RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780416|ref|YP_003064829.1| putative ferredoxin protein [Candidatus Liberibacter asiaticus str. psy62] (113 letters) >gnl|CDD|152388 pfam11953, DUF3470, Domain of unknown function (DUF3470). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 50 amino acids in length. This domain is found associated with pfam00037. This domain has a single completely conserved residue N that may be functionally important. Length = 49 Score = 64.5 bits (158), Expect = 5e-12 Identities = 23/50 (46%), Positives = 32/50 (64%), Gaps = 2/50 (4%) Query: 58 DTEPGLEL-WLKINSEYATQWPNITTKKESLPSAAKMDGVKQKYEKYFSP 106 D PG + ++++N+E A +WPNIT KK+ LP A + DGV K E Y S Sbjct: 1 DDLPGDQEKFIELNAELAKKWPNITEKKDPLPDAEEWDGVPDKLE-YLSR 49 >gnl|CDD|162616 TIGR01944, rnfB, electron transport complex, RnfABCDGE type, B subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit. Length = 165 Score = 44.0 bits (104), Expect = 8e-06 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 3/55 (5%) Query: 3 YVVTENCILCKHTDCVEVCPVDCFYEGENFL-AIHPDECIDCGVCEPECPVDAIK 56 + +NCI C T C++ CPVD + + DEC C +C CP D I+ Sbjct: 109 LIDEDNCIGC--TKCIQACPVDAIVGAAKAMHTVIADECTGCDLCVEPCPTDCIE 161 >gnl|CDD|131747 TIGR02700, flavo_MJ0208, archaeoflavoprotein, MJ0208 family. This model describes one of two paralogous families of archaealflavoprotein. The other, described by TIGR02699 and typified by the partially characterized AF1518 of Archaeoglobus fulgidus, is a homodimeric FMN-containing flavoprotein that accepts electrons from ferredoxin and can transfer them to various oxidoreductases. The function of this protein family is unknown. Length = 234 Score = 40.2 bits (94), Expect = 1e-04 Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 1/46 (2%) Query: 12 CKHTD-CVEVCPVDCFYEGENFLAIHPDECIDCGVCEPECPVDAIK 56 CK CV+ CP + I +C+ CG C+ CP +AI Sbjct: 150 CKGCGICVDACPRSAIDMVDGKAFIRLLKCVGCGKCKEACPYNAIH 195 Score = 26.0 bits (57), Expect = 2.0 Identities = 17/43 (39%), Positives = 18/43 (41%), Gaps = 7/43 (16%) Query: 18 VEVCPVDCFYEGENFLAIHP-----DECIDCGVCEPECPVDAI 55 V V PVD YE I P C CG+C CP AI Sbjct: 125 VWVVPVD--YEEGIIRTITPYMIDRKRCKGCGICVDACPRSAI 165 >gnl|CDD|181550 PRK08764, PRK08764, ferredoxin; Provisional. Length = 135 Score = 39.9 bits (93), Expect = 2e-04 Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 3/57 (5%) Query: 1 MTYVVTENCILCKHTDCVEVCPVDCFYEGENFL-AIHPDECIDCGVCEPECPVDAIK 56 + ++V +CI C T C++ CPVD G + + C C +C P CPVD I+ Sbjct: 79 VAWIVEADCIGC--TKCIQACPVDAIVGGAKHMHTVIAPLCTGCELCVPACPVDCIE 133 >gnl|CDD|182135 PRK09898, PRK09898, hypothetical protein; Provisional. Length = 208 Score = 39.4 bits (92), Expect = 2e-04 Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 2/48 (4%) Query: 6 TENCILCKHTDCVEVCPVDCFYEGENFLAIHPDE--CIDCGVCEPECP 51 + C CK C+ VCP+ + I D CI C C CP Sbjct: 120 ADTCRQCKEPQCMNVCPIGAITWQQKEGCITVDHKRCIGCSACTTACP 167 >gnl|CDD|179124 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D; Provisional. Length = 263 Score = 39.5 bits (93), Expect = 2e-04 Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 3/59 (5%) Query: 5 VTENCILCKHTDCVEVCPVDCFYEGENFLAIH-PDECIDCGVCEPECPVDAIKPDTEPG 62 V+E+C C+ CVE CP E L + C C +CE CP AI+ + Sbjct: 167 VSEDCDECE--KCVEACPRGVLELKEGKLVVTDLLNCSLCKLCERACPGKAIRVSDDEN 223 >gnl|CDD|162631 TIGR01971, NuoI, NADH-quinone oxidoreductase, chain I. This model represents the I subunit (one of 14: A->N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes "I" subunits from the closely related F420H2 dehydrogenase and formate hydrogenlyase complexes. Length = 122 Score = 39.3 bits (92), Expect = 2e-04 Identities = 26/60 (43%), Positives = 29/60 (48%), Gaps = 12/60 (20%) Query: 7 ENCILCKHTDCVEVCPVDCF----YEGEN------FLAIHPDECIDCGVCEPECPVDAIK 56 E CI C T C VCP D EGE+ F I+ CI CG+CE CP DAI Sbjct: 43 EKCIGC--TLCAAVCPADAIRVVPAEGEDGKRRLKFYQINFGRCIFCGLCEEACPTDAIV 100 Score = 33.5 bits (77), Expect = 0.011 Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 3/39 (7%) Query: 27 YEGENFLAIHP---DECIDCGVCEPECPVDAIKPDTEPG 62 + G L P ++CI C +C CP DAI+ G Sbjct: 29 FRGRIVLTRDPNGEEKCIGCTLCAAVCPADAIRVVPAEG 67 Score = 30.8 bits (70), Expect = 0.077 Identities = 9/24 (37%), Positives = 9/24 (37%), Gaps = 2/24 (8%) Query: 9 CILCKHTDCVEVCPVDCFYEGENF 32 CI C C E CP D F Sbjct: 84 CIFCGL--CEEACPTDAIVLTPEF 105 >gnl|CDD|163201 TIGR03287, methan_mark_16, putative methanogenesis marker 16 metalloprotein. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This protein is a predicted to bind FeS clusters, based on the presence of two copies of the Fer4 domain (pfam00037), with each copy having four Cys residues invariant across all members. Length = 391 Score = 39.4 bits (92), Expect = 2e-04 Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 3/53 (5%) Query: 7 ENCILCKHTDCVEVCPVDCFYEGENFLAIHPDECIDCGVCEPECPVDAIKPDT 59 E C C E CPV + ++ ++C CG C CP A + + Sbjct: 302 ERCENCDPCLVEEACPVPAIKKDGT---LNTEDCFGCGYCAEICPGGAFEVNL 351 Score = 36.7 bits (85), Expect = 0.001 Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 2/33 (6%) Query: 35 IHPDECIDCGVCEPE--CPVDAIKPDTEPGLEL 65 +P+ C +C C E CPV AIK D E Sbjct: 299 YNPERCENCDPCLVEEACPVPAIKKDGTLNTED 331 >gnl|CDD|180786 PRK06991, PRK06991, ferredoxin; Provisional. Length = 270 Score = 39.0 bits (91), Expect = 3e-04 Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 3/48 (6%) Query: 9 CILCKHTDCVEVCPVDCFYEGENFL-AIHPDECIDCGVCEPECPVDAI 55 CI C T C++ CPVD + + D C C +C P CPVD I Sbjct: 87 CIGC--TLCMQACPVDAIVGAPKQMHTVLADLCTGCDLCVPPCPVDCI 132 Score = 31.7 bits (72), Expect = 0.041 Identities = 11/21 (52%), Positives = 12/21 (57%) Query: 35 IHPDECIDCGVCEPECPVDAI 55 I CI C +C CPVDAI Sbjct: 82 IDEQLCIGCTLCMQACPVDAI 102 >gnl|CDD|180852 PRK07118, PRK07118, ferredoxin; Validated. Length = 280 Score = 38.8 