RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

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



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

 Score =  890 bits (2303), Expect = 0.0
 Identities = 296/724 (40%), Positives = 409/724 (56%), Gaps = 54/724 (7%)

Query: 14  SRVIILLLQAVSGPYIYSVPSAMKVELGSIVRVPLRSRTVLGIVWYNSEEKYKIDSLKLR 73
               +LL   +  P+ Y +P  ++V+ G  VRVP  +R ++G+V    EE  ++ + KL+
Sbjct: 3   KIARVLLPVPLPRPFDYLIPEGLEVQPGDRVRVPFGNRKLIGVVV-GVEEGSEVPADKLK 61

Query: 74  PIEYVFDC-PPLSRQMCEFVKWVADYTFSPMGLVARMVVSALSETEKMEEKIQFTGIFPR 132
           PI  V D  P L  ++   + W ADY  SP+G V R+ +                     
Sbjct: 62  PILEVLDLEPLLPPELLRLLDWAADYYLSPLGEVLRLAL--------------------- 100

Query: 133 INTVARLRVLDKIKDGKIWEKRDLIRASQVSSHVIDGLKAQGVIKQIFEVISPVVDSPNL 192
                                 +L  A   SS V+ GL  +G+I+     +  +   P+ 
Sbjct: 101 --------------------LAEL--ALAASSAVLKGLVKKGLIELEEVEVLRLRPPPDP 138

Query: 193 YFSLPILDKNQQDVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLIL 252
            F  P L+  Q   VE +      GF+  L+ GVTGSGKTEVYL+ +A VL  GKQ L+L
Sbjct: 139 AFEPPTLNPEQAAAVEAIRAA--AGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVL 196

Query: 253 LPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPF 312
           +PEI+LT  +L RF+ RFG   A  HS LS   R   WR+  RG   V++G RSALFLPF
Sbjct: 197 VPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPF 256

Query: 313 KKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRR 372
           K LGLI++DEEHD SYKQ+EG  Y+ARD+++VR K+E+ PVVL SATPS+ES  N    R
Sbjct: 257 KNLGLIIVDEEHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQGR 316

Query: 373 YHSVHLSTRYRNSALPHLQVIDMRGQTIAQGKS-LSPEMIDGIRHTLARNEQTLLFLNRR 431
           Y  + L+ R   + LP +++IDMR     +  S LSP +++ I+  L R EQ LLFLNRR
Sbjct: 317 YRLLRLTKRAGGARLPEVEIIDMRELLRGENGSFLSPPLLEAIKQRLERGEQVLLFLNRR 376

Query: 432 GYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIAC 491
           GYAP  LC+ CG   +C HC   L  HR +++L CH CG+     ++C  CGS+  ++  
Sbjct: 377 GYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTD-LVPV 435

Query: 492 GFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHN 551
           G G ER+ EE+ E FP ARI  +  D     G L+  L+  A+GE DI+IGTQ++AKGH+
Sbjct: 436 GPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHD 495

Query: 552 FPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQ 611
           FP ++LVGV+D DLGL + D R+SERTFQLL+QV GRAGR       LIQ Y P HPV+Q
Sbjct: 496 FPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQ 555

Query: 612 ALVSGDADSFYESEIRARESVNLPPFGRLAAVIISGTKYQEVENYAYNLKEHAPRS---S 668
           AL++ D D+F E E+  R +   PPFGRLA +  S    ++ E +A  L    P      
Sbjct: 556 ALLAQDYDAFAEQELEERRAAGYPPFGRLALLRASAKDEEKAEKFAQQLAALLPNLLPLL 615

Query: 669 DIVVFGPAESPLFMVRGRYRFRLLIHGKRNSNLQGFFSQMYDNTIKRSNA--LRVQFDID 726
           D+ V GPA +P+  + GRYR++LL+     ++LQ           K   A  +R   D+D
Sbjct: 616 DVEVLGPAPAPIAKIAGRYRYQLLLKSPSRADLQKLLRAWLALLQKLPQARKVRWSIDVD 675

Query: 727 PQNF 730
           PQ+F
Sbjct: 676 PQSF 679


>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 =  546 bits (1410), Expect = e-156
 Identities = 226/509 (44%), Positives = 323/509 (63%), Gaps = 8/509 (1%)

Query: 222 LISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSL 281
           L+ GVTGSGKTEVYL+ +  VL LGK VL+L+PEI+LT  +++RF+ RFG + A  HS L
Sbjct: 1   LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGL 60

Query: 282 STSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDM 341
           S S + + WR+V  G I V++G RSALFLPFK LGLI++DEEHD SYKQEEG  Y+ARD+
Sbjct: 61  SDSEKLQAWRKVKNGEILVVIGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDV 120

Query: 342 SIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDMRGQTIA 401
           ++ R K  + PVVL SATPS+ES  N   + Y  + L+ R      P +++IDMR +   
Sbjct: 121 AVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLLVLTRRVSGRKPPEVKLIDMRKE--P 178

Query: 402 QGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSK 461
           +   LSPE+I  I  TLA  EQ++LFLNRRGY+   LC+ CG  L C +C   L  H+ +
Sbjct: 179 RQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKE 238

