RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780399|ref|YP_003064812.1| DNA mismatch repair protein
[Candidatus Liberibacter asiaticus str. psy62]
         (594 letters)



>gnl|CDD|178860 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
          Length = 617

 Score =  698 bits (1805), Expect = 0.0
 Identities = 255/622 (40%), Positives = 379/622 (60%), Gaps = 34/622 (5%)

Query: 1   MKIRKLSEKIINQIAAGEIIERPSIAIKELIENSLDAESSRVETVIAGGGKSFFQITDNG 60
           M I+ L  ++ NQIAAGE++ERP+  +KEL+EN+LDA ++R++  I  GG    ++ DNG
Sbjct: 1   MPIQLLPPQLANQIAAGEVVERPASVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNG 60

Query: 61  FGMTSEEIPMAVQRHCTSKIS--DDFSNIHTFGFRGEALPSIGAVSHLTLMSRPPQNNTG 118
            G++ E++ +A+ RH TSKI+  DD   I T GFRGEALPSI +VS LTL SR      G
Sbjct: 61  CGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEALPSIASVSRLTLTSRTADAAEG 120

Query: 119 AQIAISGEKISSVRPVAMNPGTIVEVRDLFFTIPARLNFLKSEQVETNLITDVIRRMAIA 178
            QI   G +I  V+P A   GT +EVRDLFF  PAR  FLKSE+ E   I DV+ R+A+A
Sbjct: 121 WQIVYEGGEIVEVKPAAHPVGTTIEVRDLFFNTPARRKFLKSEKTELGHIDDVVNRLALA 180

Query: 179 YPKVSFTFSTIKSNRYKMNFQ-STNGNFPERISQVIGEDFINNAVELNEKSNEITLQGYT 237
           +P V+FT +    N  K+  Q    G   +R++ ++G +F  NA+ ++ +  ++ L GY 
Sbjct: 181 HPDVAFTLT---HNG-KLVLQTRGAGQLLQRLAAILGREFAENALPIDAEHGDLRLSGYV 236

Query: 238 GIPTFNRGNANQFYVFINGRTVQDKFILSTIRTAYAETIPLGRYPVVVLLLEIDPRQVDV 297
           G+PT +R N +  Y+F+NGR V+DK +   IR AY + +P GRYP  VL LE+DP QVDV
Sbjct: 237 GLPTLSRANRDYQYLFVNGRYVRDKLLNHAIRQAYHDLLPRGRYPAFVLFLELDPHQVDV 296

Query: 298 NVHPAKSYIRFRNPTIIRNFIIQSIQKAINKKGISTSSVLSKKMISSFHQDNAPKTHLPK 357
           NVHPAK  +RFR+  ++ + I+Q+IQ+A+ + G+  ++  + +++     +  P    P 
Sbjct: 297 NVHPAKHEVRFRDERLVHDLIVQAIQEALAQSGLIPAAAGANQVLEPAEPEPLPLQQTPL 356

Query: 358 YA---------------TSLTNTQEKLFLQENRLSTNDLLPSDDPTYSED---------- 392
           YA                    +QE+   ++N L  N          S +          
Sbjct: 357 YASGSSPPASSPSSAPPEQSEESQEESSAEKNPLQPNASQSEAAAAASAEAAAAAPAAAP 416

Query: 393 NDPVEESEATHYQLGIACAQIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKI 452
                  EA  + LG A  Q+H  YI+++  DGL +VDQHAAHERL++E+++       +
Sbjct: 417 EPAEAAEEADSFPLGYALGQLHGTYILAENEDGLYLVDQHAAHERLLYEQLKDKLAEVGL 476

Query: 453 TSQTLLTPEIIDLLEGECALIMEHDEDLHRLGIKAERFGPNAIAIREIPAILSKKNIPQL 512
            SQ LL P +++L E E   + EH E L RLG++ E FGPN+ A+RE+PA+L ++ + +L
Sbjct: 477 ASQPLLIPLVLELSEDEADRLEEHKELLARLGLELEPFGPNSFAVREVPALLGQQELEEL 536

