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)