RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781005|ref|YP_003065418.1| hypothetical protein CLIBASIA_04530 [Candidatus Liberibacter asiaticus str. psy62] (85 letters) >gnl|CDD|37273 KOG2062, KOG2062, KOG2062, 26S proteasome regulatory complex, subunit RPN2/PSMD1 [Posttranslational modification, protein turnover, chaperones]. Length = 929 Score = 28.4 bits (63), Expect = 0.48 Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 1/61 (1%) Query: 9 ASLISSTVIMSGCSETLDPE-NGIRELGARMKQERKKADQPIGGGKTGETLPKGGGRKIS 67 +LI+ +IM +E L P+ NG R+ ++ ++ + G + + GGR ++ Sbjct: 643 GALIALAMIMIQQTEQLCPKVNGFRKQLEKVINDKHEDGMAKFGAILAQGILDAGGRNVT 702 Query: 68 L 68 + Sbjct: 703 I 703 >gnl|CDD|99858 cd06105, ScCit1-2_like, Saccharomyces cerevisiae (Sc) citrate synthases Cit1-2_like. Citrate synthases (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). ScCit1 is a nuclear-encoded mitochondrial CS with highly specificity for AcCoA. In addition to its CS function, ScCit1 plays a part in the construction of the TCA cycle metabolon. Yeast cells deleted for Cit1 are hyper-susceptible to apoptosis induced by heat and aging stress. ScCit2 is a peroxisomal CS involved in the glyoxylate cycle; in addition to having activity with AcCoA, it may have activity with PrCoA. Chicken and pig heart CS, two Arabidopsis thaliana (Ath) CSs, CSY4 and -5, and Aspergillus niger (An) CS also belong to this group. Ath CSY4 has a mitochondrial targeting sequence; AthCSY5 has no identifiable targeting sequence. AnCS encoded by the citA gene has both an N-terminal mitochondrial import signal and a C-terminal peroxisiomal target sequence; it is not known if both these signals are functional in vivo. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS.. Length = 427 Score = 26.2 bits (58), Expect = 2.2 Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 3/37 (8%) Query: 25 LDPENGIRELGARMKQERKKADQPIGGGKTGETLPKG 61 LDPE GIR G + + +K + GG E LP+G Sbjct: 53 LDPEEGIRFRGLSIPECQKLLPKAPGG---EEPLPEG 86 >gnl|CDD|35417 KOG0196, KOG0196, KOG0196, Tyrosine kinase, EPH (ephrin) receptor family [Signal transduction mechanisms]. Length = 996 Score = 24.5 bits (53), Expect = 6.7 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 7/67 (10%) Query: 26 DPENGIRELGARMKQERKKADQPIGGGKTGE----TLPKGGGRKISLDSNNL---STELR 78 DP +RE + K ++ IG G+ GE L G R+I++ L TE + Sbjct: 614 DPNQAVREFAKEIDPSCVKIEKVIGAGEFGEVCSGRLKLPGKREITVAIKTLKAGYTEKQ 673 Query: 79 SQNFLRK 85 ++FL + Sbjct: 674 RRDFLSE 680 >gnl|CDD|38806 KOG3600, KOG3600, KOG3600, Thyroid hormone receptor-associated protein complex, subunit TRAP240 [Transcription]. Length = 2238 Score = 23.9 bits (51), Expect = 8.9 Identities = 8/31 (25%), Positives = 13/31 (41%) Query: 2 DIKGLIVASLISSTVIMSGCSETLDPENGIR 32 DI + S S I+S C ++P+ Sbjct: 1962 DICRMCGISAADSPSILSACLVAMEPQGSFV 1992 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 0.311 0.132 0.358 Gapped Lambda K H 0.267 0.0667 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 915,253 Number of extensions: 37821 Number of successful extensions: 60 Number of sequences better than 10.0: 1 Number of HSP's gapped: 60 Number of HSP's successfully gapped: 8 Length of query: 85 Length of database: 6,263,737 Length adjustment: 54 Effective length of query: 31 Effective length of database: 5,096,851 Effective search space: 158002381 Effective search space used: 158002381 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 (21.7 bits) S2: 51 (23.6 bits)