bits (91), Expect = 3e-04 Identities = 20/48 (41%), Positives = 24/48 (50%), Gaps = 4/48 (8%) Query: 9 CILCKHTDCVEVCPVDCFYEGENFLA-IHPDECIDCGVCEPECPVDAI 55 CI C CV+ CP EN LA I ++C CG C +CP AI Sbjct: 215 CIGCGK--CVKACPAGAI-TMENNLAVIDQEKCTSCGKCVEKCPTKAI 259 Score = 36.1 bits (84), Expect = 0.002 Identities = 13/40 (32%), Positives = 17/40 (42%) Query: 16 DCVEVCPVDCFYEGENFLAIHPDECIDCGVCEPECPVDAI 55 CV CP D + + D+C CG C CP + I Sbjct: 146 SCVAACPFDAIHIENGLPVVDEDKCTGCGACVKACPRNVI 185 Score = 30.3 bits (69), Expect = 0.11 Identities = 9/17 (52%), Positives = 9/17 (52%) Query: 40 CIDCGVCEPECPVDAIK 56 CI CG C CP AI Sbjct: 215 CIGCGKCVKACPAGAIT 231 >gnl|CDD|184955 PRK14993, PRK14993, tetrathionate reductase subunit B; Provisional. Length = 244 Score = 38.7 bits (90), Expect = 4e-04 Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 4/48 (8%) Query: 11 LCKHTD---CVEVCPVDCFYEGEN-FLAIHPDECIDCGVCEPECPVDA 54 LC H D CV VCPV ++ E+ + + C+ C C CP DA Sbjct: 99 LCNHCDNPPCVPVCPVQATFQREDGIVVVDNKRCVGCAYCVQACPYDA 146 >gnl|CDD|179940 PRK05113, PRK05113, electron transport complex protein RnfB; Provisional. Length = 191 Score = 38.4 bits (90), Expect = 5e-04 Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 7/52 (13%) Query: 7 ENCILCKHTDCVEVCPVDCFYEGENFLAIH---PDECIDCGVCEPECPVDAI 55 +NCI C T C++ CPVD A+H D C C +C CP D I Sbjct: 114 DNCIGC--TKCIQACPVDAIVGATK--AMHTVISDLCTGCDLCVAPCPTDCI 161 Score = 33.4 bits (77), Expect = 0.015 Identities = 12/21 (57%), Positives = 12/21 (57%) Query: 35 IHPDECIDCGVCEPECPVDAI 55 I D CI C C CPVDAI Sbjct: 111 IDEDNCIGCTKCIQACPVDAI 131 >gnl|CDD|163157 TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S protein. Members of this protein family are the Fe-S protein, NrfC, of a cytochrome c nitrite reductase system for which the pentaheme cytochrome c protein, NrfB (family TIGR03146) is an unambiguous marker. Members of this protein family show similarity to other ferredoxin-like proteins, including a subunit of a polysulfide reductase. Length = 225 Score = 37.8 bits (88), Expect = 6e-04 Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 2/47 (4%) Query: 7 ENCILCKHTDCVEVCPVDCFYEGEN--FLAIHPDECIDCGVCEPECP 51 ++C C + CV VCP ++ E + +H D C+ C C CP Sbjct: 92 KSCQHCDNAPCVAVCPTGASFKDEETGIVDVHKDLCVGCQYCIAACP 138 >gnl|CDD|131234 TIGR02179, PorD_KorD, 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family. A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of delta subunits, representing mostly pyruvate, 2-ketoisovalerate, and 2-oxoglutarate specific enzymes. The delta subunit is the smallest and resembles ferredoxins. Length = 78 Score = 37.7 bits (88), Expect = 6e-04 Identities = 22/51 (43%), Positives = 26/51 (50%), Gaps = 3/51 (5%) Query: 7 ENCILCKHTDCVEVCPVDCFYEGEN-FLAIHPDECIDCGVCEPECPVDAIK 56 E CI CK +C CP E E F+ I D C CG+C CPV AI+ Sbjct: 25 EKCIKCK--NCWLYCPEGAIQEDEGGFVGIDYDYCKGCGICANVCPVKAIE 73 Score = 26.1 bits (58), Expect = 2.3 Identities = 9/24 (37%), Positives = 13/24 (54%) Query: 35 IHPDECIDCGVCEPECPVDAIKPD 58 + ++CI C C CP AI+ D Sbjct: 22 VDKEKCIKCKNCWLYCPEGAIQED 45 >gnl|CDD|180305 PRK05888, PRK05888, NADH dehydrogenase subunit I; Provisional. Length = 164 Score = 37.2 bits (87), Expect = 0.001 Identities = 21/59 (35%), Positives = 24/59 (40%), Gaps = 12/59 (20%) Query: 7 ENCILCKHTDCVEVCPVDCFY-------EGENFLAIHP---DECIDCGVCEPECPVDAI 55 E CI CK C +CP D +G + CI CG CE CP DAI Sbjct: 58 ERCIACKL--CAAICPADAITIEAAEREDGRRRTTRYDINFGRCIFCGFCEEACPTDAI 114 Score = 34.1 bits (79), Expect = 0.008 Identities = 10/24 (41%), Positives = 11/24 (45%), Gaps = 2/24 (8%) Query: 9 CILCKHTDCVEVCPVDCFYEGENF 32 CI C C E CP D E +F Sbjct: 99 CIFCGF--CEEACPTDAIVETPDF 120 Score = 32.2 bits (74), Expect = 0.033 Identities = 9/23 (39%), Positives = 11/23 (47%) Query: 40 CIDCGVCEPECPVDAIKPDTEPG 62 CI C +C CP DAI + Sbjct: 60 CIACKLCAAICPADAITIEAAER 82 >gnl|CDD|179919 PRK05035, PRK05035, electron transport complex protein RnfC; Provisional. Length = 695 Score = 36.9 bits (86), Expect = 0.001 Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 12/53 (22%) Query: 9 CILCKHTDCVEVCPVDC-------FYEGENF---LAIHPDECIDCGVCEPECP 51 CI C C + CP F + E + +CI+CG C CP Sbjct: 372 CIRC--GACADACPASLLPQQLYWFAKAEEHDKAQEYNLFDCIECGACAYVCP 422 Score = 24.1 bits (53), Expect = 7.2 Identities = 7/14 (50%), Positives = 7/14 (50%) Query: 40 CIDCGVCEPECPVD 53 CI CG C CP Sbjct: 372 CIRCGACADACPAS 385 >gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional. Length = 590 Score = 36.7 bits (86), Expect = 0.001 Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 11/57 (19%) Query: 11 LCK----HTDCVEVCPV-----DC--FYEGENFLAIHPDECIDCGVCEPECPVDAIK 56 C+ + +C++ CPV + E + I + CI CG+C +CP DAI Sbjct: 11 RCQPKKCNYECIKYCPVVRTGEETIEIDEDDGKPVISEELCIGCGICVKKCPFDAIS 67 >gnl|CDD|132268 TIGR03224, benzo_boxA, benzoyl-CoA oxygenase/reductase, BoxA protein. Members of this protein family are BoxA, the A component of the BoxAB benzoyl-CoA oxygenase/reductase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation. BoxA is a homodimeric iron-sulphur-flavoprotein and acts as an NADPH-dependent reductase for BoxB. Length = 411 Score = 36.4 bits (84), Expect = 0.002 Identities = 17/49 (34%), Positives = 20/49 (40%), Gaps = 2/49 (4%) Query: 7 ENCILCKHTDCVEVCPVDCFYEGENFLAIHPDECIDCGVCEPECPVDAI 55 E CI C C E CP+D + + D C C C CP AI Sbjct: 10 EICIRC--NTCEETCPIDAITHDDRNYVVKADVCNGCMACVSPCPTGAI 56 Score = 35.6 bits (82), Expect = 0.003 Identities = 13/24 (54%), Positives = 15/24 (62%) Query: 35 IHPDECIDCGVCEPECPVDAIKPD 58 I P+ CI C CE CP+DAI D Sbjct: 7 IDPEICIRCNTCEETCPIDAITHD 30 >gnl|CDD|162887 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein family. This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0 to 8 additional cysteines. Length = 295 Score = 35.4 bits (82), Expect = 0.004 Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 7/59 (11%) Query: 3 YVVTENCILCKHTDCVEVCP-----VDCFYEGENFLAIHPDECIDCGVCEPECPVDAIK 56 C+ C CVEVCP + +G N + I ++C CG C CP A+ Sbjct: 44 LFKENRCLGCG--KCVEVCPAGTARLSELADGRNRIIIRREKCTHCGKCTEACPSGALS 100 >gnl|CDD|163218 TIGR03336, IOR_alpha, indolepyruvate ferredoxin oxidoreductase, alpha subunit. Indolepyruvate ferredoxin oxidoreductase (IOR) is an alpha 2/beta 2 tetramer related to ketoacid oxidoreductases for pyruvate (1.2.7.1, POR), 2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate (1.2.7.7, VOR). These multi-subunit enzymes typically are found in anaerobes and are inactiviated by oxygen. IOR in Pyrococcus acts in fermentation of all three aromatic amino acids, following removal of the amino group by transamination. In Methanococcus maripaludis, by contrast, IOR acts in the opposite direction, in pathways of amino acid biosynthesis from phenylacetate, indoleacetate, and p-hydroxyphenylacetate. In M. maripaludis and many other species, iorA and iorB are found next to an apparent phenylacetate-CoA ligase. Length = 595 Score = 35.1 bits (81), Expect = 0.004 Identities = 20/54 (37%), Positives = 24/54 (44%), Gaps = 7/54 (12%) Query: 4 VVTENCILCKHTDCVEV--CPVDCFYEGENFLAIHPDECIDCGVCEPECPVDAI 55 V + CI CK C++ CP + I P C CGVC CP DAI Sbjct: 547 VDQDKCIGCK--KCIKELGCP--AIEPEDKEAVIDP-LCTGCGVCAQICPFDAI 595 >gnl|CDD|184331 PRK13795, PRK13795, hypothetical protein; Provisional. Length = 636 Score = 33.8 bits (78), Expect = 0.010 Identities = 17/47 (36%), Positives = 17/47 (36%), Gaps = 2/47 (4%) Query: 17 CVEVCPVDCFYEGENFLAIHPDE--CIDCGVCEPECPVDAIKPDTEP 61 CV CP E I DE CI CG C CPV K Sbjct: 589 CVGACPTGAIRIEEGKRKISVDEEKCIHCGKCTEVCPVVKYKDKRNG 635 Score = 32.7 bits (75), Expect = 0.025 Identities = 10/18 (55%), Positives = 12/18 (66%) Query: 39 ECIDCGVCEPECPVDAIK 56 EC+ CGVC CP AI+ Sbjct: 582 ECVGCGVCVGACPTGAIR 599 Score = 25.0 bits (55), Expect = 4.5 Identities = 11/21 (52%), Positives = 11/21 (52%), Gaps = 2/21 (9%) Query: 3 YVVTENCILCKHTDCVEVCPV 23 V E CI C C EVCPV Sbjct: 608 SVDEEKCIHCG--KCTEVCPV 626 >gnl|CDD|131996 TIGR02951, DMSO_dmsB, DMSO reductase, iron-sulfur subunit. This family consists of the iron-sulfur subunit, or chain B, of an enzyme called the anaerobic dimethyl sulfoxide reductase. Chains A and B are catalytic, while chain C is a membrane anchor. Length = 161 Score = 33.6 bits (77), Expect = 0.013 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 2/63 (3%) Query: 2 TYVVTENCILCKHTDCVEVCPVDCFYEGEN--FLAIHPDECIDCGVCEPECPVDAIKPDT 59 Y ++ +C C CV+ CP Y+ E + + D+CI C C CP A + D Sbjct: 57 AYYISISCNHCADPACVKNCPTGAMYKREEDGLVLVDQDKCIGCRYCVWACPYGAPQYDP 116 Query: 60 EPG 62 + G Sbjct: 117 QQG 119 >gnl|CDD|182001 PRK09626, oorD, 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed. Length = 103 Score = 33.5 bits (77), Expect = 0.013 Identities = 20/53 (37%), Positives = 23/53 (43%), Gaps = 9/53 (16%) Query: 12 CKHTD-CVEVCPVDCF---YEGENFLA-----IHPDECIDCGVCEPECPVDAI 55 CK D CV VCP + L +HP+ CI C CE CP AI Sbjct: 18 CKACDICVSVCPAGVLAMRIDPHAVLGKMIKVVHPESCIGCRECELHCPDFAI 70 >gnl|CDD|170016 PRK09623, vorD, 2-ketoisovalerate ferredoxin oxidoreductase subunit delta; Reviewed. Length = 105 Score = 33.4 bits (76), Expect = 0.015 Identities = 22/61 (36%), Positives = 28/61 (45%), Gaps = 3/61 (4%) Query: 1 MTYVVTENCILCKHTDCVEVCPVDCFYEGEN-FLAIHPDECIDCGVCEPECPVDAIKPDT 59 M V C+ C C + CP Y E+ ++AI D C CG+C ECP AI Sbjct: 45 MPVVDESKCVKC--YICWKFCPEPAIYIKEDGYVAIDYDYCKGCGICANECPTKAITMVK 102 Query: 60 E 60 E Sbjct: 103 E 103 >gnl|CDD|183762 PRK12809, PRK12809, putative oxidoreductase Fe-S binding subunit; Reviewed. Length = 639 Score = 33.1 bits (75), Expect = 0.018 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 3/54 (5%) Query: 6 TENCILCKHTD---CVEVCPVDCFYEGENFLAIHPDECIDCGVCEPECPVDAIK 56 N + C H + CV CPV+ + + + +CI C C CP ++ Sbjct: 50 AANPVACHHCNNAPCVTACPVNALTFQSDSVQLDEQKCIGCKRCAIACPFGVVE 103 >gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor; Provisional. Length = 1147 Score = 32.8 bits (75), Expect = 0.018 Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 3/42 (7%) Query: 52 VDAIKPDTEPGLELWLKINSEYA--TQWPNITTKKESLPSAA 91 VD ++P P LWL+++ ++ WP + K E LP+ A Sbjct: 308 VDPMRPLLPPE-SLWLRVDELFSELKNWPRVQLKTEHLPTKA 348 >gnl|CDD|183733 PRK12769, PRK12769, putative oxidoreductase Fe-S binding subunit; Reviewed. Length = 654 Score = 32.8 bits (75), Expect = 0.019 Identities = 12/53 (22%), Positives = 21/53 (39%) Query: 9 CILCKHTDCVEVCPVDCFYEGENFLAIHPDECIDCGVCEPECPVDAIKPDTEP 61 C C+ C CP ++ + ++ +CI C C CP ++ P Sbjct: 56 CHHCEDAPCARSCPNGAISHVDDSIQVNQQKCIGCKSCVVACPFGTMQIVLTP 108 >gnl|CDD|183735 PRK12771, PRK12771, putative glutamate synthase (NADPH) small subunit; Provisional. Length = 564 Score = 32.2 bits (74), Expect = 0.029 Identities = 15/56 (26%), Positives = 19/56 (33%), Gaps = 4/56 (7%) Query: 8 NCILCKHTDCVEVCPVDCFY--EGENFLAIHPDECIDCGVCEPECPVDAIKPDTEP 61 NC C +C CP D D+C C +C CP AI+ Sbjct: 511 NCFECD--NCYGACPQDAIIKLGPGRRYHFDYDKCTGCHICADVCPCGAIEMGPGE 564 >gnl|CDD|162737 TIGR02163, napH_, ferredoxin-type protein, NapH/MauN family. Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase. Length = 255 Score = 32.3 bits (74), Expect = 0.029 Identities = 17/55 (30%), Positives = 20/55 (36%), Gaps = 8/55 (14%) Query: 7 ENCILCKHTDCVEVCPVDCFYE-----GENFLAIHPDECIDCGVCEPECPVDAIK 56 E C C DC VCP G + L + D C CG C C D + Sbjct: 201 EKCTNC--MDCFNVCPEPQVLRMPLKKGGSTLVLSGD-CTLCGRCIDVCHEDVLG 252 Score = 26.9 bits (60), Expect = 1.3 Identities = 14/63 (22%), Positives = 20/63 (31%), Gaps = 10/63 (15%) Query: 11 LCKHTDCVEVCPVDCFYE--GENFL----AIHPDECIDCGVCEPECPV----DAIKPDTE 60 + C +CP+ FY G L A ++C +C C CP Sbjct: 168 FSERGWCGHLCPLGAFYGLIGRKSLIKIAASDREKCTNCMDCFNVCPEPQVLRMPLKKGG 227 Query: 61 PGL 63 L Sbjct: 228 STL 230 >gnl|CDD|162617 TIGR01945, rnfC, electron transport complex, RnfABCDGE type, C subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the C subunit. Length = 435 Score = 32.3 bits (74), Expect = 0.031 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 12/53 (22%) Query: 9 CILCKHTDCVEVCPVDCFYEGENFLAIHPD----------ECIDCGVCEPECP 51 CI C CV+VCP++ + N+LA+ + +CI+CG C CP Sbjct: 365 CIRC--GKCVQVCPMNLLPQQLNWLALADEFDEAEEHNLMDCIECGCCSYVCP 415 >gnl|CDD|182382 PRK10330, PRK10330, formate dehydrogenase-H ferredoxin subunit; Provisional. Length = 181 Score = 32.2 bits (73), Expect = 0.031 Identities = 15/53 (28%), Positives = 22/53 (41%) Query: 9 CILCKHTDCVEVCPVDCFYEGENFLAIHPDECIDCGVCEPECPVDAIKPDTEP 61 C C+ C VCP + F+ + + CI C C CP A++ P Sbjct: 58 CRQCEDAPCANVCPNGAISRDKGFVHVMQERCIGCKTCVVACPYGAMEVVVRP 110 >gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional. Length = 604 Score = 31.7 bits (72), Expect = 0.049 Identities = 10/19 (52%), Positives = 12/19 (63%) Query: 38 DECIDCGVCEPECPVDAIK 56 ++CI CG C CP DAI Sbjct: 45 EKCIGCGTCSKICPTDAIT 63 Score = 28.6 bits (64), Expect = 0.37 Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 9/42 (21%) Query: 38 DECIDCGVCEPECP--------VDAI-KPDTEPGLELWLKIN 70 C++CG+C CP + AI K D E GL K N Sbjct: 185 ARCVECGICTDTCPAHMDIPQYIKAIYKDDLEEGLRWLYKTN 226 >gnl|CDD|162896 TIGR02512, Fe_only_hydrog, hydrogenases, Fe-only. This model describes iron-only hydrogenases of anaerobic and microaerophilic bacteria and protozoa. This model is narrower, and covers a longer stretch of sequence, than Pfam model pfam02906. This family represents a division among families that belong to pfam02906, which also includes proteins such as nuclear prelamin A recognition factor in animals. Note that this family shows some heterogeneity in terms of periplasmic, cytosolic, or hydrogenosome location, NAD or NADP dependence, and overal protein protein length. Length = 374 Score = 31.1 bits (71), Expect = 0.062 Identities = 17/66 (25%), Positives = 17/66 (25%), Gaps = 16/66 (24%) Query: 9 CILCKHTDCVEVCP----VDCFYEGENFLAIHP----------DECIDCGVCEPECPVDA 54 CI C CV C V CI CG C CPV A Sbjct: 9 CIGC--GRCVRACTNVQIVGALGFLNRGGKTEVAPKFGRLLDESNCIGCGQCSLVCPVGA 66 Query: 55 IKPDTE 60 I Sbjct: 67 ITEKDH 72 >gnl|CDD|170017 PRK09624, porD, pyuvate ferredoxin oxidoreductase subunit delta; Reviewed. Length = 105 Score = 30.8 bits (69), Expect = 0.075 Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 1/40 (2%) Query: 17 CVEVCPVDCFY-EGENFLAIHPDECIDCGVCEPECPVDAI 55 C CP Y + E + D C CG+C ECP AI Sbjct: 59 CYIYCPEPAIYLDEEGYPVFDYDYCKGCGICANECPTKAI 98 >gnl|CDD|162996 TIGR02745, ccoG_rdxA_fixG, cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum. Length = 434 Score = 30.4 bits (69), Expect = 0.10 Identities = 17/53 (32%), Positives = 21/53 (39%), Gaps = 26/53 (49%) Query: 9 CILCKHTDCVEVCPVDCFYEGENFLAIHPD-------ECIDCGVCEPECPVDA 54 CI C CV+VCP D ECI+CG+C +DA Sbjct: 233 CIDCNL--CVQVCPT------------GIDIRDGLQLECINCGLC-----IDA 266 >gnl|CDD|131231 TIGR02176, pyruv_ox_red, pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric. This model represents a single chain form of pyruvate:ferredoxin (or flavodoxin) oxidoreductase. This enzyme may transfer electrons to nitrogenase in nitrogen-fixing species. Portions of this protein are homologous to gamma subunit of the four subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase. Length = 1165 Score = 30.5 bits (69), Expect = 0.11 Identities = 18/74 (24%), Positives = 23/74 (31%), Gaps = 29/74 (39%) Query: 5 VTENCILCKHTDCVEVCP---------------------VDCFYEGENF------LAIHP 37 V +NCI C C VCP +G+ + I P Sbjct: 681 VPDNCIQCNQ--CAFVCPHAAIRPKLADEEELENAPAGFKSLDAKGKELEGMKFRIQISP 738 Query: 38 DECIDCGVCEPECP 51 +C CG C CP Sbjct: 739 LDCTGCGNCVDICP 752 Score = 29.4 bits (66), Expect = 0.24 Identities = 11/21 (52%), Positives = 12/21 (57%) Query: 37 PDECIDCGVCEPECPVDAIKP 57 PD CI C C CP AI+P Sbjct: 682 PDNCIQCNQCAFVCPHAAIRP 702 >gnl|CDD|183008 PRK11168, glpC, sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional. Length = 396 Score = 29.8 bits (68), Expect = 0.15 Identities = 10/21 (47%), Positives = 11/21 (52%) Query: 38 DECIDCGVCEPECPVDAIKPD 58 D CI C VC CPV + P Sbjct: 7 DSCIKCTVCTTACPVARVNPL 27 Score = 29.5 bits (67), Expect = 0.19 Identities = 17/63 (26%), Positives = 22/63 (34%), Gaps = 20/63 (31%) Query: 7 ENCILCKHTDCVEVCPV---DCFY--------EGENF-----LAIHP--DECIDCGVCEP 48 ++CI C T C CPV + Y +GE C +C CE Sbjct: 7 DSCIKC--TVCTTACPVARVNPLYPGPKQAGPDGERLRLKDGALYDESLKYCSNCKRCEV 64 Query: 49 ECP 51 CP Sbjct: 65 ACP 67 >gnl|CDD|183763 PRK12810, gltD, glutamate synthase subunit beta; Reviewed. Length = 471 Score = 29.7 bits (68), Expect = 0.16 Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 9/33 (27%) Query: 38 DECIDCGV--CEPECPVDAIKPDTEPGLELWLK 68 C+DCG+ C CPV P+ W Sbjct: 44 ARCMDCGIPFCHWGCPVHNYIPE-------WND 69 >gnl|CDD|183492 PRK12387, PRK12387, formate hydrogenlyase complex iron-sulfur subunit; Provisional. Length = 180 Score = 30.0 bits (68), Expect = 0.16 Identities = 24/68 (35%), Positives = 28/68 (41%), Gaps = 8/68 (11%) Query: 7 ENCILCKHTDCVEVCPVDC----FYEGENFLA--IHPDECIDCGVCEPECPVDAIKPDTE 60 + CI C CV CP + LA + CI CG CE CP AIK E Sbjct: 38 QQCIGC--AACVNACPSNALTVETDLATGELAWEFNLGRCIFCGRCEEVCPTAAIKLSQE 95 Query: 61 PGLELWLK 68 L +W K Sbjct: 96 FELAVWKK 103 Score = 27.3 bits (61), Expect = 0.91 Identities = 9/25 (36%), Positives = 15/25 (60%) Query: 36 HPDECIDCGVCEPECPVDAIKPDTE 60 +P +CI C C CP +A+ +T+ Sbjct: 36 NPQQCIGCAACVNACPSNALTVETD 60 >gnl|CDD|131115 TIGR02060, aprB, adenosine phosphosulphate reductase, beta subunit. During dissimilatory sulfate reduction and sulfur oxidation, adenylylsulfate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulfite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. Described