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Conserved domains on  [gi|507075962|ref|WP_016146734|]
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rubrerythrin [Butyricicoccus pullicaecorum]

Protein Classification

rubrerythrin family protein( domain architecture ID 11446349)

rubrerythrin family protein such as Clostridium acetobutylicum rubrerythrin-1 and -2, which function as the terminal components of an NADH peroxidase (NADH:H(2)O(2) oxidoreductase)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YotD COG1592
Rubrerythrin [Energy production and conversion];
3-176 3.07e-101

Rubrerythrin [Energy production and conversion];


:

Pssm-ID: 441200 [Multi-domain]  Cd Length: 180  Bit Score: 289.03  E-value: 3.07e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962   3 NLKGTKTEANLMAAFAGESQARNKYTYYASKAKKDGYEQIAQLFLETANNEKEHAKIWFKLLHD-----GIPSTVENLKD 77
Cdd:COG1592    2 SLKGTKTEKNLLAAFAGESQARNRYTAFAKKAKKEGYPQIARLFRATAEAEKEHAKNHFKLLKGaagpvGIGDTAENLKA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962  78 AADGENYEWTDMYATFAKEAREEGFDDIAFLFEQVGEIEKEHEARYRKLLANIESGLVFSRDGDMIWQCSNCGHIVVGKQ 157
Cdd:COG1592   82 AIEGETYEWTEMYPEFAKVAEEEGFKEAARSFRYAAEAEKIHAERYKKLLENLEAGKVFKKDEEVVWVCPVCGYIHEGKE 161

                        170
                 ....*....|....*....
gi 507075962 158 APEVCPVCAHPKAYFQIKA 176
Cdd:COG1592  162 APEKCPVCGHPKSYFELFA 180
 
Name Accession Description Interval E-value
YotD COG1592
Rubrerythrin [Energy production and conversion];
3-176 3.07e-101

Rubrerythrin [Energy production and conversion];


Pssm-ID: 441200 [Multi-domain]  Cd Length: 180  Bit Score: 289.03  E-value: 3.07e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962   3 NLKGTKTEANLMAAFAGESQARNKYTYYASKAKKDGYEQIAQLFLETANNEKEHAKIWFKLLHD-----GIPSTVENLKD 77
Cdd:COG1592    2 SLKGTKTEKNLLAAFAGESQARNRYTAFAKKAKKEGYPQIARLFRATAEAEKEHAKNHFKLLKGaagpvGIGDTAENLKA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962  78 AADGENYEWTDMYATFAKEAREEGFDDIAFLFEQVGEIEKEHEARYRKLLANIESGLVFSRDGDMIWQCSNCGHIVVGKQ 157
Cdd:COG1592   82 AIEGETYEWTEMYPEFAKVAEEEGFKEAARSFRYAAEAEKIHAERYKKLLENLEAGKVFKKDEEVVWVCPVCGYIHEGKE 161

                        170
                 ....*....|....*....
gi 507075962 158 APEVCPVCAHPKAYFQIKA 176
Cdd:COG1592  162 APEKCPVCGHPKSYFELFA 180
Rubrerythrin cd01041
Rubrerythrin, ferritin-like diiron-binding domain; Rubrerythrin domain is a nonheme iron ...
 8-131 1.35e-62

Rubrerythrin, ferritin-like diiron-binding domain; Rubrerythrin domain is a nonheme iron binding domain found in many air-sensitive bacteria and archaea and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The homodimeric rubrerythrin protein contains a binuclear metal center located within a four helix bundle. Many, but not all, rubrerythrin proteins have a second domain with a rubredoxin-like hexacoordinated iron center. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system but its function is still poorly understood.


