RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780776|ref|YP_003065189.1| ribosome recycling factor [Candidatus Liberibacter asiaticus str. psy62] (186 letters) >gnl|CDD|145100 pfam01765, RRF, Ribosome recycling factor. The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth. Thus ribosomes are "recycled" and ready for another round of protein synthesis. Length = 165 Score = 228 bits (583), Expect = 8e-61 Identities = 83/164 (50%), Positives = 119/164 (72%) Query: 21 LKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVE 80 LKK++ +RTGR +PS+LD ++V+ YGS PLNQ+A+++V E R L+++ WDK ++ ++E Sbjct: 2 LKKELSKIRTGRANPSLLDNIRVDYYGSPTPLNQLASISVPEARTLLITPWDKSLIKAIE 61 Query: 81 RGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHL 140 + I S+LGLNP +GQV+RIP+P TEERR LVK A AE++K+++RNIRRD D L Sbjct: 62 KAILASDLGLNPQNDGQVIRIPIPPLTEERRKELVKQAKKLAEEAKVAIRNIRRDANDKL 121 Query: 141 KKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184 KK K + SED V E +IQK+TD IK ID ++K+KE+M Sbjct: 122 KKLEKDKEISEDEVKKAEKEIQKLTDKYIKKIDELLKKKEKELM 165 >gnl|CDD|30582 COG0233, Frr, Ribosome recycling factor [Translation, ribosomal structure and biogenesis]. Length = 187 Score = 215 bits (548), Expect = 8e-57 Identities = 90/186 (48%), Positives = 126/186 (67%) Query: 1 MNQVIDLQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTV 60 M L++ +++M + LK ++ +RTGR +PS+LD + VE YGS PLNQ+A+++V Sbjct: 2 MMINEILKDAEEKMEKALEALKNELSKIRTGRANPSLLDRITVEYYGSPTPLNQLASISV 61 Query: 61 LEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHA 120 E R LV+ +DK MV ++E+ I SNLGLNP +G V+R+P+P TEERR LVKVA Sbjct: 62 PEARTLVIKPFDKSMVKAIEKAILASNLGLNPNNDGNVIRVPLPPLTEERRKELVKVAKK 121 Query: 121 YAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKK 180 YAE++K++VRNIRRD D +KK K + SED V E +IQK+TD IK ID ++K+ Sbjct: 122 YAEEAKVAVRNIRRDANDKIKKLEKDKEISEDEVKKAEEEIQKLTDEYIKKIDELLKDKE 181 Query: 181 KEIMHF 186 KEIM Sbjct: 182 KEIMEV 187 >gnl|CDD|29621 cd00520, RRF, Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species.. Length = 179 Score = 186 bits (475), Expect = 2e-48 Identities = 79/178 (44%), Positives = 123/178 (69%) Query: 7 LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRML 66 L+ K++M ++ LK+++ +RTGR +P++LD + VE YG+ PLNQ+A+++V EPR + Sbjct: 2 LKEAKEKMEKSLEALKEELNKIRTGRANPALLDSITVEYYGAPTPLNQLASISVPEPRTI 61 Query: 67 VVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSK 126 V++ +DK + ++E+ I S+LGLNP +G V+R+ +P TEERR LVK A AE++K Sbjct: 62 VINPFDKSAIKAIEKAILNSDLGLNPNNDGAVIRVNLPPLTEERRKELVKDAKKIAEEAK 121 Query: 127 ISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184 +++RNIRRD D +KK K + SED V E D+QK+TD IK ID + K+KE++ Sbjct: 122 VAIRNIRRDANDKIKKLEKEKEISEDEVKKAEEDLQKLTDEYIKKIDELLKSKEKELL 179 >gnl|CDD|39956 KOG4759, KOG4759, KOG4759, Ribosome recycling factor [Translation, ribosomal structure and biogenesis]. Length = 263 Score = 123 bits (310), Expect = 3e-29 Identities = 61/179 (34%), Positives = 100/179 (55%), Gaps = 3/179 (1%) Query: 7 LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRML 66 +M TI LK+D +R GR +P MLD + V+A G PLN++A V++ P+ + Sbjct: 85 EAKANSQMEKTIEALKEDFNKIRQGRFNPGMLDKIVVKANGPKRPLNEIAQVSLKGPQTI 