RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780477|ref|YP_003064890.1| DSBA oxidoreductase [Candidatus Liberibacter asiaticus str. psy62] (232 letters) >gnl|CDD|31837 COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]. Length = 244 Score = 96.0 bits (238), Expect = 7e-21 Identities = 54/180 (30%), Positives = 72/180 (40%), Gaps = 10/180 (5%) Query: 52 PSTMKDVSIGQKDAPVTMVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFPLD 111 KDV +G APVT+VE+ TC +C E + L+ KYI GK+R +LREFP Sbjct: 71 TPDGKDVVLGNPYAPVTVVEFFDYTCPYCKEAFPE----LKKKYIDDGKVRLVLREFPFL 126 Query: 112 S----VSTVAVMLARCAEKRMDGGYWGFVSLLFNKQDDWINSKNYRDALLNMAKFAGFSK 167 A ARCA + YW F LF Q + + L A A Sbjct: 127 DPACPYCRRAAQAARCAADQGIVRYWAFHDALFGSQAEAWAASILCAKDLAKADLAAL-D 185 Query: 168 NDFDTCLNDQNILDDIKAGKKRASEDFAIDSTPVFFIGGNLYLGDMSEGVFSKIIDSMIQ 227 LN + I K A + ++ TP F + G L G IID ++ Sbjct: 186 EGKKAKLNQKACDALIAKNYKLA-QQLGVNGTPTFIVNGKLVPGLPDLDELKAIIDEALK 244 >gnl|CDD|48572 cd03023, DsbA_Com1_like, DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.. Length = 154 Score = 56.3 bits (136), Expect = 6e-09 Identities = 42/164 (25%), Positives = 65/164 (39%), Gaps = 11/164 (6%) Query: 61 GQKDAPVTMVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFP-LDSVSTVAVM 119 G + VT+VE+ C +C K LE + +R + +EFP L S +A Sbjct: 1 GNPNGDVTIVEFFDYNCGYCK----KLAPELEKLLKEDPDVRVVFKEFPILGESSVLAAR 56 Query: 120 LARCAEKRMDGGYWGFVSLLFNKQDDWINSKNYRDALLNMAKFAGFSKNDFDTCLNDQNI 179 +A K G Y F + L + ++LL +AK AG + ++D I Sbjct: 57 VALAVWKNGPGKYLEFHNALMAT-----RGRLNEESLLRIAKKAGLDEAKLKKDMDDPEI 111 Query: 180 LDDIKAGKKRASEDFAIDSTPVFFIGGNLYLGDMSEGVFSKIID 223 I ++ A I TP F IG + G + + ID Sbjct: 112 EATIDKNRQLA-RALGITGTPAFIIGDTVIPGAVPADTLKEAID 154 >gnl|CDD|73335 cd02972, DsbA_family, DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins.. Length = 98 Score = 39.7 bits (92), Expect = 6e-04 Identities = 20/80 (25%), Positives = 29/80 (36%), Gaps = 9/80 (11%) Query: 69 MVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFPLDSV----STVAVMLARCA 124 +VE+ C +C F + K L Y G +R + R FPL S A A A Sbjct: 1 IVEFFDPLCPYCYLFEPELEKLL---YADDGGVRVVYRPFPLLGGMPPNSLAAARAALAA 57 Query: 125 EKRMDGGYWGFVSLLFNKQD 144 + G + L + Sbjct: 58 AAQ--GKFEALHEALADTAL 75 >gnl|CDD|48568 cd03019, DsbA_DsbA, DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.. Length = 178 Score = 36.4 bits (84), Expect = 0.006 Identities = 29/179 (16%), Positives = 60/179 (33%), Gaps = 23/179 (12%) Query: 58 VSIGQKDAPVTMVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFPLDSVSTVA 117 +S ++E+ S C HC F +++ + P+ Sbjct: 8 LSPPIPSGKPEVIEFFSYGCPHCYNFEP---ILEAWVKKLPKDVKF--EKVPVVFGGGEG 62 Query: 118 VMLARC--------AEKRMDGGYWGFVSLLFNKQDDWINSKNYRDALLNMAKFAGFSKND 169 LAR E ++ + + K+ ++ + R L+ G K Sbjct: 63 EPLARAFYAAEALGLEDKLHAALFEAI---HEKRKRLLDPDDIRKIFLS----QGVDKKK 115 Query: 170 FDTCLNDQNILDDIKAGKKRASEDFAIDSTPVFFIGGNLYLGDMSEGVFS--KIIDSMI 226 FD N ++ + +K A + + I P F + G + + G +++D +I Sbjct: 116 FDAAYNSFSVKALVAKAEKLA-KKYKITGVPAFVVNGKYVVNPSAIGGDDTLQVLDELI 173 >gnl|CDD|39778 KOG4578, KOG4578, KOG4578, Uncharacterized conserved protein, contains KAZAL and TY domains [General function prediction only]. Length = 421 Score = 30.0 bits (67), Expect = 0.59 Identities = 28/119 (23%), Positives = 38/119 (31%), Gaps = 14/119 (11%) Query: 66 PVTMVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFPLDSVSTVAVMLARCA- 124 P T Y C A K K L LD++ T VM A Sbjct: 264 PGTSTRYGKPKCEETARTAVDPKKVRRLNGCPEKKKTEFLTSL-LDALKTDMVMSGINAS 322 Query: 125 --------EKRMDGGYWGFVSLLFNKQDDWINS--KNYRDALLNMAKFAGFSKNDFDTC 173 E+R+ +W F L N +D K ++ LL +K S+ F C Sbjct: 323 NGRKSEPDEERV--VHWYFNQLDKNSNNDIERREWKPFKRVLLKKSKPRKCSRKFFKYC 379 >gnl|CDD|37090 KOG1879, KOG1879, KOG1879, UDP-glucose:glycoprotein glucosyltransferase [Carbohydrate transport and metabolism]. Length = 1470 Score = 28.0 bits (62), Expect = 2.2 Identities = 12/53 (22%), Positives = 16/53 (30%), Gaps = 5/53 (9%) Query: 57 DVSIGQKDAPVTMVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFP 109 V G + Y + FH K K GK+ Y+ R F Sbjct: 162 HVVPGSNTESPVAILYGELGTIDFRNFHKLLEKL-----AKNGKINYVFRHFL 209 >gnl|CDD|38644 KOG3434, KOG3434, KOG3434, 60S ribosomal protein L22 [Translation, ribosomal structure and biogenesis]. Length = 125 Score = 27.2 bits (60), Expect = 3.6 Identities = 21/73 (28%), Positives = 29/73 (39%), Gaps = 2/73 (2%) Query: 36 PIPDGVVDFRALLAASPSTMKDVS-IGQKDAPVTMVEYASMTCFHC-AEFHNKTFKYLED 93 P+ DG++D L +K +G VT+ S F + KYL Sbjct: 27 PVEDGILDIADLEKFLQERIKVNGKVGNLGNVVTIERSKSKITVVSTVHFSKRYLKYLTK 86 Query: 94 KYIKTGKLRYILR 106 KY+K LR LR Sbjct: 87 KYLKKNNLRDWLR 99 >gnl|CDD|33703 COG3917, NahD, 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]. Length = 203 Score = 27.2 bits (60), Expect = 3.8 Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 1/58 (1%) Query: 154 DALLNMAKFAGFSKNDFDTCLNDQNILDDIKAGKKRASEDFAIDSTPVFFIGGNLYLG 211 + + +A AG L D I +KA A + P F +G L+ G Sbjct: 133 EVVYAVANAAGLDGAALLALLGDDEIKARLKANTAEAVSR-GVFGAPTFIVGDQLFWG 189 >gnl|CDD|29489 cd02865, Heme_Cu_Oxidase_III_2, Heme-copper oxidase subunit III subfamily. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The heme-copper oxidase superfamily is diverse in terms of electron donors, subunit composition, and heme types. This superfamily includes cytochrome c and ubiquinol oxidases. Bacterial oxidases typically contain 3 or 4 subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunits I, II and III of ubiquinol oxidase are homologous to the corresponding subunits in CcO. Although not required for catalytic activity, subunit III is believed to play a role in assembly of the multimer complex. Rhodobacter CcO subunit III stabilizes the integrity of the binuclear center in subunit I. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria.. Length = 184 Score = 27.2 bits (60), Expect = 4.4 Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 2/50 (4%) Query: 8 IGVLGGIVLLFIASYFFYTRKGSALNELPIPDGVVDF--RALLAASPSTM 55 + V G + L I++YF G P+P + A+LAAS M Sbjct: 17 MAVEGTLFALLISAYFMRMTSGDWQPGAPLPLPNLLSLNTAVLAASSVAM 66 >gnl|CDD|31616 COG1427, COG1427, Predicted periplasmic solute-binding protein [General function prediction only]. Length = 252 Score = 26.8 bits (59), Expect = 5.5 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 2/54 (3%) Query: 32 LNELPIPDGVVDFRALLAASPSTM-KDVSIGQKD-APVTMVEYASMTCFHCAEF 83 +N LP+ G+ ++ A PS + + + G+ D A V+ V YA Sbjct: 12 INSLPLFLGLEQRERVVKAVPSELNELLLSGRIDAALVSSVAYAEDDLKLLPGL 65 >gnl|CDD|48072 cd01968, Nitrogenase_NifE_I, Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN. NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The NifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this NifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).. Length = 410 Score = 26.7 bits (59), Expect = 5.7 Identities = 15/31 (48%), Positives = 16/31 (51%), Gaps = 3/31 (9%) Query: 179 ILDDIKAGKKRASEDFAIDSTPV---FFIGG 206 I DDI A K ASE F I PV F+G Sbjct: 101 IGDDIDAVCKTASEKFGIPVIPVHSPGFVGN 131 >gnl|CDD|32194 COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]. Length = 222 Score = 26.2 bits (58), Expect = 7.7 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 4/55 (7%) Query: 1 MVMSTTRIGVLGGIVLLFIASYFFYTRK-GSALNELPIPDGVVDFRALLAASPST 54 +++ T+ IG IV L I + F R SAL E + GV++ + ASP Sbjct: 86 LIVGTS-IGTTAAIVPLTIGAAPFVARLVESALRE--VDKGVIEAAQAMGASPWQ 137 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 0.323 0.138 0.410 Gapped Lambda K H 0.267 0.0681 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,777,452 Number of extensions: 142069 Number of successful extensions: 394 Number of sequences better than 10.0: 1 Number of HSP's gapped: 388 Number of HSP's successfully gapped: 16 Length of query: 232 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 141 Effective length of database: 4,297,318 Effective search space: 605921838 Effective search space used: 605921838 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 56 (25.4 bits)