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Conserved domains on  [gi|496059557|ref|WP_008784064|]
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MULTISPECIES: YbdD/YjiX family protein [Citrobacter]

Protein Classification

YbdD/YjiX family protein( domain architecture ID 10006762)

YbdD/YjiX family protein might be an uncharacterized selenoprotein, similar to Escherichia coli YbdD and YijX

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbdD COG2879
Uncharacterized short protein YbdD, DUF466 family [Function unknown];
1-65 4.40e-35

Uncharacterized short protein YbdD, DUF466 family [Function unknown];


:

Pssm-ID: 442126  Cd Length: 64  Bit Score: 112.68  E-value: 4.40e-35
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 496059557  1 MFETLAKAGKYLGQTARLMIGMPDYDNYVEHMRVTHPDQTPMTYEEFFRERQDARYGGKGGaKCC 65
Cdd:COG2879   1 MLARLRRALRRLRQTARLMVGVPDYDRYVAHMRRHHPDQPPMTEREFFRERQDARYGGPGG-RCC 64
 
Name Accession Description Interval E-value
YbdD COG2879
Uncharacterized short protein YbdD, DUF466 family [Function unknown];
1-65 4.40e-35

Uncharacterized short protein YbdD, DUF466 family [Function unknown];


Pssm-ID: 442126  Cd Length: 64  Bit Score: 112.68  E-value: 4.40e-35
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 496059557  1 MFETLAKAGKYLGQTARLMIGMPDYDNYVEHMRVTHPDQTPMTYEEFFRERQDARYGGKGGaKCC 65
Cdd:COG2879   1 MLARLRRALRRLRQTARLMVGVPDYDRYVAHMRRHHPDQPPMTEREFFRERQDARYGGPGG-RCC 64
Sel_put pfam04328
Selenoprotein, putative; This entry includes a group of putative selenoproteins from ...
 7-65 1.03e-30

Selenoprotein, putative; This entry includes a group of putative selenoproteins from Proteobacteria, Actinobacteria and Firmicutes. The invariant cysteine at the C terminus is encoded by a TGA Sec codon in some Epsilonproteobacteria, suggesting a redox activity for the protein. Some members of this family have been suggested to be required for pyruvate transport in diverse bacteria, along with a CstA-like transporter found adjacent in the genome (see Supplementary note 5 in.)


Pssm-ID: 427871  Cd Length: 58  Bit Score: 101.51  E-value: 1.03e-30
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 496059557   7 KAGKYLGQTARLMIGMPDYDNYVEHMRVTHPDQTPMTYEEFFRERQDARYGGKGGaKCC 65
Cdd:pfam04328  1 RALRRVRQYARLMVGVPDYDRYVAHMRRHHPDKPPMSEREFFRERQDARYGGPGG-RCC 58
KCU-star NF033934
KCU-star family selenoprotein; This family is named KCU-star because nearly all member ...
 18-64 3.48e-15

KCU-star family selenoprotein; This family is named KCU-star because nearly all member proteins end with tripeptide lysine-cysteine-selenocysteine, followed immediately by a stop codon (represented by an asterisk, or star). Members occur in primarily in species of Helicobacter (although not Helicobacter pylori, in which selenocysteine incorporation capability has been lost) and Campylobacter. This small family belongs to the larger YbdD/YjiX (DUF466) family described by Pfam model PF04328, which regularly occur in the company of CstA family pyruvate transport proteins, and may be part of the transporter.


Pssm-ID: 411492  Cd Length: 57  Bit Score: 62.50  E-value: 3.48e-15
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 496059557 18 LMIGMPDYDNYVEHMRVTHPDQTPMTYEEFFRERQDARYGGkGGAKC 64
Cdd:NF033934 11 PLVGLPSYDKYLEHMRKNHPDKIPKSRKEFFKEALEAKYGA-GRNKC 56
 
Name Accession Description Interval E-value
YbdD COG2879
Uncharacterized short protein YbdD, DUF466 family [Function unknown];
1-65 4.40e-35

Uncharacterized short protein YbdD, DUF466 family [Function unknown];


Pssm-ID: 442126  Cd Length: 64  Bit Score: 112.68  E-value: 4.40e-35
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 496059557  1 MFETLAKAGKYLGQTARLMIGMPDYDNYVEHMRVTHPDQTPMTYEEFFRERQDARYGGKGGaKCC 65
Cdd:COG2879   1 MLARLRRALRRLRQTARLMVGVPDYDRYVAHMRRHHPDQPPMTEREFFRERQDARYGGPGG-RCC 64
Sel_put pfam04328
Selenoprotein, putative; This entry includes a group of putative selenoproteins from ...
 7-65 1.03e-30

Selenoprotein, putative; This entry includes a group of putative selenoproteins from Proteobacteria, Actinobacteria and Firmicutes. The invariant cysteine at the C terminus is encoded by a TGA Sec codon in some Epsilonproteobacteria, suggesting a redox activity for the protein. Some members of this family have been suggested to be required for pyruvate transport in diverse bacteria, along with a CstA-like transporter found adjacent in the genome (see Supplementary note 5 in.)


Pssm-ID: 427871  Cd Length: 58  Bit Score: 101.51  E-value: 1.03e-30
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 496059557   7 KAGKYLGQTARLMIGMPDYDNYVEHMRVTHPDQTPMTYEEFFRERQDARYGGKGGaKCC 65
Cdd:pfam04328  1 RALRRVRQYARLMVGVPDYDRYVAHMRRHHPDKPPMSEREFFRERQDARYGGPGG-RCC 58
KCU-star NF033934
KCU-star family selenoprotein; This family is named KCU-star because nearly all member ...
 18-64 3.48e-15

KCU-star family selenoprotein; This family is named KCU-star because nearly all member proteins end with tripeptide lysine-cysteine-selenocysteine, followed immediately by a stop codon (represented by an asterisk, or star). Members occur in primarily in species of Helicobacter (although not Helicobacter pylori, in which selenocysteine incorporation capability has been lost) and Campylobacter. This small family belongs to the larger YbdD/YjiX (DUF466) family described by Pfam model PF04328, which regularly occur in the company of CstA family pyruvate transport proteins, and may be part of the transporter.


Pssm-ID: 411492  Cd Length: 57  Bit Score: 62.50  E-value: 3.48e-15
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 496059557 18 LMIGMPDYDNYVEHMRVTHPDQTPMTYEEFFRERQDARYGGkGGAKC 64
Cdd:NF033934 11 PLVGLPSYDKYLEHMRKNHPDKIPKSRKEFFKEALEAKYGA-GRNKC 56
 
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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