RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= 537021.9.peg.788_1 (270 letters) >gnl|CDD|162764 TIGR02212, lolCE, lipoprotein releasing system, transmembrane protein, LolC/E family. This model describes the LolC protein, and its paralog LolE found in some species. These proteins are homologous to permease proteins of ABC transporters. In some species, two paralogs occur, designated LolC and LolE. In others, a single form is found and tends to be designated LolC. Length = 411 Score = 233 bits (596), Expect = 4e-62 Identities = 95/262 (36%), Positives = 145/262 (55%), Gaps = 3/262 (1%) Query: 6 RFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGIN 65 + +A RYL + R+N F+S S S IG+ +GV ALIVV+SVMNGF ++++R+LG+ Sbjct: 1 PLSLFIALRYLRAKRRNRFVSFISLFSIIGIALGVAALIVVLSVMNGFERELLQRILGVI 60 Query: 66 GHVVIQQKYYPLVDYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSD 125 H +I+ K P++D+Q + R+ P V P VSGQA V + SGV VRG+ SD Sbjct: 61 PHAIIESKQNPIIDWQELLERILKNPGVKAAAPIVSGQALVQS-AGKVSGVQVRGVDPSD 119 Query: 126 FSYLQNSFSRFYGNVSNDFDRGK-GVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGI 184 L + F G+ +IIG+ LA LG+S+GDKI ++SP +VTP G Sbjct: 120 EDKLSAISNNVKQGALKGFKPGEYNIIIGEQLAEKLGVSVGDKITLISPESNVTPFGEIP 179 Query: 185 RSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTHENI 244 R K +TV+G+F + D + M L++AQ + + V+G+ + + DP + + + Sbjct: 180 RQKRFTVIGIFSTGG-EVDGYLALMPLEDAQRFLRYGDQVTGLRLKLDDPFQADALAQQV 238 Query: 245 VRILGNGVVVIDWQQRYQIFFS 266 LG + V DW + FS Sbjct: 239 EPELGPELYVRDWTDQNGELFS 260 >gnl|CDD|182995 PRK11146, PRK11146, outer membrane-specific lipoprotein transporter subunit LolE; Provisional. Length = 412 Score = 103 bits (258), Expect = 7e-23 Identities = 67/263 (25%), Positives = 118/263 (44%), Gaps = 25/263 (9%) Query: 11 VAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVI 70 + R+ R+ +S+ S IS IG+ +GV LIV +S MNGF ++ R+L + H I Sbjct: 7 IGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRILAVVPHGEI 66 Query: 71 QQKYYPLVDYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGS---GVLVRGISNSDFS 127 + P ++Q R+ +P + P+V+ +GL G+ V V+G+ Sbjct: 67 EAVNQPFTNWQEALARVQKVPGIAAAAPYVN----FTGLVENGAKLKAVQVKGVDPQ--- 119 Query: 128 YLQNSFSRFYGNVSND----FDRGK-GVIIGKDLARNLGISIGDKINILSPYGDVTPMGM 182 + S V ND F G+ +I+GK +A L + GD + ++ P + + Sbjct: 120 -QEQRVSALPSFVQNDAWQNFKAGEQQIILGKGVADALKVKQGDWVTLMIPNSNPDHKLL 178 Query: 183 GIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTHE 242 + V G+ ++ D+ + + L +AQ Y ++ ++V+GI + V D K Sbjct: 179 QPKRVRLQVAGILQLS-GQLDHSLALIPLADAQQYLDMGDSVTGIALKVTDVFNANK--- 234 Query: 243 NIVRILGNG----VVVIDWQQRY 261 +VR G V + W Y Sbjct: 235 -LVRDAGEVTNSYVYIKSWIGTY 256 >gnl|CDD|131268 TIGR02213, lolE_release, lipoprotein releasing system, transmembrane protein LolE. This protein is part of an unusual ABC transporter complex that releases lipoproteins from the periplasmic side of the bacterial inner membrane, rather than transport any substrate across the inner membrane. In some species, the permease-like transmembrane protein is represented by two paralogs, LolC and LolE, both in the LolCDE complex. This family consists of LolE, as found in E. coli and related species. Length = 411 Score = 100 bits (250), Expect = 4e-22 Identities = 65/257 (25%), Positives = 118/257 (45%), Gaps = 11/257 (4%) Query: 10 IVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVV 69 ++ WR+ ++N +S+ S S IG+ +GV LIV +S MNGF ++ +R+L + H Sbjct: 5 LIGWRFSRGKQRNPMVSLISKFSTIGIALGVAVLIVGLSAMNGFERELNQRILAVVPHAE 64 Query: 70 IQQKYYPLVDYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGS---GVLVRGISNSDF 126 I+ P+ ++Q + RL P + P+VS +GL GS V V+G+ Sbjct: 65 IESVPPPIHNWQNLEKRLQQNPQIKAAAPYVS----FTGLVENGSKLKAVQVKGV-EPQA 119 Query: 127 SYLQNSFSRFY-GNVSNDFDRGKG-VIIGKDLARNLGISIGDKINILSPYGDVTPMGMGI 184 +S F N F++G+G +I+G +A+ L + +GD + +L P + Sbjct: 120 EQKVSSIGNFVQEQAWNKFEKGEGQLILGSGVAKELDVKVGDWVTLLIPQQNGDEKFAQP 179 Query: 185 RSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTHENI 244 + V G+ R+ D+ + L +AQ Y + V+GI + + D ++ Sbjct: 180 KRVRVQVTGILRLD-GQLDHSYALLPLADAQQYLTYGDQVTGIALKLDDVFNARNLVRSM 238 Query: 245 VRILGNGVVVIDWQQRY 261 V + W ++ Sbjct: 239 GNDYPQYVYMQSWISKF 255 >gnl|CDD|182753 PRK10814, PRK10814, outer membrane-specific lipoprotein transporter subunit LolC; Provisional. Length = 399 Score = 88.2 bits (219), Expect = 2e-18 Identities = 72/257 (28%), Positives = 126/257 (49%), Gaps = 16/257 (6%) Query: 14 RYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQK 73 RY+ + F S++S IG+ +GVMAL+ V+SVMNGF ++ +LG+ +I + Sbjct: 12 RYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNILGLMPQAIITSE 71 Query: 74 YYPLVDYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSF 133 + L Q A+ L + V ++ P +G + S GV++ GI + L Sbjct: 72 HGSLNPQQLPASALK-LDGVNRIAPLTTGDVVLQSARSVAVGVML-GIDPAQKDPL---- 125 Query: 134 SRFYGNVS-NDFDRGK-GVIIGKDLARNLGISIGDKINILSP-YGDVTPMGMGIRSKSYT 190 + + NV D GK VI+G+ LA LG+ GD+I ++ P TPMG + +T Sbjct: 126 TPYLVNVKQTDLQPGKYNVILGEQLAGQLGVKRGDQIRLMVPSASQFTPMGRIPSQRLFT 185 Query: 191 VLGMFRMRFPDYDNGMVYMSLQEAQ--LYFNLENAVSGIEVFVKDPDAIEKTHENIVRIL 248 V+G F + D + ++ Q+A + + N ++G +++ +P ++ + + L Sbjct: 186 VIGTFAAN-SEVDGYQMLVNQQDASRLMRYPAGN-ITGWRLWLDEPLKVDSLSQ---QKL 240 Query: 249 GNGVVVIDWQQRYQIFF 265 G V DW++R F Sbjct: 241 PEGTVWKDWRERKGELF 257 >gnl|CDD|147920 pfam06021, Gly_acyl_tr_N, Aralkyl acyl-CoA:amino acid N-acyltransferase. This family consists of several mammalian specific aralkyl acyl-CoA:amino acid N-acyltransferase (glycine N-acyltransferase) proteins EC:2.3.1.13. Length = 205 Score = 29.0 bits (65), Expect = 1.4 Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 10/66 (15%) Query: 198 RFPDYDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTHENIVRILGNGVVVIDW 257 ++PD++ V + QE ++ +L++ + +V+ KDP ++ LG+ V I+W Sbjct: 48 KWPDFN--TVVIRPQEQEMTDDLDHYTNTYQVYSKDPKKCQE-------FLGSSEV-INW 97 Query: 258 QQRYQI 263 +Q QI Sbjct: 98 KQHLQI 103 >gnl|CDD|163029 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid synthase PfaA. Members of the seed for this alignment are involved in omega-3 polyunsaturated fatty acid biosynthesis, such as the protein PfaA from the eicosapentaenoic acid biosynthesis operon in Photobacterium profundum strain SS9. PfaA is encoded together with PfaB, PfaC, and PfaD, and the functions of the individual polypeptides have not yet been described. More distant homologs of PfaA, also included with the reach of this model, appear to be involved in polyketide-like