RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780556|ref|YP_003064969.1| hypothetical protein CLIBASIA_02215 [Candidatus Liberibacter asiaticus str. psy62] (120 letters) >gnl|CDD|36212 KOG0994, KOG0994, KOG0994, Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]. Length = 1758 Score = 29.7 bits (66), Expect = 0.19 Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 1/42 (2%) Query: 30 ESLRMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARL 71 ++L MV+EAK+ EA + A+ +EQAN + E+SN L Sbjct: 1433 QTLSMVREAKLSASEAQQSAQRALEQAN-ASRSQMEESNREL 1473 >gnl|CDD|36831 KOG1618, KOG1618, KOG1618, Predicted phosphatase [General function prediction only]. Length = 389 Score = 29.6 bits (66), Expect = 0.20 Identities = 19/92 (20%), Positives = 39/92 (42%), Gaps = 13/92 (14%) Query: 28 RIESLRMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARLLKGLG------MDDLV 81 + +L V+ + +V+++H + VE +RV + S + +G G +D+L Sbjct: 91 ELSALLGVEVSADQVIQSHSPFRLLVEYHYKRVLVVGQGSVREVAEGYGFKNVVTVDELA 150 Query: 82 RYFMNLDSQNQAFFIDTIQNKYQDEMEELSEF 113 +YF LD F D ++ + + Sbjct: 151 KYFPLLDP-----FTDL--SRELKTTKLARDR 175 >gnl|CDD|109977 pfam00942, CBM_3, Cellulose binding domain. Length = 83 Score = 26.1 bits (58), Expect = 2.2 Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 2/25 (8%) Query: 78 DDL-VRYFMNLDS-QNQAFFIDTIQ 100 DL RY+ LD + Q F+ D Q Sbjct: 32 SDLKFRYYYTLDGNKAQGFWCDWAQ 56 >gnl|CDD|37862 KOG2651, KOG2651, KOG2651, rRNA adenine N-6-methyltransferase [RNA processing and modification]. Length = 476 Score = 26.1 bits (57), Expect = 2.3 Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 1/52 (1%) Query: 69 ARLLKGLGMDDLVRYFMNLDSQNQAFFIDTIQNKYQDEMEELSEFGEKVSDY 120 R+ + + SQ A F ++ K Q E+ LSE +SD+ Sbjct: 101 TRMQGIQTPSEFLENPSQS-SQLTALFRKHVRPKKQHEIRRLSELVSSISDF 151 >gnl|CDD|31731 COG1542, COG1542, Uncharacterized conserved protein [Function unknown]. Length = 593 Score = 25.3 bits (55), Expect = 4.1 Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 9/87 (10%) Query: 35 VKEAKMEVLEA-HKLAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRYFM-NLDSQNQ 92 + E ++ +L+A KL K++ +K E++ + +DDLV + L+S Sbjct: 282 ILEDEIRLLKAIDKLKKKHETNPAPEIKPIEKE----IKWETKIDDLVTAALYTLESFG- 336 Query: 93 AFFIDTIQNKYQDEMEELSEFGEKVSD 119 I K D L+EFGEKV + Sbjct: 337 --LIKREVVKNGDLTYVLTEFGEKVLE 361 >gnl|CDD|30536 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]. Length = 635 Score = 25.5 bits (56), Expect = 4.2 Identities = 10/32 (31%), Positives = 17/32 (53%) Query: 2 RAKTLLASTLVTTAITIIGCSLVEDNRIESLR 33 R +L + + T IT +G + +D +E LR Sbjct: 458 RLDKILKNEEIQTIITALGTGIGKDFDLEKLR 489 >gnl|CDD|35692 KOG0471, KOG0471, KOG0471, Alpha-amylase [Carbohydrate transport and metabolism]. Length = 545 Score = 25.4 bits (55), Expect = 4.3 Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 7/50 (14%) Query: 76 GMDDLVRYFMNLDSQNQAFFIDTIQNKYQDEM------EELSEFGEKVSD 119 + + +R F L+ F ID ++ + E + + GEK+ D Sbjct: 193 AIKEWLRDFW-LEKGVDGFRIDAVKGYAGENFKNMWPDEPVFDVGEKLQD 241 >gnl|CDD|146587 pfam04029, 2-ph_phosp, 2-phosphosulpholactate phosphatase. Thought to catalyse 2-phosphosulpholactate = sulpholactate + phosphate. Probable magnesium cofactor. Involved in the second step of coenzyme M biosynthesis. Inhibited by vanadate in Methanococcus jannaschii. Also known as the ComB family. Length = 231 Score = 25.2 bits (56), Expect = 4.7 Identities = 13/59 (22%), Positives = 27/59 (45%) Query: 33 RMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRYFMNLDSQN 91 ++ + E+ + + A Q N ++ S+ R LK LG++D + + LD + Sbjct: 160 LLLGLGEEELNDEARAALALYRQENDLLELLRNSSHGRRLKALGLEDDLEFCAQLDILD 218 >gnl|CDD|145014 pfam01650, Peptidase_C13, Peptidase C13 family. Members of this family are asparaginyl peptidases. