RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781226|ref|YP_003065639.1| hypothetical protein CLIBASIA_05665 [Candidatus Liberibacter asiaticus str. psy62] (129 letters) >gnl|CDD|99740 cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary metabolites. Some well studied proteins in this CD are AHBA_synthase, protein product of pleiotropic regulatory gene degT, Arnb aminotransferase and pilin glycosylation protein. The prototype of this family, the AHBA_synthase, is a dimeric PLP dependent enzyme. AHBA_syn is the terminal enzyme of 3-amino-5-hydroxybenzoic acid (AHBA) formation which is involved in the biosynthesis of ansamycin antibiotics, including rifamycin B. Some members of this CD are involved in 4-amino-6-deoxy-monosaccharide D-perosamine synthesis. Perosamine is an important element in the glycosylation of several cell products, such as antibiotics and lipopolysaccharides of gram-positive and gram-negative bacteria. The pilin glycosylation protein encoded by gene pglA, is a galactosyltransferase involved in pilin glycosylation. Additionally, this CD consists of ArnB (PmrH) aminotransferase, a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme. This CD also consists of several predicted pyridoxal phosphate-dependent enzymes apparently involved in regulation of cell wall biogenesis. The catalytic lysine which is present in all characterized PLP dependent enzymes is replaced by histidine in some members of this CD.. Length = 352 Score = 29.8 bits (68), Expect = 0.23 Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 23/70 (32%) Query: 24 LKNRDKILERRRRRY------LKN---------KDKIRESYHQYYLKNKDKYREYKRRYY 68 L+ D+I+ RRR L + ++ SYH Y ++ + E Sbjct: 227 LEKLDEIIARRREIAERYKELLADLPGIRLPDVPPGVKHSYHLYVIRLDPEAGE------ 280 Query: 69 LKNRDKMREK 78 +RD++ E Sbjct: 281 --SRDELIEA 288 >gnl|CDD|163652 cd07409, MPP_CD73_N, CD73 ecto-5'-nucleotidase and related proteins, N-terminal metallophosphatase domain. CD73 is a mammalian ecto-5'-nucleotidase expressed in endothelial cells and lymphocytes that catalyzes the conversion of 5'-AMP to adenosine in the final step of a pathway that generates adenosine from ATP. This pathway also includes a CD39 nucleoside triphosphate dephosphorylase that mediates the dephosphorylation of ATP to ADP and then to 5'-AMP. These enzymes all have an N-terminal metallophosphatase domain and a C-terminal 5'nucleotidase domain. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. Length = 281 Score = 27.5 bits (62), Expect = 1.00 Identities = 9/21 (42%), Positives = 16/21 (76%) Query: 105 EIEALEREIARLKAKPIEELI 125 EIEA ++E +LKA+ + ++I Sbjct: 167 EIEAAQKEADKLKAQGVNKII 187 >gnl|CDD|144201 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A. Length = 428 Score = 27.5 bits (62), Expect = 1.00 Identities = 25/108 (23%), Positives = 53/108 (49%), Gaps = 11/108 (10%) Query: 21 RYYLKNRDKILERRRRRYLKNKDKIRESYH--QYYLKNKDKYREYKRRYYLKNRDKMREK 78 + +L++R ++ +RR+ L+ K+ E H + LK +K ++ + + Sbjct: 312 KEFLEHRLEVYKRRKEYLLE---KLEERLHILEGLLKALNKIDFVIEV--IRGSIDLNKA 366 Query: 79 ARQSYRKLYSKDS-WIAPEEPMG-MTKAEIEALEREIARLKAKPIEEL 124 ++ +L + ++ + + +TK EIE LE+EI L+ + I EL Sbjct: 367 KKELIEELSEIQADYLL-DMRLRRLTKEEIEKLEKEIEELEKE-IAEL 412 >gnl|CDD|30998 COG0653, SecA, Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]. Length = 822 Score = 27.5 bits (61), Expect = 1.0 Identities = 17/81 (20%), Positives = 27/81 (33%) Query: 36 RRYLKNKDKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAP 95 R +L D +RE H KD EYKR + D + + ++L+ Sbjct: 727 REHLDAMDALREGIHLRGYAQKDPLIEYKREAFELFEDMLEDIKEDVVKRLFKVQVAEVE 786 Query: 96 EEPMGMTKAEIEALEREIARL 116 EE + E + Sbjct: 787 EEDRSLLAQEKALTQARALGK 807 >gnl|CDD|38228 KOG3018, KOG3018, KOG3018, Malonyl-CoA decarboxylase [Carbohydrate