RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781075|ref|YP_003065488.1| hypothetical protein CLIBASIA_04885 [Candidatus Liberibacter asiaticus str. psy62] (266 letters) >gnl|CDD|151372 pfam10925, DUF2680, Protein of unknown function (DUF2680). Members in this family of proteins are annotated as yckD however currently no function is known. Length = 59 Score = 31.5 bits (72), Expect = 0.24 Identities = 12/55 (21%), Positives = 30/55 (54%), Gaps = 3/55 (5%) Query: 145 EEERKALSDIQEQLLNDASKKIVFSSDREEYIGLHQKQIDLIHQNIDRHLARMKN 199 ++++K + + +Q+ + K+++ E + ++Q D I +NID+ + MK Sbjct: 3 DQQKKEIEALYKQIA-ELRKQVI--DKYVEAGVITKEQADHIKKNIDKRVEYMKQ 54 >gnl|CDD|150893 pfam10292, 7TM_GPCR_Srab, Serpentine type 7TM GPCR receptor class ab chemoreceptor. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srab is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The expression pattern of the srab genes is biologically intriguing. Of the six promoters successfully expressed in transgenic organisms, one was exclusively expressed in the tail phasmid neurons, two were exclusively expressed in a head amphid neuron, and two were expressed both in the head and tail neurons as well as a limited number of other cells. Length = 324 Score = 31.1 bits (71), Expect = 0.32 Identities = 19/107 (17%), Positives = 37/107 (34%), Gaps = 13/107 (12%) Query: 48 KRTFFCFAFFITIIYVFFPIFINFLISYIYKNIGYKISS-QYYSLTEYTWHDIETFLALL 106 R+ F + +F + I G +S Y++L E + L L Sbjct: 229 LRSITTLKIFANLDTIF--VVIQITGFLFLHFFGSSMSKPTYFALIE-----LNHCLPLY 281 Query: 107 YM-SCILVATDDRKLRMIEDGDRIIEIIQSIRRAFDQYKEEERKALS 152 + S I++ +K+R + ++ FD Y + K + Sbjct: 282 AIISIIILYRKIKKIR----VKIKTSLEAHMQADFDAYFDNFNKQWT 324 >gnl|CDD|132362 TIGR03319, YmdA_YtgF, conserved hypothetical protein YmdA/YtgF. Length = 514 Score = 30.3 bits (69), Expect = 0.55 Identities = 21/109 (19%), Positives = 46/109 (42%), Gaps = 16/109 (14%) Query: 131 EIIQSIRRAFDQYKEEERKALSDIQEQLLNDA---SKKIVFSSDREEYIGLHQKQIDLIH 187 E + +R ++ +E R L ++ +LL +K+ +EE + +K++ Sbjct: 58 EEVHKLRAELERELKERRNELQRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKE 117 Query: 188 QNIDRHLARMKNQLVAESDELEDILSRYSIESIPLDLPEMSQDEAIKYI 236 +N+D + +L E + L R S ++Q+EA + + Sbjct: 118 KNLD----EKEEELEELIAEQREELERIS---------GLTQEEAKEIL 153 >gnl|CDD|181733 PRK09259, PRK09259, putative oxalyl-CoA decarboxylase; Validated. Length = 569 Score = 29.6 bits (67), Expect = 0.84 Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 1/38 (2%) Query: 200 QLVAESDELEDILSRYSIESIPL-DLPEMSQDEAIKYI 236 LV ++ +L I + Y + IP+ DL ++Q E I+YI Sbjct: 14 HLVIDALKLNGIDTIYGVVGIPITDLARLAQAEGIRYI 51 >gnl|CDD|181632 PRK09060, PRK09060, dihydroorotase; Validated. Length = 444 Score = 29.5 bits (67), Expect = 0.97 Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 5/35 (14%) Query: 122 MIEDGDRIIEIIQSIRR--AF---DQYKEEERKAL 151 ++ED + + I+++ RR AF D+Y+ ERK L Sbjct: 160 LVEDDEGLRRILRNGRRRAAFHSEDEYRLRERKGL 194 >gnl|CDD|178869 PRK00108, mraY, phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional. Length = 344 Score = 29.3 bits (67), Expect = 1.0 Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 