Query: 513 LRDIIDEIIDSSTTYTLQDRIENILATMACYGSIRSGRKMQSIEMNRLLREMEKNPNSSQ 572
           +RD++DE+ +   + TL++R   +LATMAC+G+IR+GR++   EMN LLR++E   N   
Sbjct: 537 IRDLLDELAEEGDSDTLKER--ELLATMACHGAIRAGRRLTLEEMNALLRQLEATENPGT 594

Query: 573 CNHGRPTFIKLKLSDIEKLFGR 594
           C HGRPT+I+L LSD+EKLF R
Sbjct: 595 CPHGRPTYIELSLSDLEKLFKR 616


>gnl|CDD|161941 TIGR00585, mutl, DNA mismatch repair protein MutL.  All proteins in
           this family for which the functions are known are
           involved in the process of generalized mismatch repair.
           This family is based on the phylogenomic analysis of JA
           Eisen (1999, Ph.D. Thesis, Stanford University).
          Length = 312

 Score =  299 bits (769), Expect = 1e-81
 Identities = 126/312 (40%), Positives = 182/312 (58%), Gaps = 5/312 (1%)

Query: 1   MKIRKLSEKIINQIAAGEIIERPSIAIKELIENSLDAESSRVETVIAGGGKSFFQITDNG 60
           M I+ L  +++N+IAAGE+IERP+  +KEL+ENSLDA ++R++  I  GG    +++DNG
Sbjct: 1   MTIKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNG 60

Query: 61  FGMTSEEIPMAVQRHCTSKISD--DFSNIHTFGFRGEALPSIGAVSHLTLMSRPPQNN-T 117
            G+  E++P+A +RH TSKI    D   I T GFRGEAL SI +VS LT+ ++    +  
Sbjct: 61  SGIDKEDLPLACERHATSKIQSFEDLERIETLGFRGEALASISSVSRLTITTKTSAADGL 120

Query: 118 GAQIAISGEKISSVRPVAMNPGTIVEVRDLFFTIPARLNFLKSEQVETNLITDVIRRMAI 177
             Q  + G  I  ++P     GT VEVRDLF+ +P R  FLKS + E   I D++ R A+
Sbjct: 121 AWQALLEGGMIEEIKPAPRPVGTTVEVRDLFYNLPVRRKFLKSPKKEFRKILDLLNRYAL 180

Query: 178 AYPKVSFTFSTIKSNRYKMNFQSTNGNFPERISQVIGEDFINNAVELNE-KSNEITLQGY 236
            +P VSF+ +       +++ +        RI  V G   ++    L E +  ++ L+G+
Sbjct: 181 IHPDVSFSLTHDGKKVLQLSTKPNQSLKERRIRSVFGTAVLSKLFPLLEWEDGDLQLEGF 240

Query: 237 TGIPTFNRGNA-NQFYVFINGRTVQDKFILSTIRTAYAETIPLGRYPVVVLLLEIDPRQV 295
              P   R       ++FINGR V+ K +L  IR  Y E +P G+YPV VL LEIDP  V
Sbjct: 241 ISEPNVTRSRRSGWQFLFINGRPVELKLLLKAIREVYHEYLPKGQYPVFVLNLEIDPELV 300

Query: 296 DVNVHPAKSYIR 307
           DVNVHP K  +R
Sbjct: 301 DVNVHPDKKEVR 312


>gnl|CDD|149660 pfam08676, MutL_C, MutL C terminal dimerization domain.  MutL and
           MutS are key components of the DNA repair machinery that
           corrects replication errors. MutS recognizes mispaired
           or unpaired bases in a DNA duplex and in the presence of
           ATP, recruits MutL to form a DNA signaling complex for
           repair. The N terminal region of MutL contains the
           ATPase domain and the C terminal is involved in
           dimerization.
          Length = 142