Query: 462 KKLYCHQCGHSAIYSQSCVVCGSSGKMIA-CGFGIERIAEEVCEYFPLARISILSSDLEG 520
            KL CH CG+     ++C  CGS  + +   G+G E++ EE+ + FP ARI+ + SD   
Sbjct: 239 GKLRCHYCGYQEPIPKTCPQCGS--EDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTS 296

Query: 521 GGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQ 580
             G  +  L+  A G+ DI+IGTQ++AKGH+FP ++LVGV+D D GL + D R++ER FQ
Sbjct: 297 RKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQ 356

Query: 581 LLSQVTGRAGRFGLKSLGLIQAYQPTHPVMQALVSGDADSFYESEIRARESVNLPPFGRL 640
           LL+QV GRAGR       +IQ Y P HP +QA ++GD ++FYE E+  R ++N PPF RL
Sbjct: 357 LLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYEAFYEQELAQRRALNYPPFTRL 416

Query: 641 AAVIISGTKYQEVENYAYNLKEHAPRS--SDIVVFGPAESPLFMVRGRYRFRLLIHGKRN 698
             +I  G   ++ +  A    E   ++    + V GP+ +P+  + GRYR+++L+  K  
Sbjct: 417 IRLIFRGKNEEKAQQTAQAAHELLKQNLDEKLEVLGPSPAPIAKIAGRYRYQILLKSKSF 476

Query: 699 SNLQGFFSQMYDNTIKRSNALRVQFDIDP 727
             LQ   ++     I  S+++  + D+DP
Sbjct: 477 LVLQKLVNKTLLKEIP-SSSVYCEVDVDP 504


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

 Score =  109 bits (274), Expect = 3e-24
 Identities = 118/517 (22%), Positives = 192/517 (37%), Gaps = 64/517 (12%)

Query: 237 EIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKP-AEWHSSLSTSMREKIWRQVAR 295
              AA L  G+  L+++P+      +    +   G    A   + L  + R + W  V R
Sbjct: 179 AAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLR 238

Query: 296 GAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVL 355
           G   V+VG RSA+F P + LGL+ I ++ D    +      +AR+++++R       +++
Sbjct: 239 GQARVVVGTRSAVFAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLI 298

Query: 356 VSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQV-----IDMRGQTIAQGKSLSPEM 410
                + E++    S   H +        +  P ++      + +     A+   L    
Sbjct: 299 GGHARTAEAQALVESGWAHDLVAPRPVVRARAPRVRALGDSGLALERDPAARAARLPSLA 358

Query: 411 IDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCG 470
               R  L      L+ + RRGY P   C  C    +C HC+  L    +     C  CG
Sbjct: 359 FRAARDALEHGP-VLVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCG 417

Query: 471 HSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLS 530
            +A     C  CGS  ++ A   G  R AEE+   FP   + + S    GG   +     
Sbjct: 418 RAAP-DWRCPRCGSD-RLRAVVVGARRTAEELGRAFPGVPV-VTS----GGDQVVD---- 466

Query: 531 AIAKGEID----IIIGT---QLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERT----F 579
                 +D    +++ T   +   +G          ++D    L   DLR++E T     
Sbjct: 467 -----TVDAGPALVVATPGAEPRVEGG----YGAALLLDAWALLGRQDLRAAEDTLRRWM 517

Query: 580 QLLSQVTGRA--GRFGLKSLGLIQAYQPTHPVMQALVSGDADSFYESEIRARESVNLPPF 637
              + V  RA  G+       ++ A + + P +QAL+  D     E E+  R  V  PP 
Sbjct: 518 AAAALVRPRADGGQ------VVVVA-ESSLPTVQALIRWDPVGHAERELAERAEVGFPPA 570

Query: 638 GRLAAVIISGTKYQEVENYAYNLKEHAPRSSDIVVFGPAESPLFMVR------GRYRFRL 691
            R+AAV   G     V      L E A       V GP   P  + R         R R 
Sbjct: 571 VRMAAV--DGRP-AAVA----ALLEAAGLPDGAEVLGPVPLPPGVRRPAGIDAREDRVRA 623

Query: 692 LI---HGKRNSNLQGFFSQMYDNTIKR-SNALRVQFD 724
           L+     +           +   + +R    LRVQ D
Sbjct: 624 LVRVPRARGAELAAALRRAVAVRSARREPGPLRVQID 660



 Score = 34.5 bits (80), Expect = 0.094
 Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 30 YSVPSAMK--VELGSIVRVPLRSRTVLGIVW-YNSEEKYKIDSLKLRPIEYVF-DCPPLS 85
          Y VP  +    + G  VRV    R V G V    S+  +     KLR +E V    P L+
Sbjct: 31 YLVPEELSDDAQPGVRVRVRFGGRLVDGFVLERRSDSDH---EGKLRWLERVVSPEPVLT 87

Query: 86 RQMCEFVKWVAD 97
           ++    + VAD
Sbjct: 88 PEIRRLARAVAD 99


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

 Score = 86.4 bits (214), Expect = 2e-17
 Identities = 34/167 (20%), Positives = 64/167 (38%), Gaps = 14/167 (8%)

Query: 208 EQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVL--HLGKQVLILLPEISLTSAILER 265
           ++ +     G    +++  TGSGKT   L      L    GK+VL+L+P   L     E 
Sbjct: 14  KEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEE 73