biosynthetic mechanisms of polyunsaturated fatty acid biosynthesis, an alternative to the more familiar iterated mechanism of chain extension and desaturation, and in most cases are encoded near genes for homologs of PfaB, PfaC, and/or PfaD. Length = 2582 Score = 28.0 bits (62), Expect = 2.3 Identities = 31/119 (26%), Positives = 50/119 (42%), Gaps = 28/119 (23%) Query: 40 VMALIVVMSVMN------GFREDMIKRVLGINGHVVIQQKYYPLVDYQFIANRLDFIPDV 93 +++L+V V+N G+ D I LG+ G Q++ L RL + P + Sbjct: 95 LLSLVVAKEVLNDAGLPDGYDRDKIGITLGVGGG---QKQSSSL------NARLQY-PVL 144 Query: 94 IKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNV-----SNDFDRG 147 KV SG+ S +L++ + + +NSF GNV +N FD G Sbjct: 145 KKVFK-------ASGVEDEDSEMLIKKFQDQYIHWEENSFPGSLGNVISGRIANRFDLG 196 >gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733 Score = 27.9 bits (62), Expect = 2.7 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 3/54 (5%) Query: 120 GISNSDFSYLQNSFSRFYGNVSNDF--DRGKGVI-IGKDLARNLGISIGDKINI 170 G+ DF ++ V D G+G+I + L N G++IGD + + Sbjct: 30 GVEPGDFVEIEKGDRSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTV 83 >gnl|CDD|162554 TIGR01840, esterase_phb, esterase, PHB depolymerase family. This model describes a subfamily among lipases of the ab-hydrolase family. This subfamily includes bacterial depolymerases for poly(3-hydroxybutyrate) (PHB) and related polyhydroxyalkanoates (PHA), as well as acetyl xylan esterases, feruloyl esterases, and others from fungi. Length = 212 Score = 27.8 bits (62), Expect = 3.3 Identities = 9/24 (37%), Positives = 14/24 (58%) Query: 103 QAFVSGLSSGGSGVLVRGISNSDF 126 + +V+GLS+GG V G + D Sbjct: 96 RVYVTGLSAGGGMTAVLGCTYPDV 119 >gnl|CDD|117906 pfam09364, XFP_N, XFP N-terminal domain. Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.22. This family is distantly related to transketolases e.g. pfam02779. Length = 379 Score = 27.4 bits (61), Expect = 3.9 Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 7/41 (17%) Query: 105 FVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDFD 145 +V G GG ++ SYL+ S+S FY ++ D + Sbjct: 76 YVVGPGHGGPAMVSP-------SYLEGSYSEFYPEITFDEE 109 >gnl|CDD|181450 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated. Length = 819 Score = 27.4 bits (61), Expect = 4.4 Identities = 10/58 (17%), Positives = 25/58 (43%), Gaps = 2/58 (3%) Query: 123 NSDFSYLQNSFSRF--YGNVSNDFDRGKGVIIGKDLARNLGISIGDKINILSPYGDVT 178 YL N ++F + N + + + G+ + + + L + GD + + ++T Sbjct: 720 IGINIYLANPITQFNNFTNKAENLNEKAGLYVSEAFLKKLNLKDGDNVTLKKEEEELT 777 >gnl|CDD|152078 pfam11642, Blo-t-5, Mite allergen Blo t 5. This family of proteins is Blo t 5, an allergen protein from Blomia tropicalis mites. This protein shoes strong reactivity with IgE in asthmatic and rhinitis patients. The structure of the protein contains three alpha helices which form a coiled-coil. Length = 112 Score = 27.0 bits (60), Expect = 5.2 Identities = 8/22 (36%), Positives = 13/22 (59%) Query: 218 FNLENAVSGIEVFVKDPDAIEK 239 FN E A++ +V +KD + K Sbjct: 83 FNFEAALATGKVLLKDLKELAK 104 >gnl|CDD|183542 PRK12465, PRK12465, xylose isomerase; Provisional. Length = 445 Score = 26.9 bits (59), Expect = 5.2 Identities = 19/48 (39%), Positives = 22/48 (45%) Query: 156 LARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYD 