RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780823|ref|YP_003065236.1| double-strand break repair
protein AddB [Candidatus Liberibacter asiaticus str. psy62]
         (1040 letters)



>gnl|CDD|163020 TIGR02786, addB_alphas, double-strand break repair protein AddB,
            alphaproteobacterial type.  AddAB is a system well
            described in the Firmicutes as a replacement for RecBCD
            in many prokaryotes for the repair of double stranded
            break DNA damage. More recently, a distantly related gene
            pair conserved in many alphaproteobacteria was shown also
            to function in double-stranded break repair in Rhizobium
            etli. This family consists of AddB proteins of the
            alphaproteobacteial type.
          Length = 1021

 Score =  870 bits (2250), Expect = 0.0
 Identities = 383/1038 (36%), Positives = 568/1038 (54%), Gaps = 29/1038 (2%)

Query: 8    VFTIAPSSPFFREMIPALLNGTLVENFRYDPLNPLLLASVTIYVPTKRAIQELRSEFIEI 67
            VF+I P  PF   +   LL G LV  F  D  +PL LA  TIYVPT+RA + LR  F+++
Sbjct: 2    VFSIPPGRPFLDALAEGLLKGRLVAGFEADGDDPLALADATIYVPTRRAARALREAFVDV 61

Query: 68   TGKKSTILPIIKSLGDVVEEK--FTADLLLSYNLNPPVSNIQRLLELARLILIWRNKLPD 125
               ++ +LP I+ LGDV E++  F A+     +L P +S ++RLLELARLI  WR+KL +
Sbjct: 62   LDGRAALLPRIRPLGDVDEDEALFAAEGPAILDLPPAISPLERLLELARLIRAWRDKLVE 121

Query: 126  IIKDLYPESPLSLPISPANAIWLAKNLADIIDIIETEEKKWEDLHALKNEKYGMWWLLAA 185
                      +  P  PA+AIWLA++LAD++D +ETE   W  L  L        W +  
Sbjct: 122  ---------DVLAPAGPADAIWLARDLADLMDEMETEGVDWSKLDDLAEGDLARHWQVTL 172

Query: 186  DFLKIASKYWTERLVELNASSPVGYQIALMRAEAEHLM-KGTKGPIIIAGSTGSIPATAR 244
             FL+I ++ W +RL EL  S+P   +  L+RA A        +GP+I AGSTGSIPATA 
Sbjct: 173  KFLEIVTRAWPKRLAELGRSNPAARRNRLLRALAARWATNPPEGPVIAAGSTGSIPATAD 232

Query: 245  LMSTVANHPNGAIVLPGLDCHIPTAIWNTITEKSTNITSSNTTYSTHPQYSLAKLLDFLD 304
            L++ VA  P GA+VLPGLD  +    W  +    T+  S       HPQY L +LLD L 
Sbjct: 233  LLAVVARLPQGAVVLPGLDLDMDEEAWQALGPAGTDPPSV----FGHPQYGLKRLLDRLG 288

Query: 305  IKREDVKRLGNVSNEMYGRSMVISKSFLPPDTSDMRNTDILENKIPNIQKCFSDVALIEA 364
            + R++V+  G     +  R  ++S++  P +T+D   +   +     I + F++++LIEA
Sbjct: 289  VSRKEVREWGPADRGLRKRERLVSEALRPAETTDRWGSQREQPAEAGIAEAFANLSLIEA 348

Query: 365  DNEREEAISIAIALRMSLDENKKKSALITADRNLARRVKLELTRFGINIDISAGIPLSTT 424
             NEREEA++IA+ALR ++++  K +AL+T DR LARRV  EL RFGI+ D SAG PLS T
Sbjct: 349  ANEREEALAIALALREAVEDPGKTAALVTPDRALARRVAAELKRFGIDADDSAGRPLSLT 408