4/32 (12%) Query: 43 FGYFTKRTFFCF--AFFITIIYVFFPIFINFL 72 F Y T R A I++I P FI FL Sbjct: 4 FRYLTFRALLALLTALLISLI--LGPRFIRFL 33 >gnl|CDD|162694 TIGR02089, TTC, tartrate dehydrogenase. Tartrate dehydrogenase catalyzes the oxidation of both meso- and (+)-tartrate as well as a D-malate. These enzymes are closely related to the 3-isopropylmalate and isohomocitrate dehydrogenases found in TIGR00169 and TIGR02088, respectively. Length = 352 Score = 29.0 bits (65), Expect = 1.3 Identities = 19/61 (31%), Positives = 23/61 (37%), Gaps = 1/61 (1%) Query: 136 IRRAFDQYKE-EERKALSDIQEQLLNDASKKIVFSSDREEYIGLHQKQIDLIHQNIDRHL 194 IRR FDQY K L + L N F RE G + IH+ D + Sbjct: 95 IRREFDQYANVRPAKLLPGVTSPLRNCGPGDFDFVVVRENSEGEYSGVGGRIHRGTDEEV 154 Query: 195 A 195 A Sbjct: 155 A 155 >gnl|CDD|147876 pfam05960, DUF885, Bacterial protein of unknown function (DUF885). This family consists of several hypothetical bacterial proteins several of which are putative membrane proteins. Length = 536 Score = 28.8 bits (65), Expect = 1.3 Identities = 9/59 (15%), Positives = 21/59 (35%) Query: 93 EYTWHDIETFLALLYMSCILVATDDRKLRMIEDGDRIIEIIQSIRRAFDQYKEEERKAL 151 + L+ ++ +D +ED + + + +I R DQ + R+ Sbjct: 72 RPWYRYPLNQLSGAHLGLPSFLSDQAPFETVEDAEAYLARLAAIPRLLDQARANLREGA 130 >gnl|CDD|131830 TIGR02783, TrbL_P, P-type conjugative transfer protein TrbL. The TrbL protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbL is a homolog of the F-type TraG protein (which is believed to be a mating pair stabilization pore-forming protein, pfam07916) as well as the vir system VirB6 protein. Length = 298 Score = 28.9 bits (65), Expect = 1.4 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 4/72 (5%) Query: 43 FGYFTKRTFFCFAFFITIIYVFFPIFINFLISYIYKNIGYKISSQYYSLTEYTWHDIETF 102 FG F + + + V +F+ LI+ IG +Q+++ I+ Sbjct: 174 FGGSRWTRDFAWNYLKYALSVGVKLFVLTLIA----GIGSSFFAQFHTALPAGTIGIQAL 229 Query: 103 LALLYMSCILVA 114 L ++ S +++ Sbjct: 230 LVVVGASVVILG 241 >gnl|CDD|184048 PRK13428, PRK13428, F0F1 ATP synthase subunit delta; Provisional. Length = 445 Score = 28.5 bits (64), Expect = 1.9 Identities = 25/91 (27%), Positives = 37/91 (40%), Gaps = 20/91 (21%) Query: 124 EDGDRIIEIIQSIRRAFDQYKEEERK----ALSD---IQEQLLNDASKKIVFSSDRE-EY 175 DR+ E Q+ +A + K E + A D I EQL A D E E Sbjct: 46 TAADRLAEADQAHTKAVEDAKAEAARVVEEAREDAERIAEQLRAQA--------DAEAER 97 Query: 176 IGLH-QKQIDLIHQNIDRHLARMKNQLVAES 205 I + +Q+ L+ + R L + +L ES Sbjct: 98 IKVQGARQVQLLRAQLTRQL---RLELGHES 125 >gnl|CDD|182955 PRK11089, PRK11089, PTS system glucose-specific transporter subunits IIBC; Provisional. Length = 477 Score = 28.1 bits (63), Expect = 2.2 Identities = 12/36 (33%), Positives = 18/36 (50%) Query: 51 FFCFAFFITIIYVFFPIFINFLISYIYKNIGYKISS 86 FF F+ II IF ++S+I+ IG I + Sbjct: 146 FFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQT 181 >gnl|CDD|180864 PRK07168, PRK07168, bifunctional uroporphyrinogen-III methyltransferase/uroporphyrinogen-III synthase; Reviewed. Length = 474 Score = 28.0 bits (62), Expect = 2.6 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 5/72 (6%) Query: 154 IQEQLLNDA--SKKIVFSSDREEYIGLHQKQIDLIHQNIDRHLARMKNQLVAES--DELE 