Pssm-ID: 153100  Cd Length: 134  Bit Score: 189.33  E-value: 1.35e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962   8 KTEANLMAAFAGESQARNKYTYYASKAKKDGYEQIAQLFLETANNEKEHAKIWFKLLHD----------GIPSTVENLKD 77
Cdd:cd01041    1 KTEKNLLAAFAGESQARNRYTYFAEKARKEGYEQIARLFRATAENEKEHAKGHFKLLKGlgggdtgppiGIGDTLENLKA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 507075962  78 AADGENYEWTDMYATFAKEAREEGFDDIAFLFEQVGEIEKEHEARYRKLLANIE 131
Cdd:cd01041   81 AIAGETYEYTEMYPEFAEVAEEEGFKEAARSFEAIAEAEKVHAERYKKALENLE 134
Rubrerythrin pfam02915
Rubrerythrin; This domain has a ferritin-like fold.
 12-127 9.12e-27

Rubrerythrin; This domain has a ferritin-like fold.


Pssm-ID: 397180  Cd Length: 137  Bit Score: 98.58  E-value: 9.12e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962   12 NLMAAFAGESQARNKYTYYASKAKKDgYEQIAQLFLETANNEKEHAKIWFKLLHDGIPS--------------------- 70
Cdd:pfam02915   2 NLEKAIAGESSARRRYKELAEKAKNE-YPQIAELFEEMAEEERRHAGFLNKLLKDLFPGleliplehvrgyaefppkflt 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 507075962   71 TVENLKDAADGENYEWTDMYATFAKEAREEGFDDIAFLFEQVGEIEKEHEARYRKLL 127
Cdd:pfam02915  81 TATNLEEAIEGEYAEEEEMYRFYEELAEKEGYPEARKLFEDLAEAEKRHEERFRKLL 137
 
Name Accession Description Interval E-value
YotD COG1592
Rubrerythrin [Energy production and conversion];
3-176 3.07e-101

Rubrerythrin [Energy production and conversion];


Pssm-ID: 441200 [Multi-domain]  Cd Length: 180  Bit Score: 289.03  E-value: 3.07e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962   3 NLKGTKTEANLMAAFAGESQARNKYTYYASKAKKDGYEQIAQLFLETANNEKEHAKIWFKLLHD-----GIPSTVENLKD 77
Cdd:COG1592    2 SLKGTKTEKNLLAAFAGESQARNRYTAFAKKAKKEGYPQIARLFRATAEAEKEHAKNHFKLLKGaagpvGIGDTAENLKA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962  78 AADGENYEWTDMYATFAKEAREEGFDDIAFLFEQVGEIEKEHEARYRKLLANIESGLVFSRDGDMIWQCSNCGHIVVGKQ 157
Cdd:COG1592   82 AIEGETYEWTEMYPEFAKVAEEEGFKEAARSFRYAAEAEKIHAERYKKLLENLEAGKVFKKDEEVVWVCPVCGYIHEGKE 161

                        170
                 ....*....|....*....
gi 507075962 158 APEVCPVCAHPKAYFQIKA 176
Cdd:COG1592  162 APEKCPVCGHPKSYFELFA 180
Rubrerythrin cd01041
Rubrerythrin, ferritin-like diiron-binding domain; Rubrerythrin domain is a nonheme iron ...
 8-131 1.35e-62

Rubrerythrin, ferritin-like diiron-binding domain; Rubrerythrin domain is a nonheme iron binding domain found in many air-sensitive bacteria and archaea and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The homodimeric rubrerythrin protein contains a binuclear metal center located within a four helix bundle. Many, but not all, rubrerythrin proteins have a second domain with a rubredoxin-like hexacoordinated iron center. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system but its function is still poorly understood.


Pssm-ID: 153100  Cd Length: 134  Bit Score: 189.33  E-value: 1.35e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962   8 KTEANLMAAFAGESQARNKYTYYASKAKKDGYEQIAQLFLETANNEKEHAKIWFKLLHD----------GIPSTVENLKD 77
Cdd:cd01041    1 KTEKNLLAAFAGESQARNRYTYFAEKARKEGYEQIARLFRATAENEKEHAKGHFKLLKGlgggdtgppiGIGDTLENLKA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 507075962  78 AADGENYEWTDMYATFAKEAREEGFDDIAFLFEQVGEIEKEHEARYRKLLANIE 131
Cdd:cd01041   81 AIAGETYEYTEMYPEFAEVAEEEGFKEAARSFEAIAEAEKVHAERYKKALENLE 134
Rubrerythrin pfam02915
Rubrerythrin; This domain has a ferritin-like fold.
 12-127 9.12e-27

Rubrerythrin; This domain has a ferritin-like fold.