Query: 425  LHSSILTSLLNAIFKLNDFMAIATLVKHPLAKFGFPEKYLSRAKNALELVALRGNKNSYD 484
              + +L  L  A+F   D +A+ +L+KHPL + G        A   LELVALRG      
Sbjct: 409  PPAVLLRLLAEAVFAPLDPVALLSLLKHPLVRLGEERDDWRAAAELLELVALRGGTPRAG 468

Query: 485  IMDLKSLVLDRIATQKNNTHVPHWQSRLSEEDKELAVLLVDHILQCITPLVTYKTNKNST 544
            I+ L +    R+    ++  VP W S L E+  E A  L + +   I PL +    +   
Sbjct: 469  ILALPAFFERRLLALGDDPEVPAWHSALPEQSIEAARPLCELLEIAIEPLESLAGRREEL 528

Query: 545  CGNLSISDWTKLTVTCLQNVCLDEHRKLPNLWFEEEGKTLSSLFSKIIETGSCIKANAIE 604
                  ++  + TV  ++ +  DE   L  L+  E G  L+SLF++++ +   +  +A +
Sbjct: 529  -----DAELAEATVELMEALSRDEEGWLAALYEGEAGHKLASLFAELLSSAHGLDFDARD 583

Query: 605  WIDIITRLIDGETVKPKIEKSSTLFILGTLESRLLNFDTLILGGLNEGVWPKNTAKNPFL 664
            W D++  L+  E V+P+      +FI G LE+RL   D +++GGLNEGVWP     +PFL
Sbjct: 584  WPDVLQALMATEAVRPRDGGHPRIFIWGALEARLQTADLVVIGGLNEGVWPPAPRNDPFL 643

Query: 665  SRVMQSDLNLKTAEKYIGQAAHDFEMANGTRHLIYTRSLRENNIPTIASRWLQRLLVLGG 724
            SR M+ +L L   E+ IG +AHDF+ A G + ++ TR+ R    P + SRWLQRL  L G
Sbjct: 644  SRPMRHELGLPPPERRIGLSAHDFQQALGAKEVVLTRAARSGGAPAVPSRWLQRLEALAG 703

Query: 725  TDFFDNLKKRGQCYLDWTRKLDYTTKQPHYKRPKPFPPLEAQPRTYSFSEIKQLINDPYA 784
             D  + +++RG+ YL W R LD         RP P PP+  +PR +S +EI+ L  DPYA
Sbjct: 704  ADVLEEMRRRGERYLHWARALDEPQDVAPATRPAPRPPVADRPRHFSVTEIETLRRDPYA 763

Query: 785  VYARRILKLDFIPHFKKDPDRTDRGTLFHNIITELIKKRINKNTPEINHLMKQIIDSHFE 844
            +YAR ILKL  +    +DP+  DRGTL H+I+   +++  +    +    +++I  + F 
Sbjct: 764  IYARHILKLRPLDPLDRDPEAADRGTLIHDILERFVREYPDPLPADAADALRKIGRAEFA 823

Query: 845  KENLPPHIDIIWRHLFHKISHSFLEHEEKIQSSIEKIFVNIPA-KMAIESIGIHLTGFAD 903
              NLPP  + +W   F + +  F + E   +  + +IF      K  +   G  L+G AD
Sbjct: 824  SLNLPPTAEALWWPRFARAADWFADWERARRLDVRRIFAEARGRKELVGERGFTLSGRAD 883

Query: 904  RIDLLKSGFVDITDYKTGDNPKKETAQKLIDPQLSLEAAALKAGSFSQIDCRKVANLFYI 963
            RID    G   I DYKTG  P  +  +  + PQL+LEAA L  G+F  I     ANL+Y+
Sbjct: 884  RIDRTPDGSAAILDYKTGAPPSGKQVRAGLSPQLALEAALLMRGAFKDIGAPTPANLYYV 943

