RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781180|ref|YP_003065593.1| hypothetical protein CLIBASIA_05435 [Candidatus Liberibacter asiaticus str. psy62] (71 letters) >gnl|CDD|133285 cd01885, EF2, EF2 (for archaea and eukarya). Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins. Two major mechanisms are known to regulate protein elongation and both involve eEF2. First, eEF2 can be modulated by reversible phosphorylation. Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes. Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2. In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation. Second, the protein can be post-translationally modified by ADP-ribosylation. Various bacterial toxins perform this reaction after modification of a specific histidine residue to diphthamide, but there is evidence for endogenous ADP ribosylase activity. Similar to the bacterial toxins, it is presumed that modification by the endogenous enzyme also inhibits eEF2 activity. Length = 222 Score = 27.2 bits (61), Expect = 1.0 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 6/59 (10%) Query: 13 LVNNEQLTEIEEPQKV--TVDQINNAIASLIPEERRDLQDRMAKYSTRKLKPRGRVIFA 69 L+ +L+ E Q++ ++Q+N I + EE ++ D +S +K G V F Sbjct: 138 LILELKLSPEEAYQRLARIIEQVNAIIGTYADEEFKEKDDEKWYFSPQK----GNVAFG 192 >gnl|CDD|100023 cd06059, Tubulin, The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. The alpha/beta-tubulin heterodimer is the structural subunit of microtubules. The alpha- and beta-tubulins share 40% amino-acid sequence identity, exist in several isotype forms, and undergo a variety of posttranslational modifications. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three regions based on function: the amino-terminal nucleotide-binding region, an intermediate taxol-binding region and the carboxy-terminal region which probably constitutes the binding surface for motor proteins. Also included in this group is the mitochondrial Misato/DML1 protein family, involved in mitochondrial fusion and in mitochondrial distribution and morphology.. Length = 382 Score = 26.5 bits (59), Expect = 1.6 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 7/47 (14%) Query: 3 SIHQSTNSCDLVN---NEQL----TEIEEPQKVTVDQINNAIASLIP 42 S++ + D V NE L T + + + D +NN IA +I Sbjct: 147 SLNHLLENSDSVILFDNEALYNILTRQLDIDEPSFDDLNNIIAQIIS 193 >gnl|CDD|33927 COG4192, COG4192, Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]. Length = 673 Score = 26.2 bits (57), Expect = 2.3 Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 5/56 (8%) Query: 3 SIHQSTNSCDLVNNEQLTEIEEPQKVTVDQINNAIASLIPEERRDLQDRMAKYSTR 58 +IH S L + + + + QIN+ +++ I D+ R+A ++ + Sbjct: 96 AIHALLASLPQNEQAALQQGLQELRQLLQQINDLVSARI-----DVDRRLALFAEQ 146 >gnl|CDD|36180 KOG0962, KOG0962, KOG0962, DNA repair protein RAD50, ABC-type ATPase/SMC superfamily [Replication, recombination and repair]. Length = 1294 Score = 26.0 bits (57), Expect = 2.5 Identities = 14/51 (27%), Positives = 21/51 (41%) Query: 16 NEQLTEIEEPQKVTVDQINNAIASLIPEERRDLQDRMAKYSTRKLKPRGRV 66 +L E+E QI A + EER L++ K S+ K G + Sbjct: 1014 ERKLKELERELSELDKQILEADIKSVKEERVKLEEEREKLSSEKNLLLGEM 1064 >gnl|CDD|30399 COG0050, TufB, GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]. Length = 394 Score = 26.0 bits (57), Expect = 2.6 Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 2/50 (4%) Query: 21 EIEEPQKVTVDQINNAIASLIPEERRDLQD--RMAKYSTRKLKPRGRVIF 68 E + + ++++ +A+ S IP RD+ M + RG V+ Sbjct: 180 EGDAKWEAKIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVT 229 >gnl|CDD|30569 COG0220, COG0220, Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]. Length = 227 Score = 25.3 bits (55), Expect = 3.4 Identities = 13/29 (44%), Positives = 15/29 (51%) Query: 43 EERRDLQDRMAKYSTRKLKPRGRVIFADD 71 +RR Q K RKLKP G + FA D Sbjct: 137 HKRRLTQPEFLKLYARKLKPGGVLHFATD 165 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 0.314 0.129 0.353 Gapped Lambda K H 0.267 0.0735 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 781,439 Number of extensions: 30279 Number of successful extensions: 91 Number of sequences better than 10.0: 1 Number of HSP's gapped: 91 Number of HSP's successfully gapped: 12 Length of query: 71 Length of database: 6,263,737 Length adjustment: 42 Effective length of query: 29 Effective length of database: 5,356,159 Effective search space: 155328611 Effective search space used: 155328611 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 51 (23.4 bits)