transport and metabolism]. Length = 362 Score = 26.2 bits (57), Expect = 2.9 Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 4/71 (5%) Query: 44 KIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAPEEPMGMTK 103 + L++ K E + + + NR+ +RE+ YR+ +P EP+ Sbjct: 74 DLERGTWSSPLEDLQKLLEVEAVHPVVNREDVRERVGP-YRRCLGFSHPASPREPLVFIH 132 Query: 104 AEIEALEREIA 114 AL IA Sbjct: 133 V---ALMETIA 140 >gnl|CDD|34782 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA processing and modification]. Length = 1175 Score = 26.2 bits (57), Expect = 2.9 Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 3/67 (4%) Query: 33 RRRRRYLKNKDKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKDSW 92 R RRR L N I ES + ++ R R+ R+ R+ + S + + S Sbjct: 215 RLRRRMLMNPRAILESISR---ESAQLERNTARQQGEHARENGRDLSSDSNNNVINPVSD 271 Query: 93 IAPEEPM 99 P M Sbjct: 272 NVPSRDM 278 >gnl|CDD|31325 COG1129, MglA, ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]. Length = 500 Score = 25.9 bits (57), Expect = 3.2 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 6/56 (10%) Query: 61 REYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAPEEPMG-MTKAEIEALEREIAR 115 RE RR+ L +R MR +AR+ +L I P+ +G ++ A+ + + EIAR Sbjct: 108 REPTRRFGLIDRKAMRRRARELLARL---GLDIDPDTLVGDLSIAQRQMV--EIAR 158 >gnl|CDD|35636 KOG0415, KOG0415, KOG0415, Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]. Length = 479 Score = 26.1 bits (57), Expect = 3.2 Identities = 13/78 (16%), Positives = 28/78 (35%) Query: 7 TPEERMLCRREYKRRYYLKNRDKILERRRRRYLKNKDKIRESYHQYYLKNKDKYREYKRR 66 ++R +R ER R ++ RE + + + + E + R Sbjct: 369 NSDDRERSESAQRRSPGEGRHQHSDERDDGRRQHRREDARELDRKSRFRKERESNEDEDR 428 Query: 67 YYLKNRDKMREKARQSYR 84 + R++ R K+ + R Sbjct: 429 RSRRKRERTRNKSSRRER 446 >gnl|CDD|111439 pfam02538, Hydantoinase_B, Hydantoinase B/oxoprolinase. This family includes N-methylhydaintoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase EC:3.5.2.9 which catalyses the formation of L-glutamate from 5-oxo-L-proline. These enzymes are part of the oxoprolinase family and are related to pfam01968. Length = 527 Score = 25.5 bits (56), Expect = 4.4 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 6/59 (10%) Query: 69 LKNRDKMREKARQSYRKLYSKDSWIA--PEEPMGMTKAEIEALEREIARLKAKPIEELI 125 L + E + R+L+ ++ + + PE +G KA+I A ++ I R+ K I+E Sbjct: 152 LVKNGEFNE---ELIRQLFVRNPYPSRNPECNIGDLKAQIAANQKGIDRIG-KLIDEYG 206 >gnl|CDD|38823 KOG3617, KOG3617, KOG3617, WD40 and TPR repeat-containing protein [General function prediction only]. Length = 1416 Score = 25.4 bits (55), Expect = 4.5 Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 1/63 (1%) Query: 20 RRYYLKNRDKILERRRRRYLKNKDKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKA 79 +Y + RD+ L +YL++ ++ + +Y KD + + + DK A Sbjct: 903 EQYVRRKRDESLYSWWGQYLESVGEMDAALS-FYSSAKDYFSMVRIKCIQGKTDKAARIA 961 Query: 80 RQS 82 +S Sbjct: 962 EES 964 >gnl|CDD|30540 COG0191, Fba, Fructose/tagatose bisphosphate aldolase [Carbohydrate transport and metabolism]. Length = 286 Score = 25.5 bits (56), Expect = 4.6 Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 6/48 (12%) Query: 43 DKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKD 90 +RE Y +N +Y R+Y + M+E ++ ++ S Sbjct: 243 AAVRE----YLAENPKEYDP--RKYLKPAIEAMKEVVKEKIKEFGSAG 284 >gnl|CDD|32946 COG3132, COG3132, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 215 Score = 25.4 bits (55), Expect = 4.8 Identities = 11/26 (42%), Positives = 17/26 (65%) Query: 94 APEEPMGMTKAEIEALEREIARLKAK 119 AP +A +EALE+E+A L+A+ Sbjct: 182 APAAASSDLEARVEALEQEVAELRAR 207 >gnl|CDD|143419 cd07101, ALDH_SSADH2_GabD2, Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 2-like. Succinate-semialdehyde dehydrogenase 2 (SSADH2) and similar proteins are in this CD. SSADH1 (GabD1, EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation of succinate semialdehyde to succinate. SSADH activity in Mycobacterium tuberculosis is encoded by both gabD1 (Rv0234c) and gabD2 (Rv1731), however ,the Vmax of GabD1 was shown to be much higher than that of GabD2, and GabD2 (SSADH2) is likely to serve physiologically as a dehydrogenase for a different aldehyde(s). Length = 454 Score = 25.0 bits (55), Expect = 5.7 Identities = 8/17 (47%), Positives = 13/17 (76%) Query: 21 RYYLKNRDKILERRRRR 37 RYY + +++L+ RRRR Sbjct: 87 RYYARRAERLLKPRRRR 103 >gnl|CDD|35965 KOG0746, KOG0746, KOG0746, 60S ribosomal protein L3 and related proteins [Translation, ribosomal structure and biogenesis]. Length = 384 Score = 25.0 bits (54), Expect = 5.8 Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%) Query: 62 EYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAPEE 97 E KRR+Y KN K ++KA Y K + + E Sbjct: 100 ECKRRFY-KNWHKSKKKAFTKYCKKWQDEDGKKQLE 134 >gnl|CDD|147119 pfam04802, SMK-1, Component of IIS longevity pathway SMK-1. SMK-1 is a component of the IIs longevity pathway which regulates aging in C.elegans. Specifically, SMK-1 influences DAF-16-dependant regulation of the aging process by regulating the transcriptional specificity of DAF-16 activity. SMK-1 plays a role in longevity by modulating the transcriptional specificity of DAF-16. Length = 193 Score = 24.8 bits (55), Expect = 6.4 Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 4/41 (9%) Query: 50 HQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKD 90 H+ +L K++E +KN ++R+K Q+YR Y KD Sbjct: 74 HRQFLTQNAKFKEVIP---IKN-PELRQKIHQTYRLQYLKD 110 >gnl|CDD|36758 KOG1545, KOG1545, KOG1545, Voltage-gated shaker-like K+ channel KCNA [Inorganic ion transport and metabolism]. Length = 507 Score = 24.5 bits (53), Expect = 7.9 Identities = 9/17 (52%), Positives = 13/17 (76%) Query: 8 PEERMLCRREYKRRYYL 24 PEER L R E++R+ +L Sbjct: 163 PEERPLPRNEFQRQVWL 179 >gnl|CDD|39002 KOG3798, KOG3798, KOG3798, Predicted Zn-dependent hydrolase (beta-lactamase superfamily) [General function prediction only]. Length = 343 Score = 24.6 bits (53), Expect = 9.0 Identities = 8/23 (34%), Positives = 13/23 (56%) Query: 51 QYYLKNKDKYREYKRRYYLKNRD 73 +YYL+ +DK +E LK+ Sbjct: 307 EYYLEPRDKLKELMEAEGLKDTS 329 >gnl|CDD|132756 cd07071, NR_LBD_Nurr1, The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 238 Score = 24.6 bits (53), Expect = 9.2 Identities = 10/21 (47%), Positives = 13/21 (61%) Query: 8 PEERMLCRREYKRRYYLKNRD 28 PE R LC + +R +YLK D Sbjct: 200 PELRTLCTQGLQRIFYLKLED 220 >gnl|CDD|145880 pfam02956, TT_ORF1, TT viral orf 1. TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525 Score = 24.5 bits (54), Expect = 9.3 Identities = 9/24 (37%), Positives = 13/24 (54%) Query: 15 RREYKRRYYLKNRDKILERRRRRY 38 R +RR ++ R + RRRRR Sbjct: 25 ARRRRRRRRVRRRRRGRRRRRRRR 48 >gnl|CDD|33234 COG3428, COG3428, Predicted membrane protein [Function unknown]. Length = 494 Score = 24.5 bits (53), Expect = 9.9 Identities = 13/34 (38%), Positives = 17/34 (50%) Query: 96 EEPMGMTKAEIEALEREIARLKAKPIEELIYKRG 129 E G +AE E +EREIA A + E K+ Sbjct: 117 ETAGGGGEAEAELVEREIAFELAALVREARVKKL 150 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 0.320 0.136 0.389 Gapped Lambda K H 0.267 0.0615 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,749,306 Number of extensions: 94668 Number of successful extensions: 717 Number of sequences better than 10.0: 1 Number of HSP's gapped: 680 Number of HSP's successfully gapped: 163 Length of query: 129 Length of database: 6,263,737 Length adjustment: 83 Effective length of query: 46 Effective length of database: 4,470,190 Effective search space: 205628740 Effective search space used: 205628740 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.1 bits)