144 Query: 67 VVSVWDK-EMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKS 125 +++ +D + ++ + I S L L P ++G VLR+ +P T+E R L KV Y E+ Sbjct: 145 LINPFDFPVDIKAILKAIEASGLNLTPNLDGTVLRVSIPPVTKESREKLAKVLKRYFEEY 204 Query: 126 KISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184 K S+R IR + KK++KS SED V E ++QK+ + +D + K+KE++ Sbjct: 205 KQSLRKIRTKSIKKSKKNKKS--LSEDEVKKAEAELQKLAKDAVNKLDDLLKSKEKELL 261 >gnl|CDD|145770 pfam02789, Peptidase_M17_N, Cytosol aminopeptidase family, N-terminal domain. Length = 126 Score = 27.8 bits (62), Expect = 1.7 Identities = 14/77 (18%), Positives = 36/77 (46%), Gaps = 13/77 (16%) Query: 67 VVSVWDKEMVASVERGIHESNLG-LNPIVE--------GQVLRIPVPETTEERRLALVKV 117 VV V++ ++ + E+ G L+ +++ G+ L +P + +R+ LV + Sbjct: 1 VVGVFEDGKLSPAAEKLDEALDGLLSELLKEGDFSGKAGETLLLPSLPGVKAKRVLLVGL 60 Query: 118 AHAYAEKSKISVRNIRR 134 ++ ++S +R+ Sbjct: 61 ----GKEEELSAEALRK 73 >gnl|CDD|146948 pfam04556, DpnII, DpnII restriction endonuclease. Members of this family are type II restriction enzymes (EC:3.1.21.4). They recognize the double-stranded unmethylated sequence GATC and cleave before G-1. http://rebase.neb.com/rebase/enz/DpnII.html. Length = 284 Score = 27.6 bits (62), Expect = 2.3 Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 7/49 (14%) Query: 136 GMD-HLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEI 183 G+D + +K+R SGKA E +V E ++KI D K I + EI Sbjct: 138 GLDSNARKNR-SGKAMELLV---ERLLKKICD--KKGITYKKQATIDEI 180 >gnl|CDD|35900 KOG0681, KOG0681, KOG0681, Actin-related protein - Arp5p [Cytoskeleton]. Length = 645 Score = 27.3 bits (60), Expect = 2.7 Identities = 22/105 (20%), Positives = 38/105 (36%), Gaps = 5/105 (4%) Query: 80 ERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDH 139 + + L ++ L + E +E+RL A KI+ R RR+ Sbjct: 257 DENRNYFQLPYTEVLAEVELALTA-EKKQEKRLQ---EQAALKRVEKINARENRREDEQQ 312 Query: 140 LKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184 L+ K+ E LE + + D E+KK+ I+ Sbjct: 313 LESYNKAQGEQESN-LDLEQKFPLLNVPAELDEDQLKEKKKQRIL 356 >gnl|CDD|145968 pfam03105, SPX, SPX domain. We have named this region the SPX domain after (SYG1, Pho81 and XPR1). This 180 residue length domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1, the N-terminus directly binds to the G- protein beta subunit and inhibits transduction of the mating pheromone signal. This finding suggests that all the members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2. NUC-2 contains several ankyrin repeats pfam00023. Several members of this family are annotated as XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with murine leukaemia viruses (MLV). The similarity between SYG1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae. In addition, given the similarities between XPR1 and SYG1 and phosphate regulatory proteins, it has been proposed that XPR1 might be involved in G-protein associated signal transduction and may itself function as a phosphate sensor. Length = 178 Score = 27.0 bits (60), Expect = 3.1 Identities = 11/60 (18%), Positives = 30/60 (50%) Query: 126 KISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIMH 185 K R + ++ S +E+ + E++ + D ++ ++SF++EK++E++ Sbjct: 30 KELTRAKLSLTTEEDEEDESSNLLNEEELEEDESEFFEALDKELEKVNSFYKEKEEELLE 89 >gnl|CDD|176343 cd01267, CED6_AIDA1b, Phosphotyrosine-binding (PTB) domain, phosphotyrosine-interaction (PI) domain. Phosphotyrosine-binding (PTB) domain, phosphotyrosine-interaction (PI) domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether. Length = 132 Score = 26.6 bits (59), Expect = 4.2 Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 2/51 (3%) Query: 136 GMDHLKKSRKSGKASEDMVASLENDIQKIT-DSTIKNIDSFFEEKKKEIMH 185 G + +++ + K S + + I K+ D +IK + + K K ++H Sbjct: 19 GTEVAREAIRKLKFSRILKTAEWEKIPKVELDISIKGV-KIIDPKTKTVLH 68 >gnl|CDD|36394 KOG1179, KOG1179, KOG1179, Very long-chain acyl-CoA synthetase/fatty acid transporter [Lipid transport and metabolism]. Length = 649 Score = 26.4 bits (58), Expect = 5.4 Identities = 14/41 (34%), Positives = 20/41 (48%) Query: 11 KDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVP 51 KDR GDT + +++ T V ++ L V YG VP Sbjct: 507 KDRTGDTFRWKGENVSTTEVEDVLSALDFLQDVNVYGVTVP 547 >gnl|CDD|99907 cd05565, PTS_IIB_lactose, PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.. Length = 99 Score = 26.2 bits (58), Expect = 5.8 Identities = 8/22 (36%), Positives = 13/22 (59%) Query: 44 EAYGSHVPLNQVANVTVLEPRM 65 AYGSH + ++ +L P+M Sbjct: 36 GAYGSHYDMIPDYDLVILAPQM 57 >gnl|CDD|112900 pfam04104, DNA_primase_lrg, Eukaryotic and archaeal DNA primase, large subunit. DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae). The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase. Length = 217 Score = 25.8 bits (57), Expect = 7.1 Identities = 24/147 (16%), Positives = 52/147 (35%), Gaps = 35/147 (23%) Query: 63 PRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYA 122 P+ ++ + + + +E+ ++ + L ++E E E+ L++ A Sbjct: 29 PKEELLRLLVEAFRSRLEKALNLTYESLPELLEEYE------EDIREKLEPLLEHLSKEA 82 Query: 123 EKSKISVRNIR-----------RDGMDHLKK--SRK-----------SGKASEDMVASLE 158 E KIS NI R+ ++ L+ K G SL+ Sbjct: 83 EDGKISAENIDKLSPEHFPPCMRNLLEGLRAGGHLKHEGRFQLTLFLKGIGL-----SLD 137 Query: 159 NDIQKITDSTIKNIDSFFEEKKKEIMH 185 ++ ++ + F +E + I H Sbjct: 138 EILEFWREAFTRTSPDFDKEYRYNIRH 164 >gnl|CDD|35775 KOG0555, KOG0555, KOG0555, Asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 545 Score = 25.7 bits (56), Expect = 7.1 Identities = 15/66 (22%), Positives = 30/66 (45%) Query: 118 AHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFE 177 + Y SK +++ I++ + KKS K+ + + E ++++ TI S Sbjct: 50 SEEYEPISKSALKKIKKGWVRECKKSAKASQKEAEASEKREKNLEEAKKITISEDKSLPA 109 Query: 178 EKKKEI 183 KK +I Sbjct: 110 AKKIKI 115 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 0.316 0.131 0.355 Gapped Lambda K H 0.267 0.0793 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,067,434 Number of extensions: 99482 Number of successful extensions: 302 Number of sequences better than 10.0: 1 Number of HSP's gapped: 298 Number of HSP's successfully gapped: 27 Length of query: 186 Length of database: 6,263,737 Length adjustment: 88 Effective length of query: 98 Effective length of database: 4,362,145 Effective search space: 427490210 Effective search space used: 427490210 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)