209 QE+L+ SK+ FSSD Y+G + +I I + I M ++ + DE+ Sbjct: 340 TQEKLMQYGLLSKEAKFSSDTTVYLGRNINRIAFIQEKIGAGSYMMTHKYTIDHRFDEVH 399 Query: 210 D-ILSRYSIESI 220 +LS + +SI Sbjct: 400 SRMLSEFLWDSI 411 >gnl|CDD|152113 pfam11677, DUF3273, Protein of unknown function (DUF3273). Some members in this family of proteins are annotated as multi-transmembrane proteins however this cannot be confirmed. Currently this family has no known function. Length = 265 Score = 27.7 bits (62), Expect = 2.8 Identities = 15/85 (17%), Positives = 28/85 (32%), Gaps = 10/85 (11%) Query: 37 HLLRDDFGYFTKRTFFCFAFFITIIYVFFPIFINFLISYIYKNIG--YKISSQYYSLTEY 94 + LR F + + I + ++S+ + K+ S ++ Sbjct: 22 YNLRSGF------LLQLLSLTLLFISYWS-GGGLGILSFDLYALPESVKVGSAFFLSI-S 73 Query: 95 TWHDIETFLALLYMSCILVATDDRK 119 H LL MS ++ DD K Sbjct: 74 LLHGGYLLGTLLIMSFQVLLADDSK 98 >gnl|CDD|149633 pfam08644, SPT16, FACT complex subunit (SPT16/CDC68). Proteins in this family are subunits the FACT complex. The FACT complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin. Length = 152 Score = 28.0 bits (63), Expect = 2.9 Identities = 11/44 (25%), Positives = 23/44 (52%), Gaps = 4/44 (9%) Query: 129 IIEIIQSIRRAFDQYKEEERKALSDI--QEQL-LNDASKKIVFS 169 + + I+ +++ + +E ERK +D+ QE+L LN + Sbjct: 83 VFKAIKELQKRVKK-RETERKEKADVVEQEKLILNRNKRPPRLK 125 >gnl|CDD|183402 PRK12284, PRK12284, tryptophanyl-tRNA synthetase; Reviewed. Length = 431 Score = 27.7 bits (62), Expect = 2.9 Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 3/28 (10%) Query: 188 QNIDRHLARMK---NQLVAESDELEDIL 212 + IDR LA M+ L+A ++EDIL Sbjct: 280 ERIDRELAPMRERYEALIARPADIEDIL 307 >gnl|CDD|180186 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated. Length = 619 Score = 27.8 bits (63), Expect = 3.0 Identities = 10/65 (15%), Positives = 31/65 (47%), Gaps = 5/65 (7%) Query: 124 EDGDRIIEIIQSIRRAFDQYKE--EERKALSDIQEQLLNDASKKIVFSSDREEYIGLHQK 181 E ++++E +++ + + + ++ E++ Q + +K+ + + + L K Sbjct: 215 ELPEKVLEKFKALAKQYKKLRKAQEKKVEGRLAQHKKYAKLREKLK---EELKSLRLTSK 271 Query: 182 QIDLI 186 QID + Sbjct: 272 QIDEL 276 >gnl|CDD|129888 TIGR00806, rfc, RFC reduced folate carrier. Proteins of the RFC family are so-far restricted to animals. RFC proteins possess 12 putative transmembrane a-helical spanners (TMSs) and evidence for a 12 TMS topology has been published for the human RFC. The RFC transporters appear to transport reduced folate by an energy-dependent, pH-dependent, Na+-independent mechanism. Folate:H+ symport, folate:OH- antiport and folate:anion antiport mechanisms have been proposed, but the energetic mechanism is not well defined. Length = 511 Score = 27.5 bits (61), Expect = 3.4 Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 5/62 (8%) Query: 60 IIYVFFPIFINFLISYIYKNIGYKISSQYYSLTEYTWHDIETFLALLYMSCI-LVATDDR 118 + YV F FL+ I +S + +L I TF+A + I V +D R Sbjct: 358 VTYVLFRGIYQFLVPIATFQIASSLSKELCALV----FGINTFVATALKTIITAVVSDKR 413 Query: 119 KL 120 L Sbjct: 414 GL 415 >gnl|CDD|172952 PRK14477, PRK14477, bifunctional nitrogenase molybdenum-cofactor biosynthesis protein NifE/NifN; Provisional. Length = 917 Score = 27.4 bits (61), Expect = 3.5 Identities = 11/22 (50%), Positives = 14/22 (63%) Query: 212 LSRYSIESIPLDLPEMSQDEAI 233 LSR+ ESI L+ MS+ AI Sbjct: 531 LSRHFKESIALNTTAMSEVTAI 552 >gnl|CDD|147793 pfam05832, DUF846, Eukaryotic protein of unknown function (DUF846). This family consists of several of unknown function from a variety of eukaryotic organisms. Length = 140 Score = 27.6 bits (62), Expect = 3.8 Identities = 6/27 (22%), Positives = 13/27 (48%) Query: 50 TFFCFAFFITIIYVFFPIFINFLISYI 76 F ++Y+ +F NF++ +I Sbjct: 10 FHLLFKLLAILLYLLGGLFSNFILQFI 36 >gnl|CDD|151461 pfam11014, DUF2852, Protein of unknown function (DUF2852). This bacterial family of proteins has no known function. Length = 115 Score = 27.2 bits (61), Expect = 4.0 Identities = 7/20 (35%), Positives = 11/20 (55%) Query: 138 RAFDQYKEEERKALSDIQEQ 157 AFD+Y+ E + L + Q Sbjct: 70 EAFDEYRAETLRRLEEEQRA 89 >gnl|CDD|179718 PRK04028, PRK04028, glutamyl-tRNA(Gln) amidotransferase subunit E; Validated. Length = 630 Score = 27.1 bits (61), Expect = 4.3 Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 5/43 (11%) Query: 111 ILVATDDRKLRMIEDGDRIIEIIQSIRRAFDQYKEEERKALSD 153 ILVA ++ K + +I+ + A + EE R AL D Sbjct: 376 ILVADEEEKAEKALE-----AVIERAKEALEGVPEETRGALPD 413 >gnl|CDD|165201 PHA02867, PHA02867, C-type lectin protein; Provisional. Length = 167 Score = 27.0 bits (59), Expect = 5.4 Identities = 10/65 (15%), Positives = 19/65 (29%), Gaps = 12/65 (18%) Query: 45 YFTKRTFFCFAFFITIIYVFFPIFINFLIS--YIYKN---------IGYKISSQYYSLTE 93 + + + F I + Y + IGY Y+++ E Sbjct: 9 VSEVSCYAITVLG-ILCLILFTILVVVTCKWYYAFPYFSKVCPDEWIGYNSKCYYFTINE 67 Query: 94 YTWHD 98 W+D Sbjct: 68 TNWND 72 >gnl|CDD|165227 PHA02909, PHA02909, hypothetical protein; Provisional. Length = 72 Score = 26.8 bits (59), Expect = 5.5 Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 5/45 (11%) Query: 38 LLRDDFG-----YFTKRTFFCFAFFITIIYVFFPIFINFLISYIY 77 +L D+G Y+T+ TF FI + +F +F SY+Y Sbjct: 14 MLSVDYGNGKKVYYTENTFCIMVSFILFVIIFLSMFTILACSYVY 58 >gnl|CDD|152563 pfam12128, DUF3584, Protein of unknown function (DUF3584). This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. There are two conserved sequence motifs: GKT and YLP. Length = 1192 Score = 26.9 bits (60), Expect = 6.2 Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 22/92 (23%) Query: 122 MIEDGDRIIEIIQSIRRAFDQ----YKEEERKALSDIQEQLLNDASKKIVFSSDREEYIG 177 + D + Q I+R +++ KE+ + L + REE Sbjct: 362 VEARLDLLTGKHQDIQRKYERRKQKIKEQLERDLEKNNARRAA----------IREE--- 408 Query: 178 LHQKQIDLIHQNIDRHLARMKNQLVAESDELE 209 I+ L+ +++QL + + L+ Sbjct: 409 -----KARQKAAIEEALSALESQLRQQLEALK 435 >gnl|CDD|149949 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal. Length = 426 Score = 26.7 bits (59), Expect = 6.2 Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 3/63 (4%) Query: 134 QSIRRAFDQYKEEERKALSDIQEQLLNDASKKIVFSSDREEYIGLHQKQIDLIHQNIDRH 193 + +RRA + K ER+ L + S + EE L K +DL Q ++ Sbjct: 7 KKLRRALKKAKGFERQKLGRRIKNAEKKKSDNDKLARIEEEIEAL--KTLDL-DQLAKKY 63 Query: 194 LAR 196 L Sbjct: 64 LFS 66 >gnl|CDD|162068 TIGR00852, pts-Glc, PTS system, maltose and glucose-specific subfamily, IIC component. permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the