RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780134|ref|YP_003064547.1| phage-related integrase/recombinase [Candidatus Liberibacter asiaticus str. psy62] (348 letters) >gnl|CDD|162771 TIGR02224, recomb_XerC, tyrosine recombinase XerC. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. Length = 295 Score = 54.5 bits (132), Expect = 4e-08 Identities = 35/159 (22%), Positives = 68/159 (42%), Gaps = 14/159 (8%) Query: 71 LKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVES---RK 127 L++L E S H R +++ + + + G ++T +RS + R Sbjct: 4 LEYLRVERNYSPH---TVRAYRRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARG 60 Query: 128 HTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWS 187 + S + L+++R +++ VR+ + NP V PK+ + + ++++M+ Sbjct: 61 LSRRSLARKLSALRSFYRFLVRRGLIKANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPD 120 Query: 188 EGSQPRLA------FEFLLY-SGLRCSDSCRAGVQHLQN 219 E + LA E LLY SGLR S+ + L Sbjct: 121 EDDEDWLALRDRAILE-LLYSSGLRVSELVGLDLDDLDL 158 >gnl|CDD|162772 TIGR02225, recomb_XerD, tyrosine recombinase XerD. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. Length = 291 Score = 46.8 bits (112), Expect = 8e-06 Identities = 39/224 (17%), Positives = 80/224 (35%), Gaps = 29/224 (12%) Query: 95 FESYFDQIIRKSGDFDYRKITTKHIRSGVESRK---HTPSSAIQFLTSMRVLFKWAVRQE 151 F + ++ D ++ I + K + S + L+++R +++ +R+ Sbjct: 28 FLEFLEER-----GIDLEEVDRGDIVDFLAELKEAGLSARSIARALSALRSFYRFLLREG 82 Query: 152 YVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSEGSQP-----RLAFEFLLYSGLRC 206 +P +E PK + + T E+++ + + P R E L +GLR Sbjct: 83 IREDDPSALIEPPKVARKLPKVLTVEEVEALLAA-PDVDTPLGLRDRAMLELLYATGLRV 141 Query: 207 SDSC--RAGVQHLQNNIFSIK-----------TQKTGTIITVELPDGFMKLLAMTPIGKE 253 S+ R +L ++ ++ + L + LL + Sbjct: 142 SELVGLRLEDVNLDEGFVRVRGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVKESD 201 Query: 254 TFFINNDKQKMNATQFSIWFKAKATKAGVNK--SAHGVRKFSAT 295 F+N ++ K A +AG+ K S H +R AT Sbjct: 202 ALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFAT 245 >gnl|CDD|178959 PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed. Length = 299 Score = 42.1 bits (100), Expect = 2e-04 Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 7/85 (8%) Query: 87 LAVNSRISFE---SYFDQIIRKSGDFDYRKITTKHIRSGVESRKH---TPSSAIQFLTSM 140 LA N+ S+ F + + G + T +++ + +S+ + L+++ Sbjct: 22 LAENTLSSYRRDLELFAEWLAARGL-SLAEATRDDLQAFLAELAEGGYKATSSARRLSAL 80 Query: 141 RVLFKWAVRQEYVAINPCLSVERPK 165 R F++ +R+ +P ++ PK Sbjct: 81 RRFFQFLLREGLREDDPSALLDSPK 105 >gnl|CDD|178942 PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed. Length = 297 Score = 35.5 bits (83), Expect = 0.023 Identities = 29/157 (18%), Positives = 54/157 (34%), Gaps = 31/157 (19%) Query: 71 LKWLISEYRKSAHWGSLAVNSRISFESYFDQI--------IRKSGDFDYRKITTKHIRSG 122 L++L E S H + +Y + + +RS Sbjct: 14 LEYLRVERGLSPH----------TLRAYRRDLRAFLAFLEEHGISSLQ--DLDAADLRSF 61 Query: 123 VESRK---HTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDM 179 + R+ + S + L+++R ++W VR+ + NP + PK +P + Sbjct: 62 LARRRRQGLSARSLARRLSALRSFYRWLVRRGLLKANPAAGLRAPKIPKRLPKPLDVDQA 121 Query: 180 QQFKSFWSEGSQPRLA------FEFLLYSGLRCSDSC 210 ++ + LA E L SGLR S+ Sbjct: 122 KRL--LDAIDEDDPLALRDRAILELLYGSGLRLSELV 156 >gnl|CDD|152161 pfam11725, AvrE, Pathogenicity factor. This family is secreted by gram-negative Gammaproteobacteria such as Pseudomonas syringae of tomato and the fire blight plant pathogen Erwinia amylovora, amongst others. It is an essential pathogenicity factor of approximately 198 kDa. Its injection into the host-plant is dependent upon the bacterial type III or Hrp secretion system. The family is long and carries a number of predicted functional regions, including an ERMS or endoplasmic reticulum membrane retention signal at both the C- and the N-termini, a leucine-zipper motif from residues 539-560, and a nuclear localisation signal at 1358-1361. this conserved AvrE-family of effectors is among the few that are required for full virulence of many phytopathogenic pseudomonads, erwinias and pantoeas. Length = 1771 Score = 33.6 bits (77), Expect = 0.071 Identities = 29/116 (25%), Positives = 49/116 (42%), Gaps = 10/116 (8%) Query: 226 TQKTGTIITV--ELPDGFMKLL---AMTPIGKETFFINNDKQKMNATQFSIWFKAKAT-K 279 TQ+ G TV E DGF+ L + P+ I ++ ++ F + A + Sbjct: 1312 