Pssm-ID: 397180  Cd Length: 137  Bit Score: 98.58  E-value: 9.12e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962   12 NLMAAFAGESQARNKYTYYASKAKKDgYEQIAQLFLETANNEKEHAKIWFKLLHDGIPS--------------------- 70
Cdd:pfam02915   2 NLEKAIAGESSARRRYKELAEKAKNE-YPQIAELFEEMAEEERRHAGFLNKLLKDLFPGleliplehvrgyaefppkflt 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 507075962   71 TVENLKDAADGENYEWTDMYATFAKEAREEGFDDIAFLFEQVGEIEKEHEARYRKLL 127
Cdd:pfam02915  81 TATNLEEAIEGEYAEEEEMYRFYEELAEKEGYPEARKLFEDLAEAEKRHEERFRKLL 137
rubredoxin_SM cd00729
Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present ...
 142-173 5.13e-15

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: 65.29  E-value: 5.13e-15
                         10        20        30
                 ....*....|....*....|....*....|..
gi 507075962 142 MIWQCSNCGHIVVGKQAPEVCPVCAHPKAYFQ 173
Cdd:cd00729    1 KVWVCPVCGYIHEGEEAPEKCPICGAPKEKFE 32
rubredoxin_like cd00350
Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family ...
 143-173 3.90e-12

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: 57.56  E-value: 3.90e-12
                         10        20        30
                 ....*....|....*....|....*....|.
gi 507075962 143 IWQCSNCGHIVVGKQAPEVCPVCAHPKAYFQ 173
Cdd:cd00350    1 KYVCPVCGYIYDGEEAPWVCPVCGAPKDKFE 31
Rubrerythrin_like cd01046
rubrerythrin-like, diiron-binding domain; Rubrerythrin-like domain, similar to rubrerythrin, a ...
 8-127 1.01e-08

rubrerythrin-like, diiron-binding domain; Rubrerythrin-like domain, similar to rubrerythrin, a nonheme iron binding domain found in many air-sensitive bacteria and archaea, and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system. The rubrerythrin protein has two domains, a binuclear metal center located within a four-helix bundle of the rubrerythrin domain, and a rubredoxin domain. The Rubrerythrin-like domains in this CD are singular domains (no C-terminus rubredoxin domain) and are phylogenetically distinct from rubrerythrin domains of rubrerythrin-rubredoxin proteins.


Pssm-ID: 153105  Cd Length: 123  Bit Score: 51.15  E-value: 1.01e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962   8 KTEANLMAAFAGESQARNKYTYYASKAKKDGYEQIAQLFLETANNEKEHAKIWFKLLHDGIPSTVENLKDAADGENYEwT 87
Cdd:cd01046    1 DLEEDLEANFKGETTEVGMYLAMARVAQREGYPEVAEELKRIAMEEAEHAARFAELLGKVSEDTKENLEMMLEGEAGA-N 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 507075962  88 DMYATFAKEAREEGFDDIAFLFEQVGEIEKEHEARYRKLL 127
Cdd:cd01046   80 EGKKDAATEAKAEGLDEAHDFFHEAAKDEARHGKMLKGLL 119
YhjR COG1633
Rubrerythrin, includes spore coat protein YhjR [Inorganic ion transport and metabolism];
13-130 2.86e-08

Rubrerythrin, includes spore coat protein YhjR [Inorganic ion transport and metabolism];


Pssm-ID: 441240  Cd Length: 141  Bit Score: 50.11  E-value: 2.86e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962  13 LMAAFAGESQARNKYTYYASKAKKdgyEQIAQLFLETANNEKEHAKIWFKLLH-------------------------DG 67
Cdd:COG1633    6 LKEAIAMEEEAIEFYLELAEKAKD---PELKKLFEELAEEEKKHAELLEKLYEklggkpvappeeesqpglaelmdklDG 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 507075962  68 IPSTVENLKDAADGENyEWTDMYATFAKEAREEgfdDIAFLFEQVGEIEKEHEARYRKLLANI 130
Cdd:COG1633   83 SVSDAEALELAIATEK-DAIEFYRELAAKVGDP---EIKKLFEELAADEKEHAALLEGLYDRL 141
Ferritin_like cd00657
Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, ...
 13-127 5.15e-06

Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF).