E. coli PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-cellobiose (ASC), trehalose (Tre), putative glucoside (Glv) and sucrose (Scr) permeases of E. coli. Most, but not all Scr permeases of other bacteria also lack a IIA domain. This model is specific for the IIC domain of the Glc family PTS transporters. Length = 289 Score = 26.5 bits (59), Expect = 7.0 Identities = 18/98 (18%), Positives = 31/98 (31%), Gaps = 17/98 (17%) Query: 2 WERIANTIVATSKKWSFLFAILSPTEVYNVHRRIWHLLRDDFGYFTKRT-----FFCFAF 56 W +A + IL +H R + K+ FF Sbjct: 50 WGNFFGFEIAKVGYTGVVGPILVGAIALALHER----------FLDKKLPDVLGFFLGPR 99 Query: 57 FITIIYVFFPIFINFLISYIYKNIGYKISSQYYSLTEY 94 F+ II F I + + ++ +G IS+ + L Sbjct: 100 FVVIIAGFVAILLIGPLGRVWPPVG--ISALLHWLYSA 135 >gnl|CDD|178902 PRK00149, dnaA, chromosomal replication initiation protein; Reviewed. Length = 450 Score = 26.7 bits (60), Expect = 7.3 Identities = 32/133 (24%), Positives = 58/133 (43%), Gaps = 39/133 (29%) Query: 129 IIEIIQSIRR-AFDQYKEEERKA----LSDIQ---------EQL------LNDASKKIVF 168 + + ++R +++KE+ R + DIQ E+ L++A K+IV Sbjct: 190 TNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVL 249 Query: 169 SSDREEYIGLHQKQIDLIHQNIDRHLARMKNQLVA--ESDELED---ILSRYSIESIPLD 223 +SDR K++ + +R +R + L E +LE IL + E +D Sbjct: 250 TSDR------PPKELPGLE---ERLRSRFEWGLTVDIEPPDLETRIAIL-KKKAEEEGID 299 Query: 224 LPEMSQDEAIKYI 236 LP DE +++I Sbjct: 300 LP----DEVLEFI 308 >gnl|CDD|152507 pfam12072, DUF3552, Domain of unknown function (DUF3552). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with pfam00013, pfam01966. This domain has a single completely conserved residue A that may be functionally important. Length = 201 Score = 26.4 bits (59), Expect = 8.2 Identities = 19/109 (17%), Positives = 43/109 (39%), Gaps = 16/109 (14%) Query: 131 EIIQSIRRAFDQYKEEERKALSDIQEQLL---NDASKKIVFSSDREEYIGLHQKQIDLIH 187 E I +R ++ +E R L +++LL +K +EE + +K++ Sbjct: 60 EEIHKLRAEAERELKERRNELQRQEKRLLQKEETLDRKDESLEKKEESLEEKEKELAARQ 119 Query: 188 QNIDRHLARMKNQLVAESDELEDILSRYSIESIPLDLPEMSQDEAIKYI 236 Q ++ ++ + + ELE I ++ +EA + + Sbjct: 120 QQLEEKEEELEELIEEQQQELERI-------------SGLTAEEAKEIL 155 >gnl|CDD|151445 pfam10998, DUF2838, Protein of unknown function (DUF2838). This bacterial family of proteins has no known function. Length = 111 Score = 26.1 bits (58), Expect = 8.6 Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 3/42 (7%) Query: 17 SFLFAILSPTEVYNVHRRIWHLLRDDFGYFTKRTFFCFAFFI 58 + L+ P Y ++ +H D YF F FI Sbjct: 31 TVLYFYFMPIRFYTYRKKGYHYFLADLCYF---VNFLLLLFI 69 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.326 0.141 0.418 Gapped Lambda K H 0.267 0.0769 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,531,069 Number of extensions: 303775 Number of successful extensions: 1379 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1369 Number of HSP's successfully gapped: 109 Length of query: 266 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 174 Effective length of database: 4,006,537 Effective search space: 697137438 Effective search space used: 697137438 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 56 (25.3 bits)