TQRNGLNFTVPDEEIDGFVDGLFEGKLNPLDLLKKGIEHEMKQGKRFNFDLTAGAALDLR 1371 Query: 280 AGVNKSAHGVRKFSATISADAGATAHELMATYGWKTV----DQAETYTKGADRIRL 331 AG+N + G + +AT A G A +A+Y + D++ T +R R Sbjct: 1372 AGINLTEPGSKPLTATARAGVGLNASANLASYTDYSSTQKNDKSSTREASDNRPRF 1427 >gnl|CDD|179273 PRK01287, xerC, site-specific tyrosine recombinase XerC; Reviewed. Length = 358 Score = 30.9 bits (70), Expect = 0.49 Identities = 13/57 (22%), Positives = 27/57 (47%), Gaps = 9/57 (15%) Query: 109 FDYRKITTKHIRSGVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPK 165 + YRK + + + + L+ +RV F+W +++ ++ NP +E PK Sbjct: 80 YGYRKANGEPL---------STRTQRTQLSPLRVWFRWLLKRHHILYNPAEDLELPK 127 >gnl|CDD|181403 PRK08367, porA, pyruvate ferredoxin oxidoreductase subunit alpha; Reviewed. Length = 394 Score = 29.1 bits (65), Expect = 1.6 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 10/73 (13%) Query: 243 KLLAMTPIGKETF-------FINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSAT 295 K++A PI T F+ N + ++A + + A A V SA GVR F+AT Sbjct: 23 KVIAAFPITPSTLVPEKISEFVANGE--LDAEFIKVESEHSAISACVGASAAGVRTFTAT 80 Query: 296 ISADAGATAHELM 308 S A HE++ Sbjct: 81 ASQGL-ALMHEVL 92 >gnl|CDD|180751 PRK06922, PRK06922, hypothetical protein; Provisional. Length = 677 Score = 27.9 bits (62), Expect = 4.1 Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 1/60 (1%) Query: 72 KWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSG-DFDYRKITTKHIRSGVESRKHTP 130 K +I +Y + + +SF+ D+ ++ + F + + I VE+ K Sbjct: 311 KRVIEKYLREYRENEKPNTTHVSFQVKVDEDMKTAYVSFRFSAVGEALITFCVEAEKIDM 370 >gnl|CDD|178220 PLN02610, PLN02610, probable methionyl-tRNA synthetase. Length = 801 Score = 27.4 bits (61), Expect = 5.4 Identities = 26/110 (23%), Positives = 40/110 (36%), Gaps = 22/110 (20%) Query: 244 LLAMTPIGKETFFINNDKQKMNATQF----------SIWFKAKATKAGVNKSAHGVRKFS 293 LL P +T F D Q ++ + F AK AG + Sbjct: 376 LLTNRPEVSDTLFTWADLQAKLNSELLNNLGNFINRVLSFIAKPPGAG----------YG 425 Query: 294 ATISADAGATAHELMATYGWKTVDQAETYTKGADRIRL--GIKNSRRISS 341 + I GA +H L K E Y + ++++L G+K + ISS Sbjct: 426 SVIPDAPGAESHPLTKKLAEKVGKLVEQYVEAMEKVKLKQGLKTAMSISS 475 >gnl|CDD|183690 PRK12698, flgH, flagellar basal body L-ring protein; Reviewed. Length = 224 Score = 27.4 bits (61), Expect = 5.7 Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 1/23 (4%) Query: 216 HLQNNIFS-IKTQKTGTIITVEL 237 N+++S IK K G IITV L Sbjct: 52 SQANSLYSDIKAHKVGDIITVVL 74 >gnl|CDD|178415 PLN02820, PLN02820, 3-methylcrotonyl-CoA carboxylase, beta chain. Length = 569 Score = 27.5 bits (61), Expect = 5.8 Identities = 10/24 (41%), Positives = 17/24 (70%), Gaps = 1/24 (4%) Query: 161 VERPKRKTEGIRPWTKEDMQQFKS 184 +ER +K +GI W+KE+ + FK+ Sbjct: 491 IERENKKRQGI-QWSKEEEEAFKA 513 >gnl|CDD|184758 PRK14596, PRK14596, peptide deformylase; Provisional. Length = 199 Score = 27.1 bits (60), Expect = 6.9 Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 3/28 (10%) Query: 145 KWAVRQEYVAINPCLSVERPKRK--TEG 170 + V +EYV +NP ++ R + EG Sbjct: 78 RSRVLREYVMVNPVITY-RKGDQSGQEG 104 >gnl|CDD|129541 TIGR00449, tgt_general, tRNA-guanine transglycosylases, various specificities. Different tRNA-guanine transglycosylases catalyze different tRNA base modifications. Two guanine base substitutions by different enzymes described by the model are involved in generating queuosine at position 34 in bacterial tRNAs and archaeosine at position 15 in archaeal tRNAs. This model is designed for fragment searching, so the superfamily is used loosely. Length = 367 Score = 27.0 bits (60), Expect = 8.6 Identities = 13/30 (43%), Positives = 14/30 (46%) Query: 28 GHGRRIRLPYPHESTFIPAYMSALTGSTPK 57 GH R RL PH S P +M T T K Sbjct: 8 GHARVGRLKTPHGSVETPVFMPVGTLGTVK 37 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 0.320 0.132 0.399 Gapped Lambda K H 0.267 0.0789 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,577,515 Number of extensions: 339420 Number of successful extensions: 574 Number of sequences better than 10.0: 1 Number of HSP's gapped: 573 Number of HSP's successfully gapped: 16 Length of query: 348 Length of database: 5,994,473 Length adjustment: 94 Effective length of query: 254 Effective length of database: 3,963,321 Effective search space: 1006683534 Effective search space used: 1006683534 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 (21.8 bits) S2: 58 (26.0 bits)