 Score =  172 bits (438), Expect = 3e-43
 Identities = 62/147 (42%), Positives = 101/147 (68%), Gaps = 6/147 (4%)

Query: 406 LGIACAQIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKITSQTLLTPEIIDL 465
           LG A  Q+H  YI+++  DGL +VDQHAAHER+++EK++       + SQ LL P  ++L
Sbjct: 2   LGKALGQVHGTYILAENEDGLYLVDQHAAHERILYEKLKSKLKE-GLQSQPLLIPLTLEL 60

Query: 466 LEGECALIMEHDEDLHRLGIKAERFGPNAIAIREIPAILSKKNIPQLLRDIIDEIIDSST 525
              E AL+ EH E L RLG + E FGPN++ +R +PA+L ++N+ +L+R+++DE+ +   
Sbjct: 61  SPEEAALLEEHKELLARLGFELEEFGPNSLIVRSVPALLRQQNLEELIRELLDELAEKG- 119

Query: 526 TYTLQDRIENILATMACYGSIRSGRKM 552
               ++ +E +LATMAC+ +IR+GR++
Sbjct: 120 ----EELLEELLATMACHSAIRAGRRL 142


>gnl|CDD|129086 smart00853, MutL_C, MutL C terminal dimerisation domain.  MutL and
           MutS are key components of the DNA repair machinery that
           corrects replication errors. MutS recognises mispaired
           or unpaired bases in a DNA duplex and in the presence of
           ATP, recruits MutL to form a DNA signaling complex for
           repair. The N terminal region of MutL contains the
           ATPase domain and the C terminal is involved in
           dimerisation.
          Length = 136

 Score =  150 bits (380), Expect = 1e-36
 Identities = 52/137 (37%), Positives = 92/137 (67%), Gaps = 2/137 (1%)

Query: 406 LGIACAQIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKIT-SQTLLTPEIID 464
           LG    Q+H  YI++++ DGLV++DQHAAHER+++E+++    +  +  SQ LL P I++
Sbjct: 1   LGRVLGQVHGTYILAESEDGLVLIDQHAAHERILYEQLKAKLQAGLLEKSQPLLIPVILE 60

Query: 465 LLEGECALIMEHDEDLHRLGIKAERFGPNAIAIREIPAILSKKNIPQLLRDIIDEIIDSS 524
           L   E AL+ EH E L RLG + E FG  ++ +R +PA+L ++N+ +L+ +++D + +  
Sbjct: 61  LSPEEAALLEEHQELLARLGFELEIFGGQSVILRSVPALLRQQNLQELIPELLDLLAEGG 120

Query: 525 TTYTLQDRIENILATMA 541
           +T +L   +E +LA++A
Sbjct: 121 ST-SLPQLVEALLASLA 136


>gnl|CDD|179773 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
          Length = 535

 Score = 38.7 bits (91), Expect = 0.005
 Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 9/56 (16%)

Query: 25 IAIKELIENSLDA-ESS------RVETVIAGGGKSFFQIT--DNGFGMTSEEIPMA 71
            +KEL++NSLDA E +      ++E      GK  +++T  DNG G+  EEIP  
Sbjct: 39 TTVKELVDNSLDACEEAGILPDIKIEIKRVDEGKDHYRVTVEDNGPGIPPEEIPKV 94


>gnl|CDD|184494 PRK14083, PRK14083, HSP90 family protein; Provisional.
          Length = 601

 Score = 36.8 bits (86), Expect = 0.014
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 14/58 (24%)

Query: 23 PSIAIKELIENSLDAESSR------------VETVIAGGGKSFFQITDNGFGMTSEEI 68
          P + ++EL++N++DA ++R            +E   AGGG     + DNG G+T EE+
Sbjct: 24 PRVYVRELLQNAVDAITARRALDPTAPGRIRIELTDAGGGT--LIVEDNGIGLTEEEV 79