Query: 266 FQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALF-------LPFKKLGLI 318
            +K       +         + +  R++  G   ++V     L        L    + L+
Sbjct: 74  LKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLV 133

Query: 319 VIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPSIESR 365
           ++DE H +        L       +++   ++  ++L+SATP  E  
Sbjct: 134 ILDEAHRLLDGGFGDQL-----EKLLKLLPKNVQLLLLSATPPEEIE 175


>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 = 63.1 bits (154), Expect = 2e-10
 Identities = 65/220 (29%), Positives = 97/220 (44%), Gaps = 37/220 (16%)

Query: 222 LISGVTGSGKTEVYLE-IVAAVLHLGKQVLILLPEISLTSAILERFQKRF---GVKPAEW 277
           L+ G  G GKTEV +     AVL  GKQV +L+P   L     E F++RF    V     
Sbjct: 476 LVCGDVGFGKTEVAMRAAFKAVLD-GKQVAVLVPTTLLAQQHFETFKERFANFPVTIELL 534

Query: 278 HSSLSTSMREKIWRQVARGAISVIVGVRSAL--FLPFKKLGLIVIDEEHDISYKQEEGIL 335
               S   + +I +++A G I +++G    L   + FK LGL++IDEE     KQ+E + 
Sbjct: 535 SRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKL- 593

Query: 336 YNARDMSIVRGKIESFPVVLVSATPSIESRVNGISRRYHSVHLSTRYRNSALPHLQVIDM 395
              +++        S  V+ +SATP        I R   ++H+S     S +  L +I  
Sbjct: 594 ---KELRT------SVDVLTLSATP--------IPR---TLHMSM----SGIRDLSIIAT 629

Query: 396 ----RGQTIAQGKSLSPEMI-DGIRHTLARNEQTLLFLNR 430
               R           PE++ + IR  L R  Q     NR
Sbjct: 630 PPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNR 669



 Score = 31.9 bits (73), Expect = 0.55
 Identities = 28/112 (25%), Positives = 49/112 (43%), Gaps = 23/112 (20%)

Query: 494 GIERIAEEVCEYFPLARISILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFP 553
            IE++A ++ E  P ARI+I    +      L+  +    KGE  +++ T ++  G + P
Sbjct: 672 SIEKLATQLRELVPEARIAIAHGQM--TENELEEVMLEFYKGEFQVLVCTTIIETGIDIP 729

Query: 554 RMSLVGVVDGDLGLTNADLRSSERTFQL--LSQVTGRAGRFGLKSLGLIQAY 603
             + + +++       AD       F L  L Q+ GR GR         +AY
Sbjct: 730 NANTI-IIE------RAD------KFGLAQLYQLRGRVGR------SKKKAY 762



 Score = 29.6 bits (67), Expect = 3.1
 Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 2/35 (5%)

Query: 529 LSAIAKGEIDIIIGT-QLVAKGHNFPRMSLVGVVD 562
           L  +A G+IDI+IGT +L+ K   F  + L+ ++D
Sbjct: 547 LKELASGKIDILIGTHKLLQKDVKFKDLGLL-IID 580


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

 Score = 60.8 bits (148), Expect = 1e-09
 Identities = 47/147 (31%), Positives = 70/147 (47%), Gaps = 18/147 (12%)

Query: 222 LISGVTGSGKTEV-YLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRF---GVKPAEW 277
           L+ G  GSGKT V  L ++AA+   G QV ++ P   L        +      G++ A  
Sbjct: 260 LLQGDVGSGKTLVAALAMLAAIEA-GYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALL 318

Query: 278 HSSLSTSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVIDEEHDISYKQEEGI 334
             SL    R+++   +A G I ++VG   AL    + FK+L L++IDE+H    +Q    
Sbjct: 319 TGSLKGKRRKELLETIASGQIHLVVGTH-ALIQEKVEFKRLALVIIDEQHRFGVEQ---- 373

Query: 335 LYNARDMSIVRGKIESFPVVLV-SATP 360
               R     +G+    P VLV SATP
Sbjct: 374 ----RKKLREKGQGGFTPHVLVMSATP 396



 Score = 33.9 bits (78), Expect = 0.16
 Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 3/43 (6%)

Query: 521 GGGRLQLQLSAIAKGEIDIIIGTQ-LVAKGHNFPRMSLVGVVD 562
           G  R +L L  IA G+I +++GT  L+ +   F R++LV ++D
Sbjct: 324 GKRRKEL-LETIASGQIHLVVGTHALIQEKVEFKRLALV-IID 364



 Score = 31.2 bits (71), Expect = 0.93
 Identities = 29/136 (21%), Positives = 59/136 (43%), Gaps = 28/136 (20%)

Query: 500 EEVCEYFPLARISILSSDLEGGGGRLQ--LQLSAIAK---GEIDIIIGTQLVAKGHNFPR 554
           E + + FP   + +L        GR++   + + + +   GE+DI++ T ++  G + P 
Sbjct: 474 ERLKKAFPKYNVGLLH-------GRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN 526

