RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780144|ref|YP_003064557.1| 50S ribosomal protein L12P [Candidatus Liberibacter asiaticus str. psy62] (126 letters) >gnl|CDD|100102 cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and contain binding sites for other molecules. Initiation factors, elongation factors, and release factors are known to interact with the L7/L12 stalk during their GTP-dependent cycles. The binding site for the factors EF-Tu and EF-G comprises L7/L12, L10, L11, the L11-binding region of 23S rRNA, and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12 has minimal effect on factor binding and it has been proposed that L7/L12 induces the catalytically active conformation of EF-Tu and EF-G, thereby stimulating the GTPase activity of both factors. In eukaryotes, the proteins that perform the equivalent function to L7/L12 are called P1 and P2, which do not share sequence similarity with L7/L12. However, a bacterial L7/L12 homolog is found in some eukaryotes, in mitochondria and chloroplasts. In archaea, the protein equivalent to L7/L12 is called aL12 or L12p, but it is closer in sequence to P1 and P2 than to L7/L12.. Length = 127 Score = 130 bits (330), Expect = 7e-32 Identities = 81/127 (63%), Positives = 96/127 (75%), Gaps = 5/127 (3%) Query: 3 NIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAAS----EKTEF 58 +E IVE L LTL+EAAEL K LE+++GVSASA + A A A +AA+ EKTEF Sbjct: 2 KVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAAAAAAAPAAAAAAAAEAEEKTEF 61 Query: 59 EVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLED 118 +VVL+ F KKIAVIKEVR IT LGLKEAK+LVESAPK LK G+SK+EA E+KKKLE+ Sbjct: 62 DVVLESFGA-AKKIAVIKEVREITGLGLKEAKDLVESAPKVLKEGVSKEEAEEIKKKLEE 120 Query: 119 AGATVEL 125 AGA VEL Sbjct: 121 AGAKVEL 127 >gnl|CDD|177022 CHL00083, rpl12, ribosomal protein L12. Length = 131 Score = 118 bits (298), Expect = 4e-28 Identities = 71/131 (54%), Positives = 95/131 (72%), Gaps = 6/131 (4%) Query: 1 MSNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPV-----SVVAPVAAEAGSAASEK 55 + I I+E+L SLTL+EAAEL K++E+ +GV ASAPV S A AA+A EK Sbjct: 2 STKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMMSAPAAAAAQAAEEVEEK 61 Query: 56 TEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKK 115 TEF+V+L+ K+ IAV+K VR++T LGLKEAKELVES PK++K G+SK+EA E KK+ Sbjct: 62 TEFDVILEEVPADKR-IAVLKVVRSLTGLGLKEAKELVESLPKTIKEGISKEEAEEAKKQ 120 Query: 116 LEDAGATVELR 126 LE+AGA V ++ Sbjct: 121 LEEAGAKVIIK 131 >gnl|CDD|30571 COG0222, RplL, Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]. Length = 124 Score = 99 bits (249), Expect = 1e-22 Identities = 75/126 (59%), Positives = 93/126 (73%), Gaps = 3/126 (2%) Query: 1 MSNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEV 60 E I+E L LT++E +EL K LE+++GV+A+APV+ A AA A AA EKTEF+V Sbjct: 2 ALTKEQIIEALKELTVLELSELVKALEEKFGVTAAAPVAAAAAGAA-AAEAAEEKTEFDV 60 Query: 61 VLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAG 120 VLK KKIAVIK VR +T LGLKEAK+LVE APK LK G+SK+EA E+KKKLE+AG Sbjct: 61 VLKSAGG--KKIAVIKVVRELTGLGLKEAKDLVEGAPKVLKEGVSKEEAEEIKKKLEEAG 118 Query: 121 ATVELR 126 A VEL+ Sbjct: 119 AKVELK 124 >gnl|CDD|36927 KOG1715, KOG1715, KOG1715, Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]. Length = 187 Score = 91.2 bits (226), Expect = 7e-20 Identities = 62/130 (47%), Positives = 82/130 (63%), Gaps = 7/130 (5%) Query: 2 SNIESIVEKLSSLTLIEAAELSKRLEKEWGVS------ASAPVSVVAPVAAEAGSAASEK 55 I IV+++SSLTL+E ++L L+K+ + A+A + A EK Sbjct: 58 PKISKIVDEISSLTLLETSDLVDLLKKKLNIPELPLAPAAAAGAAAPDAGGAEEEAKKEK 117 Query: 56 TEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKK 115 T F+V L+ FD KI VIKEVRA+T LGLKEAK+LVE APK LK G++K+EA E+K+K Sbjct: 118 TTFDVKLEKFD-ASSKIKVIKEVRALTGLGLKEAKKLVEKAPKILKEGVTKEEAEEIKEK 176 Query: 116 LEDAGATVEL 125 LE AGA V L Sbjct: 177 LEAAGAKVVL 186 >gnl|CDD|144215 