>gnl|CDD|128669 smart00387, HATPase_c, Histidine kinase-like ATPases.  Histidine
          kinase-, DNA gyrase B-, phytochrome-like ATPases.
          Length = 111

 Score = 31.9 bits (73), Expect = 0.44
 Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 3/47 (6%)

Query: 26 AIKELIENSLDA--ESSRVE-TVIAGGGKSFFQITDNGFGMTSEEIP 69
           +  L++N++    E  R+  T+   G      + DNG G+  E++ 
Sbjct: 9  VLSNLLDNAIKYTPEGGRITVTLERDGDHLEITVEDNGPGIPPEDLE 55


>gnl|CDD|162176 TIGR01052, top6b, DNA topoisomerase VI, B subunit.  This model
          describes DNA topoisomerase VI, an archaeal type II DNA
          topoisomerase (DNA gyrase).
          Length = 488

 Score = 30.9 bits (70), Expect = 0.91
 Identities = 18/54 (33%), Positives = 22/54 (40%), Gaps = 7/54 (12%)

Query: 25 IAIKELIENSLDAESS-------RVETVIAGGGKSFFQITDNGFGMTSEEIPMA 71
            I EL+ NSLDA          +VE    G       + DNG G+  E IP  
Sbjct: 31 TVIHELVTNSLDACEEAGILPDIKVEIEKIGKDHYKVTVEDNGPGIPEEYIPKV 84


>gnl|CDD|173589 PTZ00398, PTZ00398, phosphoenolpyruvate carboxylase; Provisional.
          Length = 974

 Score = 30.5 bits (69), Expect = 1.3
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 58  DNGFGMTSEEIPMAVQRHCTSKISDDFS-NIHTFGFRGEALPSIGAVSHLTLMSRPPQN- 115
           D G   ++ E+  A +    S I+  +   I  F  RG ++   G   HL ++S+PP   
Sbjct: 631 DGGRLTSAWELYKAQE--RLSNIARQYGVEIRFFHGRGGSVSRGGGPQHLAILSQPPNTI 688

Query: 116 NTGAQIAISGEKISS 130
            +  +I I GE I+ 
Sbjct: 689 KSYLRITIQGETITQ 703


>gnl|CDD|163071 TIGR02916, PEP_his_kin, putative PEP-CTERM system histidine kinase.
            Members of this protein family have a novel N-terminal
           domain, a single predicted membrane-spanning helix, and
           a predicted cystosolic histidine kinase domain. We
           designate this protein PrsK, and its companion
           DNA-binding response regulator protein (TIGR02915) PrsR.
           These predicted signal-transducing proteins appear to
           enable enhancer-dependent transcriptional activation.
           The prsK gene is often associated with exopolysaccharide
           biosynthesis genes.
          Length = 679

 Score = 29.7 bits (67), Expect = 2.3
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 21  ERPSIAIKELIENSLDA--ESSRVE-TVIAGGGKSFFQITDNGFGMTSEEI 68
           ER    +  L++N+L+A     RV   V    G +  +I D+G GM+   I
Sbjct: 578 ERLERVLGHLVQNALEATPGEGRVAIRVERECGAARIEIEDSGCGMSPAFI 628


>gnl|CDD|184870 PRK14868, PRK14868, DNA topoisomerase VI subunit B; Provisional.
          Length = 795

 Score = 29.0 bits (65), Expect = 3.3
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 10/52 (19%)

Query: 26 AIKELIENSLDAESSR-------VETVIAGGGKSF-FQITDNGFGMTSEEIP 69
          A+KE ++N+LDA           VE  I   G  +   + DNG G+T E+IP
Sbjct: 50 AVKEAVDNALDATEEAGILPDIYVE--IEEVGDYYRLVVEDNGPGITKEQIP 99


>gnl|CDD|179965 PRK05218, PRK05218, heat shock protein 90; Provisional.
          Length = 613

