RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781214|ref|YP_003065627.1| hypothetical protein CLIBASIA_05605 [Candidatus Liberibacter asiaticus str. psy62] (110 letters) >gnl|CDD|36350 KOG1135, KOG1135, KOG1135, mRNA cleavage and polyadenylation factor II complex, subunit CFT2 (CPSF subunit) [RNA processing and modification]. Length = 764 Score = 30.3 bits (68), Expect = 0.12 Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 3/48 (6%) Query: 46 DTIGGFFGSSQKEGKKEEEGVR---PLEGDELAEVRRQESLRAYEMNR 90 T+ S + K+ E VR LEG+EL E E LR + R Sbjct: 359 GTLARELISMPERAKRIELKVRKRVKLEGEELLEYLEGERLRNEDALR 406 >gnl|CDD|144263 pfam00606, Glycoprotein_B, Herpesvirus Glycoprotein B. This family of proteins contains a transmembrane region. Length = 711 Score = 27.9 bits (63), Expect = 0.67 Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 5/37 (13%) Query: 20 LGSIF---GPVGGVIGGLMGGAAGLYSEWDTIGGFFG 53 L F G VG +G ++ G AG + G Sbjct: 625 LDDFFQGLGAVGKAVGNVVSGVAGAVG--SIVSGVVS 659 >gnl|CDD|109790 pfam00747, Viral_DNA_bp, ssDNA binding protein. This protein is found in herpesviruses and is needed for replication. Length = 1111 Score = 26.6 bits (59), Expect = 1.8 Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 1/48 (2%) Query: 33 GLMGGAAGLYSEWDTIGGFFGSSQKEGKKEEEGVRPLEGDEL-AEVRR 79 G+ + Y++ D +G F E K + E + D A V R Sbjct: 507 GVFTTMSRAYNDCDVLGNFARRYALEKKDDGEAAKADMQDTYRASVER 554 >gnl|CDD|133006 cd02513, CMP-NeuAc_Synthase, CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety. CMP-N-acetylneuraminic acid synthetase (CMP-NeuAc synthetase) or acylneuraminate cytidylyltransferase catalyzes the transfer the CMP moiety of CTP to the anomeric hydroxyl group of NeuAc in the presence of Mg++. It is the second to last step in the sialylation of the oligosaccharide component of glycoconjugates by providing the activated sugar-nucleotide cytidine 5'-monophosphate N-acetylneuraminic acid (CMP-Neu5Ac), the substrate for sialyltransferases. Eukaryotic CMP-NeuAc synthetases are predominantly located in the nucleus. The activated CMP-Neu5Ac diffuses from the nucleus into the cytoplasm. Length = 223 Score = 26.0 bits (58), Expect = 2.3 Identities = 9/34 (26%), Positives = 15/34 (44%) Query: 56 QKEGKKEEEGVRPLEGDELAEVRRQESLRAYEMN 89 + ++ G+ P+ E RRQ+ AY N Sbjct: 142 WRALGLDDNGLEPVNYPEDKRTRRQDLPPAYHEN 175 >gnl|CDD|34102 COG4395, COG4395, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 281 Score = 26.1 bits (57), Expect = 2.4 Identities = 11/26 (42%), Positives = 13/26 (50%) Query: 28 GGVIGGLMGGAAGLYSEWDTIGGFFG 53 G++GGL GG S G FFG Sbjct: 30 SGMLGGLAGGLLMGLSGMFFGGLFFG 55 >gnl|CDD|145626 pfam02585, PIG-L, GlcNAc-PI de-N-acetylase. Members of this family are related to PIG-L an N-acetylglucosaminylphosphatidylinositol de-N-acetylase (EC:3.5.1.89) that catalyses the second step in GPI biosynthesis. Length = 111 Score = 26.1 bits (58), Expect = 2.4 Identities = 7/18 (38%), Positives = 11/18 (61%) Query: 68 PLEGDELAEVRRQESLRA 85 L +EL +RR+E+ A Sbjct: 40 GLSPEELGAIRRREARAA 57 >gnl|CDD|29406 cd02111, eukary_SO_Moco, molybdopterin binding domain of sulfite oxidase (SO). SO catalyzes the terminal reaction in the oxidative degradation of the sulfur-containing amino acids cysteine and methionine. Common features of all known members of the sulfite oxidase (SO) family of molybdopterin binding domains are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate.. Length = 365 Score = 26.1 bits (57), Expect = 2.5 Identities = 8/18 (44%), Positives = 10/18 (55%) Query: 79 RQESLRAYEMNRIPIPAR 96 + L AYEMN P+P Sbjct: 161 