Query: 964  RLK--QKFKIDCITNDKKKY-----SADELSEKSLKNLIEIVTLLQNGEQPFISHLRLSE 1016
            RL        + I ++K K       A +L+E++ + LI+++    + +Q + S      
Sbjct: 944  RLGGNGPVGEESILSEKGKGGKEPQDAPDLAEEAWERLIQLIRAYDDPDQGYTSRALPFG 1003

Query: 1017 KSNIQSEYDHLARVAEWR 1034
            K     +YDHLARV EW 
Sbjct: 1004 KKEYYGDYDHLARVDEWS 1021


>gnl|CDD|163360 TIGR03623, TIGR03623, probable DNA repair protein.  Members of this
           protein family are bacterial proteins of about 900 amino
           acids in length. Members show extended homology to
           proteins in TIGR02786, the AddB protein of double-strand
           break repair via homologous recombination. Members of
           this family, therefore, may be DNA repair proteins.
          Length = 874

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 17/40 (42%), Positives = 22/40 (55%)

Query: 630 ILGTLESRLLNFDTLILGGLNEGVWPKNTAKNPFLSRVMQ 669
           +LG LE+  L FD L + GL +  WP     NPFL   +Q
Sbjct: 461 VLGLLEAAGLQFDALWVMGLTDEQWPAPPRPNPFLPLALQ 500



 Score = 39.3 bits (92), Expect = 0.006
 Identities = 40/155 (25%), Positives = 64/155 (41%), Gaps = 26/155 (16%)

Query: 807 DRGTLFHNIITELIKKRI-------NKNTPEINHLMKQIIDSHFEKEN------LPPHID 853
           +RGTL H ++ EL  +R+         +  E+  L+ + I+    +E        P    
Sbjct: 635 ERGTLVHRVL-ELFWERLKNQEALNALDEAELEQLIAEAIEEALAEERARHSQTFPERFL 693

Query: 854 IIWRHLFHKISHSFLEHEEKIQ----SSIEKIFVNIPAKMAIESIGIHLTGFADRIDLLK 909
            + +    ++   +LE E K       + E          +IE  G+ L    DRID L 
Sbjct: 694 ELEQERLLQLLLEWLELERKRPPFEVVATE-------QNHSIEIGGLELKLRIDRIDRLA 746

Query: 910 SGFVDITDYKTGDNPKKETA-QKLIDPQLSLEAAA 943
            G   I DYKTG    K+   ++ ++PQL L A  
Sbjct: 747 DGSRLIIDYKTGAPSVKDWLGERPVEPQLPLYALL 781


>gnl|CDD|163010 TIGR02773, addB_Gpos, ATP-dependent nuclease subunit B.  DNA repair
           is accomplished by several different systems in
           prokaryotes. Recombinational repair of double-stranded
           DNA breaks involves the RecBCD pathway in some lineages,
           and AddAB (also called RexAB) in other. The AddA protein
           is conserved between the firmicutes and the
           alphaproteobacteria, while the partner protein is not.
           Nevertheless, the partner is designated AddB in both
           systems. This model describes the AddB protein as found
           Bacillus subtilis and related species. Although the RexB
           protein of Streptococcus and Lactococcus is considered
           to be orthologous, functionally equivalent, and merely
           named differently, all members of this protein family
           have a P-loop nucleotide binding motif GxxGxGK[ST] at
           the N-terminus, unlike RexB proteins, and a CxxCxxxxxC
           motif at the C-terminus, both of which may be relevant
           to function.
          Length = 1158

 Score = 37.0 bits (86), Expect = 0.025
 Identities = 44/225 (19%), Positives = 83/225 (36%), Gaps = 53/225 (23%)

Query: 740 DWTRKLDYTTKQPHYK-RPKPFPPLEAQ---PRT--YSFSEIKQLINDPYAVYARRILKL 793
            W   L+Y      Y    K     +A+     T   S S +++    P+A +A+  LKL
Sbjct: 747 KWKNGLEYVLSGLTYDNETKKLQEPKAKKLYGETIQASVSRLEKYNACPFAHFAQYGLKL 806

