RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780901|ref|YP_003065314.1| single-stranded-DNA-specific exonuclease protein [Candidatus Liberibacter asiaticus str. psy62] (600 letters) >gnl|CDD|161976 TIGR00644, recJ, single-stranded-DNA-specific exonuclease RecJ. All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair. Length = 539 Score = 536 bits (1382), Expect = e-153 Identities = 211/553 (38%), Positives = 325/553 (58%), Gaps = 16/553 (2%) Query: 39 IPDIVARVLVNRNV-SIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMI 97 + I+A++LV+R + + + ++FL P + L PDP +L D +KA RI++AI N+EKI+I Sbjct: 1 LNPILAQILVSRGIKTAEEFENFLEPDLIDL-PDPFLLKDMEKAVERIIEAIENNEKILI 59 Query: 98 FGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVD 157 FGDYDVDG S A+++ FL VN + YIP+RI +GYG +P + + I G LIITVD Sbjct: 60 FGDYDVDGITSTAILVEFLKDLGVNVDYYIPNRITEGYGLSPEALREAIENGVSLIITVD 119 Query: 158 CGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFL 217 G ++++ + YA GIDVIV DHH+ + A A+VNPNR D L AGV F Sbjct: 120 NGISAHEEIDYAKELGIDVIVTDHHEPPEDLPEAAAIVNPNRPDCDYPNKELAGAGVAFK 179 Query: 218 VLVLIYRILRQDNKVPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLMVARRQGNP 277 + + L + L+ LDLVA+ T+ DV+PL G NRA V KGL R+ P Sbjct: 180 LCTALDEELPKLKPDLLDL-----LDLVAIGTIADVMPLTGENRALVKKGLKALRKGKRP 234 Query: 278 GLKALIERVNIS-SPITAENLGYMIGPSINAGGRIGESNLGSRLLISDDSQELEMLAMKL 336 GLKAL++ + P+++ ++G+ IGP INA GR+G+++L LL++DD ++ LA +L Sbjct: 235 GLKALLKVAGFNGKPLSSTDIGFSIGPRINAAGRLGDASLAVELLLTDDPKQARQLAEEL 294 Query: 337 DVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGIVGLLAARLKEKFGR 396 D LN+ R+ +E +L +AE + SVIVV G+ WHPG++G++A+RL E F + Sbjct: 295 DELNEERKKIEQEVLAEAEKIAEAN--LLPNDSVIVVAGENWHPGVLGIVASRLAETFNK 352 Query: 397 PSFAISFEEDGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVERVNFGRL 456 P ++ +E GS RSI G D+ ++S + E + +K GGHAMAAGLT++R N Sbjct: 353 PVIVLAIDEGKGAKGSARSISGIDLYDLLS-ELREALFLKFGGHAMAAGLTLKRENLEEF 411 Query: 457 CDFFQKFAHNIVPALITTPVFKIDGVLNASAVNIALIDMLESAGPYGAGNPNPVFAFPNH 516 + ++ I+ A + + +D L A + LI+ +E P+G GNP P+F N Sbjct: 412 REKLEEKFKKILFADESEEILPVDAELKAEEITRELIEQIEKLEPFGQGNPEPLFLLKNL 471 Query: 517 KLQSIRVVNLAHLQMTFESQDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYW 576 +++ I+++ HL+++ +S ++AIAF L + G+ + V G L +N W Sbjct: 472 RVEDIKLLGENHLKLSLKSGGK-NIEAIAFNAGDLE----LELNLGRPLDVAGKLSINEW 526 Query: 577 RGSKRCQLRVLDA 589 RG + QL + D Sbjct: 527 RGRETPQLIIQDL 539 >gnl|CDD|182944 PRK11070, PRK11070, ssDNA exonuclease RecJ; Provisional. Length = 575 Score = 291 bits (748), Expect = 3e-79 Identities = 186/531 (35%), Positives = 286/531 (53%), Gaps = 36/531 (6%) Query: 39 IPDIVARVLVNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIF 98 +P ++ R+ +R V + L S++ L+P L+ +KA + A+ +I++ Sbjct: 20 LPPLLRRLYASRGVR---SAQELERSVKGLLPWQQ-LSGIEKAVELLYNALREGTRIIVV 75 Query: 99 GDYDVDGAASVALMMRFL-SHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVD 157 GD+D DGA S AL + L S N + +P+R DGYG +P ++++ GAQLI+TVD Sbjct: 76 