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Conserved domains on  [gi|499172655|ref|WP_010870242|]
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MULTISPECIES: rubredoxin-like domain-containing protein [Methanocaldococcus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YotD super family cl27730
Rubrerythrin [Energy production and conversion];
4-26 5.54e-09

Rubrerythrin [Energy production and conversion];


The actual alignment was detected with superfamily member COG1592:

Pssm-ID: 441200 [Multi-domain]  Cd Length: 180  Bit Score: 48.66  E-value: 5.54e-09
                         10        20
                 ....*....|....*....|...
gi 499172655   4 WKCSNCGYVFEAEKPPERCPNCG 26
Cdd:COG1592  148 WVCPVCGYIHEGKEAPEKCPVCG 170
PolC_DP2 super family cl29799
DNA polymerase II large subunit DP2;
5-49 5.85e-03

DNA polymerase II large subunit DP2;


The actual alignment was detected with superfamily member pfam03833:

Pssm-ID: 427537  Cd Length: 866  Bit Score: 32.51  E-value: 5.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 499172655    5 KCSNCGyvfeAEKPPERCPNCGEKCTFYDVsCytPECGFKGYDPK 49
Cdd:pfam03833 622 RCPNCG----KETFENRCPDCGAHTEPVYV-C--PKCGIEVEDEK 659
 
Name Accession Description Interval E-value
YotD COG1592
Rubrerythrin [Energy production and conversion];
4-26 5.54e-09

Rubrerythrin [Energy production and conversion];


Pssm-ID: 441200 [Multi-domain]  Cd Length: 180  Bit Score: 48.66  E-value: 5.54e-09
                         10        20
                 ....*....|....*....|...
gi 499172655   4 WKCSNCGYVFEAEKPPERCPNCG 26
Cdd:COG1592  148 WVCPVCGYIHEGKEAPEKCPVCG 170
rubredoxin_SM cd00729
Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present ...
 4-26 3.25e-06

Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.


Pssm-ID: 238371 [Multi-domain]  Cd Length: 34  Bit Score: 38.71  E-value: 3.25e-06
                        10        20
                ....*....|....*....|...
gi 499172655  4 WKCSNCGYVFEAEKPPERCPNCG 26
Cdd:cd00729   3 WVCPVCGYIHEGEEAPEKCPICG 25
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 4-34 1.64e-04

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 37.25  E-value: 1.64e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 499172655   4 WKCSNCGYV--FEAEKPPERCPNCGEKCTFYDV 34
Cdd:PRK07225 545 YVCAKCGMIaiYDKKRNRKYCPICGEETDIYPV 577
HypA pfam01155
Hydrogenase/urease nickel incorporation, metallochaperone, hypA; HypA is a metallochaperone ...
 5-26 3.01e-04

Hydrogenase/urease nickel incorporation, metallochaperone, hypA; HypA is a metallochaperone that binds nickel to bring it safely to its target. The targets for Hypa are the nickel-containing enzymes [Ni,Fe]-hydrogenase and urease. The nickel coordinates with four nitrogens within the protein. The four conserved cysteines towards the C-terminus bind one zinc moiety probably to stabilize the protein fold.


Pssm-ID: 460085  Cd Length: 111  Bit Score: 35.58  E-value: 3.01e-04
                          10        20
                  ....*....|....*....|..
gi 499172655    5 KCSNCGYVFEAEKPPERCPNCG 26
Cdd:pfam01155  71 RCRDCGKEFELEERDLVCPRCG 92
PolC_DP2 pfam03833
DNA polymerase II large subunit DP2;
5-49 5.85e-03

DNA polymerase II large subunit DP2;


Pssm-ID: 427537  Cd Length: 866  Bit Score: 32.51  E-value: 5.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 499172655    5 KCSNCGyvfeAEKPPERCPNCGEKCTFYDVsCytPECGFKGYDPK 49
Cdd:pfam03833 622 RCPNCG----KETFENRCPDCGAHTEPVYV-C--PKCGIEVEDEK 659
 
Name Accession Description Interval E-value
YotD COG1592
Rubrerythrin [Energy production and conversion];
4-26 5.54e-09

Rubrerythrin [Energy production and conversion];


Pssm-ID: 441200 [Multi-domain]  Cd Length: 180  Bit Score: 48.66  E-value: 5.54e-09
                         10        20
                 ....*....|....*....|...
gi 499172655   4 WKCSNCGYVFEAEKPPERCPNCG 26
Cdd:COG1592  148 WVCPVCGYIHEGKEAPEKCPVCG 170
rubredoxin_SM cd00729
Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present ...
 4-26 3.25e-06

Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.