203 LAR+ G SIG K N L + PM S TV+G R D D Sbjct: 223 LARDYGRSIGFKGNFLIEPKPMEPMKHQYDFDSATVIGFLRQHGLDQD 270 >gnl|CDD|185385 PRK15488, PRK15488, thiosulfate reductase PhsA; Provisional. Length = 759 Score = 26.6 bits (59), Expect = 6.9 Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 9/42 (21%) Query: 150 VIIGKDLARNLGISIGDKINILSPYGD------VTPMGMGIR 185 V I A LGI GD+I + + G VTP GIR Sbjct: 668 VWIHPQTAGKLGIKNGDEIRLENSVGKEKGKALVTP---GIR 706 >gnl|CDD|178542 PLN02956, PLN02956, PSII-Q subunit. Length = 185 Score = 26.3 bits (58), Expect = 8.4 Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 2/35 (5%) Query: 216 LYFNLENAVSGIEVFVKDPDA--IEKTHENIVRIL 248 LY +L N+V+ ++ +D D + + +ENIV L Sbjct: 144 LYSDLFNSVTKLDYAARDKDETRVWEYYENIVASL 178 >gnl|CDD|185160 PRK15248, PRK15248, fimbrial outer membrane usher protein StbC; Provisional. Length = 853 Score = 26.3 bits (58), Expect = 8.6 Identities = 9/27 (33%), Positives = 15/27 (55%) Query: 168 INILSPYGDVTPMGMGIRSKSYTVLGM 194 I++ P G + PMG + + T +GM Sbjct: 773 ISVKMPDGGIPPMGADVFNGEGTNIGM 799 >gnl|CDD|149560 pfam08547, CIA30, Complex I intermediate-associated protein 30 (CIA30). This protein is associated with mitochondrial Complex I intermediate-associated protein 30 (CIA30) in human and mouse. The family is also present in Schizosaccharomyces pombe which does not contain the NADH dehydrogenase component of complex I, or many of the other essential subunits. This means it is possible that this family of protein may not be directly involved in oxidative phosphorylation. Length = 161 Score = 26.4 bits (59), Expect = 8.6 Identities = 7/22 (31%), Positives = 11/22 (50%) Query: 120 GISNSDFSYLQNSFSRFYGNVS 141 G+S S + + F GN+S Sbjct: 22 GVSTSSLQLSPDGTAVFSGNLS 43 >gnl|CDD|182528 PRK10535, PRK10535, macrolide transporter ATP-binding /permease protein; Provisional. Length = 648 Score = 26.2 bits (58), Expect = 8.9 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%) Query: 24 FISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQ 72 F+++ + IS + IGVM +++V SV RE I+ +G V+QQ Sbjct: 524 FLTLVAVISLVVGGIGVMNIMLV-SVTERTREIGIRMAVGARASDVLQQ 571 >gnl|CDD|162815 TIGR02349, DnaJ_bact, chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family. Length = 354 Score = 26.0 bits (58), Expect = 9.7 Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 4/64 (6%) Query: 102 GQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDFDRGK--GVIIGKDLARN 159 G A +G GG G G F + F F+G R + G G+DL + Sbjct: 65 GHAGFNG-GGGGGGGGFNGFDIGFFGDFGDIFGDFFGG-GGGSGRRRRSGPRRGEDLRYD 122 Query: 160 LGIS 163 L ++ Sbjct: 123 LELT 126 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 0.143 0.419 Gapped Lambda K H 0.267 0.0760 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,711,929 Number of extensions: 319772 Number of successful extensions: 1002 Number of sequences better than 10.0: 1 Number of HSP's gapped: 994 Number of HSP's successfully gapped: 40 Length of query: 270 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 178 Effective length of database: 4,006,537 Effective search space: 713163586 Effective search space used: 713163586 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 (21.6 bits) S2: 56 (25.3 bits)