Query: 555 MSLVGVVDGD-LGLTNADLRSSERTFQLLSQVTGRAGRFGLKSLGLIQAYQP-THPVMQA 612
            +++ + D +  GL+             L Q+ GR GR   +S  L+    P +    + 
Sbjct: 527 ATVMVIEDAERFGLSQ------------LHQLRGRVGRGDHQSYCLLVYKNPKSESAKKR 574

Query: 613 L--VSGDADSFYESEI 626
           L  ++   D F  +E 
Sbjct: 575 LRVMADTLDGFVIAEE 590


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

 Score = 54.4 bits (131), Expect = 1e-07
 Identities = 37/118 (31%), Positives = 57/118 (48%), Gaps = 5/118 (4%)

Query: 222 LISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPA--EWHS 279
           L+ G  G GKTEV +      +   KQV +L+P   L     + F+ RF   P   E  S
Sbjct: 625 LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLS 684

Query: 280 SL-STSMREKIWRQVARGAISVIVGVRSALF--LPFKKLGLIVIDEEHDISYKQEEGI 334
              S   + +I  + A G I +++G    L   + +K LGL+++DEEH    + +E I
Sbjct: 685 RFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERI 742


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

 Score = 48.6 bits (117), Expect = 5e-06
 Identities = 33/111 (29%), Positives = 49/111 (44%), Gaps = 23/111 (20%)

Query: 228 GSGKTEVYLEIVAAVLHL---GKQVLILLP-EI-------SLTSAILERFQKRFGVKPAE 276
           GSGKT V      A L     G Q  ++ P EI       +L      +  +  G++ A 
Sbjct: 292 GSGKTVV---AALAALAAIEAGYQAALMAPTEILAEQHYENLK-----KLLEPLGIRVAL 343

Query: 277 WHSSLSTSMREKIWRQVARGAISVIVGVRSALF---LPFKKLGLIVIDEEH 324
              SL    R +I   +A G   +++G   AL    + F  LGL++IDE+H
Sbjct: 344 LTGSLKGKERREILEAIASGEADIVIGTH-ALIQDDVEFHNLGLVIIDEQH 393



 Score = 36.7 bits (86), Expect = 0.020
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 496 ERIAEEVCEYFPLARISI--LSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQ-LVAKGHNF 552
           E+  E + +      I +  L+  L  G  R ++ L AIA GE DI+IGT  L+     F
Sbjct: 324 EQHYENLKKLLEPLGIRVALLTGSL-KGKERREI-LEAIASGEADIVIGTHALIQDDVEF 381

Query: 553 PRMSLVGVVD 562
             + LV ++D
Sbjct: 382 HNLGLV-IID 390


>gnl|CDD|161969 TIGR00631, uvrb, excinuclease ABC, B subunit.  This family is based
           on the phylogenomic analysis of JA Eisen (1999, Ph.D.
           Thesis, Stanford University).
          Length = 655

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 31/98 (31%), Positives = 55/98 (56%), Gaps = 13/98 (13%)

Query: 497 RIAEEVCEYFPLARISI--LSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLVAKGHNFPR 554
           ++AE++ +Y     I +  L S+++    R+++ +  +  GE D+++G  L+ +G + P 
Sbjct: 453 KMAEDLTDYLKELGIKVRYLHSEIDTLE-RVEI-IRDLRLGEFDVLVGINLLREGLDLPE 510

Query: 555 MSLVGVVDGDL-GLTNADLRSSERTFQLLSQVTGRAGR 591
           +SLV ++D D  G     LR SER+   L Q  GRA R
Sbjct: 511 VSLVAILDADKEGF----LR-SERS---LIQTIGRAAR 540



 Score = 30.0 bits (68), Expect = 2.3
 Identities = 26/84 (30%), Positives = 33/84 (39%), Gaps = 19/84 (22%)

Query: 247 KQVLILLPEISLTSAILER----------------FQKRFGVKPAEWHSSLSTSMREKIW 290
            QV  LL EI    A  ER                + K  G+K    HS + T  R +I 
Sbjct: 426 GQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEII 485

Query: 291 RQVARGAISVIVGV---RSALFLP 311
           R +  G   V+VG+   R  L LP
Sbjct: 486 RDLRLGEFDVLVGINLLREGLDLP 509


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

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 23/98 (23%), Positives = 36/98 (36%), Gaps = 20/98 (20%)

Query: 500 EEVCEYFPLARISILSSDLEGGGGRLQLQLSAI----AKGEIDIIIGTQLVAKGHNFPRM 555
           EE+ E      I +        GG  Q +   I      G+I +++ T +  +G + P +
Sbjct: 1   EELAELLKELGIKVARLH----GGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGV 56

Query: 556 SLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFG 593
            LV + D               +     Q  GRAGR G
Sbjct: 57  DLVIIYDLP------------WSPASYIQRIGRAGRAG 82


>gnl|CDD|162341 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
           putative.  This model represents a family of proteins in
           Gram-positive bacteria. The N-terminal region of about
           200 amino acids resembles the epsilon subunit of E. coli
           DNA polymerase III and the homologous region of the
           Gram-positive type DNA polymerase III alpha subunit. The
           epsilon subunit contains an exonuclease domain. The
           remainder of this protein family resembles a predicted
           ATP-dependent helicase, the DNA damage-inducible protein
           DinG of E. coli.
          Length = 850