EADVLLAYEMNGTPLPRD 178 >gnl|CDD|146831 pfam04391, DUF533, Protein of unknown function (DUF533). Some family members may be secreted or integral membrane proteins. Length = 187 Score = 25.6 bits (57), Expect = 2.7 Identities = 11/24 (45%), Positives = 15/24 (62%) Query: 17 GFKLGSIFGPVGGVIGGLMGGAAG 40 G LG G +GG++G L+GG G Sbjct: 1 GDLLGGGGGGLGGLLGALLGGKKG 24 >gnl|CDD|133122 cd06591, GH31_xylosidase_XylS, XylS is a glycosyl hydrolase family 31 (GH31) alpha-xylosidase found in prokaryotes, eukaryotes, and archaea, that catalyzes the release of alpha-xylose from the non-reducing terminal side of the alpha-xyloside substrate. XylS has been characterized in Sulfolobus solfataricus where it hydrolyzes isoprimeverose, the p-nitrophenyl-beta derivative of isoprimeverose, and xyloglucan oligosaccharides, and has transxylosidic activity. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. The XylS family corresponds to subgroup 3 in the Ernst et al classification of GH31 enzymes. Length = 319 Score = 25.7 bits (57), Expect = 3.0 Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 4/37 (10%) Query: 30 VIGGLMGGAAGL-YSEWDT-IGGFFGSSQKEGKKEEE 64 + GL G +G+ + W T IGGFF + G + E Sbjct: 241 IAAGLNMGLSGIPW--WTTDIGGFFVGNPPAGLDDPE 275 >gnl|CDD|177107 MTH00028, COX3, cytochrome c oxidase subunit III; Provisional. Length = 297 Score = 25.4 bits (55), Expect = 3.6 Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 12/75 (16%) Query: 10 FGSSLSSGFKLGSIFGPVG------------GVIGGLMGGAAGLYSEWDTIGGFFGSSQK 57 F SSL+ +LGS++ P G L GA ++ IG +S + Sbjct: 102 FHSSLAPSVELGSVWPPKGIEALDPFAVPLLNTTILLSSGATVTWAHHAIIGTGNPASLE 161 Query: 58 EGKKEEEGVRPLEGD 72 +G + EG P G Sbjct: 162 KGTQGIEGPNPSNGA 176 >gnl|CDD|39042 KOG3838, KOG3838, KOG3838, Mannose lectin ERGIC-53, involved in glycoprotein traffic [Intracellular trafficking, secretion, and vesicular transport]. Length = 497 Score = 25.3 bits (55), Expect = 4.2 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 4/44 (9%) Query: 29 GVIGGLMGGAAGLYSEWDTIGGFFGSSQKEGKKEEEGVRPLEGD 72 G +G + GG W+ IG FF S +G+K + L D Sbjct: 121 GHVGPVFGGLD----SWNGIGIFFDSFDNDGQKNNPAISVLLND 160 >gnl|CDD|145952 pfam03073, TspO_MBR, TspO/MBR family. Tryptophan-rich sensory protein (TspO) is an integral membrane protein that acts as a negative regulator of the expression of specific photosynthesis genes in response to oxygen/light. It is involved in the efflux of porphyrin intermediates from the cell. This reduces the activity of coproporphyrinogen III oxidase, which is thought to lead to the accumulation of a putative repressor molecule that inhibits the expression of specific photosynthesis genes. Several conserved aromatic residues are necessary for TspO function: they are thought to be involved in binding porphyrin intermediates. In, the rat mitochondrial peripheral benzodiazepine receptor (MBR) was shown to not only retain its structure within a bacterial outer membrane, but also to be able to functionally substitute for TspO in TspO- mutants, and to act in a similar manner to TspO in its in situ location: the outer mitochondrial membrane. The biological significance of MBR remains unclear, however. It is thought to be involved in a variety of cellular functions, including cholesterol transport in steroidogenic tissues. Length = 144 Score = 24.8 bits (55), Expect = 5.2 Identities = 11/21 (52%), Positives = 13/21 (61%) Query: 21 GSIFGPVGGVIGGLMGGAAGL 41 +FGPV V+ LMG AA L Sbjct: 36 NWVFGPVWTVLYILMGIAAYL 56 >gnl|CDD|32224 COG2041, COG2041, Sulfite oxidase and related enzymes [General function prediction