RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780144|ref|YP_003064557.1| 50S ribosomal protein L12P [Candidatus Liberibacter asiaticus str. psy62] (126 letters) >gnl|CDD|178906 PRK00157, rplL, 50S ribosomal protein L7/L12; Reviewed. Length = 123 Score = 131 bits (331), Expect = 7e-32 Identities = 76/125 (60%), Positives = 94/125 (75%), Gaps = 4/125 (3%) Query: 1 MSNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEV 60 E I+E L +T++E +EL K LE+++GVSA+APV+ A AA A +AA EKTEF+V Sbjct: 2 ALTKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAAA--AAAAAAAAEEKTEFDV 59 Query: 61 VLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAG 120 VLK D KKIAVIK VR IT LGLKEAK+LVE APK +K G+SK+EA E+KKKLE+AG Sbjct: 60 VLKSAGD--KKIAVIKAVREITGLGLKEAKDLVEGAPKVVKEGVSKEEAEEIKKKLEEAG 117 Query: 121 ATVEL 125 A VEL Sbjct: 118 AKVEL 122 >gnl|CDD|162069 TIGR00855, L12, ribosomal protein L7/L12. THis model resembles Pfam model pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus. Length = 126 Score = 111 bits (278), Expect = 8e-26 Identities = 75/124 (60%), Positives = 96/124 (77%), Gaps = 2/124 (1%) Query: 3 NIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVL 62 + E I+E L +T++E +EL K LE+++GVSA+APV+ A AA A +AA EKTEF+V+L Sbjct: 5 SKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAGAAGAAAAAAAAEEKTEFDVIL 64 Query: 63 KGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAGAT 122 KG D KIAVIK VR IT LGLKEAK+LVE APK LK G+SK+EA E+KKKLE+AGA Sbjct: 65 KGAGD--NKIAVIKVVREITGLGLKEAKDLVEGAPKVLKEGVSKEEAEELKKKLEEAGAK 122 Query: 123 VELR 126 VE++ Sbjct: 123 VEVK 126 >gnl|CDD|183148 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional. Length = 914 Score = 33.3 bits (76), Expect = 0.019 Identities = 24/92 (26%), Positives = 35/92 (38%), Gaps = 14/92 (15%) Query: 14 LTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDDPKKKIA 73 L LIE L++R+ E ++ A V V AA+A F L FD P Sbjct: 684 LLLIEDNPLTQRITAEMLNTSGAQVVAVGN-AAQALETLQNSEPFAAALVDFDLPDYD-- 740 Query: 74 VIKEVRAITDLGLKEAKELVESAPKSLKTGLS 105 G+ A++L + P + G S Sbjct: 741 -----------GITLARQLAQQYPSLVLIGFS 761 >gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional. Length = 936 Score = 32.5 bits (74), Expect = 0.034 Identities = 24/113 (21%), Positives = 50/113 (44%), Gaps = 4/113 (3%) Query: 5 ESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAAS---EKTEFEVV 61 E +++KL+++ + +EL+ R + S + EAG ++E Sbjct: 681 EELLQKLNAVHIYTVSELASREPEALAKSLGLSKKEAEKLIREAGDVLELLRRRSELRKF 740 Query: 62 LKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLK-TGLSKDEANEMK 113 ++ P++ + K ++A+ G+ + L + P LK GLS+ EA + Sbjct: 741 VRKHVPPRRGRSHAKIMKALISSGINDIAALARADPADLKKAGLSEAEAASLL 793 >gnl|CDD|178963 PRK00290, dnaK, molecular chaperone DnaK; Provisional. Length = 627 Score = 28.1 bits (64), Expect = 0.71 Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 3/43 (6%) Query: 79 RAITDLGLK---EAKELVESAPKSLKTGLSKDEANEMKKKLED 118 + + +LG K + KE +E+A K LK L ++ +K K E+ Sbjct: 541 KTLKELGDKVPADEKEKIEAAIKELKEALKGEDKEAIKAKTEE 583 >gnl|CDD|184895 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional. Length = 444 Score = 27.8 bits (63), Expect = 0.76 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 14/71 (19%) Query: 66 DDPKKKIAV--------IKEVRAITDLGLKEAKELVES----APKSLKTGLSKDEANEMK 113 DP K++++ +K R I G ++A++++ES S++ K E+ Sbjct: 137 KDPVKRLSIKYSHPVWLVK--RWIDQYGEEKAEKILESLNEPPKASIRVNTLKISVEELI 194 Query: 114 KKLEDAGATVE 124 +KLE+ G VE Sbjct: 195 EKLEEEGYEVE 205 >gnl|CDD|181825 PRK09405, aceE, pyruvate dehydrogenase subunit E1; Reviewed. Length = 891 Score = 27.4 bits (62), Expect = 1.1 Identities = 8/18 (44%), Positives = 14/18 (77%), Gaps = 3/18 (16%) Query: 17 IEAAELSKRLEKEWGVSA 34 +EAAE+ L +++GV+A Sbjct: 743 LEAAEI---LAEDYGVAA 757 >gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift. Length = 360 Score = 26.2 bits (58), Expect = 2.1 Identities = 23/114 (20%), Positives = 47/114 (41%), Gaps = 23/114 (20%) Query: 5 ESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKG 64 S++EKL SL EL L V++ + + E ++ E ++ Sbjct: 3 PSLLEKLESLL-ERYEELEALLSD---------PEVISDQD-KLRKLSKEYSQLEEIVDC 51 Query: 65 FDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLED 118 + + ++ IKE + I + E +E+ K+E E+++K+E+ Sbjct: 52 YREYQQAQEDIKEAKEILEESDPEMREMA------------KEELEELEEKIEE 93 >gnl|CDD|162912 TIGR02544, III_secr_YscJ, type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF. Length = 193 Score = 26.1 bits (58), Expect = 2.5 Identities = 12/25 (48%), Positives = 14/25 (56%) Query: 100 LKTGLSKDEANEMKKKLEDAGATVE 124 L +GLS+ EANEM L G E Sbjct: 22 LYSGLSEREANEMLAVLMRHGIDAE 46 >gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase. Length = 684 Score = 25.9 bits (57), Expect = 3.4 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 12/77 (15%) Query: 51 AASEKTEFEVVLK-GFDDPKK-KIAVIKEVRAITDLGL---KEAKELVESAPKSLKTGLS 105 A S+K++ +V F +P++ ++ VI + +LGL + K +VE+ ++ Sbjct: 426 AHSDKSKVPLVAHEKFAEPREVEVLVIVPNK--KELGLAFKGDQKVVVEA-----LEAMN 478 Query: 106 KDEANEMKKKLEDAGAT 122 + EA EMK KLE G Sbjct: 479 EKEAMEMKAKLESKGEA 495 >gnl|CDD|183840 PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional. Length = 896 Score = 24.9 bits (55), Expect = 5.4 Identities = 8/18 (44%), Positives = 10/18 (55%), Gaps = 3/18 (16%) Query: 17 IEAAELSKRLEKEWGVSA 34 + AA L L +WGV A Sbjct: 748 LAAARL---LADDWGVDA 762 >gnl|CDD|183393 PRK12273, aspA, aspartate ammonia-lyase; Provisional. Length = 472 Score = 25.1 bits (56), Expect = 5.6 Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 12/45 (26%) Query: 74 VIKEVRAITDLGLKEAKELVE------------SAPKSLKTGLSK 106 V++++ IT L L A++L+E A K L LSK Sbjct: 248 VVEKLAEITGLPLVPAEDLIEATQDTGAFVEVSGALKRLAVKLSK 292 >gnl|CDD|150561 pfam09902, DUF2129, Uncharacterized protein conserved in bacteria (DUF2129). This domain, found in various hypothetical prokaryotic proteins, has no known function. Length = 71 Score = 24.8 bits (55), Expect = 5.7 Identities = 11/25 (44%), Positives = 14/25 (56%) Query: 1 MSNIESIVEKLSSLTLIEAAELSKR 25 +E IVEKLS L ++ E S R Sbjct: 39 QEEVEEIVEKLSKLKFVKKVEPSYR 63 >gnl|CDD|181508 PRK08628, PRK08628, short chain dehydrogenase; Provisional. Length = 258 Score = 24.9 bits (55), Expect = 5.8 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 6/53 (11%) Query: 26 LEKEWGVS-ASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDDPKKKIAVIKE 77 L +EW V+ A V V A + AE + E + FDDP+ K+A I Sbjct: 163 LTREWAVALAKDGVRVNAVIPAEVMTPLYENW-----IATFDDPEAKLAAITA 210 >gnl|CDD|162857 TIGR02438, catachol_actin, catechol 1,2-dioxygenase, Actinobacterial. Members of this family are catechol 1,2-dioxygenases of the Actinobacteria. They are more closely related to actinobacterial chlorocatechol 1,2-dioxygenases than to proteobacterial catechol 1,2-dioxygenases, and so are built in this separate model. The member from Rhodococcus rhodochrous NCIMB 13259 (GB|AAC33003.1) is described as a homodimer with bound Fe, similarly active on catechol, 3-methylcatechol and 