Query: 794 DFIPHFKKDPDRTDRGTLFHNIITELIKKRINKNTPEINHLMKQIIDSHFEK---ENLPP 850
                +K +    D G +FH  + + I   + +   + + L K+           ENL P
Sbjct: 807 KERKIYKLEA--PDLGQIFHEAL-KEISDELKEEDLDWSDLTKEQC-RALANEAVENLVP 862

Query: 851 HIDIIWRHLFHKISHSFLEHE---EKIQSSIEKI------------FVNI---------- 885
            I        H+I  S   +    ++++  + +             FV +          
Sbjct: 863 KIQ-------HEILLSSKRYRYVQKRLKRIVTRAVKVLSEQAKRSKFVPVGLELGFGFGG 915

Query: 886 ----PAKMAIES-IGIHLTGFADRIDLLKSG---FVDITDYKTGD 922
               P K+ +++   ++L G  DR+D  +     ++ I DYK+  
Sbjct: 916 NELPPLKLILKNGEELNLRGRIDRVDKAEKEDETYLRIIDYKSSS 960


>gnl|CDD|163019 TIGR02785, addA_Gpos, recombination helicase AddA, Firmicutes type.
            AddAB, also called RexAB, substitutes for RecBCD in
            several bacterial lineages. These DNA recombination
            proteins act before synapse and are particularly
            important for DNA repair of double-stranded breaks by
            homologous recombination. The term AddAB is used broadly,
            with AddA homologous between the Firmicutes (as modeled
            here) and the alphaproteobacteria, while the partner AddB
            proteins show no strong homology across the two groups of
            species.
          Length = 1232

 Score = 33.9 bits (78), Expect = 0.22
 Identities = 54/236 (22%), Positives = 86/236 (36%), Gaps = 51/236 (21%)

Query: 771  SFSEIKQLINDPY--------AVYARRILKLDF-IPHF---KKDPDRTDRGTLFHNIITE 818
            S SEIK++  DP         +V   R  K+   +P F    K     + GT  H ++  
Sbjct: 1013 SVSEIKRIFEDPMEDEGSERASVKQSRGKKISLELPKFLTKTKGLTAAEIGTATHLVMQH 1072

Query: 819  L-IKKRINKNTPEINHLMKQIIDSHFEKENLPP------HIDIIWRHLFHK-ISHSFLEH 870
            L + K +++        ++  ID   + E L        +ID I    F   +    L+ 
Sbjct: 1073 LDLSKDLSEEE------LQAQIDRLVKNELLTEEQAEKINIDKI-VAFFDTPLGKQILKA 1125

Query: 871  EEKIQSSIEKIFVNIPAKMAI---------ESIGIHLTGFADRIDLLKSGFVDITDYKTG 921
            +E ++   E  F  + +             E I +   G  D     + G V   DYKT 
Sbjct: 1126 KEVLRR--EPFFSMLISAEIYFDDRDEADEEDILVQ--GIIDGYLESEDGIVLF-DYKTD 1180

Query: 922  --DNPKKETAQKLIDP---QLSLEAAALKAGSFSQIDCRKVANLFYIRLKQKFKID 972
              + P  E   +L +    QL+L   AL      +I  +KV   +   L     ID
Sbjct: 1181 HVEGPSFEKINQLKERYRGQLALYEKAL-----EEIYKKKVKGKYLYLLDGDVVID 1231


>gnl|CDD|177789 PLN00197, PLN00197, beta-amylase; Provisional.
          Length = 573

 Score = 32.3 bits (73), Expect = 0.65
 Identities = 14/34 (41%), Positives = 21/34 (61%)

