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Conserved domains on  [gi|1080273633|gb|OFK66005|]
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autonomous glycyl radical cofactor GrcA [Corynebacterium sp. HMSC074A09]

Protein Classification

autonomous glycyl radical cofactor GrcA( domain architecture ID 10013746)

autonomous glycyl radical cofactor GrcA is similar to pyruvate formate-lyase-activating protein and may act as a radical domain for damaged PFL or other radical proteins

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11127 PRK11127
autonomous glycyl radical cofactor GrcA; Provisional
 1-82 3.57e-41

autonomous glycyl radical cofactor GrcA; Provisional


:

Pssm-ID: 182983 [Multi-domain]  Cd Length: 127  Bit Score: 131.12  E-value: 3.57e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080273633   1 MATKTFDERLASMKANRTANN----------------------------MNSGLYHANINVLDKSTLEDAVEHPEKYPNL 52
Cdd:PRK11127   17 NSFWLLDSEKGEARCIVAKAGyaedqvvavsklgeieyrevpvevkpevRVEGGQHLNVNVLRRETLEDAVKHPEKYPQL 96

                          90       100       110
                  ....*....|....*....|....*....|
gi 1080273633  53 TVRVSGYAVNFVKLTREQQLDVISRTFHQG 82
Cdd:PRK11127   97 TIRVSGYAVRFNSLTPEQQRDVIARTFTES 126
 
Name Accession Description Interval E-value
PRK11127 PRK11127
autonomous glycyl radical cofactor GrcA; Provisional
 1-82 3.57e-41

autonomous glycyl radical cofactor GrcA; Provisional


Pssm-ID: 182983 [Multi-domain]  Cd Length: 127  Bit Score: 131.12  E-value: 3.57e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080273633   1 MATKTFDERLASMKANRTANN----------------------------MNSGLYHANINVLDKSTLEDAVEHPEKYPNL 52
Cdd:PRK11127   17 NSFWLLDSEKGEARCIVAKAGyaedqvvavsklgeieyrevpvevkpevRVEGGQHLNVNVLRRETLEDAVKHPEKYPQL 96

                          90       100       110
                  ....*....|....*....|....*....|
gi 1080273633  53 TVRVSGYAVNFVKLTREQQLDVISRTFHQG 82
Cdd:PRK11127   97 TIRVSGYAVRFNSLTPEQQRDVIARTFTES 126
PflD COG1882
Pyruvate-formate lyase [Energy production and conversion]; Pyruvate-formate lyase is part of ...
 22-81 1.73e-34

Pyruvate-formate lyase [Energy production and conversion]; Pyruvate-formate lyase is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 441486 [Multi-domain]  Cd Length: 789  Bit Score: 123.34  E-value: 1.73e-34
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080273633  22 MNSGLYHANINVLDKSTLEDAVEHPEKYPNLTVRVSGYAVNFVKLTREQQLDVISRTFHQ 81
Cdd:COG1882   729 FDLGGHHIQFNVVDRETLLDAQKHPEKYPDLTVRVAGYSAYFVELSKEQQDDIIARTEHE 788
PFL1 cd01678
Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, ...
 25-80 5.05e-34

Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate in which two cysteines and one glycine form radicals that are required for catalysis. PFL has a ten-stranded alpha/beta barrel domain that is structurally similar to those of all three ribonucleotide reductase (RNR) classes as well as benzylsuccinate synthase and B12-independent glycerol dehydratase.


Pssm-ID: 153087 [Multi-domain]  Cd Length: 738  Bit Score: 122.09  E-value: 5.05e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1080273633  25 GLYHANINVLDKSTLEDAVEHPEKYPNLTVRVSGYAVNFVKLTREQQLDVISRTFH 80
Cdd:cd01678   683 GGHHLNVNVLNRETLLDAMEHPEKYPQLTIRVSGYAVNFVKLTREQQLDVISRTFH 738
Gly_radical pfam01228
Glycine radical;
25-64 3.04e-21

Glycine radical;


Pssm-ID: 426140 [Multi-domain]  Cd Length: 106  Bit Score: 79.90  E-value: 3.04e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1080273633  25 GLYHANINVLDKSTLEDAVEHPEKYPNLTVRVSGYAVNFV 64
Cdd:pfam01228  67 GGHHLQFNVVDRETLPDAQKHPEKYPDLTVRVSGYSANFV 106
choline_CutC TIGR04394
choline trimethylamine-lyase; Members of this family, homologs to pyruvate formate-lyases and ...
 17-78 3.98e-13

choline trimethylamine-lyase; Members of this family, homologs to pyruvate formate-lyases and benzylsuccinate synthases, are glycine radical enzymes that appear to act as choline TMA-lyase, that is, to perform a C-N bond cleavage turning choline into trimethylamine (TMA) plus acetaldehyde. The gene symbol is cutC, for choline utilization. The activase, CutD, is a radical SAM enzyme. [Energy metabolism, Amino acids and amines]


Pssm-ID: 275187 [Multi-domain]  Cd Length: 789  Bit Score: 62.51  E-value: 3.98e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1080273633  17 RTANNMNSGlyHANINVLDKSTLEDAVEHPEKYPNLTVRVSGYAVNFVKLTREQQLDVISRT 78
Cdd:TIGR04394 725 RTASILGNG--EMQFNYLDNETLLDAQQHPEKYRDLVVRVAGYSAFFVELCKDVQDEIISRT 784
 
