RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780995|ref|YP_003065408.1| Endonuclease/exonuclease/phosphatase [Candidatus Liberibacter asiaticus str. psy62] (125 letters) >gnl|CDD|146159 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase family. This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin. Length = 255 Score = 33.0 bits (75), Expect = 0.020 Identities = 22/126 (17%), Positives = 32/126 (25%), Gaps = 25/126 (19%) Query: 9 LKKWADQKIKTGIPFVIAGDFNRKINSIG---------DTDDFWQKMDPDGLLIRFPQEK 59 L +D +I P ++ GDFN + +S T + D Sbjct: 139 LDFLSDLRIPKSDPVILCGDFNARPDSWDSALLKSIGKSTLFLLLERDLVFDGFDELPIG 198 Query: 60 -------ESTCNVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHC 112 + K S LD L+ S S L S H Sbjct: 199 FPPTWWSYRNSSEKKNTGSRLDR---------ILVSGSLLRRVVILSLLLLVIFTGSDHR 249 Query: 113 PLTIEY 118 P+ Sbjct: 250 PVLATL 255 >gnl|CDD|31052 COG0708, XthA, Exonuclease III [DNA replication, recombination, and repair]. Length = 261 Score = 30.6 bits (69), Expect = 0.12 Identities = 29/143 (20%), Positives = 51/143 (35%), Gaps = 37/143 (25%) Query: 7 EWLKKWADQKIKTGIPFVIAGDFN--RKINSIGDTDDFWQKMDPDGLLIR---------- 54 + L+ + ++ +K G P V+ GDFN + + + W G L Sbjct: 127 DALRNYLEELLKKGKPVVLCGDFNIAPEEIDVANPKKRWLNEGNSGFLPEERAWFRRLLN 186 Query: 55 ----------FPQEKESTC-----NVIKRNKSS-LDYFVIDRDNKNFLIDNSFSIVSYDQ 98 P+ ++ T N +RN+ +DY ++ + L D Sbjct: 187 AGFVDTFRLFHPEPEKYTWWDYRANAARRNRGWRIDYILVSPALADRLKDAGI------- 239 Query: 99 SDLDTRR-SKLSTHCPLTIEYDF 120 D + R K S H P+ +E D Sbjct: 240 -DREVRGWEKPSDHAPVWVELDL 261 >gnl|CDD|88569 cd05129, RasGAP_RAP6, Rab5-activating protein 6 (RAP6) is an endosomal protein with a role in the regulation of receptor-mediated endocytosis. RAP6 contains a Vps9 domain, which is involved in the activation of Rab5, and a Ras GAP domain (RGD). Rab5 is a small GTPase required for the control of the endocystic route, and its activity is regulated by guanine nucleotide exchange factor, such as Rabex5, and GAPs, such as RN-tre. Human Rap6 protein is localized on the plasma membrane and on the endosome. RAP6 binds to Rab5 and Ras through the Vps9 and RGD domains, respectively.. Length = 353 Score = 28.3 bits (63), Expect = 0.62 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 3/55 (5%) Query: 40 DDFWQKMDPDGLLIRFP---QEKESTCNVIKRNKSSLDYFVIDRDNKNFLIDNSF 91 D+FW +DPD L+ RF +EK K + + + + + K + N F Sbjct: 118 DEFWLDIDPDKLMERFSPDEREKRFGEKGTKEYERRVQEYRAEVEAKLVALVNKF 172 >gnl|CDD|33370 COG3568, ElsH, Metal-dependent hydrolase [General function prediction only]. Length = 259 Score = 27.6 bits (61), Expect = 0.89 Identities = 23/122 (18%), Positives = 34/122 (27%), Gaps = 17/122 (13%) Query: 3 SQQGEWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDP-----DGLLIRFPQ 57 S+ + A + P V+ GDFN + + ++ L F Sbjct: 147 SRLRQAAALLALAGLPALNPTVLMGDFNNE----PGSAEYRLAARSPLNAQAALTGAFAP 202 Query: 58 EKESTCNVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIE 117 T N L +DR + +I S D S H PL E Sbjct: 203 AVGRTIRTFPSNTPLLR---LDR----IFVSKELAIRSVHVLT-DRLARVASDHLPLLAE 254 Query: 118 YD 119 Sbjct: 255 LR 256 >gnl|CDD|37661 KOG2450, KOG2450, KOG2450, Aldehyde dehydrogenase [Energy production and conversion]. Length = 501 Score = 26.7 bits (59), Expect = 1.9 Identities = 7/18 (38%), Positives = 9/18 (50%) Query: 6 GEWLKKWADQKIKTGIPF 23 E A +K+K G PF Sbjct: 319 VEKFVAAAKKKLKVGDPF 336 >gnl|CDD|34040 COG4318, COG4318, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 221 Score = 26.1 bits (57), Expect = 2.6 Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 6/39 (15%) Query: 14 DQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLL 52 + +K G+P V+A S DDFW+ MD + + Sbjct: 92 REGVKQGLPVVVAD------LSPLAKDDFWEVMDENHWV 124 >gnl|CDD|147340 pfam05112, Baculo_p47, Baculovirus P47 protein. This family consists of several Baculovirus P47 proteins which is one of the primary components of Baculovirus encoded RNA polymerase, which initiates transcription from late and very late promoters. Length = 313 Score = 26.1 bits (58), Expect = 2.9 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 6/46 (13%) Query: 61 STCNVIKRNKSSLDYFV--IDRDNK----NFLIDNSFSIVSYDQSD 100 S +VIKR+KSS Y V +D +N L+ N+F+++ D Sbjct: 191 SISDVIKRHKSSKKYIVLELDPNNAAELVKLLLKNNFTVIENAHID 236 >gnl|CDD|176468 cd01596, Aspartase_like, aspartase (L-aspartate ammonia-lyase) and fumarase class II enzymes. This group contains aspartase (L-aspartate ammonia-lyase), fumarase class II enzymes, and related proteins. It is a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. Aspartase catalyzes the reversible deamination of aspartic acid. Fumarase catalyzes the reversible hydration/dehydration of fumarate to L-malate during the Krebs cycle. Length = 450 Score = 25.1 bits (56), Expect = 5.3 Identities = 7/24 (29%), Positives = 10/24 (41%), Gaps = 3/24 (12%) Query: 19 TGIPFVIAGDFNRKINSIGDTDDF 42 TG+PFV A + + D Sbjct: 249 TGLPFVTAPN---LFEATAAHDAL 269 >gnl|CDD|31981 COG1796, POL4, DNA polymerase IV (family X) [DNA replication, recombination, and repair]. Length = 326 Score = 24.4 bits (53), Expect = 7.5 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 11/77 (14%) Query: 16 KIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLLIRFPQ-----------EKESTCN 64 ++ I IAG R ++GD D P+ +L + E + + Sbjct: 176 ELTPIIQASIAGSLRRGRETVGDIDILISTSHPESVLEELLEMPNVQEVIAKGETKVSML 235 Query: 65 VIKRNKSSLDYFVIDRD 81 +I +S+D+ V+ + Sbjct: 236 LILDEGTSVDFRVVPPE 252 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.319 0.137 0.416 Gapped Lambda K H 0.267 0.0757 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,568,367 Number of extensions: 74458 Number of successful extensions: 180 Number of sequences better than 10.0: 1 Number of HSP's gapped: 180 Number of HSP's successfully gapped: 21 Length of query: 125 Length of database: 6,263,737 Length adjustment: 82 Effective length of query: 43 Effective length of database: 4,491,799 Effective search space: 193147357 Effective search space used: 193147357 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: 51 (23.4 bits)