RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781146|ref|YP_003065559.1| hypothetical protein CLIBASIA_05265 [Candidatus Liberibacter asiaticus str. psy62] (122 letters) >gnl|CDD|58519 cd01842, SGNH_hydrolase_like_5, SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.. Length = 183 Score = 26.1 bits (57), Expect = 2.5 Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 1/32 (3%) Query: 37 DFSKYGRKVIKNLREEKPEQYLRLISQILPRE 68 D S+Y R +K RE + +L +LP E Sbjct: 62 DLSRYQRNSMKTYRENLERLFSKL-DSVLPIE 92 >gnl|CDD|73272 cd01493, APPBP1_RUB, Ubiquitin activating enzyme (E1) subunit APPBP1. APPBP1 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. ABPP1 contains part of the adenylation domain.. Length = 425 Score = 26.0 bits (57), Expect = 3.0 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 6/63 (9%) Query: 6 LLPIRKKYPCINRLSHKEISLQYLYQSVLTDD---FSKYGRKVIKNL---REEKPEQYLR 59 LLP+ P + + K I LQ +Y+ D KY R+++K+L + ++ ++ Sbjct: 306 LLPLPGTLPDMTADTEKYIKLQNIYREKAEKDAAEVEKYVREILKSLGRSPDSISDKEIK 365 Query: 60 LIS 62 L Sbjct: 366 LFC 368 >gnl|CDD|144174 pfam00481, PP2C, Protein phosphatase 2C. Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase. Length = 253 Score = 25.4 bits (56), Expect = 4.0 Identities = 8/20 (40%), Positives = 15/20 (75%), Gaps = 2/20 (10%) Query: 73 DGITNGDQLTDEQLCEIIRS 92 DG+ D L+D+++ +I+RS Sbjct: 209 DGLW--DVLSDQEVVDIVRS 226 >gnl|CDD|143970 pfam00213, OSCP, ATP synthase delta (OSCP) subunit. The ATP D subunit from E. coli is the same as the OSCP subunit which is this family. The ATP D subunit from metazoa are found in family pfam00401. Length = 171 Score = 25.2 bits (56), Expect = 5.2 Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 5/73 (6%) Query: 31 QSVLTDDFSKYGRKVIKNLREEKPEQYLRLISQILPREKIKQDGITNGD-----QLTDEQ 85 ++V S+ + +K L E L I++ + GI L++EQ Sbjct: 58 KAVFGGKLSELTKNFLKLLAENGRLSLLPEIAEEFEELYNEHRGIVEATVTSAVPLSEEQ 117 Query: 86 LCEIIRSLEKELQ 98 L + +LEK+ Sbjct: 118 LKALKAALEKKTG 130 >gnl|CDD|147746 pfam05761, 5_nucleotid, 5' nucleotidase family. This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5. Length = 448 Score = 24.9 bits (55), Expect = 5.3 Identities = 4/26 (15%), Positives = 12/26 (46%) Query: 87 CEIIRSLEKELQIFTDFKNKDAHSRE 112 ++ LE+E++I + + + Sbjct: 320 ALVVPELEREIEILNTEQYRFEELQR 345 >gnl|CDD|176141 cd08450, PBP2_HcaR, The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 196 Score = 25.0 bits (55), Expect = 5.8 Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 2/31 (6%) Query: 44 KVIKNLREEKPEQYLRLISQILPR--EKIKQ 72 +V+ LREE P+ + L S P+ E + + Sbjct: 17 EVLPILREEHPDLDVELSSLFSPQLAEALMR 47 >gnl|CDD|144807 pfam01346, FKBP_N, Domain amino terminal to FKBP-type peptidyl-prolyl isomerase. This family is only found at the amino terminus of pfam00254. This domain is of unknown function. Length = 124 Score = 24.8 bits (55), Expect = 5.8 Identities = 9/28 (32%), Positives = 20/28 (71%), Gaps = 1/28 (3%) Query: 72 QDGITNGD-QLTDEQLCEIIRSLEKELQ 98 QD + + +LTDE++ + +++ +K+LQ Sbjct: 55 QDALAGKELKLTDEEIQKALQAFQKKLQ 82 >gnl|CDD|111230 pfam02316, Mu_DNA_bind, Mu DNA-binding domain. This family consists of MuA-transposase and repressor protein CI. These proteins contain homologous DNA-binding domains at their N-termini which compete for the same DNA site within the Mu bacteriophage genome. Length = 136 Score = 25.0 bits (54), Expect = 6.0 Identities = 12/60 (20%), Positives = 27/60 (45%) Query: 7 LPIRKKYPCINRLSHKEISLQYLYQSVLTDDFSKYGRKVIKNLREEKPEQYLRLISQILP 66 LP+ + + R E ++ T + Y R++I + + P++ R + ++LP Sbjct: 46 LPVETRAALLLRQGEIETGAGLFEKARPTLEAHTYDRELIWSKWDLAPDEQRRALEKLLP 105 >gnl|CDD|29049 cd00992, PDZ_signaling, PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.. Length = 82 Score = 24.4 bits (53), Expect = 7.3 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 11/63 (17%) Query: 48 NLREEKPEQYLRLISQILPREKIKQDGITNGDQL-----------TDEQLCEIIRSLEKE 96 +LR K +S++ P ++ G+ GD++ T E+ E++++ E Sbjct: 17 SLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGDE 76 Query: 97 LQI 99 + + Sbjct: 77 VTL 79 >gnl|CDD|31056 COG0712, AtpH, F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]. Length = 178 Score = 24.0 bits (52), Expect = 9.5 Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 8/87 (9%) Query: 19 LSHKEISLQY---LYQSVLTDDFSKYGRKVIKNLREEKPEQYLRLISQILPREKIKQDGI 75 LS +S + L S+ + ++ L E K L I + + + GI Sbjct: 49 LSSPAVSAEDKKELLISIFKKIGDPLLQNFLRLLAENKRLNLLPEILEEFLKLAAESRGI 108 Query: 76 TNGD-----QLTDEQLCEIIRSLEKEL 97 + +L+DEQL ++ LEK+ Sbjct: 109 VEAEVTSAFELSDEQLTKLEAKLEKKF 135 >gnl|CDD|37920 KOG2709, KOG2709, KOG2709, Uncharacterized conserved protein [Function unknown]. Length = 560 Score = 23.9 bits (51), Expect = 9.8 Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 1/42 (2%) Query: 64 ILPREKIKQDGITNGDQLTDE-QLCEIIRSLEKELQIFTDFK 104 + P + G+T G L+ E Q +I LE LQ FTDF Sbjct: 256 LFPDPTPQNPGMTVGILLSSEIQERRLIEELEIVLQEFTDFL 297 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 0.315 0.132 0.362 Gapped Lambda K H 0.267 0.0760 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,377,000 Number of extensions: 65568 Number of successful extensions: 180 Number of sequences better than 10.0: 1 Number of HSP's gapped: 180 Number of HSP's successfully gapped: 30 Length of query: 122 Length of database: 6,263,737 Length adjustment: 82 Effective length of query: 40 Effective length of database: 4,491,799 Effective search space: 179671960 Effective search space used: 179671960 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: 42 (22.0 bits) S2: 51 (23.4 bits)