RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780961|ref|YP_003065374.1| hypothetical protein CLIBASIA_04310 [Candidatus Liberibacter asiaticus str. psy62] (200 letters) >gnl|CDD|32922 COG3108, COG3108, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 185 Score = 155 bits (394), Expect = 6e-39 Identities = 69/149 (46%), Positives = 95/149 (63%), Gaps = 2/149 (1%) Query: 54 EEVRTLKIYVVSTGSKAIVTFKRGSQYNQEGLSQLNRLLYDWHSKQSIDMDPQLFDFLWE 113 E R LK+Y + TG KA FK Y+Q LS LNRLL DW + + MDP+LFD +++ Sbjct: 35 PEPRILKLYNLHTGEKAEAEFKDNGGYDQASLSGLNRLLRDWRQNEVVRMDPRLFDLVYQ 94 Query: 114 IQQYFSVPEYIYILSGYRTQETNKMLSRRNRKIARKSQHVLGKAVDFYIPGVSLRSLYKI 173 ++ + + SGYR+ TN+ML R+R +A+KS H+LG+A+DF IPGVSL L Sbjct: 95 LKTLEGHRRPVQVTSGYRSPATNRMLRSRSRGVAKKSLHMLGQAMDFQIPGVSLWELRNA 154 Query: 174 AIRLKRGGVGYY--SKFLHIDVGRVRSWT 200 A+ ++ GGVGYY S +H+DVG VR W Sbjct: 155 ALSMQGGGVGYYPHSNSVHMDVGPVRDWN 183 >gnl|CDD|145604 pfam02557, VanY, D-alanyl-D-alanine carboxypeptidase. Length = 131 Score = 28.8 bits (65), Expect = 0.99 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 12/54 (22%) Query: 123 YIYILSGYRTQETNKML---SRRNRKI--ARK-------SQHVLGKAVDFYIPG 164 ++I SGYR+ E + L + A + S+H G A+D P Sbjct: 25 DLFIASGYRSYEYQQALYDKYVKGEGKEAALRYSAPPGYSEHQTGLAIDIGDPD 78 >gnl|CDD|37703 KOG2492, KOG2492, KOG2492, CDK5 activator-binding protein [Signal transduction mechanisms]. Length = 552 Score = 27.3 bits (60), Expect = 2.9 Identities = 10/33 (30%), Positives = 16/33 (48%) Query: 137 KMLSRRNRKIARKSQHVLGKAVDFYIPGVSLRS 169 ++L R +R++ L + IPGV L S Sbjct: 366 RVLEIMRRGYSREAYLELVAHIRSMIPGVGLSS 398 >gnl|CDD|36001 KOG0782, KOG0782, KOG0782, Predicted diacylglycerol kinase [Signal transduction mechanisms]. Length = 1004 Score = 27.4 bits (60), Expect = 2.9 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 1/43 (2%) Query: 33 LSPDLIKYHQQSSMSSDLLDQ-EEVRTLKIYVVSTGSKAIVTF 74 LS DL+K + LL Q + +L Y TG+ IV + Sbjct: 875 LSSDLMKLQETHLNGGSLLIQGPDHCSLLHYAAKTGNGEIVKY 917 >gnl|CDD|37762 KOG2551, KOG2551, KOG2551, Phospholipase/carboxyhydrolase [Amino acid transport and metabolism]. Length = 230 Score = 27.2 bits (60), Expect = 3.0 Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 3/61 (4%) Query: 115 QQYFSVP--EYIYILSGYRTQETNKMLSRRNRKIARKSQHVLGKAVDFYIPGVSLRSLYK 172 Y P ++ +SG++ S R ++ S H+ G+ D +P L + Sbjct: 129 LPYVKQPPFKFAVFISGFKFPSKKLDESAYKRPLSTPSLHIFGET-DTIVPSERSEQLAE 187 Query: 173 I 173 Sbjct: 188 S 188 >gnl|CDD|37702 KOG2491, KOG2491, KOG2491, Nuclear matrix protein [Nuclear structure]. Length = 674 Score = 27.3 bits (60), Expect = 3.2 Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 14/66 (21%) Query: 100 SIDMDPQLFDFLWEIQQYFSVPEYIY--------------ILSGYRTQETNKMLSRRNRK 145 SI +D L+ W +Q YFS P +Y +L +++ + N K Sbjct: 222 SIKVDYNLYRKFWSLQDYFSNPNSLYEKIKWKKFLKYLEEVLQVFKSYKLEDTFGESNEK 281 Query: 146 IARKSQ 151 + + Sbjct: 282 MEELAT 287 >gnl|CDD|48525 cd02976, NrdH, NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase activity that is dependent on TRX reductase, not glutathione (GSH). It is part of the NrdHIEF operon, where NrdEF codes for class Ib ribonucleotide reductase (RNR-Ib), an efficient enzyme at low oxygen levels. Under these conditions when GSH is mostly conjugated to spermidine, NrdH can still function and act as a hydrogen donor for RNR-Ib. It has been suggested that the NrdHEF system may be the oldest RNR reducing system, capable of functioning in a microaerophilic environment, where GSH was not yet available. NrdH from Corynebacterium ammoniagenes can form domain-swapped dimers, although it is unknown if this happens in vivo. Domain-swapped dimerization, which results in the blocking of the TRX reductase binding site, could be a mechanism for regulating the oxidation state of the protein.. Length = 73 Score = 26.3 bits (58), Expect = 6.1 Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 3/42 (7%) Query: 101 IDMDPQLFDFLWEIQQYFSVPEYIY---ILSGYRTQETNKML 139 +D DP+ + L ++ Y SVP + LSG+R + +L Sbjct: 32 VDEDPEALEELKKLNGYRSVPVVVIGDEHLSGFRPDKLRALL 73 >gnl|CDD|147498 pfam05343, Peptidase_M42, M42 glutamyl aminopeptidase. These peptidases are found in Archaea and Bacteria. The example in Lactococcus lactis, PepA, aids growth on milk. Pyrococcus horikoshii contain a thermostable de-blocking aminopeptidase member of this family used commercially for N-terminal protein sequencing. Length = 292 Score = 26.0 bits (58), Expect = 7.1 Identities = 8/30 (26%), Positives = 15/30 (50%) Query: 103 MDPQLFDFLWEIQQYFSVPEYIYILSGYRT 132 P+L FL E+ + ++P + + G T Sbjct: 221 YHPKLRKFLLELAKKNNIPYQVEVYPGGGT 250 >gnl|CDD|133086 cd06228, Peptidase_M14-like_3, A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. Length = 332 Score = 25.9 bits (57), Expect = 8.0 Identities = 8/12 (66%), Positives = 10/12 (83%) Query: 108 FDFLWEIQQYFS 119 FDFLW+ Q+YF Sbjct: 130 FDFLWDFQKYFD 141 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 0.323 0.137 0.403 Gapped Lambda K H 0.267 0.0798 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,432,974 Number of extensions: 121372 Number of successful extensions: 328 Number of sequences better than 10.0: 1 Number of HSP's gapped: 326 Number of HSP's successfully gapped: 18 Length of query: 200 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 111 Effective length of database: 4,340,536 Effective search space: 481799496 Effective search space used: 481799496 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 55 (24.8 bits)