 Score = 37.9 bits (88), Expect = 0.009
 Identities = 17/46 (36%), Positives = 21/46 (45%)

Query: 220 VSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILER 265
            SLI   TG+GKT  YL          K V+I      L S +LE+
Sbjct: 266 KSLIEAPTGTGKTLGYLLPALYYAITEKPVVISTNTKVLQSQLLEK 311


>gnl|CDD|161845 TIGR00376, TIGR00376, DNA helicase, putative.  The gene product may
           represent a DNA helicase. Eukaryotic members of this
           family have been characterized as binding certain
           single-stranded G-rich DNA sequences (GGGGT and GGGCT).
           A number of related proteins are characterized as
           helicases.
          Length = 637

 Score = 37.1 bits (86), Expect = 0.015
 Identities = 26/102 (25%), Positives = 44/102 (43%), Gaps = 15/102 (14%)

Query: 169 GLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVS-----LI 223
             +    I    E  S   +  +  F  P L+++Q++ V          FA+S     LI
Sbjct: 129 HSRLLEFILGR-EAPSKASEIHDFQFFDPNLNESQKEAV---------SFALSSKDLFLI 178

Query: 224 SGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILER 265
            G  G+GKT   +E++  ++  G +VL+  P       +LER
Sbjct: 179 HGPPGTGKTRTLVELIRQLVKRGLRVLVTAPSNIAVDNLLER 220


>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 = 34.4 bits (79), Expect = 0.096
 Identities = 24/106 (22%), Positives = 44/106 (41%), Gaps = 10/106 (9%)

Query: 227 TGSGKTEVYLEIVAAVLHLGKQVLILLPEISL---TSAILERFQKRFGVKPAEW---HSS 280
           TG GKT   L +   +   GK+  I+LP   L    +  +    ++ GV        HS 
Sbjct: 102 TGVGKTTFGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSR 161

Query: 281 LSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLG----LIVIDE 322
           L T  +++   ++  G   +++     L   + +LG     I +D+
Sbjct: 162 LPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDFIFVDD 207


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

 Score = 34.5 bits (80), Expect = 0.099
 Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 227 TGSGKTEVYLEIVAAVLHL-GKQVLILLPEISLTSAILERFQKR-----FGVKPAEWHSS 280
           TG GKT  +  +++  L   GK+  I+ P   L   ++E+ +K       GVK   +HSS
Sbjct: 104 TGVGKT-TFGLVMSLYLAKKGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSS 162

Query: 281 LSTSMREKIWRQVARGAISVIV 302
           L    +E+   ++  G   ++V
Sbjct: 163 LKKKEKEEFLERLKEGDFDILV 184


>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 = 34.3 bits (79), Expect = 0.10
 Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 227 TGSGKTEVYLEIVAAVLHLGK--QVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTS 284
           TG GKTE  L      +   K  +V+I LP  +  +A+  R ++ FG      HSS S  
Sbjct: 8   TGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGSNLGLLHSSSSFK 67


>gnl|CDD|185380 PRK15483, PRK15483, type III restriction-modification system StyLTI
           enzyme res; Provisional.
          Length = 986

 Score = 34.2 bits (79), Expect = 0.13
 Identities = 19/71 (26%), Positives = 26/71 (36%), Gaps = 4/71 (5%)

Query: 165 HVIDGLKAQGVIKQIFEVISPVVDSPNLYFSLPILDKNQQDVVEQVVPLCTKGFAVSLIS 224
           H    L A   I   F  I      PN Y + P++    ++ +           A   I 
Sbjct: 10  HQEQALAA---ILAAFTGIDIASADPNHY-ANPLIKLRYENGIPGRSRTRIDDKANIDIK 65

Query: 225 GVTGSGKTEVY 235
             TG+GKT VY
Sbjct: 66  METGTGKTYVY 76


>gnl|CDD|163164 TIGR03158, cas3_cyano, CRISPR-associated helicase, Cyano-type.
           subtype of CRISPR/Cas locus, found in several species of
           Cyanobacteria and several archaeal species. It contains
           helicase motifs and appears to represent the Cas3
           protein of the Cyano subtype of CRISPR/Cas system.
          Length = 357

 Score = 32.6 bits (74), Expect = 0.41
 Identities = 15/49 (30%), Positives = 22/49 (44%)

Query: 313 KKLGLIVIDEEHDISYKQEEGILYNARDMSIVRGKIESFPVVLVSATPS 361
            K   ++ DE H    KQ  G+L+    M ++R        V +SATP 
Sbjct: 144 TKFSTVIFDEFHLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPD 192


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

 Score = 31.7 bits (72), Expect = 0.68
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 9/65 (13%)

Query: 529 LSAIAKGEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGR 588
           L  +  G +DI+I T + A+G +  R+SLV          N D+     ++      TGR
Sbjct: 288 LERLKDGRLDILIATDVAARGLDVERISLV---------VNYDIPMDSESYVHRIGRTGR 338