pfam00542, Ribosomal_L12, Ribosomal protein L7/L12 C-terminal domain. Length = 68 Score = 88.7 bits (221), Expect = 4e-19 Identities = 48/69 (69%), Positives = 55/69 (79%), Gaps = 2/69 (2%) Query: 57 EFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKL 116 EF+VVL D KKIAVIK VR IT LGLKEAK+LVE APK +K G+SK+EA E+KKKL Sbjct: 1 EFDVVLTSAGD--KKIAVIKVVREITGLGLKEAKDLVEGAPKVIKEGVSKEEAEEIKKKL 58 Query: 117 EDAGATVEL 125 E+AGA VEL Sbjct: 59 EEAGAKVEL 67 >gnl|CDD|34618 COG5013, NarG, Nitrate reductase alpha subunit [Energy production and conversion]. Length = 1227 Score = 25.7 bits (56), Expect = 4.1 Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 7/87 (8%) Query: 18 EAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDD-------PKK 70 E EL+K + GV+ P A AAE A S +T +V +K + Sbjct: 919 EYDELAKLNGTKAGVAKGRPRIDTAIDAAEVILALSPETNGQVAVKAWAALEEITGRDHT 978 Query: 71 KIAVIKEVRAITDLGLKEAKELVESAP 97 +A+ KE I ++ + S+P Sbjct: 979 HLALNKEDEKIRFRDIQAQPRKIISSP 1005 >gnl|CDD|37077 KOG1866, KOG1866, KOG1866, Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]. Length = 944 Score = 25.3 bits (55), Expect = 4.1 Identities = 8/31 (25%), Positives = 15/31 (48%) Query: 1 MSNIESIVEKLSSLTLIEAAELSKRLEKEWG 31 + N++ V+ L +L + A S + EW Sbjct: 52 VYNLKRSVDCLMTLYYMFKATTSCQALYEWE 82 >gnl|CDD|37247 KOG2036, KOG2036, KOG2036, Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]. Length = 1011 Score = 24.9 bits (54), Expect = 6.7 Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 13/70 (18%) Query: 4 IESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAA-------EAGSAASEKT 56 ++IVEK T+ A + G SA+ +S+ VA + S + KT Sbjct: 266 FDAIVEKTLRSTVSLTASRGR------GKSAALGLSIAGAVAFGYSNIYVTSPSPENLKT 319 Query: 57 EFEVVLKGFD 66 FE V KGFD Sbjct: 320 LFEFVFKGFD 329 >gnl|CDD|110511 pfam01514, YscJ_FliF, Secretory protein of YscJ/FliF family. This family includes proteins that are related to the YscJ lipoprotein, and the amino terminus of FliF, the flageller M-ring protein. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flageller proteins, based on the similarity to YscJ proteins. Length = 206 Score = 24.6 bits (54), Expect = 8.1 Identities = 11/21 (52%), Positives = 14/21 (66%) Query: 100 LKTGLSKDEANEMKKKLEDAG 120 L TGLS+ +ANE+ L AG Sbjct: 30 LYTGLSEKDANEVLAALLQAG 50 >gnl|CDD|176462 cd01357, Aspartase, Aspartase. This subgroup contains Escherichia coli aspartase (L-aspartate ammonia-lyase), Bacillus aspartase and related proteins. It is a member of the Lyase class I family, which includes both aspartase (L-aspartate ammonia-lyase) and fumarase class II enzymes. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. Aspartase catalyzes the reversible deamination of aspartic acid. Length = 450 Score = 24.4 bits (54), Expect = 9.5 Identities = 8/21 (38%), Positives = 15/21 (71%) Query: 74 VIKEVRAITDLGLKEAKELVE 94 V++++ IT L LK A+ L++ Sbjct: 241 VVEKLSEITGLPLKRAENLID 261 >gnl|CDD|145572 pfam02503, PP_kinase, Polyphosphate kinase. Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. Length = 678 Score = 24.3 bits (54), Expect = 9.8 Identities = 8/19 (42%), Positives = 13/19 (68%), Gaps = 2/19 (10%) Query: 107 DEANEMK--KKLEDAGATV 123 DE N ++ ++LE+AG V Sbjct: 402 DEENNIRWARRLEEAGVHV 420 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 0.304 0.122 0.305 Gapped Lambda K H 0.267 0.0784 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,221,838 Number of extensions: 54474 Number of successful extensions: 186 Number of sequences better than 10.0: 1 Number of HSP's gapped: 177 Number of HSP's successfully gapped: 48 Length of query: 126 Length of database: 6,263,737 Length adjustment: 83 Effective length of query: 43 Effective length of database: 4,470,190 Effective search space: 192218170 Effective search space used: 192218170 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 (23.3 bits)