RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781067|ref|YP_003065480.1| elongation factor P [Candidatus Liberibacter asiaticus str. psy62] (189 letters) >gnl|CDD|30580 COG0231, Efp, Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]. Length = 131 Score = 132 bits (333), Expect = 8e-32 Identities = 47/131 (35%), Positives = 82/131 (62%) Query: 1 MVKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTE 60 M + AS +RKG + +DG+ Y+V+ + PGKG +V+++ + G KV ++ + Sbjct: 1 MAMISASELRKGLYIVIDGEPYVVVEISHVKPGKGGAFVRVKLKNLFTGKKVEKTFKADD 60 Query: 61 QVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG 120 +VE A VE + Q+LY D + + FM+ ETY+Q + ++ IGD + +EGMEV++L++ G Sbjct: 61 KVEVAIVERKTAQYLYIDGDFYVFMDLETYEQYELPKDQIGDAAKFLKEGMEVEVLLYNG 120 Query: 121 VALSVEVPRHV 131 ++VE+P V Sbjct: 121 EPIAVELPNFV 131 >gnl|CDD|88435 cd04470, S1_EF-P_repeat_1, S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P has 3 domains (domains I, II, and III). Domains II and III are S1-like domains. This CD includes domain II (the first S1 domain of EF_P). Domains II and III have structural homology to the eIF5A domain C, suggesting that domains II and III evolved by duplication.. Length = 61 Score = 81.3 bits (201), Expect = 2e-16 Identities = 24/61 (39%), Positives = 42/61 (68%) Query: 68 EDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVEV 127 E++ Q+LY+D + + FM+ ETY+Q+ + +E +GD + +EGMEV +L + G + VE+ Sbjct: 1 EEREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVEL 60 Query: 128 P 128 P Sbjct: 61 P 61 >gnl|CDD|144650 pfam01132, EFP, Elongation factor P (EF-P) OB domain. Length = 55 Score = 78.6 bits (195), Expect = 9e-16 Identities = 20/55 (36%), Positives = 36/55 (65%) Query: 69 DQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVAL 123 + Q+LY+D + + FM+ ETY+Q+ + +E +GD + +EGMEV +L + G + Sbjct: 1 RREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVTVLFYNGEPI 55 >gnl|CDD|88469 cd05794, S1_EF-P_repeat_2, S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P has 3 domains (domains I, II, and III). Domains II and III are S1-like domains. This CD includes domain III (the second S1 domain of EF_P). Domains II and III of have structural homology to the eIF5A domain C, suggesting that domains II and III evolved by duplication.. Length = 56 Score = 68.6 bits (168), Expect = 1e-12 Identities = 22/56 (39%), Positives = 27/56 (48%) Query: 131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER 186 V V +TEP KG T ++ KPA L VP I G+ I + T YVER Sbjct: 1 VELEVTETEPGVKGDTASSGTKPATLETGAEVQVPLFIKEGEKIKVDTRTGEYVER 56 >gnl|CDD|37159 KOG1948, KOG1948, KOG1948, Metalloproteinase-related collagenase pM5 [Posttranslational modification, protein turnover, chaperones]. Length = 1165 Score = 29.2 bits (65), Expect = 0.66 Identities = 11/49 (22%), Positives = 18/49 (36%) Query: 60 EQVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQ 108 +ER+F +D +G +FM ++ EV D Q Sbjct: 970 SPIERSFPRSFTVSVGNEDVKGLNFMAFIQAKTTDITVEVGMDTNEELQ 1018 >gnl|CDD|133365 cd04165, GTPBP1_like, GTPBP1-like. Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12. Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6. The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and survival. This fusion product may contribute to the onset of GBM. Length = 224 Score = 28.8 bits (65), Expect = 0.97 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 2/70 (2%) Query: 118 HEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVIL 177 H G+AL++ +P VV T ID P++ Q K + +R P DD V+L Sbjct: 130 HLGLALALNIPVFVVVTKIDLAPANILQETLKDLKRILKVPGVRK--LPVPVKSDDDVVL 187 Query: 178 TEDNSYVERV 187 N ER+ Sbjct: 188 AASNFSSERI 197 >gnl|CDD|35684 KOG0463, KOG0463, KOG0463, GTP-binding protein GP-1 [General function prediction only]. Length = 641 Score = 28.1 bits (62), Expect = 1.6 Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 2/70 (2%) Query: 118 HEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVIL 177 H G+AL++ VP VV T ID P++ Q + S R +P + DD V+ Sbjct: 265 HLGLALALHVPVFVVVTKIDMCPANILQETMKLLTRLLKSPGCR-KLPVLVRSMDD-VVH 322 Query: 178 TEDNSYVERV 187 N ERV Sbjct: 323 AAVNFPSERV 332 >gnl|CDD|176260 cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases. Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes or ketones. Like many zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these FDHs form dimers, with 4 zinc ions per dimer. The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Length = 368 Score = 26.4 bits (59), Expect = 4.8 Identities = 9/31 (29%), Positives = 16/31 (51%) Query: 69 DQRFQFLYQDQEGFHFMNPETYDQVTVSEEV 99 D +F + + +HFM T+ + TV E+ Sbjct: 120 DGTSRFSCKGKPIYHFMGTSTFSEYTVVAEI 150 >gnl|CDD|176645 cd05282, ETR_like, 2-enoyl thioester reductase-like. 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Candida tropicalis enoyl thioester reductase (Etr1p) catalyzes the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis. Etr1p forms homodimers with each subunit containing a nucleotide-binding Rossmann fold domain and a catalytic domain. Length = 323 Score = 25.7 bits (57), Expect = 8.5 Identities = 7/20 (35%), Positives = 11/20 (55%) Query: 170 IGDDIVILTEDNSYVERVKK 189 +G D VI + +RVK+ Sbjct: 182 LGADEVIDSSPEDLAQRVKE 201 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 0.318 0.135 0.381 Gapped Lambda K H 0.267 0.0876 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,205,434 Number of extensions: 109059 Number of successful extensions: 264 Number of sequences better than 10.0: 1 Number of HSP's gapped: 264 Number of HSP's successfully gapped: 14 Length of query: 189 Length of database: 6,263,737 Length adjustment: 88 Effective length of query: 101 Effective length of database: 4,362,145 Effective search space: 440576645 Effective search space used: 440576645 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 (21.7 bits) S2: 54 (24.3 bits)