Query: 589 AGRFG 593
           AGR G
Sbjct: 339 AGRAG 343


>gnl|CDD|150993 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein
           DNA-binding domain.  The plasmid conjugative coupling
           protein TrwB forms hexamers from six structurally very
           similar protomers. This hexamer contains a central
           channel running from the cytosolic pole (made up by the
           AADs) to the membrane pole ending at the transmembrane
           pore shaped by 12 transmembrane helices, rendering an
           overall mushroom-like structure. The TrwB_AAD (all-alpha
           domain) domain appears to be the DNA-binding domain of
           the structure. TrwB, a basic integral inner-membrane
           nucleoside-triphosphate-binding protein, is the
           structural prototype for the type IV secretion system
           coupling proteins, a family of proteins essential for
           macromolecular transport between cells and export.
          Length = 386

 Score = 30.6 bits (70), Expect = 1.4
 Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)

Query: 222 LISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERF 266
           LI G TG+GKT+   E++  +   G + +I       T   +ERF
Sbjct: 19  LIVGTTGTGKTQALRELLDQIRARGDRAIIY----DPTGTFVERF 59


>gnl|CDD|151048 pfam10486, PI3K_1B_p101, Phosphoinositide 3-kinase gamma adapter
           protein p101 subunit.  Class I PI3Ks are dual-specific
           lipid and protein kinases involved in numerous
           intracellular signaling pathways. Class IB PI3K,
           p110gamma, is mainly activated by seven-transmembrane
           G-protein-coupled receptors (GPCRs), through its
           regulatory subunit p101 and G-protein beta-gamma
           subunits.
          Length = 856

 Score = 30.3 bits (68), Expect = 1.6
 Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 9/80 (11%)

Query: 536 EIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGLK 595
           E+   I T+L A G ++ R+     V  + GL N    SS  T  L++    +A    + 
Sbjct: 120 ELLTFISTELKAPGISYQRL-----VRAEQGLPNRSYPSSTVTVLLVNPEEVQAEFLSVA 174

Query: 596 SLGLIQAYQPTHPVMQALVS 615
                +  Q   P    LV 
Sbjct: 175 ----EKLSQAEQPPHTTLVH 190


>gnl|CDD|181473 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
            Provisional.
          Length = 1103

 Score = 30.3 bits (69), Expect = 1.9
 Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 6/40 (15%)

Query: 455  LVEHRSKKKLY-CHQCGHSAIYSQS-----CVVCGSSGKM 488
            L++   K  +Y C  CGH A Y +      C + G  G +
Sbjct: 1033 LLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNI 1072


>gnl|CDD|163455 TIGR03743, SXT_TraD, conjugative coupling factor TraD, SXT/TOL
           subfamily.  Members of this protein family are the
           putative conjugative coupling factor, TraD (or TraG),
           rather distantly related to the well-characterized TraD
           of the F plasmid. Members are associated with
           conjugative-transposon-like mobile genetic elements of
           the class that includes SXT, an antibiotic resistance
           transfer element in some Vibrio cholerae strains.
          Length = 634

 Score = 30.3 bits (69), Expect = 1.9
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 221 SLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLP 254
           +L+ G TG GKT +   ++   +  G  V+++ P
Sbjct: 179 TLVLGTTGVGKTRLAELLITQDIRRGDVVIVIDP 212


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

 Score = 29.5 bits (66), Expect = 3.1
 Identities = 35/122 (28%), Positives = 54/122 (44%), Gaps = 31/122 (25%)

Query: 535 GEIDIIIGTQLVAKGHNFPRMSLVGVVD----GDLG---LTNADLRSSERTFQLLSQVTG 587
             I +I+ T  +A G N P   LV V D    G+ G   L+N +++          Q+ G
Sbjct: 310 RYIKVIVATPTLAAGVNLP-ARLVIVRDITRYGNGGIRYLSNMEIK----------QMIG 358

Query: 588 RAGRFGLKS--LGLIQAYQP-THPVMQALVSGD---ADSFYESEIRARESVNLPPFGRLA 641
           RAGR G     +G I A  P ++   +  +SG+     S+  S+ + R       F  LA
Sbjct: 359 RAGRPGYDQYGIGYIYAASPASYDAAKKYLSGEPEPVISYMGSQRKVR-------FNTLA 411

Query: 642 AV 643
           A+
Sbjct: 412 AI 413


>gnl|CDD|131024 TIGR01969, minD_arch, cell division ATPase MinD, archaeal.  This
           model represents the archaeal branch of the MinD family.
           MinD, a weak ATPase, works in bacteria with MinC as a
           generalized cell division inhibitor and, through
           interaction with MinE, prevents septum placement
           inappropriate sites. Often several members of this
           family are found in archaeal genomes, and the function
           is uncharacterized. More distantly related proteins
           include flagellar biosynthesis proteins and ParA
           chromosome partitioning proteins. The exact roles of the
           various archaeal MinD homologs are unknown.
          Length = 251

 Score = 29.3 bits (66), Expect = 3.4
 Identities = 14/40 (35%), Positives = 25/40 (62%)

Query: 219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISL 258
            +++ SG  G+GKT +   +  A+  LGK+VL L  +I++
Sbjct: 2   IITIASGKGGTGKTTITANLGVALAKLGKKVLALDADITM 41


>gnl|CDD|128434 smart00129, KISc, Kinesin motor, catalytic domain. ATPase.
           Microtubule-dependent molecular motors that play
           important roles in intracellular transport of organelles
           and in cell division.
          Length = 335

 Score = 29.5 bits (67), Expect = 3.7
 Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 5/36 (13%)

