RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780203|ref|YP_003064616.1| hypothetical protein CLIBASIA_00440 [Candidatus Liberibacter asiaticus str. psy62] (82 letters) >gnl|CDD|176195 cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase. (2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent medium chain alcohol dehydrogenase, catalyzes the NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and meso-butanediol to acetoin. BDH functions as a homodimer. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. 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. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit. Length = 351 Score = 28.7 bits (65), Expect = 0.33 Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 2/36 (5%) Query: 1 MDDRKYRPSKEEVRDAFPELIKALEKGLSTFDVEPL 36 + ++ S R+ F E+I L G D EPL Sbjct: 287 LKEKTLTGSICYTREDFEEVIDLLASGK--IDAEPL 320 >gnl|CDD|145544 pfam02461, AMO, Ammonia monooxygenase. Ammonia monooxygenase plays a key role in the nitrogen cycle and degrades a wide range of hydrocarbons and halogenated hydrocarbons. Length = 245 Score = 27.4 bits (61), Expect = 0.90 Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 3/27 (11%) Query: 13 VRDAFPELIKALEKG-LSTF--DVEPL 36 VR PE I+ +E+G L TF DV P+ Sbjct: 188 VRTGTPEYIRMVERGTLRTFGKDVVPV 214 >gnl|CDD|111365 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548 Score = 25.8 bits (57), Expect = 2.8 Identities = 9/19 (47%), Positives = 12/19 (63%) Query: 11 EEVRDAFPELIKALEKGLS 29 EEVR E I+ LE+ L+ Sbjct: 332 EEVRATVAEAIRLLEEELT 350 >gnl|CDD|145578 pfam02514, CobN-Mg_chel, CobN/Magnesium Chelatase. This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN is implicated in the conversion of hydrogenobyrinic acid a,c-diamide to cobyrinic acid. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis. Length = 1064 Score = 25.2 bits (56), Expect = 3.9 Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 5/34 (14%) Query: 14 RDAFPELIKALEKG---LSTFDVEPLK-NPVKSH 43 RDAFP LI+ +++ ++ D EP + N V+ H Sbjct: 787 RDAFPNLIELIDEAVRLVAALD-EPDEMNYVRKH 819 >gnl|CDD|176479 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. Length = 378 Score = 24.9 bits (55), Expect = 5.1 Identities = 8/22 (36%), Positives = 14/22 (63%) Query: 50 YISHVCELIELLKNKDFDGVEI 71 Y+ + EL+K+ DFD +E+ Sbjct: 126 YLKDLDLARELVKSGDFDALEL 147 >gnl|CDD|146970 pfam04587, ADP_PFK_GK, ADP-specific Phosphofructokinase/Glucokinase conserved region. In archaea a novel type of glycolytic pathway exists that is deviant from the classical Embden-Meyerhof pathway. This pathway utilizes two novel proteins: an ADP-dependent Glucokinase and an ADP-dependent Phosphofructokinase. This conserved region is present at the C-terminal of both these proteins. Interestingly this family contains sequences from higher eukaryotes.. Length = 444 Score = 24.7 bits (54), Expect = 5.3 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 10/57 (17%) Query: 10 KEEVRDAFPELIKALE----KGLSTFDVEPLKNPVKSHGKGYESYISHVCELIELLK 62 KEE+R+ E+ + ++ GL + S GK E Y+ V E I+LLK Sbjct: 196 KEELREFLEEIGEQVDLAILSGLQMLTLF------YSDGKDAEYYLKRVKEDIKLLK 246 >gnl|CDD|37414 KOG2203, KOG2203, KOG2203, GTP-binding protein [General function prediction only]. Length = 772 Score = 24.6 bits (53), Expect = 5.6 Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 6/64 (9%) Query: 8 PSKEEVRDAFPELIKALEKGLSTFDVEPLKNPVKSHGK----GYESYISHVCELIELLKN 63 KE D F E + +L + + P HG G+ Y + ++IE +N Sbjct: 218 SHKELKEDQFKEQVASLRQRFVHSGISPYGFAGDYHGVIPADGFSFYAEQIWDVIE--EN 275 Query: 64 KDFD 67 KD D Sbjct: 276 KDLD 279 >gnl|CDD|119349 cd00598, GH18_chitinase-like, The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel. The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins. The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model.. Length = 210 Score = 24.6 bits (54), Expect = 6.6 Identities = 8/15 (53%), Positives = 10/15 (66%) Query: 57 LIELLKNKDFDGVEI 71 L+ LK FDGV+I Sbjct: 96 LVSFLKTYGFDGVDI 110 >gnl|CDD|145454 pfam02309, AUX_IAA, AUX/IAA family. Transcription of the AUX/IAA family of genes is rapidly induced by the plant hormone auxin. Some members of this family are longer and contain an N terminal DNA binding domain. The function of this region is uncertain. Length = 192 Score = 24.2 bits (53), Expect = 8.4 Identities = 11/31 (35%), Positives = 14/31 (45%) Query: 17 FPELIKALEKGLSTFDVEPLKNPVKSHGKGY 47 + EL ALEK S F + K +G Y Sbjct: 118 YDELSSALEKMFSCFTIGESKLLDLLNGSEY 148 >gnl|CDD|48477 cd00713, GltS, Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The N-terminal glutaminase domain catalyzes the hydrolysis of glutamine to glutamic acid and ammonia, and has a fold similar to that of other glutamine amidotransferases such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), and beta lactam synthetase (beta-LS), as well as the Ntn hydrolase folds of the proteasomal alpha and beta subunits.. Length = 413 Score = 24.0 bits (52), Expect = 9.9 Identities = 9/21 (42%), Positives = 10/21 (47%) Query: 60 LLKNKDFDGVEIERKSYNLRK 80 + DG ERK Y LRK Sbjct: 133 VGAPSGDDGEAFERKLYLLRK 153 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 0.313 0.135 0.381 Gapped Lambda K H 0.267 0.0660 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,003,449 Number of extensions: 43974 Number of successful extensions: 163 Number of sequences better than 10.0: 1 Number of HSP's gapped: 163 Number of HSP's successfully gapped: 21 Length of query: 82 Length of database: 6,263,737 Length adjustment: 52 Effective length of query: 30 Effective length of database: 5,140,069 Effective search space: 154202070 Effective search space used: 154202070 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 (21.8 bits) S2: 51 (23.6 bits)