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation. In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified. This has formerly been characterized as a 'haemoglobinase', but this term is probably incorrect. Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue. Both forms have been recombinantly expressed. Length = 258 Score = 24.9 bits (55), Expect = 4.9 Identities = 11/29 (37%), Positives = 16/29 (55%) Query: 40 MEVLEAHKLAKEYVEQANQRVKEAEEQSN 68 ME + H L+KE +EQ + VK S+ Sbjct: 210 MEDSDDHDLSKETLEQQFELVKNRTTGSH 238 >gnl|CDD|48129 cd03202, GST_C_etherase_LigE, GST_C family, Beta etherase LigE subfamily; composed of proteins similar to Sphingomonas paucimobilis beta etherase, LigE, a GST-like protein that catalyzes the cleavage of the beta-aryl ether linkages present in low-moleculer weight lignins using GSH as the hydrogen donor. This reaction is an essential step in the degradation of lignin, a complex phenolic polymer that is the most abundant aromatic material in the biosphere. The beta etherase activity of LigE is enantioselective and it complements the activity of the other GST family beta etherase, LigF. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains.. Length = 124 Score = 24.8 bits (54), Expect = 5.2 Identities = 13/47 (27%), Positives = 23/47 (48%) Query: 64 EEQSNARLLKGLGMDDLVRYFMNLDSQNQAFFIDTIQNKYQDEMEEL 110 E SN L+ GL + LD +QA+F + + ++ +EE+ Sbjct: 6 ERWSNTTLVPGLFPLIVPDIHDLLDPPDQAYFRQSREKRFGRSLEEV 52 >gnl|CDD|143803 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. Length = 598 Score = 24.9 bits (55), Expect = 5.8 Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 11/67 (16%) Query: 9 STLVTTAITIIGCSLVEDNRIESLRMVKEA---------KMEVLEAHKLAKEYVEQANQR 59 T ITI S + D+ IE RMVK+A + E +EA A+EYV + Sbjct: 486 GTGKEQKITITNSSGLSDDEIE--RMVKDAEEYAAEDKKRKERIEAKNEAEEYVYSLEKS 543 Query: 60 VKEAEEQ 66 +KE ++ Sbjct: 544 LKEEGDK 550 >gnl|CDD|37327 KOG2116, KOG2116, KOG2116, Protein involved in plasmid maintenance/nuclear protein involved in lipid metabolism [Cell motility, Lipid transport and metabolism]. Length = 738 Score = 24.6 bits (53), Expect = 6.4 Identities = 8/27 (29%), Positives = 15/27 (55%) Query: 85 MNLDSQNQAFFIDTIQNKYQDEMEELS 111 M L +AFF++ ++ +D +EL Sbjct: 74 MKLGDSGEAFFVEETEDDVEDVPDELL 100 >gnl|CDD|185706 cd07895, Adenylation_mRNA_capping, Adenylation domain of GTP-dependent mRNA capping enzymes. RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues. Length = 215 Score = 24.5 bits (54), Expect = 6.4 Identities = 5/17 (29%), Positives = 10/17 (58%) Query: 81 VRYFMNLDSQNQAFFID 97 VRY + + + + + ID Sbjct: 52 VRYLLLITGRGEVYLID 68 >gnl|CDD|177069 CHL00149, odpA, pyruvate dehydrogenase E1 component alpha subunit; Reviewed. Length = 341 Score = 24.4 bits (53), Expect = 6.9 Identities = 10/19 (52%), Positives = 14/19 (73%) Query: 40 MEVLEAHKLAKEYVEQANQ 58 M+VL ++AKE VE+A Q Sbjct: 229 MDVLAVREVAKEAVERARQ 247 >gnl|CDD|177000 