Name Accession Description Interval E-value
PRK11127 PRK11127
autonomous glycyl radical cofactor GrcA; Provisional
 1-82 3.57e-41

autonomous glycyl radical cofactor GrcA; Provisional


Pssm-ID: 182983 [Multi-domain]  Cd Length: 127  Bit Score: 131.12  E-value: 3.57e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080273633   1 MATKTFDERLASMKANRTANN----------------------------MNSGLYHANINVLDKSTLEDAVEHPEKYPNL 52
Cdd:PRK11127   17 NSFWLLDSEKGEARCIVAKAGyaedqvvavsklgeieyrevpvevkpevRVEGGQHLNVNVLRRETLEDAVKHPEKYPQL 96

                          90       100       110
                  ....*....|....*....|....*....|
gi 1080273633  53 TVRVSGYAVNFVKLTREQQLDVISRTFHQG 82
Cdd:PRK11127   97 TIRVSGYAVRFNSLTPEQQRDVIARTFTES 126
PflD COG1882
Pyruvate-formate lyase [Energy production and conversion]; Pyruvate-formate lyase is part of ...
 22-81 1.73e-34

Pyruvate-formate lyase [Energy production and conversion]; Pyruvate-formate lyase is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 441486 [Multi-domain]  Cd Length: 789  Bit Score: 123.34  E-value: 1.73e-34
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080273633  22 MNSGLYHANINVLDKSTLEDAVEHPEKYPNLTVRVSGYAVNFVKLTREQQLDVISRTFHQ 81
Cdd:COG1882   729 FDLGGHHIQFNVVDRETLLDAQKHPEKYPDLTVRVAGYSAYFVELSKEQQDDIIARTEHE 788
PFL1 cd01678
Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, ...
 25-80 5.05e-34

Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate in which two cysteines and one glycine form radicals that are required for catalysis. PFL has a ten-stranded alpha/beta barrel domain that is structurally similar to those of all three ribonucleotide reductase (RNR) classes as well as benzylsuccinate synthase and B12-independent glycerol dehydratase.


Pssm-ID: 153087 [Multi-domain]  Cd Length: 738  Bit Score: 122.09  E-value: 5.05e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1080273633  25 GLYHANINVLDKSTLEDAVEHPEKYPNLTVRVSGYAVNFVKLTREQQLDVISRTFH 80
Cdd:cd01678   683 GGHHLNVNVLNRETLLDAMEHPEKYPQLTIRVSGYAVNFVKLTREQQLDVISRTFH 738
Gly_radical pfam01228
Glycine radical;
25-64 3.04e-21

Glycine radical;


Pssm-ID: 426140 [Multi-domain]  Cd Length: 106  Bit Score: 79.90  E-value: 3.04e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1080273633  25 GLYHANINVLDKSTLEDAVEHPEKYPNLTVRVSGYAVNFV 64
Cdd:pfam01228  67 GGHHLQFNVVDRETLPDAQKHPEKYPDLTVRVSGYSANFV 106
PFL2_DhaB_BssA cd01677
Pyruvate formate lyase 2 and related enzymes; This family includes pyruvate formate lyase 2 ...
 17-78 9.17e-16

Pyruvate formate lyase 2 and related enzymes; This family includes pyruvate formate lyase 2 (PFL2), B12-independent glycerol dehydratase (DhaB) and the alpha subunit of benzylsuccinate synthase (BssA), all of which have a highly conserved ten-stranded alpha/beta barrel domain, which is similar to those of PFL1 (pyruvate formate lyase 1) and RNR (ribonucleotide reductase). Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. DhaB catalyzes the first step in the conversion of glycerol to 1,3-propanediol while BssA catalyzes the first step in the anaerobic mineralization of both toluene and m-xylene.


Pssm-ID: 153086 [Multi-domain]  Cd Length: 781  Bit Score: 70.00  E-value: 9.17e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1080273633  17 RTAnnMNSGLYHANINVLDKSTLEDAVEHPEKYPNLTVRVSGYAVNFVKLTREQQLDVISRT 78
Cdd:cd01677   721 RTY--FDLGGHHIQFNVVSAETLRDAQKHPEKYRDLIVRVAGYSAYFVELSKEVQDEIIART 780
pflD PRK09983
putative formate acetyltransferase 2; Provisional
 26-81 9.81e-14

putative formate acetyltransferase 2; Provisional


Pssm-ID: 182181 [Multi-domain]  Cd Length: 765  Bit Score: 64.46  E-value: 9.81e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1080273633  26 LYHANINVLDKSTLEDAVEHPEKYPNLTVRVSGYAVNFVKLTREQQLDVISRTFHQ 81
Cdd:PRK09983  709 LQHIQFNVVNADTLREAQQRPQDYAGLVVRVAGYSAFFVELSKEIQDDIIRRTAHQ 764
choline_CutC TIGR04394
choline trimethylamine-lyase; Members of this family, homologs to pyruvate formate-lyases and ...
 17-78 3.98e-13

choline trimethylamine-lyase; Members of this family, homologs to pyruvate formate-lyases and benzylsuccinate synthases, are glycine radical enzymes that appear to act as choline TMA-lyase, that is, to perform a C-N bond cleavage turning choline into trimethylamine (TMA) plus acetaldehyde. The gene symbol is cutC, for choline utilization. The activase, CutD, is a radical SAM enzyme. [Energy metabolism, Amino acids and amines]


Pssm-ID: 275187 [Multi-domain]  Cd Length: 789  Bit Score: 62.51  E-value: 3.98e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1080273633  17 RTANNMNSGlyHANINVLDKSTLEDAVEHPEKYPNLTVRVSGYAVNFVKLTREQQLDVISRT 78
Cdd:TIGR04394 725 RTASILGNG--EMQFNYLDNETLLDAQQHPEKYRDLVVRVAGYSAFFVELCKDVQDEIISRT 784
 
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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