaryotic RAD51 (TIGR02239), and archaeal RadB
           (TIGR02237). This protein is involved in DNA repair and
           recombination. The member from Pyrococcus horikoshii
           contains an intein.
          Length = 310

 Score = 28.6 bits (64), Expect = 3.9
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 202 VSTGIQTLDKQMGGLQRSDLII-IAGRPGMGKTSLATNIAYNV 243
           ++TG + LD+ +GG   +  I  + G  G GKT +   +A NV
Sbjct: 77  ITTGSKELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNV 119


>gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
           protein. 
          Length = 1394

 Score = 28.5 bits (64), Expect = 4.1
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 11/55 (20%)

Query: 211 KQMGGLQR-SDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGI 264
           K M GL +  +L ++ GRPG G ++L   IA N          TDG +  + G I
Sbjct: 78  KPMDGLIKPGELTVVLGRPGSGCSTLLKTIASN----------TDGFHIGVEGVI 122


>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
          Length = 197

 Score = 28.6 bits (64), Expect = 4.4
 Identities = 12/26 (46%), Positives = 17/26 (65%)

Query: 219 SDLIIIAGRPGMGKTSLATNIAYNVA 244
           S +  I G PG+GKTS++  IA + A
Sbjct: 3   STIHFIGGIPGVGKTSISGYIARHRA 28


>gnl|CDD|181283 PRK08197, PRK08197, threonine synthase; Validated.
          Length = 394

 Score = 28.0 bits (63), Expect = 5.3
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 409 DLRESGSIEQDADVVLF 425
            LRESG ++ D  VVLF
Sbjct: 359 QLRESGWLKGDERVVLF 375


>gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA.  This model describes
           orthologs of the recA protein. RecA promotes
           hybridization of homolgous regions of DNA. A segment of
           ssDNA can be hybridized to another ssDNA region, or to a
           dsDNA region. ATP is hydrolyzed in the process. Part of
           the SOS respones, it is regulated by LexA via
           autocatalytic cleavage.
          Length = 321

 Score = 28.1 bits (63), Expect = 5.6
 Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 5/50 (10%)

Query: 202 VSTGIQTLDKQMG--GLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKA 249
           +STG  +LD  +G  GL R  +I I G    GKT+LA +    +A+A KA
Sbjct: 36  ISTGSLSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHA---IAEAQKA 82


>gnl|CDD|183817 PRK12892, PRK12892, allantoate amidohydrolase; Reviewed.
          Length = 412

 Score = 28.1 bits (63), Expect = 5.7
 Identities = 20/72 (27%), Positives = 23/72 (31%), Gaps = 21/72 (29%)

Query: 148 DKSPSIQIEEAERKLFHLAENGRYDGGFH--TFSDA----------------MTVAIDMA 189
                I  +     L  LA  G    G H  T+SDA                + V ID  
Sbjct: 2   LAMLRIDGQRVLDDLMELAAIGAAKTGVHRPTYSDAHVAARRRLAAWCEAAGLAVRIDGI 61

Query: 190 GQAFNRDGRLAG 201
           G  F   GRL G
Sbjct: 62  GNVF---GRLPG 70


>gnl|CDD|148176 pfam06414, Zeta_toxin, Zeta toxin.  This family consists of several
           bacterial zeta toxin proteins. Zeta toxin is thought to
           be part of a postregulational killing system in
           bacteria. It relies on antitoxin/toxin systems that
           secure stable inheritance of low and medium copy number
           plasmids during cell division and kill cells that have
           lost the plasmid.
          Length = 191

 Score = 28.0 bits (63), Expect = 5.9
 Identities = 9/23 (39%), Positives = 15/23 (65%)

Query: 217 QRSDLIIIAGRPGMGKTSLATNI 239
           +R   +++ G+PG GKT LA  +
Sbjct: 10  ERPVAVLLGGQPGAGKTELARAL 32


>gnl|CDD|150510 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
           This domain, found in various prokaryotic proteins
           (including putative ATP/GTP binding proteins), has no
           known function.
          Length = 348

 Score = 28.0 bits (63), Expect = 6.2
 Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 8/39 (20%)

Query: 221 LIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKT 259
           + ++ G PG GKT +A N+          EL      +T
Sbjct: 3   VFLVTGGPGTGKTVVALNLFA--------ELSDSDLGRT 33