CHL00060, atpB, ATP synthase CF1 beta subunit. Length = 494 Score = 24.2 bits (53), Expect = 7.6 Identities = 12/35 (34%), Positives = 18/35 (51%) Query: 65 EQSNARLLKGLGMDDLVRYFMNLDSQNQAFFIDTI 99 E AR+ GL + YF +++ Q+ FID I Sbjct: 237 EPPGARMRVGLTALTMAEYFRDVNKQDVLLFIDNI 271 >gnl|CDD|36143 KOG0925, KOG0925, KOG0925, mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]. Length = 699 Score = 24.1 bits (52), Expect = 9.0 Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 1/40 (2%) Query: 48 LAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRY-FMN 86 KE Q + + S LK LG+DDLV + FM+ Sbjct: 389 FEKEMQPQTYPEILRSNLSSTVLQLKKLGIDDLVHFDFMD 428 >gnl|CDD|107325 cd06330, PBP1_Arsenic_SBP_like, Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds. Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Length = 346 Score = 24.1 bits (53), Expect = 9.2 Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 2/43 (4%) Query: 50 KEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRY--FMNLDSQ 90 VE+A A + A L+GL + D Q Sbjct: 294 AAAVEKAGATDGGAPPEQIAAALEGLSFETPGGPITMRAADHQ 336 >gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases, head-to-tail. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX)D) located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, protecting and stabilizing reactive carbocation intermediates. Farnesyl diphosphate synthases produce the precursors of steroids, cholesterol, sesquiterpenes, farnsylated proteins, heme, and vitamin K12; and geranylgeranyl diphosphate and longer chain synthases produce the precursors of carotenoids, retinoids, diterpenes, geranylgeranylated chlorophylls, ubiquinone, and archaeal ether linked lipids. Isoprenyl diphosphate synthases are widely distributed among archaea, bacteria, and eukareya. Length = 259 Score = 24.0 bits (53), Expect = 9.9 Identities = 10/29 (34%), Positives = 16/29 (55%) Query: 47 KLAKEYVEQANQRVKEAEEQSNARLLKGL 75 +LA+EY E+A + +K E L+ L Sbjct: 224 ELAREYEEKALEALKALPESPAREALRAL 252 >gnl|CDD|147308 pfam05059, Orbi_VP4, Orbivirus VP4 core protein. Orbiviruses are double stranded RNA retroviruses of which the bluetongue virus is a member. The core of bluetongue virus (BTV) is a multienzyme complex composed of two major proteins (VP7 and VP3) and three minor proteins (VP1, VP4 and VP6) in addition to the viral genome. VP4 has been shown to perform all RNA capping activities and has both methyltransferase type 1 and type 2 activities associated with it. Length = 642 Score = 23.9 bits (52), Expect = 10.0 Identities = 10/18 (55%), Positives = 13/18 (72%) Query: 27 NRIESLRMVKEAKMEVLE 44 NR + LR + EAK EV+E Sbjct: 581 NREQKLRDLSEAKAEVIE 598 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 0.314 0.129 0.334 Gapped Lambda K H 0.267 0.0753 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,217,809 Number of extensions: 54255 Number of successful extensions: 265 Number of sequences better than 10.0: 1 Number of HSP's gapped: 262 Number of HSP's successfully gapped: 53 Length of query: 120 Length of database: 6,263,737 Length adjustment: 82 Effective length of query: 38 Effective length of database: 4,491,799 Effective search space: 170688362 Effective search space used: 170688362 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: 41 (21.6 bits) S2: 51 (23.4 bits)