RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= 537021.9.peg.788_1 (270 letters) >gnl|CDD|34229 COG4591, LolE, ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]. Length = 408 Score = 195 bits (498), Expect = 7e-51 Identities = 97/267 (36%), Positives = 151/267 (56%), Gaps = 7/267 (2%) Query: 3 IFSRFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVL 62 +F E+ +A RYL + RK FISI S +S IG+ +GV LIVV+SVMNGF++++ R+L Sbjct: 1 MFMPLELFIALRYLRA-RKRRFISIISALSLIGIALGVAVLIVVLSVMNGFQKELENRIL 59 Query: 63 GINGHVVIQQKYYPLVDYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGIS 122 G+N HV I + P+ DY+ + + P V P++ GQA + + SGVLVRG+ Sbjct: 60 GVNPHVQITPEDGPIDDYRELIKLILKNPGVKAASPYIEGQALLQS-GNNSSGVLVRGVD 118 Query: 123 NSDFSYLQNSFSRFYGNVSNDFDRGK-GVIIGKDLARNLGISIGDKINILSPYGDVTPMG 181 D S +D G+ G+I+G LA LG+ +GDK+ +++P + P G Sbjct: 119 PKDE-DKSAISSFLKDGSEDDLKPGEFGIILGSGLAEKLGVRVGDKVTLITPESNT-PFG 176 Query: 182 MGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLE-NAVSGIEVFVKDPDAIEKT 240 G R K +TV+G+F + D + Y+ L++AQ FNL V+GI + +KDP E+ Sbjct: 177 RGPRQKRFTVVGIFSTGLSELDESLAYIPLEDAQNLFNLPKGVVTGIRLKLKDPFNAEEL 236 Query: 241 HENI-VRILGNGVVVIDWQQRYQIFFS 266 + + +L G+ DW+++ FFS Sbjct: 237 KRKLEIELLPQGLKAKDWREQNGEFFS 263 >gnl|CDD|38054 KOG2843, KOG2843, KOG2843, Fumarylacetoacetase [Carbohydrate transport and metabolism]. Length = 420 Score = 31.1 bits (70), Expect = 0.32 Identities = 35/112 (31%), Positives = 47/112 (41%), Gaps = 15/112 (13%) Query: 157 ARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMR-----FPDYDNGMVYMSL 211 A N+GI K N L P P+G R+ S V G R PD V+ + Sbjct: 134 ATNVGIMFRGKENALMPNWRHLPVGYHGRASSVVVSGTPIRRPLGQTKPDDAEKPVFGAC 193 Query: 212 QEAQLYFNLENA--VSGIEVFVKDPDAIEKTHENIVRILGNGVVVI-DWQQR 260 + L F LE A V G + +P I+K +NI G V++ DW R Sbjct: 194 K--LLDFELEMAFFVGGPGNQLGEPIPIDKAWKNIF-----GFVLMNDWSAR 238 >gnl|CDD|33190 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]. Length = 978 Score = 29.1 bits (65), Expect = 1.1 Identities = 10/29 (34%), Positives = 16/29 (55%) Query: 150 VIIGKDLARNLGISIGDKINILSPYGDVT 178 V I +LA GI GD + + S +G++ Sbjct: 857 VEISPELAAERGIEDGDLVRLTSEFGEIK 885 >gnl|CDD|37768 KOG2557, KOG2557, KOG2557, Uncharacterized conserved protein, contains TLDc domain [Function unknown]. Length = 427 Score = 28.5 bits (63), Expect = 1.9 Identities = 10/48 (20%), Positives = 22/48 (45%), Gaps = 4/48 (8%) Query: 7 FEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFR 54 V W+ L+S+ + SF +F+G G+ ++++ G+ Sbjct: 229 HHERVEWKLLYSSSVHG----QSFSTFLGHTSGMGPSVLIIKDTEGYV 272 >gnl|CDD|145483 pfam02359, CDC48_N, Cell division protein 48 (CDC48), N-terminal domain. This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a substrate 185-residue recognition domain. Length = 87 Score = 28.7 bits (65), Expect = 2.0 Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 2/34 (5%) Query: 145 DRGKGVI-IGKDLARNLGISIGDKINILSPYGDV 177 D G G+I + +N G+SIGD++ + P DV Sbjct: 55 DEGPGIIRMDGVQRKNAGVSIGDEVTV-RPAEDV 87 >gnl|CDD|30310 cd02778, MopB_CT_Thiosulfate-R-like, The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.. Length = 123 Score = 28.3 bits (63), Expect = 2.4 Identities = 11/30 (36%), Positives = 16/30 (53%) Query: 149 GVIIGKDLARNLGISIGDKINILSPYGDVT 178 + I + A LGI GD++ + S G VT Sbjct: 31 TLWINPETAARLGIKDGDRVEVSSARGKVT 60 >gnl|CDD|30324 cd02792, MopB_CT_Formate-Dh-Na-like, Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.. Length = 122 Score = 27.8 bits (62), Expect = 3.2 Identities = 11/28 (39%), Positives = 15/28 (53%) Query: 150 VIIGKDLARNLGISIGDKINILSPYGDV 177 V I +LA GI GD + + SP G + Sbjct: 37 VEISPELAAERGIKNGDMVWVSSPRGKI 64 >gnl|CDD|30306 cd00508, MopB_CT_Fdh-Nap-like, This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.. Length = 120 Score = 27.8 bits (62), Expect = 3.3 Identities = 11/29 (37%), Positives = 14/29 (48%) Query: 150 VIIGKDLARNLGISIGDKINILSPYGDVT 178 V I + A LGI GD + + S G V Sbjct: 37 VEIHPEDAARLGIKDGDLVRVSSRRGSVV 65 >gnl|CDD|30307 cd02775, MopB_CT, Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is the eukaryotic/eubacterial protein domain family of the 75-kDa subunit/Nad11/NuoG (second domain) of respiratory complex 1/NADH-quinone oxidoreductase which is postulated to have lost an ancestral formate dehydrogenase activity and only vestigial sequence evidence remains of a molybdopterin binding site. This hierarchy is of the conserved MopB_CT domain present in many, but not all, MopB homologs.. Length = 101 Score = 27.7 bits (61), Expect = 3.9 Identities = 11/29 (37%), Positives = 14/29 (48%) Query: 150 VIIGKDLARNLGISIGDKINILSPYGDVT 178 V I + A LGI GD + + S G V Sbjct: 25 VEINPEDAAALGIKDGDLVRVESRRGSVV 53 >gnl|CDD|147621 pfam05544, Pro_racemase, Proline racemase. This family consists of proline racemase (EC 5.1.1.4) proteins which catalyse the interconversion of L- and D-proline in bacteria. This family also contains several similar eukaryotic proteins including a sequence with B-cell mitogenic properties which has been characterized as a co-factor-independent proline racemase. Length = 325 Score = 26.5 bits (59), Expect = 8.7 Identities = 5/26 (19%), Positives = 14/26 (53%) Query: 86 RLDFIPDVIKVLPFVSGQAFVSGLSS 111 + ++P +SG+A+++G + Sbjct: 286 GETEVGGRPAIVPSISGRAWITGTNQ 311 >gnl|CDD|145241 pfam01959, DHQS, 3-dehydroquinate synthase (EC 4.6.1.3). 3-Dehydroquinate synthase is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides. Length = 343 Score = 26.5 bits (59), Expect = 8.7 Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 1/32 (3%) Query: 210 SLQEAQLYFN-LENAVSGIEVFVKDPDAIEKT 240 S +EA+L LE V G+ + DP+ I+ Sbjct: 121 SAEEAKLALETLEKGVDGVLLDPDDPNEIKAI 152 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 0.326 0.143 0.419 Gapped Lambda K H 0.267 0.0782 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,488,967 Number of extensions: 197451 Number of successful extensions: 793 Number of sequences better than 10.0: 1 Number of HSP's gapped: 788 Number of HSP's successfully gapped: 34 Length of query: 270 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 178 Effective length of database: 4,275,709 Effective search space: 761076202 Effective search space used: 761076202 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: 57 (25.6 bits)