RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780571|ref|YP_003064984.1| hypothetical protein CLIBASIA_02290 [Candidatus Liberibacter asiaticus str. psy62] (182 letters) >gnl|CDD|149078 pfam07811, TadE, TadE-like protein. The members of this family are similar to a region of the protein product of the bacterial tadE locus. In various bacterial species, the tad locus is closely linked to flp-like genes, which encode proteins required for the production of pili involved in adherence to surfaces. It is thought that the tad loci encode proteins that act to assemble or export an Flp pilus in various bacteria. All tad loci but TadA have putative transmembrane regions, and in fact the region in question is this family has a high proportion of hydrophobic amino acid residues. Length = 43 Score = 39.7 bits (94), Expect = 5e-04 Identities = 12/42 (28%), Positives = 24/42 (57%), Gaps = 1/42 (2%) Query: 17 GVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMG 58 G AVE A++LP+LLL+ + E+ ++++ + A+ Sbjct: 1 GAAAVEFALVLPVLLLLLFGIVELG-RLFYARQVLQNAAREA 41 >gnl|CDD|183508 PRK12408, PRK12408, glucokinase; Provisional. Length = 336 Score = 30.1 bits (68), Expect = 0.32 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 9/75 (12%) Query: 8 ILRFLSRENGVVAVEMAIILPILLLIYMAVYEI---TMLYTLSKRLTRFASHMGDMVAQE 64 +L+ L R V +E + P LL +Y A+ + T ++ +T A D +A E Sbjct: 191 LLQHLLRTRTHVPIEHVLSGPGLLNLYRALCALRGATPVHASPAAITAAALAGDDALAHE 250 Query: 65 TSINKQYLQGFENFL 79 LQ F FL Sbjct: 251 A------LQVFCGFL 259 >gnl|CDD|131469 TIGR02416, CO_dehy_Mo_lg, carbon-monoxide dehydrogenase, large subunit. This model represents the large subunits of group of carbon-monoxide dehydrogenases that include molybdenum as part of the enzymatic cofactor. There are various forms of carbon-monoxide dehydrogenase; Salicibacter pomeroyi DSS-3, for example, has two forms. Note that, at least in some species, the active site Cys is modified with a selenium attached to (rather than replacing) the sulfur atom. This is termed selanylcysteine, and created post-translationally, in contrast to selenocysteine incorporation during translation as for many other selenoproteins. Length = 770 Score = 29.9 bits (67), Expect = 0.45 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 4/49 (8%) Query: 44 YTLSKRLTR---FASHMGDMVAQETSINKQYLQGFENFLRATMYPYRTP 89 Y S R+T D +AQ ++ L+ +NF++ +PY P Sbjct: 358 YRCSFRVTEAVYAIERAVDTLAQRLEMDSADLR-IKNFIQPEQFPYTAP 405 >gnl|CDD|183189 PRK11546, zraP, zinc resistance protein; Provisional. Length = 143 Score = 27.1 bits (60), Expect = 2.9 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 11/90 (12%) Query: 98 YWLDNKQIVRKMWNWSSSNVKVEREDIPASIKD---ASTFIVRAEVS---INYRTLVFSK 151 +W MW +++ + E++ I + A T +R ++ Y L+ + Sbjct: 29 HWGGGH----GMWQQNAAPLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLTAN 84 Query: 152 ILPDSLKGDIVLRKVYYYRQRLGDQIVCRD 181 PDS K + V +++ RQ L + V RD Sbjct: 85 P-PDSSKINAVAKEMENLRQSLDELRVKRD 113 >gnl|CDD|162834 TIGR02391, hypoth_ymh, conserved hypothetical protein TIGR02391. This family consists of a relatively rare (~ 8 occurrences per 200 genomes) prokaryotic protein family. Genes for members are appear to be associated variously with phage and plasmid regions, restriction system loci, transposons, and housekeeping genes. The function is unknown. Length = 125 Score = 27.0 bits (60), Expect = 3.1 Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 9/61 (14%) Query: 36 AVYEITMLYTLSKRLTR--FASHMGDMVA-----QETSINKQYLQGFENFLRATMYPYRT 88 + E+T L F+S V E +Q +G N L + +R Sbjct: 32 KIRELTGDSLDGVELIDQAFSSKNNPKVGGNLLQTEAEQGEQ--EGLSNLLAGAITGFRN 89 Query: 89 P 89 P Sbjct: 90 P 90 >gnl|CDD|152009 pfam11573, Med23, Mediator complex subunit 23. Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice. Length = 1341 Score = 26.7 bits (59), Expect = 3.8 Identities = 37/198 (18%), Positives = 60/198 (30%), Gaps = 64/198 (32%) Query: 1 MKCIKNYILRFLSRENGVVAVEMAIILPILLLI----------YMAVYEITMLY------ 44 MK I LRF + + ++ + ++L I Y + EI L+ Sbjct: 144 MKYILEKALRFPYSVSPEIVPQLLAVEEVILHIFDRNANLLPAYFTLNEIMRLHPYQAAM 203 Query: 45 ---TLSKRLTRFASHMGDMVAQETSINKQYLQGFENFLRATMYPYRTPNHSIIVTGYWLD 101 L+ L + +AQ SI G R++M P HS Y Sbjct: 204 PPWRLTNLLANLSEEF-RPIAQMLSI-----CG-----RSSMLP--IVEHS----SYA-- 244 Query: 102 NKQIVRKMWNWSSSNVKVEREDIPASIKDASTFIVRAEVSINYRTLVFSKILPDSLKGDI 161 NW + D + F ++ + YR + L Sbjct: 245 -----DNTSNW-------WKLDP-----NTLKFELQGNHKLPYRPELLEPQLY------- 280 Query: 162 VLRKVYYYRQRLGDQIVC 179 +LR Y Q ++C Sbjct: 281 LLR--YVLEQPYSRDMLC 296 >gnl|CDD|184750 PRK14568, vanB, D-alanine--D-lactate ligase; Provisional. Length = 343 Score = 26.2 bits (58), Expect = 4.5 Identities = 10/31 (32%), Positives = 18/31 (58%) Query: 118 KVEREDIPASIKDASTFIVRAEVSINYRTLV 148 ++ +E+ P + ST IV A++S R+ V Sbjct: 242 RIHQENEPEKGSENSTIIVPADISAEERSRV 272 >gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein MsbA. This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes. Length = 571 Score = 25.4 bits (56), Expect = 9.2 Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 9/53 (16%) Query: 23 MAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQETSINKQYLQGF 75 + ++LP+L ++ V SKRL R + + + + Q T++ ++ LQG+ Sbjct: 160 VVVMLPVLSILMRRV---------SKRLRRISKEIQNSMGQVTTVAEETLQGY 203 >gnl|CDD|162277 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor regulator (CFTR). The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se. Length = 1490 Score = 25.3 bits (55), Expect = 9.8 Identities = 24/108 (22%), Positives = 44/108 (40%), Gaps = 21/108 (19%) Query: 75 FENFLRATMYPYRTP-----NHSIIVTGYWLDNKQIVRKMWNWSSSNVKVEREDIPASIK 129 F+ L M PYR + + +T ++N Q V K + W + E I +I+ Sbjct: 237 FQACLGQKMMPYRDKRAGKISERLAITSEIIENIQSV-KAYCWEEA-----MEKIIKNIR 290 Query: 130 DASTFIVRAEVSINYRT----------LVFSKILPDSLKGDIVLRKVY 167 + R + Y +VF ++P +L I+LR+++ Sbjct: 291 QDELKLTRKIAYLRYFYSSAFFFSGFFVVFLSVVPYALIKGIILRRIF 338 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 0.138 0.411 Gapped Lambda K H 0.267 0.0590 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,946,526 Number of extensions: 174247 Number of successful extensions: 426 Number of sequences better than 10.0: 1 Number of HSP's gapped: 426 Number of HSP's successfully gapped: 19 Length of query: 182 Length of database: 5,994,473 Length adjustment: 87 Effective length of query: 95 Effective length of database: 4,114,577 Effective search space: 390884815 Effective search space used: 390884815 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: 54 (24.9 bits)