Pssm-ID: 238371 [Multi-domain]  Cd Length: 34  Bit Score: 38.71  E-value: 3.25e-06
                        10        20
                ....*....|....*....|...
gi 499172655  4 WKCSNCGYVFEAEKPPERCPNCG 26
Cdd:cd00729   3 WVCPVCGYIHEGEEAPEKCPICG 25
rubredoxin_like cd00350
Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family ...
 4-26 2.53e-05

Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.


Pssm-ID: 238210 [Multi-domain]  Cd Length: 33  Bit Score: 36.76  E-value: 2.53e-05
                        10        20
                ....*....|....*....|...
gi 499172655  4 WKCSNCGYVFEAEKPPERCPNCG 26
Cdd:cd00350   2 YVCPVCGYIYDGEEAPWVCPVCG 24
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 4-34 1.64e-04

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 37.25  E-value: 1.64e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 499172655   4 WKCSNCGYV--FEAEKPPERCPNCGEKCTFYDV 34
Cdd:PRK07225 545 YVCAKCGMIaiYDKKRNRKYCPICGEETDIYPV 577
HypA pfam01155
Hydrogenase/urease nickel incorporation, metallochaperone, hypA; HypA is a metallochaperone ...
 5-26 3.01e-04

Hydrogenase/urease nickel incorporation, metallochaperone, hypA; HypA is a metallochaperone that binds nickel to bring it safely to its target. The targets for Hypa are the nickel-containing enzymes [Ni,Fe]-hydrogenase and urease. The nickel coordinates with four nitrogens within the protein. The four conserved cysteines towards the C-terminus bind one zinc moiety probably to stabilize the protein fold.


Pssm-ID: 460085  Cd Length: 111  Bit Score: 35.58  E-value: 3.01e-04
                          10        20
                  ....*....|....*....|..
gi 499172655    5 KCSNCGYVFEAEKPPERCPNCG 26
Cdd:pfam01155  71 RCRDCGKEFELEERDLVCPRCG 92
COG3357 COG3357
Predicted transcriptional regulator, contains HTH and Zn-ribbon domains [Transcription];
5-25 3.40e-04

Predicted transcriptional regulator, contains HTH and Zn-ribbon domains [Transcription];


Pssm-ID: 442585  Cd Length: 92  Bit Score: 34.87  E-value: 3.40e-04
                        10        20
                ....*....|....*....|...
gi 499172655  5 KCSNCGYVFEAEKP--PERCPNC 25
Cdd:COG3357  55 ECRDCGFVFFDDRLnkPSRCPRC 77
HybF COG0375
Hydrogenase maturation factor HypA/HybF, metallochaperone involved in Ni insertion ...
 5-26 3.67e-04

Hydrogenase maturation factor HypA/HybF, metallochaperone involved in Ni insertion [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440144  Cd Length: 113  Bit Score: 35.14  E-value: 3.67e-04
                         10        20
                 ....*....|....*....|..
gi 499172655   5 KCSNCGYVFEAEKPPERCPNCG 26
Cdd:COG0375   72 RCRDCGKEFELEELFLRCPKCG 93
Nob1 COG1439
rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis];
4-26 9.40e-04

rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441048 [Multi-domain]  Cd Length: 155  Bit Score: 34.44  E-value: 9.40e-04
                         10        20
                 ....*....|....*....|....*
gi 499172655   4 WK--CSNCGYVFEaeKPPERCPNCG 26
Cdd:COG1439  124 WRyrCTGCGREFD--EPEEECPICG 146
Mcm2 COG1241
DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and ...
 5-31 1.06e-03

DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair];


Pssm-ID: 440854 [Multi-domain]  Cd Length: 682  Bit Score: 34.78  E-value: 1.06e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 499172655   5 KCSNCGYVFEAE------KPPERCPNCGEKCTF 31
Cdd:COG1241  130 ECPRCGTETYVPqtgeklQEPHECPGCGRQGPF 162
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 4-27 2.21e-03

bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a role in recombination and recombinational repair of DNA damaged by UV radiation, X-rays, and chemical agent and is responsible for the stabilization or processing of branched DNA molecules.


