RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780776|ref|YP_003065189.1| ribosome recycling factor [Candidatus Liberibacter asiaticus str. psy62] (186 letters) >gnl|CDD|178850 PRK00083, frr, ribosome recycling factor; Reviewed. Length = 185 Score = 259 bits (664), Expect = 3e-70 Identities = 85/181 (46%), Positives = 123/181 (67%) Query: 6 DLQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRM 65 L++ ++RM + LK+++ +RTGR +PS+LD +KV+ YGS PLNQVA+++V E R Sbjct: 5 ILKDAEERMEKAVEALKRELAKIRTGRANPSLLDGIKVDYYGSPTPLNQVASISVPEART 64 Query: 66 LVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKS 125 L++ WDK M+ ++E+ I S+LGLNP +G V+R+P+P TEERR LVK AE++ Sbjct: 65 LLIQPWDKSMLKAIEKAIRASDLGLNPSNDGTVIRLPIPPLTEERRKELVKQVKKEAEEA 124 Query: 126 KISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIMH 185 K+++RNIRRD D LKK K + SED + E++IQK+TD IK ID K+KEIM Sbjct: 125 KVAIRNIRRDANDKLKKLEKDKEISEDELKRAEDEIQKLTDKYIKKIDELLAAKEKEIME 184 Query: 186 F 186 Sbjct: 185 V 185 >gnl|CDD|129587 TIGR00496, frr, ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily. Length = 176 Score = 181 bits (461), Expect = 9e-47 Identities = 81/176 (46%), Positives = 118/176 (67%) Query: 11 KDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSV 70 K+RM +I LK+++ +RTGR +PS+LD + VE YG+ PL Q+A+VTV + R LV+ Sbjct: 1 KERMDKSIQALKRELSKIRTGRANPSLLDRILVEYYGAPTPLRQLASVTVPDARTLVIQP 60 Query: 71 WDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVR 130 +DK + ++E+ I S+LGLNP +G V+R+ P TEERR LVK A AE++K++VR Sbjct: 61 FDKSNINAIEKAIQRSDLGLNPNNDGSVIRVNFPPLTEERRKELVKHAKKIAEQAKVAVR 120 Query: 131 NIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIMHF 186 N+RRD D +KK K + SED L+ +IQK+TD IK ID ++K+KE+M Sbjct: 121 NVRRDANDKVKKLEKDKEISEDEERRLQEEIQKLTDEYIKKIDEILKDKEKELMEV 176 >gnl|CDD|180891 PRK07219, PRK07219, DNA topoisomerase I; Validated. Length = 822 Score = 31.5 bits (72), Expect = 0.14 Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 13/48 (27%) Query: 149 ASEDMVASLENDIQKITDSTIK-------------NIDSFFEEKKKEI 183 SE+M A LE D+Q I D K I S +EK+KEI Sbjct: 537 VSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEI 584 >gnl|CDD|185113 PRK15191, PRK15191, fimbrial protein BcfF; Provisional. Length = 172 Score = 28.5 bits (63), Expect = 0.97 Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 7/66 (10%) Query: 5 IDLQNIKDRM-GDTISF------LKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVAN 57 IDLQN G T+SF D++ L G S + + + + +PL Q ++ Sbjct: 71 IDLQNCGSTASGVTVSFSGAADSRNTDLLALTAGESDASGIGIALYDQNKTLIPLGQESD 130 Query: 58 VTVLEP 63 V L P Sbjct: 131 VVTLSP 136 >gnl|CDD|162969 TIGR02670, cas_csx8, CRISPR-associated protein Csx8 (provisional). In three genomes so far, a member of this protein appears in the midst of a CRISPR-associated (cas) gene operon, immediately upstream of a member of family TIGR01875 (CRISPR-associated autoregulator, DevR family). The genomes so far are Nocardia farcinica IFM10152, Clostridium perfringens SM101, and Clostridium tetani E88. Length = 441 Score = 28.3 bits (63), Expect = 1.2 Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 9/71 (12%) Query: 116 KVAHAYAEKSKISVRN-IRRDGM---DHLKKSRKSGKASEDMVASLENDI----QKITDS 167 K +++YA I + IR G ++LKK++ KA N + QK+ S Sbjct: 334 KNSYSYAINELIKINQLIRNGGKEMDENLKKAKACAKAVVKKFIKENNKLASYKQKLLSS 393 Query: 168 TI-KNIDSFFE 177 + K+ D + Sbjct: 394 VVFKDHDRICD 404 >gnl|CDD|147910 pfam06007, PhnJ, Phosphonate metabolism protein PhnJ. This family consists of several bacterial phosphonate metabolism (PhnJ) sequences. The exact role that PhnJ plays in phosphonate utilisation is unknown. Length = 279 Score = 27.2 bits (61), Expect = 2.6 Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 4/43 (9%) Query: 92 PIVEGQ--VLRIPVPE--TTEERRLALVKVAHAYAEKSKISVR 130 P+ E Q VL++P+PE E A + HA A+ + V+ Sbjct: 112 PLTEDQILVLQVPIPEPLRFVEPSEAETRKMHAEADYGLMWVK 154 >gnl|CDD|117664 pfam09104, BRCA-2_OB3, BRCA2, oligonucleotide/oligosaccharide-binding, domain 3. Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding. Length = 143 Score = 27.1 bits (60), Expect = 2.8 Identities = 9/18 (50%), Positives = 16/18 (88%) Query: 168 TIKNIDSFFEEKKKEIMH 185 TI+NID+F++E +K++ H Sbjct: 118 TIENIDTFYKEAEKKLAH 135 >gnl|CDD|118189 pfam09657, Cas_Csx8, CRISPR-associated protein Csx8 (Cas_Csx8). Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes proteins of unknown function which are encoded in the midst of a cas gene operon. Length = 441 Score = 26.8 bits (59), Expect = 3.8 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 9/71 (12%) Query: 116 KVAHAYAEKSKISVRNIRRDG----MDHLKKSRKSGKASEDMVASLENDI----QKITDS 167 K +++YA I + + R+G ++LKK+ KA + N + QK+ S Sbjct: 334 KNSYSYAINELIKINQLIRNGGKEMDENLKKAIACAKAVVKKFENSLNKLASYKQKLLSS 393 Query: 168 TI-KNIDSFFE 177 + K+ D + Sbjct: 394 VVFKDHDRICD 404 >gnl|CDD|180569 PRK06456, PRK06456, acetolactate synthase catalytic subunit; Reviewed. Length = 572 Score = 26.3 bits (58), Expect = 4.3 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 6/43 (13%) Query: 147 GKASEDMVASLENDIQ-----KITDSTIKNIDSFFEEKKKEIM 184 G+A M A+LE+D + +D T + D E +KK IM Sbjct: 263 GRAEASM-AALESDAMLVVGARFSDRTFTSYDEMVETRKKFIM 304 >gnl|CDD|182685 PRK10735, tldD, protease TldD; Provisional. Length = 481 Score = 25.9 bits (57), Expect = 6.2 Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 6/46 (13%) Query: 44 EAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLG 89 E+Y +H+P+ ++ N ML +E++ SVE GI+ N G Sbjct: 353 ESY-AHLPMPRMTNTY-----MLAGKSTPQEIIESVEYGIYAPNFG 392 >gnl|CDD|152163 pfam11727, ISG65-75, Invariant surface glycoprotein. This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite. Length = 289 Score = 26.0 bits (57), Expect = 6.3 Identities = 12/69 (17%), Positives = 25/69 (36%), Gaps = 21/69 (30%) Query: 131 NIRRDGMDHLKKSRKSGKASEDMVASLENDIQKI---------------TDSTIKNIDSF 175 + + D+L K +E A+++ + ++ +DS K I Sbjct: 54 KVGNERADYLVKK------TEGFAANIKLALDRVKYYLEKLESRSDSKLSDSDKKKIKEI 107 Query: 176 FEEKKKEIM 184 E+ K +I Sbjct: 108 CEKAKDKID 116 >gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. These proteins are found in P. falciparum, P. vivax and P. yoelii. Length = 2757 Score = 25.8 bits (56), Expect = 7.4 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 3/62 (4%) Query: 124 KSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLE---NDIQKITDSTIKNIDSFFEEKK 180 K K ++N+ + H+K + K SE+ + ++ ND++ + D I N D EKK Sbjct: 1115 KIKDDIKNLDQKIDHHIKALEEIKKKSENYIDEIKAQINDLEDVADKAISNDDPEEIEKK 1174 Query: 181 KE 182 E Sbjct: 1175 IE 1176 >gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated. Length = 740 Score = 25.5 bits (56), Expect = 8.0 Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%) Query: 149 ASEDMVASLENDIQKITDSTIKNIDSFFEE 178 DM + LE D+ KI + IK D+ EE Sbjct: 528 TKPDMTSRLEEDMDKIAEGKIKE-DAVLEE 556 >gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit; Provisional. Length = 482 Score = 25.7 bits (57), Expect = 8.5 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 4/81 (4%) Query: 106 TTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKK-SRKSGKASEDMVASL---ENDI 161 T+E+R +A AEK S R +RR+ + L + + + + + A L E +I Sbjct: 340 KTKEKRETRDSIAKKIAEKLHTSKRKVRREVLPFLSIIFKHNPELAARLAAFLELTEEEI 399 Query: 162 QKITDSTIKNIDSFFEEKKKE 182 + +T S +K E Sbjct: 400 EFLTGSKKATKKIKKIVEKAE 420 >gnl|CDD|184561 PRK14192, PRK14192, bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional. Length = 283 Score = 25.6 bits (56), Expect = 8.8 Identities = 11/23 (47%), Positives = 14/23 (60%) Query: 88 LGLNPIVEGQVLRIPVPETTEER 110 L NP V G +L+ PVP +ER Sbjct: 86 LNANPDVHGILLQHPVPAQIDER 108 >gnl|CDD|151875 pfam11436, DUF3199, Protein of unknown function (DUF3199). Some members in this family of proteins with unknown function are annotated as YqbG however this cannot be confirmed. Currently the proteins has no known function. Length = 124 Score = 25.5 bits (56), Expect = 9.4 Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 3/24 (12%) Query: 101 IPVPETTEERRLALVKVAHAYAEK 124 P+PET RLAL+K+A YA K Sbjct: 50 RPLPETV---RLALLKLAQYYALK 70 >gnl|CDD|182781 PRK10854, PRK10854, exopolyphosphatase; Provisional. Length = 513 Score = 25.1 bits (55), Expect = 10.0 Identities = 11/31 (35%), Positives = 13/31 (41%) Query: 104 PETTEERRLALVKVAHAYAEKSKISVRNIRR 134 P E RR+ V A Y IS N +R Sbjct: 159 PILVESRRMGCVSFAQLYFPGGVISKENFQR 189 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 0.316 0.131 0.355 Gapped Lambda K H 0.267 0.0753 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,923,810 Number of extensions: 177526 Number of successful extensions: 426 Number of sequences better than 10.0: 1 Number of HSP's gapped: 425 Number of HSP's successfully gapped: 41 Length of query: 186 Length of database: 5,994,473 Length adjustment: 88 Effective length of query: 98 Effective length of database: 4,092,969 Effective search space: 401110962 Effective search space used: 401110962 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 54 (24.5 bits)