GDFDADGATSTALSVLALRSLGCSNVDYLVPNRFEDGYGLSPEVVDQAHARGAQLIVTVD 135 Query: 158 CGSTSYDALQYATNQGIDVIVIDHHQVKSEEIP-AYALVNPNRLDDLSGQGHLCAAGVVF 216 G +S+ + +A GI V+V DHH + E +P A A++NPN D L GV F Sbjct: 136 NGISSHAGVAHAHALGIPVLVTDHH-LPGETLPAADAIINPNLRDCNFPSKSLAGVGVAF 194 Query: 217 LVLVLIYRILRQDN-------KVPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLM 269 +++ + LR +P +L LLDLVAL TV DVVPL NR V +GL Sbjct: 195 YLMLALRAFLRDQGWFDERGIAIP---NLAELLDLVALGTVADVVPLDANNRILVWQGLS 251 Query: 270 VARR-QGNPGLKALIERVN-ISSPITAENLGYMIGPSINAGGRIGESNLGSRLLISDDSQ 327 R + PG+KAL+E N + + A +LG+ +GP +NA GR+ + ++G LL+ D+ Sbjct: 252 RIRAGKCRPGIKALLEVANRDAQKLAASDLGFALGPRLNAAGRLDDMSVGVALLLCDNIG 311 Query: 328 ELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASV-----IVVEGDRWHPGI 382 E +LA +LD LNQ R+ +E M Q EA LT C+ ++++S + + WH G+ Sbjct: 312 EARVLANELDALNQTRKEIEQGM--QVEA--LTLCEKLERSSDTLPYGLAMYHPEWHQGV 367 Query: 383 VGLLAARLKEKFGRPSFAISFEEDGKGI--GSGRSIEGFDIGKMVSF--AVEEGILVKGG 438 VG+LA+R+KE+F RP I+F G G GSGRSI+G + + + G+++K G Sbjct: 368 VGILASRIKERFHRP--VIAFAPAGDGTLKGSGRSIQGLHMRDALERLDTLYPGLILKFG 425 Query: 439 GHAMAAGLTVERVNFGRLCDFFQKFAHNIVPALITTPVFKIDGVLNASAVNIALIDMLES 498 GHAMAAGL++E F F + + + V DG L+ + +++ + ++L Sbjct: 426 GHAMAAGLSLEEDKFELFQQRFGELVTEWLDPSLLQGVVWSDGELSPAEMSLEVAELLRD 485 Query: 499 AGPYGAGNPNPVFAFPNHKLQSIRVVNLAHLQMTFESQD-SETLQAIAFRV 548 AGP+G P P+F LQ R+V HL++ E L IAF V Sbjct: 486 AGPWGQMFPEPLFDGRFRLLQQ-RLVGERHLKVMVEPVGGGPLLDGIAFNV 535 >gnl|CDD|184937 PRK14974, PRK14974, cell division protein FtsY; Provisional. Length = 336 Score = 33.0 bits (76), Expect = 0.24 Identities = 11/24 (45%), Positives = 19/24 (79%) Query: 157 DCGSTSYDALQYATNQGIDVIVID 180 D + +YDA+++A +GIDV++ID Sbjct: 206 DPAAVAYDAIEHAKARGIDVVLID 229 >gnl|CDD|149172 pfam07948, Nairovirus_M, Nairovirus M polyprotein-like. The sequences in this family are similar to the Dugbe virus M polyprotein precursor, which includes glycoproteins G1 and G2. Both are thought to be inserted in the membrane of the Golgi complex of the infected host cell, and G1 is known to have a role in infection of vertebrate hosts. Length = 645 Score = 31.7 bits (72), Expect = 0.58 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 3/61 (4%) Query: 136 GPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALV 195 G + + +G +T D G S A+N G+ +I + H +K + P + Sbjct: 98 GLTAEPFKSYYAKG---FLTFDSGYFSAKCYSAASNSGLQLINVTQHSIKIQNTPGPKIS 154 Query: 196 N 196 N Sbjct: 155 N 155 >gnl|CDD|162105 TIGR00916, 2A0604s01, protein-export membrane protein, SecD/SecF family. The SecA,SecB,SecD,SecE,SecF,SecG and SecY proteins form the protein translocation appartus in prokaryotes. This family is specific for the SecD and SecF proteins. Length = 192 Score = 31.1 bits (71), Expect = 0.92 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 4/61 (6%) Query: 167 QYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRIL 226 +A N G IV+D+ +V S P V P +L G + A ++ LVLVL+Y +L Sbjct: 11 