Query: 202 NQQDVVEQVV-PL---CTKGFAVSLIS-GVTGSGKT 232
           +Q+DV E+   PL     +G+  ++ + G TGSGKT
Sbjct: 59  SQEDVFEETAAPLVDSVLEGYNATIFAYGQTGSGKT 94


>gnl|CDD|183288 PRK11716, PRK11716, DNA-binding transcriptional regulator IlvY;
           Provisional.
          Length = 269

 Score = 29.0 bits (66), Expect = 3.9
 Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 12/67 (17%)

Query: 454 WLVEHRSKKKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAEEVCEYFPLA-RIS 512
           W   H+ K  +Y    GH AI S           M+A G G+  + E V E  P+  R+ 
Sbjct: 184 WFRRHKIKPNIYATVSGHEAIVS-----------MVALGCGVGLLPEVVLENSPVRNRVQ 232

Query: 513 ILSSDLE 519
           IL     
Sbjct: 233 ILERVPP 239


>gnl|CDD|162973 TIGR02682, cas_csx11, CRISPR-associated protein, Csx11 family.
           Members of this uncommon, sporadically distributed
           protein family are large (>900 amino acids) and strictly
           associated, so far, with CRISPR-associated (Cas) gene
           clusters. Nearby Cas genes always include members of the
           RAMP superfamily and the six-gene CRISPR-associated RAMP
           module. Species in which it is found, so far, include
           three archaea (Methanosarcina mazei, M. barkeri and
           Methanobacterium thermoautotrophicum) and two bacteria
           (Thermodesulfovibrio yellowstonii DSM 11347 and
           Sulfurihydrogenibium azorense).
          Length = 918

 Score = 29.1 bits (65), Expect = 4.0
 Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 5/43 (11%)

Query: 176 IKQIFEVISPV-----VDSPNLYFSLPILDKNQQDVVEQVVPL 213
           +K++ EV  P+      D   +YF +P LDKN+ + +  +V  
Sbjct: 271 LKKLLEVEYPLGNEIYRDDTGIYFIVPELDKNEDNNLAVLVDD 313


>gnl|CDD|183172 PRK11517, PRK11517, transcriptional regulatory protein YedW;
           Provisional.
          Length = 223

 Score = 29.1 bits (65), Expect = 4.4
 Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 19/91 (20%)

Query: 352 PVVLVSATPSIESRVNGIS--------RRYHSVHLSTRYRNSALPH------LQVIDMRG 397
           PV+ ++A  S++ RV G+         + +    L  R R     H      L++  +R 
Sbjct: 73  PVICLTARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQHHALNSTLEISGLRM 132

Query: 398 QTIAQGKSLSPEMIDGIRHTLARNEQTLLFL 428
            +++Q  S      D I  TL R E  LL+L
Sbjct: 133 DSVSQSVSR-----DNISITLTRKEFQLLWL 158


>gnl|CDD|152334 pfam11898, DUF3418, Domain of unknown function (DUF3418).  This
           presumed domain is functionally uncharacterized. This
           domain is found in bacteria. This domain is typically
           between 582 to 594 amino acids in length. This domain is
           found associated with pfam07717, pfam00271, pfam04408.
          Length = 586

 Score = 29.0 bits (66), Expect = 4.9
 Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 5/29 (17%)

Query: 383 RNSALP-HLQ----VIDMRGQTIAQGKSL 406
              ALP HL+    V+D +G+ +A+G+ L
Sbjct: 251 DLEALPPHLRMNFRVVDEKGKVLAEGRDL 279


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

 Score = 28.6 bits (64), Expect = 5.6
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 12/65 (18%)

Query: 535 GEIDIIIGTQLVAKGHNFPRMSLVGVVDGDLGLTNADLRSSERTFQLLSQVTGRAGRFGL 594
           G   ++I T L+A+G +  ++SLV          N DL +S   +  + ++ GR+GRFG 
Sbjct: 316 GSTRVLITTDLLARGIDVQQVSLV---------INYDLPASPENY--IHRI-GRSGRFGR 363

Query: 595 KSLGL 599
           K + +
Sbjct: 364 KGVAI 368


>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 = 28.5 bits (63), Expect = 6.0
 Identities = 26/138 (18%), Positives = 52/138 (37%), Gaps = 20/138 (14%)

Query: 222 LISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSL 281
           LI G  GSGKT +   +   +   G  V+ +  E  L   + +      G K A    S 
Sbjct: 6   LIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKA----SG 61

Query: 282 STSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLIVIDEEHDISYKQEEGILYNARDM 341
           S  +R ++   +AR                  K  ++++DE   +   ++E +L    ++
Sbjct: 62  SGELRLRLALALARK----------------LKPDVLILDEITSLLDAEQEALLLLLEEL 105

Query: 342 SIVRGKIESFPVVLVSAT 359
            ++        + ++  T
Sbjct: 106 RLLLLLKSEKNLTVILTT 123


>gnl|CDD|161791 TIGR00260, thrC, threonine synthase.  Involved in threonine
           biosynthesis it catalyses the reaction
           O-PHOSPHO-L-HOMOSERINE + H(2)O = L-THREONINE +
           ORTHOPHOSPHATE using pyridoxal phosphate as a cofactor.
           the enzyme is distantly related to the serine/threonine
           dehydratases which are also pyridoxal-phosphate
           dependent enzymes. the pyridoxal-phosphate binding site
           is a Lys (K) residues present at residue 70 of the
           model.
          Length = 328