4-methylcatechol. Length = 281 Score = 24.7 bits (54), Expect = 5.9 Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 18/85 (21%) Query: 42 APVAAEAGSAASEKTEFEVVLKGFDDPKKKIAVI-KEV-RAITDLGLKEAKELVESAPKS 99 AP AA +G+AA++K + E V D K+++A I ++V AI + LK Sbjct: 7 APTAAASGNAATDKFKAERVSA--DTSKERVAAIARDVLGAINETILKH----------- 53 Query: 100 LKTGLSKDEANEMKKKLEDAGATVE 124 ++ DE N +K+ L D G E Sbjct: 54 ---KVTYDEYNVLKQWLIDVGEDGE 75 >gnl|CDD|179714 PRK04023, PRK04023, DNA polymerase II large subunit; Validated. Length = 1121 Score = 24.9 bits (55), Expect = 6.0 Identities = 7/20 (35%), Positives = 11/20 (55%) Query: 66 DDPKKKIAVIKEVRAITDLG 85 DD ++ + +V I DLG Sbjct: 384 DDVEEAKEIRDDVEEILDLG 403 >gnl|CDD|178670 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional. Length = 981 Score = 24.8 bits (54), Expect = 6.8 Identities = 9/21 (42%), Positives = 13/21 (61%) Query: 103 GLSKDEANEMKKKLEDAGATV 123 G SK++ E K K+E+AG Sbjct: 403 GASKEKVTEWKAKIEEAGGVF 423 >gnl|CDD|178436 PLN02843, PLN02843, isoleucyl-tRNA synthetase. Length = 974 Score = 24.7 bits (54), Expect = 7.4 Identities = 10/20 (50%), Positives = 12/20 (60%) Query: 14 LTLIEAAELSKRLEKEWGVS 33 L LI A +L LE +WGV Sbjct: 278 LFLIVATDLVPALEAKWGVK 297 >gnl|CDD|181714 PRK09231, PRK09231, fumarate reductase flavoprotein subunit; Validated. Length = 582 Score = 24.6 bits (54), Expect = 7.9 Identities = 17/41 (41%), Positives = 20/41 (48%), Gaps = 12/41 (29%) Query: 17 IEAAELSKRLEKEWGVSASAPVSVVAP-----VAAEAGSAA 52 I AAE + L+ A +S V P VAAE GSAA Sbjct: 21 IAAAEANPNLK-------IALISKVYPMRSHTVAAEGGSAA 54 >gnl|CDD|161728 TIGR00132, gatA, glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, A subunit. This orthology group is more narrowly defined here than in Proc Natl Acad Aci USA 94, 11819-11826 (1997). In particular, a Rhodococcus homolog found in association with nitrile hydratase genes and described as an enantiomer-selective amidase active on several 2-aryl propionamides, is excluded here. It is likely, however, that the amidase subunit GatA is not exclusively a part of the Glu-tRNA(Gln) amidotransferase heterotrimer and restricted to that function in all species. Length = 460 Score = 24.6 bits (54), Expect = 7.9 Identities = 20/75 (26%), Positives = 27/75 (36%), Gaps = 20/75 (26%) Query: 50 SAASEKTEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEA 109 SA EF LK K + V+KE D KE +E E+A Sbjct: 225 SAKVPDPEFFEELKKDLKGLK-VGVVKEFSEEMD---KEVQEKFENA------------- 267 Query: 110 NEMKKKLEDAGATVE 124 + LE+ GA + Sbjct: 268 ---LEVLEELGAEIV 279 >gnl|CDD|149109 pfam07859, Abhydrolase_3, alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes. Length = 209 Score = 24.5 bits (54), Expect = 9.0 Identities = 8/21 (38%), Positives = 11/21 (52%) Query: 106 KDEANEMKKKLEDAGATVELR 126 +DE ++L AG VEL Sbjct: 178 RDEGEAYAERLRAAGVPVELV 198 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 0.304 0.122 0.305 Gapped Lambda K H 0.267 0.0623 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,868,726 Number of extensions: 109118 Number of successful extensions: 279 Number of sequences better than 10.0: 1 Number of HSP's gapped: 274 Number of HSP's successfully gapped: 62 Length of query: 126 Length of database: 5,994,473 Length adjustment: 82 Effective length of query: 44 Effective length of database: 4,222,617 Effective search space: 185795148 Effective search space used: 185795148 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 43 (21.9 bits) S2: 51 (23.7 bits)