 Score = 28.9 bits (66), Expect = 3.4
 Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 17/61 (27%)

Query: 25 IAIKELIENSLDA------ESSRVETVIAGGGK-----SF------FQITDNGFGMTSEE 67
          I ++ELI N+ DA      E+     +  G G      SF        I+DNG GMT EE
Sbjct: 29 IFLRELISNASDAIDKLRFEALTDPALYEGDGDLKIRISFDKEARTLTISDNGIGMTREE 88

Query: 68 I 68
          +
Sbjct: 89 V 89


>gnl|CDD|181750 PRK09277, PRK09277, aconitate hydratase; Validated.
          Length = 888

 Score = 28.6 bits (65), Expect = 4.3
 Identities = 8/17 (47%), Positives = 12/17 (70%)

Query: 322 IQKAINKKGISTSSVLS 338
           I+KAIN   +  ++VLS
Sbjct: 510 IEKAINDNDLVVTAVLS 526


>gnl|CDD|179380 PRK02190, PRK02190, agmatinase; Provisional.
          Length = 301

 Score = 27.9 bits (63), Expect = 7.3
 Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 16/64 (25%)

Query: 489 RFGPNAIAIREIPAILSKKNIP-QLLRDIIDE--IID-----------SSTTYTLQDRIE 534
           RFGP   AIR+    L+ ++       D+ +   ++D                 L+   E
Sbjct: 47  RFGPA--AIRQASTNLAWEDRRYPWNFDLFERLAVVDYGDLVFDYGDAEDFPEALEAHAE 104

Query: 535 NILA 538
            ILA
Sbjct: 105 KILA 108


>gnl|CDD|185569 PTZ00345, PTZ00345, glycerol-3-phosphate dehydrogenase;
           Provisional.
          Length = 365

 Score = 28.1 bits (63), Expect = 7.6
 Identities = 9/37 (24%), Positives = 16/37 (43%)

Query: 486 KAERFGPNAIAIREIPAILSKKNIPQLLRDIIDEIID 522
           +      +A AI     I+ +   P L  D+I+E + 
Sbjct: 115 ENNNLKKHARAISLTKGIIVENGKPVLCSDVIEEELG 151


>gnl|CDD|161754 TIGR00189, tesB, acyl-CoA thioesterase II.  Subunit: homotetramer.
          Length = 271

 Score = 27.7 bits (62), Expect = 9.0
 Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 5/61 (8%)

Query: 315 RNFIIQSIQKAINKKGISTSSVLSKKMISSF-HQDNAPKTHLPK----YATSLTNTQEKL 369
           R+FI + ++   + K I T     +   S   HQ   PK   P+        L       
Sbjct: 74  RSFITRRVKAVQHGKTIFTLQASFQAEESGIEHQSTMPKVPAPESELPRENQLATKYPAT 133

Query: 370 F 370
            
Sbjct: 134 L 134


>gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional.
          Length = 602

 Score = 27.4 bits (61), Expect = 10.0
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 11/57 (19%)

Query: 162 QVETNLITDVIRRMAIAYPKVSFTFSTIKSNRYKMNFQSTNGNFPERISQVIGEDFI 218
           Q   ++I D ++ +A+ +P + FTF          N +  +G F +   Q  G+D I
Sbjct: 196 QQYLDIILDRLQTLAVVFPDIKFTF----------NGKKVSGKFKKYAKQ-FGDDTI 241


  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
   0.318    0.134    0.372 

Gapped
Lambda     K      H
   0.267   0.0679    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 9,676,415
Number of extensions: 638959
Number of successful extensions: 1319
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1304
Number of HSP's successfully gapped: 28
Length of query: 594
Length of database: 5,994,473
Length adjustment: 99
Effective length of query: 495
Effective length of database: 3,855,281
Effective search space: 1908364095
Effective search space used: 1908364095
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: 60 (27.0 bits)