Pssm-ID: 153097  Cd Length: 130  Bit Score: 44.02  E-value: 5.15e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962  13 LMAAFAGESQARNKYTYYASKAKkdgYEQIAQLFLETANNEKEHAKIWFKLLHD--GIP------------------STV 72
Cdd:cd00657    3 LNDALAGEYAAIIAYGQLAARAP---DPDLKDELLEIADEERRHADALAERLRElgGTPplppahllaayalpktsdDPA 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 507075962  73 ENLKDAADGENYEwTDMYATFAKEAREEgfdDIAFLFEQVGEIEKEHEARYRKLL 127
Cdd:cd00657   80 EALRAALEVEARA-IAAYRELIEQADDP---ELRRLLERILADEQRHAAWFRKLL 130
Rubrerythrin_like cd01046
rubrerythrin-like, diiron-binding domain; Rubrerythrin-like domain, similar to rubrerythrin, a ...
 89-134 1.50e-03

rubrerythrin-like, diiron-binding domain; Rubrerythrin-like domain, similar to rubrerythrin, a nonheme iron binding domain found in many air-sensitive bacteria and archaea, and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system. The rubrerythrin protein has two domains, a binuclear metal center located within a four-helix bundle of the rubrerythrin domain, and a rubredoxin domain. The Rubrerythrin-like domains in this CD are singular domains (no C-terminus rubredoxin domain) and are phylogenetically distinct from rubrerythrin domains of rubrerythrin-rubredoxin proteins.


Pssm-ID: 153105  Cd Length: 123  Bit Score: 36.90  E-value: 1.50e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 507075962  89 MYATFAKEAREEGFDDIAFLFEQVGEIEKEHEARYRKLLANIESGL 134
Cdd:cd01046   19 MYLAMARVAQREGYPEVAEELKRIAMEEAEHAARFAELLGKVSEDT 64
Ferritin_like_AB cd01045
Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Ferritin-like ...
 13-131 3.62e-03

Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Ferritin-like domain found in archaea and bacteria (Ferritin_like_AB). This uncharacterized domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins whose function is unknown. This family includes unknown or hypothetical proteins which were sequenced from mostly anaerobic or microaerophilic metal-metabolizing and/or nitrogen-fixing microbes. The family includes sequences from ferric-, sulfate-, and arsenic-reducing bacteria, Geobacter, Magnetospirillum, Desulfovibrio, and Desulfitobacterium. Also included are several nitrogen-fixing endosymbiotic bacteria, Rhizobium, Mesorhizobium, and Bradyrhizobium; also phototrophic purple nonsulfur bacteria, Rhodobacter and Rhodopseudomonas, as well as, obligate thermophiles, Thermotoga, Thermoanaerobacter, and Pyrococcus. The conserved residues of a diiron center are present in this uncharacterized domain.


Pssm-ID: 153104  Cd Length: 139  Bit Score: 36.17  E-value: 3.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507075962  13 LMAAFAGESQARNKYTYYASKAKKDGyeqIAQLFLETANNEKEHAKIWFKLLHDGIPSTVENLKDaadgENYEWTDMYAT 92
Cdd:cd01045    3 LALAIKMEEEAAEFYLELAEKAKDPE---LKKLFEELAEEEKEHAERLEELYEKLFGEELPELEP----EDYKEEVEEEP 75

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 507075962  93 FAKEAREEGFDDIAFLfEQVGEIEKEHEARYRKLLANIE 131
Cdd:cd01045   76 EFKKALESLMDPLEAL-RLAIEIEKDAIEFYEELAEKAE 113
 
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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