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Conserved domains on  [gi|502899920|ref|WP_013134896|]
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RidA family protein [Arcobacter nitrofigilis]

Protein Classification

RidA family protein( domain architecture ID 10150280)

RidA (reactive intermediate/imine deaminase A) family protein similar to 2-iminobutanoate/2-iminopropanoate deaminase, which catalyzes the deamination of enamine/imine intermediates to yield 2-ketobutyrate and ammonia

CATH:  3.30.1330.40
PubMed:  14624641

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YjgF_YER057c_UK114_like_2 cd06150
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 9-114 2.06e-47

This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


:

Pssm-ID: 100007  Cd Length: 105  Bit Score: 147.68  E-value: 2.06e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920   9 ERMSRIVEYSGVIYLAGIVSDDKDLDIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDAWVSKE 88
Cdd:cd06150    1 ARMSQAVVHNGTVYLAGQVADDTSADITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMA-DFAAMNAVWDAWVPPG 79

                         90       100
                 ....*....|....*....|....*.
gi 502899920  89 QPPARACVEANMASSNTLVEIIFTAV 114
Cdd:cd06150   80 HAPARACVEAKLADPGYLVEIVVTAA 105
 
Name Accession Description Interval E-value
YjgF_YER057c_UK114_like_2 cd06150
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 9-114 2.06e-47

This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100007  Cd Length: 105  Bit Score: 147.68  E-value: 2.06e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920   9 ERMSRIVEYSGVIYLAGIVSDDKDLDIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDAWVSKE 88
Cdd:cd06150    1 ARMSQAVVHNGTVYLAGQVADDTSADITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMA-DFAAMNAVWDAWVPPG 79

                         90       100
                 ....*....|....*....|....*.
gi 502899920  89 QPPARACVEANMASSNTLVEIIFTAV 114
Cdd:cd06150   80 HAPARACVEAKLADPGYLVEIVVTAA 105
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 11-115 9.23e-25

Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 family [Defense mechanisms]; Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 family is part of the Pathway/BioSystem: Pyrimidine degradation


Pssm-ID: 440021  Cd Length: 125  Bit Score: 90.62  E-value: 9.23e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920  11 MSRIVEYSGVIYLAGIVSDDKDL-----DIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDAWV 85
Cdd:COG0251   17 YSQAVRVGNLVFVSGQVPLDPDTgelggDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLTDMA-DFAAVNEVYAEYF 95

                         90       100       110
                 ....*....|....*....|....*....|
gi 502899920  86 sKEQPPARACVEANMASSNTLVEIIFTAVK 115
Cdd:COG0251   96 -GEGRPARTAVGVAALPKGALVEIEAIAAL 124
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 10-114 1.96e-20

Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA. Previously thought to inhibit protein synthesis initiation. This protein may also be involved in the regulation of purine biosynthesis. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella.


Pssm-ID: 426010  Cd Length: 117  Bit Score: 79.65  E-value: 1.96e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920   10 RMSRIVEYSGVIYLAG-IVSDDKD-----LDIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDA 83
Cdd:pfam01042   8 PYSQAVKAGNLVYVSGqIPLDPDTgklveGDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMN-DFAEVNEVYAE 86

                          90       100       110
                  ....*....|....*....|....*....|.
gi 502899920   84 WVSKEQPPARACVEANMASSNTLVEIIFTAV 114
Cdd:pfam01042  87 YFDADKAPARSAVGVAALPLGALVEIEAIAV 117
TIGR00004 TIGR00004
reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of ...
 34-115 3.51e-12

reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of protein synthesis intiation, then as an endoribonuclease active on single-stranded mRNA, endoribonuclease L-PSP. Members of this family, conserved in all domains of life and often with several members per bacterial genome, appear to catalyze a reaction that minimizes toxic by-products from reactions catalyzed by pyridoxal phosphate-dependent enzymes. [Cellular processes, Other]


Pssm-ID: 129116  Cd Length: 124  Bit Score: 58.46  E-value: 3.51e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920   34 DIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDAWVsKEQPPARACVEANMASSNTLVEIIFTA 113
Cdd:TIGR00004  45 DIAEQAEQVLENLKAILEAAGLSLDDVVKTTVFLTDLN-DFAEVNEVYGQYF-DEHYPARSAVQVAALPKGVLVEIEAIA 122


                  ..
gi 502899920  114 VK 115
Cdd:TIGR00004 123 VK 124
 
Name Accession Description Interval E-value
YjgF_YER057c_UK114_like_2 cd06150
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 9-114 2.06e-47

This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100007  Cd Length: 105  Bit Score: 147.68  E-value: 2.06e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920   9 ERMSRIVEYSGVIYLAGIVSDDKDLDIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDAWVSKE 88
Cdd:cd06150    1 ARMSQAVVHNGTVYLAGQVADDTSADITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMA-DFAAMNAVWDAWVPPG 79

                         90       100
                 ....*....|....*....|....*.
gi 502899920  89 QPPARACVEANMASSNTLVEIIFTAV 114
Cdd:cd06150   80 HAPARACVEAKLADPGYLVEIVVTAA 105
YjgF_YER057c_UK114_family cd00448
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 11-113 1.50e-25

YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100004 [Multi-domain]  Cd Length: 107  Bit Score: 92.24  E-value: 1.50e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920  11 MSRIVEYSGVIYLAGIVSDDKD-----LDIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDAWV 85
Cdd:cd00448    1 YSQAVRVGNLVFVSGQIPLDPDgelvpGDIEAQTRQALENLEAVLEAAGGSLDDVVKVTVYLTDMA-DFAAVNEVYDEFF 79