by this model is the beta subunit of APS reductase, sharing common evolutionary origin with other iron-sulfur cluster-binding proteins. Length = 132 Score = 29.6 bits (66), Expect = 0.17 Identities = 22/60 (36%), Positives = 26/60 (43%), Gaps = 6/60 (10%) Query: 2 TYVVTENCILCK---HTDCVEVCPVDCFY---EGENFLAIHPDECIDCGVCEPECPVDAI 55 T+V C CK T CV +CP D + E I PD C +C C CP AI Sbjct: 3 TFVYPTKCDGCKAGEKTACVYICPNDLMHLDTEIMKAYNIEPDMCWECYSCVKACPQGAI 62 >gnl|CDD|181891 PRK09477, napH, quinol dehydrogenase membrane component; Provisional. Length = 271 Score = 29.5 bits (67), Expect = 0.19 Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 7/54 (12%) Query: 7 ENCILCKHTDCVEVCP---V--DCFYEGENFLAIHPDECIDCGVCEPECPVDAI 55 + C C DC VCP V ++ + +CI CG C C D Sbjct: 208 QKCTRC--MDCFHVCPEPQVLRPPLKGKQSPSQVTSGDCITCGRCIDVCSEDVF 259 >gnl|CDD|182807 PRK10882, PRK10882, hydrogenase 2 protein HybA; Provisional. Length = 328 Score = 29.6 bits (67), Expect = 0.20 Identities = 14/45 (31%), Positives = 18/45 (40%), Gaps = 2/45 (4%) Query: 9 CILCKHTDCVEVCPVDCFYEGE--NFLAIHPDECIDCGVCEPECP 51 C+ C +CV VCPV + + D C C C CP Sbjct: 112 CMHCVDPNCVSVCPVSALTKDPKTGIVHYDKDVCTGCRYCMVACP 156 >gnl|CDD|179457 PRK02651, PRK02651, photosystem I subunit VII; Provisional. Length = 81 Score = 29.2 bits (65), Expect = 0.22 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 10/57 (17%) Query: 5 VTENCILCKHTDCVEVCPVDCF--------YEGENFLAIHPDECIDCGVCEPECPVD 53 + + CI C T CV CP+D G+ + ++C+ C CE CP D Sbjct: 7 IYDTCIGC--TQCVRACPLDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPTD 61 >gnl|CDD|131121 TIGR02066, dsrB, sulfite reductase, dissimilatory-type beta subunit. This model describes the beta subunit of sulfite reductase. Length = 341 Score = 29.0 bits (65), Expect = 0.28 Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 4/60 (6%) Query: 12 CKHTDCVEVCPVDCF---YEGENF-LAIHPDECIDCGVCEPECPVDAIKPDTEPGLELWL 67 C+ V CP +G+N L + ++CI CG C CP I G +W+ Sbjct: 184 CEIPSVVAACPTGALKPRRDGKNKSLEVDVEKCIYCGNCYTMCPAMPIFDPENDGAAIWV 243 >gnl|CDD|116890 pfam08307, Glyco_hydro_98C, Glycosyl hydrolase family 98 C-terminal domain. This putative domain is found at the C-terminus of glycosyl hydrolase family 98 proteins. This domain is not expected to form part of the catalytic activity. Length = 231 Score = 28.8 bits (64), Expect = 0.29 Identities = 7/22 (31%), Positives = 13/22 (59%) Query: 68 KINSEYATQWPNITTKKESLPS 89 K+ SE +T+ +I K + L + Sbjct: 74 KLISENSTELSSIAAKTQYLNA 95 >gnl|CDD|179174 PRK00941, PRK00941, acetyl-CoA decarbonylase/synthase complex subunit alpha; Validated. Length = 781 Score = 28.8 bits (65), Expect = 0.33 Identities = 17/52 (32%), Positives = 19/52 (36%), Gaps = 11/52 (21%) Query: 9 CILCKHTDCVEVCP-----VDCFYEGEN----FLAIHPDECIDCGVCEPECP 51 C C CV VCP + L D+CI CG CE CP Sbjct: 406 CTECG--WCVRVCPNELPIPEAMEAAAKGDLSKLEDLYDKCIGCGRCEQVCP 455 Score = 24.2 bits (53), Expect = 7.0 Identities = 6/14 (42%), Positives = 8/14 (57%) Query: 38 DECIDCGVCEPECP 51 +C +CG C CP Sbjct: 404 KKCTECGWCVRVCP 417 >gnl|CDD|132092 TIGR03048, PS_I_psaC, photosystem I iron-sulfur protein PsaC. Members of this family are PsaC, an essential component of photosystem I (PS-I) reaction center in Cyanobacteria and chloroplasts. This small protein, about 80 amino acids in length, contains two copies of the ferredoxin-like 4Fe-4S binding site (pfam00037) and therefore eight conserved Cys residues. This protein is also called photosystem I subunit VII. Length = 80 Score = 28.3 bits (63), Expect = 0.44 Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 10/68 (14%) Query: 5 VTENCILCKHTDCVEVCPVDCF----YEG--ENFLAIHP--DECIDCGVCEPECPVDAIK 56 + + CI C T CV CP D ++G +A P ++C+ C CE CP D + Sbjct: 6 IYDTCIGC--TQCVRACPTDVLEMVPWDGCKAGQIASAPRTEDCVGCKRCESACPTDFLS 63 Query: 57 PDTEPGLE 64 G E Sbjct: 64 VRVYLGAE 71 >gnl|CDD|182113 PRK09853, PRK09853, putative selenate reductase subunit YgfK; Provisional. Length = 1019 Score = 28.0 bits (63), Expect = 0.49 Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 7/44 (15%) Query: 17 CVEVCP----VDCFYEG--ENFLAIHPDE-CIDCGVCEPECPVD 53 CV+VCP V G F +H D C +CG C CP + Sbjct: 898 CVDVCPNRANVSIAVPGFQNRFQIVHLDAMCNECGNCAQFCPWN 941 >gnl|CDD|132422 TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit. Members of this protein family are the membrane-anchoring, non-catalytic C subunit, product of the glpC gene, of a three-subunit, FAD-dependent, anaerobic glycerol-3-phosphate dehydrogenase. GlpC lasks classical hydrophobic transmembrane helices; Cole, et al suggest interaction with the membrane may involve amphipathic helices. GlcC has conserved Cys-containing motifs suggestive of iron-sulfur binding. This complex is found mostly in Escherichia coli and closely related species. Length = 397 Score = 28.2 bits (63), Expect = 0.54 Identities = 20/65 (30%), Positives = 23/65 (35%), Gaps = 20/65 (30%) Query: 7 ENCILCKHTDCVEVCPV-----------DCFYEGENFLAIHP---DE----CIDCGVCEP 48 E+CI C T C CPV +GE DE C +C CE Sbjct: 5 ESCIKC--TVCTVYCPVAKANPLYPGPKQAGPDGERLRLKSAELYDEALKYCTNCKRCEV 62 Query: 49 ECPVD 53 CP D Sbjct: 63 ACPSD 67 Score = 26.7 bits (59), Expect = 1.4 Identities = 9/20 (45%), Positives = 10/20 (50%) Query: 38 DECIDCGVCEPECPVDAIKP 57 + CI C VC CPV P Sbjct: 5 ESCIKCTVCTVYCPVAKANP 24 >gnl|CDD|161850 TIGR00384, dhsB, succinate dehydrogenase and fumarate reductase iron-sulfur protein. Succinate dehydrogenase and fumarate reductase are reverse directions of the same enzymatic interconversion, succinate + FAD+ = fumarate + FADH2 (EC 1.3.11.1). In E. coli, the forward and reverse reactions are catalyzed by distinct complexes: fumarate reductase operates under anaerobic conditions and succinate dehydrogenase operates under aerobic conditions. This model also describes a region