>gnl|CDD|129161 TIGR00051, TIGR00051, acyl-CoA thioester hydrolase, YbgC/YbaW
           family.  This model describes a subset of related
           acyl-CoA thioesterases that include several at least
           partially characterized proteins. YbgC is an acyl-CoA
           thioesterase associated with the Tol-Pal system. YbaW is
           part of the FadM regulon.
          Length = 117

 Score = 27.8 bits (62), Expect = 6.3
 Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 3/53 (5%)

Query: 410 LRESGSIEQD--ADVVLFVIRDEYYIRNKEPTNKDDILAYTKWQEDLKRVKGI 460
           LR  G  +    A+ V FV+ +   I  K+P   DD+L      E+L     +
Sbjct: 32  LRSLGFPQSVLRAEGVAFVVVN-INIEYKKPARLDDVLEIRTQIEELNGFSFV 83


>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family.  This
           model represents a rather narrowly distributed archaeal
           protein family in which members have a single copy of
           the KaiC domain. This stands in contrast to the
           circadian clock protein KaiC itself, with two copies of
           the domain. Members are expected to have weak ATPase
           activity, by homology to the
           autokinase/autophosphorylase KaiC itself.
          Length = 224

 Score = 27.7 bits (62), Expect = 6.4
 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 205 GIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYN 242
           GI  LD+ + GG     +I++ G  G GKT+ +    Y 
Sbjct: 1   GIPGLDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQ 39


>gnl|CDD|162744 TIGR02173, cyt_kin_arch, cytidylate kinase, putative.  Proteins in
           this family are believed to be cytidylate kinase.
           Members of this family are found in the archaea and in
           spirochaetes, and differ considerably from the common
           bacterial form of cytidylate kinase described by
           TIGR00017.
          Length = 171

 Score = 27.8 bits (62), Expect = 7.1
 Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 12/45 (26%)

Query: 221 LIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIV 265
           +I I+G PG GKT++A  +A  +            S K I+ G +
Sbjct: 2   IITISGPPGSGKTTVAKILAEKL------------SLKLISAGDI 34


>gnl|CDD|130080 TIGR01007, eps_fam, capsular exopolysaccharide family.  This model
           describes the capsular exopolysaccharide proteins in
           bacteria. The exopolysaccharide gene cluster consists of
           several genes which encode a number of proteins which
           regulate the exoploysaccharide biosynthesis(EPS).
           Atleast 13 genes espA to espM in streptococcus species
           seem to direct the EPS proteins and all of which share
           high homology. Functional roles were characterized by
           gene disruption experiments which resulted in
           exopolysaccharide-deficient phenotypes.
          Length = 204

 Score = 27.8 bits (62), Expect = 7.5
 Identities = 16/44 (36%), Positives = 23/44 (52%)

Query: 212 QMGGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDG 255
           Q  G +   L+I + +PG GK++ + NIA   A A    L  DG
Sbjct: 11  QFSGAEIKVLLITSVKPGEGKSTTSANIAVAFAQAGYKTLLIDG 54


>gnl|CDD|162028 TIGR00763, lon, ATP-dependent protease La.  This protein is induced
           by heat shock and other stresses in E. coli, B.
           subtilis, and other species. The yeast member,
           designated PIM1, is located in the mitochondrial matrix,
           required for mitochondrial function, and also induced by
           heat shock.
          Length = 775

 Score = 27.6 bits (62), Expect = 8.1
 Identities = 10/15 (66%), Positives = 12/15 (80%)

Query: 226 GRPGMGKTSLATNIA 240
           G PG+GKTSL  +IA
Sbjct: 354 GPPGVGKTSLGKSIA 368


>gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional.
          Length = 180

 Score = 27.5 bits (62), Expect = 9.3
 Identities = 10/20 (50%), Positives = 15/20 (75%)

Query: 221 LIIIAGRPGMGKTSLATNIA 240
           +I I+G PG GKT++A  +A
Sbjct: 2   IITISGPPGSGKTTVARLLA 21


  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
   0.317    0.133    0.364 

Gapped
Lambda     K      H
   0.267   0.0669    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 8,217,451
Number of extensions: 552258
Number of successful extensions: 1642
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1552
Number of HSP's successfully gapped: 90
Length of query: 504
Length of database: 5,994,473
Length adjustment: 97
Effective length of query: 407
Effective length of database: 3,898,497
Effective search space: 1586688279
Effective search space used: 1586688279
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.6 bits)