only]. Length = 271 Score = 24.6 bits (53), Expect = 6.3 Identities = 9/25 (36%), Positives = 12/25 (48%) Query: 70 EGDELAEVRRQESLRAYEMNRIPIP 94 G L + +L AY MN P+P Sbjct: 172 TGLPLDDALHPLTLLAYGMNGEPLP 196 >gnl|CDD|146715 pfam04226, Transgly_assoc, Transglycosylase associated protein. Bacterial protein, predicted to be an integral membrane protein. Some family members have been annotated as transglycosylase associated proteins, but no experimental evidence is provided. This family was annotated based on the information in Eschericha coli ymge. Length = 48 Score = 24.3 bits (54), Expect = 7.1 Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 1/32 (3%) Query: 23 IFGPVGGVIGGLMGGAAGLYSEWDTIGGFFGS 54 I G VG +GG + G G Y + +GG + Sbjct: 2 ILGIVGAFVGGFLFGLLGPYGGGE-LGGLIPA 32 >gnl|CDD|32559 COG2431, COG2431, Predicted membrane protein [Function unknown]. Length = 297 Score = 24.4 bits (53), Expect = 7.8 Identities = 10/42 (23%), Positives = 19/42 (45%) Query: 3 FLDSSVKFGSSLSSGFKLGSIFGPVGGVIGGLMGGAAGLYSE 44 LD + G +++SGF S+ G + G + G+ + Sbjct: 186 LLDLPLTTGLAMASGFGWYSLSGILLTEAYGPVLGSIAFLNN 227 >gnl|CDD|145216 pfam01925, TauE, Sulfite exporter TauE/SafE. This is a family of integral membrane proteins where the alignment appears to contain two duplicated modules of three transmembrane helices. The proteins are involved in the transport of anions across the cytoplasmic membrane during taurine metabolism as an exporter of sulfoacetate. This family used to be known as DUF81. Length = 236 Score = 24.1 bits (53), Expect = 8.0 Identities = 9/40 (22%), Positives = 12/40 (30%) Query: 1 MSFLDSSVKFGSSLSSGFKLGSIFGPVGGVIGGLMGGAAG 40 M S G + G + G + GL G G Sbjct: 108 MLLRPRLAAAASRRPPGALALLLAGGLIGFLSGLFGIGGG 147 >gnl|CDD|35045 COG5486, COG5486, Predicted metal-binding integral membrane protein [Function unknown]. Length = 283 Score = 24.2 bits (52), Expect = 8.2 Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%) Query: 14 LSSGFKLGSIFGPVGGVIGGLMGGAAGLYSEWDTI 48 L + LG I P+ G+ GGL AGLY ++ T+ Sbjct: 150 LHAFALLGPILSPLSGLAGGLTLLVAGLY-QFTTL 183 >gnl|CDD|36750 KOG1537, KOG1537, KOG1537, Homoserine kinase [Amino acid transport and metabolism]. Length = 355 Score = 24.3 bits (52), Expect = 8.2 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 5/70 (7%) Query: 11 GSSLSSGFKLGSIFGPVGGVIGGLMGGAAGLYSEWDTI-----GGFFGSSQKEGKKEEEG 65 G++ +G +L + +G G ++ + + D GGF GS + + E Sbjct: 113 GTAKMAGVRLVNESADLGLSKGSMLDYSLMIERHPDNAVAEMMGGFLGSFLRALLESEAK 172 Query: 66 VRPLEGDELA 75 V D + Sbjct: 173 VSGYHADNIL 182 >gnl|CDD|147783 pfam05818, TraT, Enterobacterial TraT complement resistance protein. The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between an Escherichia coli and its surroundings. Length = 215 Score = 24.3 bits (53), Expect = 8.7 Identities = 12/42 (28%), Positives = 18/42 (42%) Query: 12 SSLSSGFKLGSIFGPVGGVIGGLMGGAAGLYSEWDTIGGFFG 53 S+LS+G+ + +G +G G AG GG G Sbjct: 81 SALSTGYGGAAAGAALGAAVGAYNSGGAGAALGVGLAGGLVG 122 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 0.137 0.390 Gapped Lambda K H 0.267 0.0700 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,325,756 Number of extensions: 64043 Number of successful extensions: 255 Number of sequences better than 10.0: 1 Number of HSP's gapped: 250 Number of HSP's successfully gapped: 43 Length of query: 110 Length of database: 6,263,737 Length adjustment: 76 Effective length of query: 34 Effective length of database: 4,621,453 Effective search space: 157129402 Effective search space used: 157129402 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 (23.5 bits)