Query: 864 SHSFLEHEEKIQSSIEKIFVNIPAKMAIESIGIH 897
           S   L+H E+I SS + IF N   K++++  GIH
Sbjct: 364 SQMLLDHGERILSSAKSIFENTGVKISVKIAGIH 397


>gnl|CDD|184382 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
          Length = 900

 Score = 31.7 bits (73), Expect = 0.87
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 31/74 (41%)

Query: 112 LARLIL--IWRN--------KLPDII-------KDLYPESPLSLPISPANAIWLAKNLAD 154
           LARL++    R          L +++       K+ YPE              L +N   
Sbjct: 352 LARLVIRRTLRLLDELGLDVPLSELVDMQIDELKEDYPE--------------LKENRDY 397

Query: 155 IIDIIETEEKKWED 168
           I+DI++ EE+K+ +
Sbjct: 398 ILDIVDLEEEKYRE 411


>gnl|CDD|140232 PTZ00205, PTZ00205, DNA polymerase kappa; Provisional.
          Length = 571

 Score = 29.6 bits (66), Expect = 3.9
 Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 15/76 (19%)

Query: 382 LDENKKKSALIT----ADRNLARRVKLELTRFGINIDISAGIPLSTTLHSSILTSLLNAI 437
           L E K+KS+L T     +RN A+R + EL    I  ++ A   L T +H           
Sbjct: 89  LQELKRKSSLFTQLLGGERNAAQRKQWELKVSKIEQELEATRRLGTYIH----------- 137

Query: 438 FKLNDFMAIATLVKHP 453
             ++ F A   + KHP
Sbjct: 138 LDMDMFYAAVEIKKHP 153


>gnl|CDD|184767 PRK14611, PRK14611, 4-diphosphocytidyl-2-C-methyl-D-erythritol
           kinase; Provisional.
          Length = 275

 Score = 29.0 bits (65), Expect = 7.1
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 63  EFIE--ITGKKSTILPIIKSLGDVVEEKFTADLLLSYNLNPPVSNIQRLLELARLILIWR 120
           EF+E  I+ + + + P IKS    V  K T  +L +      + ++ R  E  ++  +  
Sbjct: 152 EFLEKPISREITLVYPNIKSSTGRVYSKVTKQILTNKEDLNIIISLLREGEEKKIEEVIE 211

Query: 121 NKLPDIIKDLYPE 133
           N L +I  +LYPE
Sbjct: 212 NTLGEIALELYPE 224


>gnl|CDD|163509 TIGR03797, NHPM_micro_ABC2, NHPM bacteriocin system ABC
           transporter, ATP-binding protein.  Members of this
           protein family are ABC transporter ATP-binding subunits,
           part of a three-gene putative bacteriocin transport
           operon. The other subunits include another ATP-binding
           subunit (TIGR03796), which has an N-terminal propeptide
           cleavage domain, and an HlyD homolog (TIGR03794). In a
           number of genomes, a conserved propeptide sequence with
           a classic Gly-Gly motif.
          Length = 686

 Score = 28.4 bits (64), Expect = 9.4
 Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 15/60 (25%)

Query: 23  PALLNGTL-VEN--FRYDPLNPLLLASVTIYVPTKRAIQELRSEFIEITGK----KSTIL 75
           P  L+G + V+   FRY P  PL+L  V++ +           EF+ I G     KST+L
Sbjct: 445 PGKLSGAIEVDRVTFRYRPDGPLILDDVSLQI---EP-----GEFVAIVGPSGSGKSTLL 496


  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
   0.319    0.135    0.394 

Gapped
Lambda     K      H
   0.267   0.0751    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 17,111,391
Number of extensions: 1138935
Number of successful extensions: 2204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2194
Number of HSP's successfully gapped: 26
Length of query: 1040
Length of database: 5,994,473
Length adjustment: 103
Effective length of query: 937
Effective length of database: 3,768,849
Effective search space: 3531411513
Effective search space used: 3531411513
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 (21.7 bits)
S2: 62 (27.6 bits)