DFAANIGKPAIVLDNAKVISA--PVVGTVGPTLGGELIKAGII--ALLIGLVLVLLYMLL 66 Query: 227 R 227 R Sbjct: 67 R 67 >gnl|CDD|131525 TIGR02472, sucr_P_syn_N, sucrose-phosphate synthase, putative, glycosyltransferase domain. This family consists of the N-terminal regions, or in some cases the entirety, of bacterial proteins closely related to plant sucrose-phosphate synthases (SPS). The C-terminal domain (TIGR02471), found with most members of this family, resembles both bona fide plant sucrose-phosphate phosphatases (SPP) and the SPP-like domain of plant SPS. At least two members of this family lack the SPP-like domain, which may have binding or regulatory rather than enzymatic activity by analogy to plant SPS. This enzyme produces sucrose 6-phosphate and UDP from UDP-glucose and D-fructose 6-phosphate, and may be encoded near the gene for fructokinase. Length = 439 Score = 30.9 bits (70), Expect = 1.0 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 2/42 (4%) Query: 29 RALAITQKHAIPDIVARVLVNRNVSIDYAK--DFLNPSIRLL 68 RALA + D+V R++ + VS DYA+ + + P R++ Sbjct: 37 RALARRSEVEQVDLVTRLIKDAKVSPDYAQPIERIAPGARIV 78 >gnl|CDD|182695 PRK10747, PRK10747, putative protoheme IX biogenesis protein; Provisional. Length = 398 Score = 30.1 bits (68), Expect = 1.9 Identities = 13/36 (36%), Positives = 21/36 (58%) Query: 340 NQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEG 375 NQ+R+ L+ A A+ L +CDD A I+++G Sbjct: 254 NQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDG 289 >gnl|CDD|180539 PRK06352, PRK06352, threonine synthase; Validated. Length = 351 Score = 30.0 bits (67), Expect = 2.0 Identities = 13/36 (36%), Positives = 19/36 (52%) Query: 144 KFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVI 179 K EGA+ +I G+TS A YAT G+ ++ Sbjct: 69 KAKEEGAEAVICASTGNTSAAAAAYATRAGLKAYIV 104 >gnl|CDD|185455 PTZ00114, PTZ00114, Heat shock protein 60; Provisional. Length = 555 Score = 29.5 bits (67), Expect = 2.6 Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 4/59 (6%) Query: 428 AVEEGILVKGGGHAMA-AGLTVERVNFGRLCDFFQKFAHNIVPALITTPVFKIDGVLNA 485 AVEEGI V GGG A+ A ++++ Q+ IV + P +I NA Sbjct: 418 AVEEGI-VPGGGVALLRASKLLDKLEEDNELTPDQRTGVKIVRNALRLPTKQI--AENA 473 >gnl|CDD|129577 TIGR00486, YbgI_SA1388, dinuclear metal center protein, YbgI/SA1388 family. The characterization of this family of uncharacterized proteins as orthologous is tentative. Members are found in all three domains of life. Several members (from Bacillus subtilis, Listeria monocytogenes, and Mycobacterium tuberculosis - all classified as Firmicutes within the Eubacteria) share a long insert relative to other members. Length = 249 Score = 29.3 bits (66), Expect = 3.3 Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 6/65 (9%) Query: 119 CSVNANMYIPD-RIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVI 177 N Y+ +V G G S + K + EG IT G S+ A G++VI Sbjct: 159 VVKNGPEYVKKVAVVSGSGL--SFIMKALREGVDAYIT---GDLSHHTAHLARELGLNVI 213 Query: 178 VIDHH 182 H+ Sbjct: 214 DAGHY 218 >gnl|CDD|182441 PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional. Length = 318 Score = 28.9 bits (66), Expect = 3.9 Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 6/34 (17%) Query: 147 NEGAQLIITVDCGSTSYDALQYATNQGIDVIVID 180 EGA D S ++DA+Q A +GIDV++ID Sbjct: 176 KEGA------DPASVAFDAIQAAKARGIDVLIID 203 >gnl|CDD|181451 PRK08506, PRK08506, replicative DNA helicase; Provisional. Length = 472 Score = 28.8 bits (65), Expect = 4.2 Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 5/42 (11%) Query: 312 GESNLGSR-LLISDDSQELEMLAMKLDV----LNQNRRLMES 348 G N R L IS+ S+ L++LA +LD+ L+Q R +ES Sbjct: 316 GSGNFKDRHLQISEISRGLKLLARELDIPIIALSQLNRSLES 357 >gnl|CDD|165230 PHA02914, PHA02914, Immunoglobulin-like domain protein; Provisional. Length = 500 Score = 28.5 bits (63), Expect = 4.7 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 6/51 (11%) Query: 9 VECSISGFRWVSLLGQEGINRALAITQKHAIPDIVARVLVNRNVSIDYAKD 59 +EC S + G E I+ A I I ++ V V D+A+D Sbjct: 284 IECFFS------MCGNENISNAKWIDTGFEIGPLIGTVKSKDIVEGDFAED 328 >gnl|CDD|180907 PRK07251, PRK07251, pyridine nucleotide-disulfide oxidoreductase; Provisional. Length = 438 Score = 28.6 bits (64), Expect = 4.9 Identities = 9/24 (37%), Positives = 16/24 (66%) Query: 147 NEGAQLIITVDCGSTSYDALQYAT 170 N+G Q+++ + + +DAL YAT Sbjct: 226 NDGDQVLVVTEDETYRFDALLYAT 249 >gnl|CDD|161686 TIGR00064, ftsY, signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein. Length = 272 Score = 28.4 bits (64), Expect = 5.7 Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 6/34 (17%) Query: 147 NEGAQLIITVDCGSTSYDALQYATNQGIDVIVID 180 EGA D + ++DA+Q A + IDV++ID Sbjct: 134 KEGA------DPAAVAFDAIQKAKARNIDVVLID 161 >gnl|CDD|161830 TIGR00344, alaS, alanine--tRNA ligase. The model describes alanine--tRNA ligase. This enzyme catalyzes the reaction (tRNAala + L-alanine + ATP = L-alanyl-tRNAala + pyrophosphate + AMP). Length = 851 Score = 28.1 bits (63), Expect = 6.8 Identities = 24/117 (20%), Positives = 48/117 (41%), Gaps = 10/117 (8%) Query: 337 DVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGIVGLLAARLKEKFGR 396 + + L ++ + + + + I V+V D + +A RLK K G Sbjct: 737 ALQKELESLKLKIADQKIDE-LKDKAETINGVKVLVEVVDAKDMKSLKTMADRLKSKLGS 795 Query: 397 PSFAISFEEDGKG-IGSGRS----IEGFDIGKMVSFAVEEGILVKGGGH---AMAAG 445 + ++ +GK + G S +G G++++ + + + KGGG A A G Sbjct: 796 AIYVLASFANGKVKLVCGVSNDVLNKGIKAGELIN-QIAQVLGGKGGGRPDLAQAGG 851 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 0.139 0.406 Gapped Lambda K H 0.267 0.0676 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 10,038,623 Number of extensions: 685056 Number of successful extensions: 1397 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1383 Number of HSP's successfully gapped: 26 Length of query: 600 Length of database: 5,994,473 Length adjustment: 99 Effective length of query: 501 Effective length of database: 3,855,281 Effective search space: 1931495781 Effective search space used: 1931495781 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: 60 (27.0 bits)