Pssm-ID: 410866 [Multi-domain]  Cd Length: 268  Bit Score: 33.66  E-value: 2.21e-03
                         10        20
                 ....*....|....*....|....
gi 499172655   4 WKCSNCGYvfEAEKPPERCPNCGE 27
Cdd:cd01121    1 YVCQECGY--ESPKWLGRCPSCGE 22
TOPRIM_TopoIA_RevGyr cd03361
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA ...
 4-28 2.64e-03

TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173781 [Multi-domain]  Cd Length: 170  Bit Score: 33.44  E-value: 2.64e-03
                         10        20
                 ....*....|....*....|....*
gi 499172655   4 WKCSNCGYVFEAEKPpeRCPNCGEK 28
Cdd:cd03361   78 KRCRDCGYQFTEDSD--KCPRCGSE 100
SIRT5_Af1_CobB cd01412
SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human ...
 5-26 4.72e-03

SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.


Pssm-ID: 238703  Cd Length: 224  Bit Score: 32.95  E-value: 4.72e-03
                         10        20
                 ....*....|....*....|....*..
gi 499172655   5 KCSNCGYVFE-----AEKPPERCPNCG 26
Cdd:cd01412  111 RCSSCGYVGEnneeiPEEELPRCPKCG 137
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 4-34 5.16e-03

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 33.01  E-value: 5.16e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 499172655    4 WKCSNCGYV--FEAEKPPERCPNCGEKCTFYDV 34
Cdd:PRK08565 1043 YVCELCGHIawYDRRKNKYVCPIHGDKGNISPV 1075
PolC_DP2 pfam03833
DNA polymerase II large subunit DP2;
5-49 5.85e-03

DNA polymerase II large subunit DP2;


Pssm-ID: 427537  Cd Length: 866  Bit Score: 32.51  E-value: 5.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 499172655    5 KCSNCGyvfeAEKPPERCPNCGEKCTFYDVsCytPECGFKGYDPK 49
Cdd:pfam03833 622 RCPNCG----KETFENRCPDCGAHTEPVYV-C--PKCGIEVEDEK 659
PfuEndoQ-like cd19067
lesion-specific endonuclease similar to Pyrococcus furiosus EndoQ; Pyrococcus furiosus EndoQ ...
 6-26 6.40e-03

lesion-specific endonuclease similar to Pyrococcus furiosus EndoQ; Pyrococcus furiosus EndoQ is a lesion-specific endonuclease which is assumed to be involved in DNA repair pathways in Thermococcales. It recognizes a deaminated base and hydrolyzes the phosphodiester bond 5' to the site of the lesion. Initially identified as a hypoxanthine-specific endonuclease, it has now been shown that EndoQ also recognizes uracil, xanthine, and apurinic/apyrimidinic (AP) sites in DNA, and that a homolog in Bacillus pumilus shares functional properties of the archaeal EndoQs.


Pssm-ID: 410989 [Multi-domain]  Cd Length: 395  Bit Score: 32.38  E-value: 6.40e-03
                         10        20
                 ....*....|....*....|....
gi 499172655   6 CSNCGYVF---EAEKPPERCPNCG 26
Cdd:cd19067  260 HRKCGVSLspeETKKLNGICPVCG 283
COG2331 COG2331
Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction ...
 5-28 8.02e-03

Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only];


Pssm-ID: 441902  Cd Length: 77  Bit Score: 31.17  E-value: 8.02e-03
                        10        20
                ....*....|....*....|....*....
gi 499172655  5 KCSNCGYVFEA-----EKPPERCPNCGEK 28
Cdd:COG2331   7 RCESCGHEFEVlqkmsDDPLTVCPECGGP 35
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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