 Score = 28.5 bits (64), Expect = 6.2
 Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 16/81 (19%)

Query: 260 SAILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIVGVRSALFLPFKKLGLI- 318
           + I+  F +    +P E  ++LST++            I        AL L  +  G   
Sbjct: 219 ADIVRAFLESGQWEPIEDPATLSTAID-----------IGNPANWERALELFRRSNGNAE 267

Query: 319 -VIDEEHDISYK---QEEGIL 335
            V DEE   + K   +EEG  
Sbjct: 268 DVSDEEILEAIKLLAREEGYF 288


>gnl|CDD|180660 PRK06696, PRK06696, uridine kinase; Validated.
          Length = 223

 Score = 28.4 bits (64), Expect = 6.9
 Identities = 12/46 (26%), Positives = 21/46 (45%)

Query: 205 DVVEQVVPLCTKGFAVSLISGVTGSGKTEVYLEIVAAVLHLGKQVL 250
           ++ E ++ L         I G+T SGKT    E+   +   G+ V+
Sbjct: 9   ELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIKKRGRPVI 54


>gnl|CDD|184910 PRK14946, PRK14946, DNA polymerase III subunit beta; Provisional.
          Length = 366

 Score = 28.3 bits (63), Expect = 7.3
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 286 REKIWRQVARGAISVIVGVRSAL---FLPFKKLGLIVIDEEHDISYK 329
           +E I +Q+ R   +++    S L   FL   + GL +I    ++SYK
Sbjct: 7   KEIIEKQIERMQSAILNNGNSPLSGFFLKLTRSGLFIISTNSELSYK 53


>gnl|CDD|178669 PLN03122, PLN03122, Poly [ADP-ribose] polymerase; Provisional.
          Length = 815

 Score = 28.2 bits (63), Expect = 7.7
 Identities = 18/68 (26%), Positives = 25/68 (36%), Gaps = 14/68 (20%)

Query: 389 HLQVIDMRGQTIAQGK-SLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLK 447
           HL +  MR      G+ S   +        +    Q  LF     Y PL  C +CG  L+
Sbjct: 74  HLSIEQMREILEENGQDSSGSD------DAVLPRCQDQLF-----YGPLEKCPLCGGALE 122

Query: 448 C--LHCSC 453
           C     +C
Sbjct: 123 CDGHRYTC 130


>gnl|CDD|184743 PRK14559, PRK14559, putative protein serine/threonine phosphatase;
           Provisional.
          Length = 645

 Score = 28.1 bits (63), Expect = 7.8
 Identities = 13/47 (27%), Positives = 17/47 (36%), Gaps = 16/47 (34%)

Query: 439 CQVCGNRLKCLHCSCWLVEHRSKKKLYCHQCGHSAIYSQS-CVVCGS 484
           CQ CG  L           H+      C QCG      ++ C  CG+
Sbjct: 18  CQKCGTSLT----------HKP-----CPQCGTEVPVDEAHCPNCGA 49


>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
           Provisional.
          Length = 784

 Score = 28.4 bits (63), Expect = 7.9
 Identities = 27/93 (29%), Positives = 42/93 (45%), Gaps = 25/93 (26%)

Query: 493 FGIERIAEEVCEYFPL-ARIS-----ILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQLV 546
           +G+ER+ + + EY  + +R++     IL      G G+  L  S IAK            
Sbjct: 325 YGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQS-IAK------------ 371

Query: 547 AKGHNFPRMSLVGVVDGDLGLTNADLRSSERTF 579
           A G  + RM+L GV D       A++R   RT+
Sbjct: 372 ATGRKYVRMALGGVRD------EAEIRGHRRTY 398


>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 = 27.8 bits (62), Expect = 9.8
 Identities = 33/149 (22%), Positives = 63/149 (42%), Gaps = 24/149 (16%)

Query: 227 TGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMR 286
           TG GK+  Y ++ A  L      L++ P ISL    + + +   G+     +SS S   +
Sbjct: 35  TGGGKSLCY-QLPA--LCSDGITLVISPLISLMEDQVLQLKA-SGIPATFLNSSQSKEQQ 90

Query: 287 EKIWRQVARGAISVIV-----GVRSALFL----PFKKLGLIVIDEEHDIS-----YKQEE 332
           + +   +  G I ++         S   L      K + LI +DE H IS     ++ + 
Sbjct: 91  KNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPD- 149

Query: 333 GILYNARDMSIVRGKIESFPVVLVSATPS 361
                 + +  ++ K  + P++ ++AT S
Sbjct: 150 -----YKALGSLKQKFPNVPIMALTATAS 173


  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    0.137    0.401 

Gapped
Lambda     K      H
   0.267   0.0746    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 11,967,995
Number of extensions: 797830
Number of successful extensions: 1732
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1701
Number of HSP's successfully gapped: 65
Length of query: 731
Length of database: 5,994,473
Length adjustment: 100
Effective length of query: 631
Effective length of database: 3,833,673
Effective search space: 2419047663
Effective search space used: 2419047663
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 (27.2 bits)