of the B subunit of a cytosolic archaeal fumarate reductase. Length = 220 Score = 28.2 bits (63), Expect = 0.57 Identities = 8/20 (40%), Positives = 9/20 (45%) Query: 39 ECIDCGVCEPECPVDAIKPD 58 CI CG C CP P+ Sbjct: 139 GCILCGCCYSSCPAFWWNPE 158 >gnl|CDD|181037 PRK07569, PRK07569, bidirectional hydrogenase complex protein HoxU; Validated. Length = 234 Score = 28.1 bits (63), Expect = 0.57 Identities = 20/62 (32%), Positives = 22/62 (35%), Gaps = 17/62 (27%) Query: 9 CILCKHTDCVEVCPV-------DCFYEGENFLAI----HP----DECIDCGVCEPECPVD 53 C+LC T CV VC D G I P + C CG C CP Sbjct: 148 CVLC--TRCVRVCDEIEGAHTWDVAGRGAKSRVITDLNQPWGTSETCTSCGKCVQACPTG 205 Query: 54 AI 55 AI Sbjct: 206 AI 207 >gnl|CDD|181301 PRK08222, PRK08222, hydrogenase 4 subunit H; Validated. Length = 181 Score = 27.8 bits (62), Expect = 0.68 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 2/32 (6%) Query: 37 PDECIDCGVCEPECPVDA--IKPDTEPGLELW 66 P +CI CG C CP +A I+ D + W Sbjct: 37 PSQCIACGACTCACPANALTIQTDDQQNSRTW 68 Score = 27.4 bits (61), Expect = 0.84 Identities = 20/62 (32%), Positives = 21/62 (33%), Gaps = 22/62 (35%) Query: 7 ENCILCKHTDCVEVCPVDCFYEGENFLAIHPDE-------------CIDCGVCEPECPVD 53 CI C C CP N L I D+ CI CG CE CP Sbjct: 38 SQCIAC--GACTCACPA-------NALTIQTDDQQNSRTWQLYLGRCIYCGRCEEVCPTR 88 Query: 54 AI 55 AI Sbjct: 89 AI 90 >gnl|CDD|132358 TIGR03315, Se_ygfK, putative selenate reductase, YgfK subunit. Members of this protein family are YgfK, predicted to be one subunit of a three-subunit, molybdopterin-containing selenate reductase. This enzyme is found, typically, in genomic regions associated with xanthine dehydrogenase homologs predicted to belong to the selenium-dependent molybdenum hydroxylases (SDMH). Therefore, the selenate reductase is suggested to play a role in furnishing selenide for SelD, the selenophosphate synthase. Length = 1012 Score = 27.8 bits (62), Expect = 0.70 Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 9/56 (16%) Query: 7 ENCILCKH--TDCVEVCP----VDCFYEGEN--FLAIHPDE-CIDCGVCEPECPVD 53 + C+ C + CV+VCP + + G F +H D C +CG C CP D Sbjct: 881 QRCLECSYVCEKCVDVCPNRANIVIYVPGFRDQFQIVHLDGMCNECGNCATFCPYD 936 >gnl|CDD|181399 PRK08348, PRK08348, NADH-plastoquinone oxidoreductase subunit; Provisional. Length = 120 Score = 27.5 bits (61), Expect = 0.79 Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 2/28 (7%) Query: 6 TENCILCKHTDCVEVCPVDCFYEGENFL 33 T C+ C CV+VCP ++FL Sbjct: 72 TGRCVFCGQ--CVDVCPTGALQMSDDFL 97 Score = 27.1 bits (60), Expect = 1.0 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 4/50 (8%) Query: 9 CILCKHTDCVEVCPVDCF--YEGENFLAIHPDECIDCGVCEPECPVDAIK 56 C+ C+ CV VCP F +A+ C+ CG C CP A++ Sbjct: 44 CVGCRM--CVTVCPAGVFVYLPEIRKVALWTGRCVFCGQCVDVCPTGALQ 91 >gnl|CDD|131958 TIGR02912, sulfite_red_C, sulfite reductase, subunit C. Members of this protein family include the C subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulfite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulfide gas from sulfite. Length = 314 Score = 27.5 bits (61), Expect = 0.79 Identities = 18/50 (36%), Positives = 22/50 (44%), Gaps = 7/50 (14%) Query: 9 CILCKHTDCVEVC---PVDCFYEGENFLAIHPDE-CIDCGVCEPECPVDA 54 CI C CV+VC V EN+ + CI CG C +CP A Sbjct: 171 CIGCGA--CVKVCKKKAVGAL-SFENYKVVRDHSKCIGCGECVLKCPTGA 217 >gnl|CDD|181779 PRK09326, PRK09326, F420H2 dehydrogenase subunit F; Provisional. Length = 341 Score = 27.5 bits (61), Expect = 0.80 Identities = 11/21 (52%), Positives = 12/21 (57%) Query: 35 IHPDECIDCGVCEPECPVDAI 55 I D C CG CE CP+ AI Sbjct: 9 IEYDVCTACGACEAVCPIGAI 29 >gnl|CDD|132337 TIGR03294, FrhG, coenzyme F420 hydrogenase, subunit gamma. This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. This protein contains two 4Fe-4S cluster binding domains (pfam00037) and scores above the trusted cutoff to model pfam01058 for the "NADH ubiquinone oxidoreductase, 20 Kd subunit" family. Length = 228 Score = 27.5 bits (61), Expect = 0.82 Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 3/52 (5%) Query: 1 MTYVVTEN-CILCKHTDCVEVCPVDCFYEGENFLAIHPDECIDCGVCEPECP 51 MT VV + C+ C C CP + ++ D CI CG C +CP Sbjct: 167 MTKVVNQGLCMGCG--TCAAACPTRAIEMEDGRPNVNRDRCIKCGACYVQCP 216 >gnl|CDD|183780 PRK12831, PRK12831, putative oxidoreductase; Provisional. Length = 464 Score = 27.3 bits (61), Expect = 0.84 Identities = 8/17 (47%), Positives = 10/17 (58%) Query: 7 ENCILCKHTDCVEVCPV 23 C+ CK CV+ CPV Sbjct: 40 SRCLQCKKPKCVKGCPV 56 >gnl|CDD|172522 PRK14028, PRK14028, pyruvate ferredoxin oxidoreductase subunit gamma/delta; Provisional. Length = 312 Score = 27.3 bits (60), Expect = 0.98 Identities = 20/61 (32%), Positives = 23/61 (37%), Gaps = 15/61 (24%) Query: 9 CILCKHTDCVEVCPVDCFYE---------GENFLAIHPD----ECIDCGVCEPECPVDAI 55 CI+C+ C CP D E G F D C CGVC CP AI Sbjct: 249 CIMCR--KCWLYCPDDAIIEAWREAEGPRGRKFRMKMIDFDYQYCKGCGVCAEVCPTGAI 306 Query: 56 K 56 + Sbjct: 307 Q 307 >gnl|CDD|129374 TIGR00273, TIGR00273, iron-sulfur cluster-binding protein. Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulfur clusters. Length = 432 Score = 26.8 bits (59), Expect = 1.4 Identities = 9/13 (69%), Positives = 10/13 (76%) Query: 40 CIDCGVCEPECPV 52 CI CG C+ ECPV Sbjct: 295 CIRCGACQNECPV 307 >gnl|CDD|181890 PRK09476, napG, quinol dehydrogenase periplasmic component; Provisional. Length = 254 Score = 26.5 bits (59), Expect = 1.6 Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 2/24 (8%) Query: 35 IHPDECIDCGVCEPECPVD--AIK 56 +H D C CG CE C ++ AIK Sbjct: 181 VHSDACTGCGKCEKACVLEKAAIK 204 Score = 24.2 bits (53), Expect = 7.4 Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 4/27 (14%) Query: 30 ENFLAIHPDECIDCGVCEPECPVDAIK 56 +FL+ CI CG+C CP D +K Sbjct: 55 NDFLS----ACIRCGLCVQACPYDTLK 77 >gnl|CDD|162107 TIGR00918, 2A060602, The Eukaryotic (Putative) Sterol Transporter (EST) Family. Length = 1145 Score = 26.4 bits (58), Expect = 1.7 Identities = 10/25 (40%), Positives = 14/25 (56%) Query: 10 ILCKHTDCVEVCPVDCFYEGENFLA 34 IL K C+ + P+DCF+EG Sbjct: 179 ILEKLIPCLIITPLDCFWEGAKLQG 203 >gnl|CDD|183604 PRK12576, PRK12576, succinate dehydrogenase iron-sulfur subunit; Provisional. Length = 279 Score = 26.3 bits (58), Expect = 1.8 Identities = 11/20 (55%), Positives = 14/20 (70%) Query: 39 ECIDCGVCEPECPVDAIKPD 58 +CI CG+C CPV AI P+ Sbjct: 153 QCIWCGLCVSACPVVAIDPE 172 >gnl|CDD|177700 PLN00071, PLN00071, photosystem I subunit VII; Provisional. Length = 81 Score = 26.1 bits (57), Expect = 2.1 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 10/57 (17%) Query: 5 VTENCILCKHTDCVEVCPVDCF----YEG--ENFLAIHP--DECIDCGVCEPECPVD 53 + + CI C T CV CP D ++G +A P ++C+ C CE CP D Sbjct: 7 IYDTCIGC--TQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPTD 61 >gnl|CDD|177602 PHA03365, PHA03365, hypothetical protein; Provisional. Length = 419 Score = 26.2 bits (58), Expect = 2.2 Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 3/32 (9%) Query: 14 HTDCVEVCPVDCFYEGENFLAIH---PDECID 42 HT EVCPV+ G+N++ + P E +D Sbjct: 218 HTVQGEVCPVNAVRLGKNYVRVSVDKPSEKLD 249 >gnl|CDD|163077 TIGR02936, fdxN_nitrog, ferredoxin III, nif-specific. Members of this family are homodimeric ferredoxins from nitrogen fixation regions of many nitrogen-fixing bacteria. As characterized in Rhodobacter capsulatus, these proteins are homodimeric, with two 4Fe-4S clusters bound per monomer. Although nif-specific, this protein family is not usiveral, as other nitrogenase systems may substitute flavodoxins, or different types of ferredoxin. Length = 91 Score = 26.2 bits (58), Expect = 2.2 Identities = 8/20 (40%), Positives = 9/20 (45%) Query: 35 IHPDECIDCGVCEPECPVDA 54 +P CI CG C CP Sbjct: 67 ANPGNCIGCGACARVCPKKC 86 Score = 24.3 bits (53), Expect = 6.8 Identities = 10/26 (38%), Positives = 10/26 (38%), Gaps = 2/26 (7%) Query: 1 MTYVVTENCILCKHTDCVEVCPVDCF 26 M NCI C C VCP C Sbjct: 64 MVVANPGNCIGCG--ACARVCPKKCQ 87 >gnl|CDD|182296 PRK10194, PRK10194, ferredoxin-type protein; Provisional. Length = 163 Score = 25.8 bits (56), Expect = 2.6 Identities = 9/24 (37%), Positives = 12/24 (50%) Query: 35 IHPDECIDCGVCEPECPVDAIKPD 58 ++ C CG C CPV AI + Sbjct: 135 LNSQLCNGCGACAASCPVSAITAE 158 >gnl|CDD|129414 TIGR00314, cdhA, CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Acetyl-CoA decarbonylase/synthase (ACDS) is a multienzyme complex. Carbon monoxide dehydrogenase is a synonym. The ACDS complex carries out an unusual reaction involving the reversible cleavage and synthesis of acetyl-CoA in methanogens. The model contains the prosite signature for 4Fe-4S ferredoxins [C-x(2)-C-x(2)-C-x(3)-C-[PEG]] between residues 448-462 of the model. Length = 784 Score = 26.0 bits (57), Expect = 2.6 Identities = 7/14 (50%), Positives = 9/14 (64%) Query: 38 DECIDCGVCEPECP 51 ++C CG CE CP Sbjct: 437 EQCYACGRCEQACP 450 >gnl|CDD|162882 TIGR02486, RDH, reductive dehalogenase. This model represents a family of corrin and 8-iron Fe-S cluster-containing reductive dehalogenases found primarily in halorespiring microorganisms such as dehalococcoides ethenogenes which contains as many as 17 enzymes of this type with varying substrate ranges. One example of a characterized species is the tetrachloroethene reductive dehalogenase (1.97.1.8) which also acts on trichloroethene converting it to dichloroethene. Length = 314 Score = 25.5 bits (56), Expect = 2.9 Identities = 11/25 (44%), Positives = 12/25 (48%) Query: 40 CIDCGVCEPECPVDAIKPDTEPGLE 64 C CG C ECP AI EP + Sbjct: 207 CETCGKCADECPSGAISKGGEPTWD 231 >gnl|CDD|181383 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B; Validated. Length = 420 Score = 25.7 bits (57), Expect = 3.1 Identities = 8/16 (50%), Positives = 9/16 (56%) Query: 35 IHPDECIDCGVCEPEC 50 I D+CI CG C C Sbjct: 339 IDQDKCIGCGRCYIAC 354 Score = 25.3 bits (56), Expect = 3.8 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 8/53 (15%) Query: 7 ENCILCKHTDCVEVC------PVDCFYEGENFLAIHPDECIDCGVCEPECPVD 53 + CI C C C ++ +G + +EC+ C +C CPV+ Sbjct: 342 DKCIGCGR--CYIACEDTSHQAIEWDEDGTRTPEVIEEECVGCNLCAHVCPVE 392 >gnl|CDD|183490 PRK12385, PRK12385, fumarate reductase iron-sulfur subunit; Provisional. Length = 244 Score = 25.4 bits (56), Expect = 3.3 Identities = 8/19 (42%), Positives = 12/19 (63%) Query: 40 CIDCGVCEPECPVDAIKPD 58 CI+CG+C CP + P+ Sbjct: 149 CINCGLCYAACPQFGLNPE 167 >gnl|CDD|132518 TIGR03478, DMSO_red_II_bet, DMSO reductase family type II enzyme, iron-sulfur subunit. This model represents the iron-sulfur subunit, typically called the beta subunit, of various proteins that also contain a molybdopterin subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase. Length = 321 Score = 25.5 bits (56), Expect = 3.5 Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 2/49 (4%) Query: 9 CILCKHTDCVEVCPVDCFY--EGENFLAIHPDECIDCGVCEPECPVDAI 55 C C + C+ CP Y E + + + + C C CP + Sbjct: 131 CNHCTNPACLAACPTGAIYKREEDGIVLVDQERCKGYRYCVEACPYKKV 179 >gnl|CDD|129498 TIGR00403, ndhI, NADH-plastoquinone oxidoreductase subunit I protein. Length = 183 Score = 25.3 bits (55), Expect = 4.1 Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 2/24 (8%) Query: 9 CILCKHTDCVEVCPVDCFYEGENF 32 CI C +CVE CP +C E + Sbjct: 104 CIFCG--NCVEYCPTNCLSMTEEY 125 Score = 24.9 bits (54), Expect = 5.1 Identities = 8/16 (50%), Positives = 11/16 (68%) Query: 38 DECIDCGVCEPECPVD 53 D+CI C VC CP++ Sbjct: 62 DKCIACEVCVRVCPIN 77 Score = 24.1 bits (52), Expect = 8.3 Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 13/60 (21%) Query: 7 ENCILCKHTDCVEVCPVDCFYEGENF-----------LAIHPDECIDCGVCEPECPVDAI 55 + CI C+ CV VCP++ F +I CI CG C CP + + Sbjct: 62 DKCIACEV--CVRVCPINLPVVDWEFNKAIKKKQLKNYSIDFGVCIFCGNCVEYCPTNCL 119 >gnl|CDD|180502 