                         90       100
                 ....*....|....*....|....*...
gi 502899920  86 SKEQPPARACVEANMASSNTLVEIIFTA 113
Cdd:cd00448   80 GEGPPPARTAVGVAALPPGALVEIEAIA 107
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 11-115 9.23e-25

Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 family [Defense mechanisms]; Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 family is part of the Pathway/BioSystem: Pyrimidine degradation


Pssm-ID: 440021  Cd Length: 125  Bit Score: 90.62  E-value: 9.23e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920  11 MSRIVEYSGVIYLAGIVSDDKDL-----DIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDAWV 85
Cdd:COG0251   17 YSQAVRVGNLVFVSGQVPLDPDTgelggDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLTDMA-DFAAVNEVYAEYF 95

                         90       100       110
                 ....*....|....*....|....*....|
gi 502899920  86 sKEQPPARACVEANMASSNTLVEIIFTAVK 115
Cdd:COG0251   96 -GEGRPARTAVGVAALPKGALVEIEAIAAL 124
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 10-114 1.96e-20

Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA. Previously thought to inhibit protein synthesis initiation. This protein may also be involved in the regulation of purine biosynthesis. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella.


Pssm-ID: 426010  Cd Length: 117  Bit Score: 79.65  E-value: 1.96e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920   10 RMSRIVEYSGVIYLAG-IVSDDKD-----LDIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDA 83
Cdd:pfam01042   8 PYSQAVKAGNLVYVSGqIPLDPDTgklveGDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMN-DFAEVNEVYAE 86

                          90       100       110
                  ....*....|....*....|....*....|.
gi 502899920   84 WVSKEQPPARACVEANMASSNTLVEIIFTAV 114
Cdd:pfam01042  87 YFDADKAPARSAVGVAALPLGALVEIEAIAV 117
TIGR00004 TIGR00004
reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of ...
 34-115 3.51e-12

reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of protein synthesis intiation, then as an endoribonuclease active on single-stranded mRNA, endoribonuclease L-PSP. Members of this family, conserved in all domains of life and often with several members per bacterial genome, appear to catalyze a reaction that minimizes toxic by-products from reactions catalyzed by pyridoxal phosphate-dependent enzymes. [Cellular processes, Other]


Pssm-ID: 129116  Cd Length: 124  Bit Score: 58.46  E-value: 3.51e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920   34 DIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDAWVsKEQPPARACVEANMASSNTLVEIIFTA 113
Cdd:TIGR00004  45 DIAEQAEQVLENLKAILEAAGLSLDDVVKTTVFLTDLN-DFAEVNEVYGQYF-DEHYPARSAVQVAALPKGVLVEIEAIA 122


                  ..
gi 502899920  114 VK 115
Cdd:TIGR00004 123 VK 124
eu_AANH_C_1 cd06155
A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine ...
 22-109 1.34e-10

A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the first of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100012  Cd Length: 101  Bit Score: 53.80  E-value: 1.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920  22 YLAGIVSDDKDLDIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIArDFAGFNEVWDAWVSKEQPPARACVEANMa 101
Cdd:cd06155   11 WISNVTASESDETVEEQMESIFSKLREILQSNGLSLSDILYVTLYLRDMS-DFAEVNSVYGTFFDKPNPPSRVCVECGL- 88


                 ....*...
gi 502899920 102 SSNTLVEI 109
Cdd:cd06155   89 PEGCDVQL 96
YjgH_like cd02198
YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, ...
 21-115 5.87e-06

YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100005  Cd Length: 111  Bit Score: 41.86  E-value: 5.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920  21 IYLAGIVSDDKDL----DIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIARDFAGFNEVWDAWVsKEQPPARACV 96
Cdd:cd02198   13 LFVSGQVGSDADGsvaeDFEAQFRLAFQNLGAVLEAAGCSFDDVVELTTFHVDMAAHLPAFAAVKDEYF-KEPYPAWTAV 91

                         90       100
                 ....*....|....*....|
gi 502899920  97 EANM-ASSNTLVEIIFTAVK 115
Cdd:cd02198   92 GVAWlARPGLLVEIKVVAVR 111
YjgF_YER057c_UK114_like_6 cd06154
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 12-113 1.03e-05

This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100011  Cd Length: 119  Bit Score: 41.39  E-value: 1.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920  12 SRIVEYSGVIYLAGIVSDDKDL-----DIKGQAQRVLAMAEERLAEAGSNKDHILRAEIFVKDIARdfagFNEVWDA--W 84
Cdd:cd06154   14 SRAVRVGNWVFVSGTTGYDYDGmvmpgDAYEQTRQCLEIIEAALAEAGASLEDVVRTRMYVTDIAD----FEAVGRAhgE 89

                         90       100       110
                 ....*....|....*....|....*....|
gi 502899920  85 VSKEQPPARACVEA-NMASSNTLVEIIFTA 113
Cdd:cd06154   90 VFGDIRPAATMVVVsLLVDPEMLVEIEVTA 119
YjgF_YER057c_UK114_like_3 cd06151
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 20-109 2.67e-04

This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.


Pssm-ID: 100008  Cd Length: 126  Bit Score: 37.68  E-value: 2.67e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502899920  20 VIYLAGIVSDDKDL-----------DIKGQAQRVLAMAEERLAEAGSNKDHILRAEIF-VKDIAR----DFAGFNEVWDA 83
Cdd:cd06151   13 TIYLSGTVPAVVNAsapkgsparygDTETQTISVLKRIETILQSQGLTMGDVVKMRVFlVADPALdgkmDFAGFMKAYRQ 92

                         90       100       110
                 ....*....|....*....|....*....|
gi 502899920  84 WV-SKEQP--PARACVE-ANMASSNTLVEI 109
Cdd:cd06151   93 FFgTAEQPnkPARSTLQvAGLVNPGWLVEI 122
 
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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