PRK06273, PRK06273, ferredoxin; Provisional. Length = 165 Score = 25.1 bits (55), Expect = 4.4 Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 1/25 (4%) Query: 38 DECIDCGVCEPECPVDAIK-PDTEP 61 + CI CG C CP AI+ EP Sbjct: 49 ELCIGCGGCANVCPTKAIEMIPVEP 73 >gnl|CDD|184136 PRK13552, frdB, fumarate reductase iron-sulfur subunit; Provisional. Length = 239 Score = 24.9 bits (55), Expect = 4.6 Identities = 8/21 (38%), Positives = 11/21 (52%) Query: 38 DECIDCGVCEPECPVDAIKPD 58 D CI+CG C C ++ D Sbjct: 149 DRCIECGCCVAACGTKQMRED 169 >gnl|CDD|181450 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated. Length = 819 Score = 25.1 bits (55), Expect = 4.8 Identities = 8/17 (47%), Positives = 10/17 (58%) Query: 39 ECIDCGVCEPECPVDAI 55 +C CG C CPV A+ Sbjct: 205 DCSFCGECIAVCPVGAL 221 >gnl|CDD|129492 TIGR00397, mauM_napG, MauM/NapG family ferredoxin-type protein. MauM is involved in methylamine utilization. NapG is associated with nitrate reductase activity. The two proteins are highly similar. Length = 213 Score = 24.5 bits (53), Expect = 5.8 Identities = 7/17 (41%), Positives = 10/17 (58%) Query: 40 CIDCGVCEPECPVDAIK 56 C+ CG+C CP D + Sbjct: 55 CVRCGLCVEACPYDILS 71 >gnl|CDD|181234 PRK08117, PRK08117, 4-aminobutyrate aminotransferase; Provisional. Length = 433 Score = 24.6 bits (54), Expect = 6.4 Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 4/51 (7%) Query: 1 MTYVVT-ENCILCKHTDCVEVCPVDCFYEGENFLA--IHPDECIDCGVCEP 48 Y C C + EVC ++C + E+ + P+E + + EP Sbjct: 166 SVYQAPYPYCDRCPKGEDPEVCFLECLRDLESLFKHQVTPEE-VAAVIIEP 215 >gnl|CDD|162435 TIGR01582, FDH-beta, formate dehydrogenase, beta subunit, Fe-S containing. In addition to the gamma proteobacteria, a sequence from Aquifex aolicus falls within the scope of this model. This appears to be the case for the alpha, gamma and epsilon (accessory protein TIGR01562) chains as well. Length = 283 Score = 24.5 bits (53), Expect = 6.4 Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 2/47 (4%) Query: 9 CILCKHTDCVEVCPVD--CFYEGENFLAIHPDECIDCGVCEPECPVD 53 C+ C+ C++ CP + +CI CG C CP + Sbjct: 93 CMHCREPGCLKACPAPGAIIQYQNGIVDFDHSKCIGCGYCIVGCPFN 139 >gnl|CDD|162880 TIGR02484, CitB, CitB domain protein. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene ) and is complemented by the characterized precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate. This model identifies the C-terminal domain of the R. capsulatus CobZ, which, in most other species exists as a separate gene adjacent to CobZ. Length = 372 Score = 24.5 bits (53), Expect = 6.5 Identities = 10/29 (34%), Positives = 12/29 (41%), Gaps = 4/29 (13%) Query: 24 DCFYEGENFLAIHPDECIDCGVCEPECPV 52 D F E + L + C CG C C V Sbjct: 4 DPFAEAKRVLNL----CNSCGYCTGLCAV 28 >gnl|CDD|161798 TIGR00276, TIGR00276, iron-sulfur cluster binding protein, putative. This series of proteins contain the prosite signature for 4Fe-4S ferredoxins iron-sulfur binding proteins (C-x(2)-C-x(2)-C-x(3)-C-[PEG]) between residues 175-188 of the model. Length = 282 Score = 24.4 bits (53), Expect = 7.2 Identities = 6/20 (30%), Positives = 8/20 (40%) Query: 36 HPDECIDCGVCEPECPVDAI 55 + C C C CP A+ Sbjct: 157 IEEYCGRCTKCIDACPTQAL 176 >gnl|CDD|183739 PRK12778, PRK12778, putative bifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta; Provisional. Length = 752 Score = 24.3 bits (53), Expect = 7.3 Identities = 9/15 (60%), Positives = 11/15 (73%) Query: 9 CILCKHTDCVEVCPV 23 C+ CK+ CVE CPV Sbjct: 331 CLDCKNPGCVEGCPV 345 >gnl|CDD|161860 TIGR00402, napF, ferredoxin-type protein NapF. The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation. Length = 101 Score = 24.1 bits (52), Expect = 8.0 Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 3/45 (6%) Query: 16 DCVEVCPVDCFYEGENFLA---IHPDECIDCGVCEPECPVDAIKP 57 +C C + G+ EC CG C CP +A P Sbjct: 41 ECASACENNILQLGQQGQPTVEFDNAECDFCGKCAEACPTNAFHP 85 >gnl|CDD|182000 PRK09625, porD, pyruvate flavodoxin oxidoreductase subunit delta; Reviewed. Length = 133 Score = 23.9 bits (52), Expect = 8.3 Identities = 25/86 (29%), Positives = 30/86 (34%), Gaps = 15/86 (17%) Query: 6 TENCILCKHTDCVEVCPVDCFY-EGENFLAIHPDECIDCGVCEPECPVDAIKPDTEPGLE 64 E CI C + C CP + + C CGVC CP T P Sbjct: 58 NEICINCFN--CWVYCPDAAILSRDKKLKGVDYSHCKGCGVCVEVCP-------TNPK-S 107 Query: 65 LWL----KINSEYATQWPNITTKKES 86 L + N TQWP KK+S Sbjct: 108 LLMFEEQIENETALTQWPKKEEKKKS 133 >gnl|CDD|183738 PRK12775, PRK12775, putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional. Length = 1006 Score = 24.1 bits (52), Expect = 8.4 Identities = 8/17 (47%), Positives = 9/17 (52%) Query: 7 ENCILCKHTDCVEVCPV 23 E CI C C+ CPV Sbjct: 331 ERCIQCAKPTCIAGCPV 347 >gnl|CDD|171592 PRK12575, PRK12575, succinate dehydrogenase iron-sulfur subunit; Provisional. Length = 235 Score = 24.1 bits (52), Expect = 9.2 Identities = 9/20 (45%), Positives = 9/20 (45%) Query: 39 ECIDCGVCEPECPVDAIKPD 58 ECI C C CP PD Sbjct: 145 ECILCACCSTACPSYWWNPD 164 >gnl|CDD|180322 PRK05950, sdhB, succinate dehydrogenase iron-sulfur subunit; Reviewed. Length = 232 Score = 24.0 bits (53), Expect = 9.8 Identities = 7/14 (50%), Positives = 7/14 (50%) Query: 39 ECIDCGVCEPECPV 52 ECI C C CP Sbjct: 142 ECILCACCSTSCPS 155 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 0.317 0.136 0.453 Gapped Lambda K H 0.267 0.0648 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,784,445 Number of extensions: 93941 Number of successful extensions: 359 Number of sequences better than 10.0: 1 Number of HSP's gapped: 312 Number of HSP's successfully gapped: 154 Length of query: 113 Length of database: 5,994,473 Length adjustment: 78 Effective length of query: 35 Effective length of database: 4,309,049 Effective search space: 150816715 Effective search space used: 150816715 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.2 bits)