NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|517269154|ref|WP_018457972|]
View 

MULTISPECIES: RidA family protein [unclassified Bradyrhizobium]

Protein Classification

RidA family protein( domain architecture ID 10000806)

RidA (reactive intermediate/imine deaminase A) family protein similar to Pseudomonas sp. 2-aminomuconate deaminase that hydrolyzes 2-aminomuconate to 4-oxalocrotonate, and releases ammonia in the modified meta-cleavage pathway by forming various compounds including acetaldehyde, pyruvic acid, acetyl-CoA, and succinate, that may enter the Krebs cycle

CATH:  3.30.1330.40
PubMed:  14624641|22094463|25975565
SCOP:  3001733

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 1-130 2.39e-27

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: 97.94  E-value: 2.39e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154   1 MHILQPAEWKKPRGFSHGVVVegpGRWVVLAGQTGGD-ETGNYAPDMAAQVGTALKRIIKLLGEAGASPEHIVRLTWYLT 79
Cdd:COG0251    3 RELINPPAPAPIGPYSQAVRV---GNLVFVSGQVPLDpDTGELGGDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLT 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 517269154  80 SRSEYEaagaGIGAAWKETLGRNFPPSTLLYIGGLVDDrAKVEIEVTAFVP 130
Cdd:COG0251   80 DMADFA----AVNEVYAEYFGEGRPARTAVGVAALPKG-ALVEIEAIAALP 125
 
Name Accession Description Interval E-value
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 1-130 2.39e-27

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: 97.94  E-value: 2.39e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154   1 MHILQPAEWKKPRGFSHGVVVegpGRWVVLAGQTGGD-ETGNYAPDMAAQVGTALKRIIKLLGEAGASPEHIVRLTWYLT 79
Cdd:COG0251    3 RELINPPAPAPIGPYSQAVRV---GNLVFVSGQVPLDpDTGELGGDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLT 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 517269154  80 SRSEYEaagaGIGAAWKETLGRNFPPSTLLYIGGLVDDrAKVEIEVTAFVP 130
Cdd:COG0251   80 DMADFA----AVNEVYAEYFGEGRPARTAVGVAALPKG-ALVEIEAIAALP 125
YjgF_YER057c_UK114_family cd00448
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 15-127 1.90e-22

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: 84.92  E-value: 1.90e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154  15 FSHGVVVegpGRWVVLAGQTGGDETGNYAP-DMAAQVGTALKRIIKLLGEAGASPEHIVRLTWYLTSRSEYEaagaGIGA 93
Cdd:cd00448    1 YSQAVRV---GNLVFVSGQIPLDPDGELVPgDIEAQTRQALENLEAVLEAAGGSLDDVVKVTVYLTDMADFA----AVNE 73

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 517269154  94 AWKETLG-RNFPPSTLLYIGGLVDDrAKVEIEVTA 127
Cdd:cd00448   74 VYDEFFGeGPPPARTAVGVAALPPG-ALVEIEAIA 107
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 14-127 9.12e-14

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: 62.70  E-value: 9.12e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154   14 GFSHGVVVegpGRWVVLAGQTGGDE-TGNYAP-DMAAQVGTALKRIIKLLGEAGASPEHIVRLTWYLTSRSEYEaagaGI 91
Cdd:pfam01042   8 PYSQAVKA---GNLVYVSGQIPLDPdTGKLVEgDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMNDFA----EV 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 517269154   92 GAAWKETLGRNFPPSTLLYIGGLVDDRAKVEIEVTA 127
Cdd:pfam01042  81 NEVYAEYFDADKAPARSAVGVAALPLGALVEIEAIA 116
 
Name Accession Description Interval E-value
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 1-130 2.39e-27

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: 97.94  E-value: 2.39e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154   1 MHILQPAEWKKPRGFSHGVVVegpGRWVVLAGQTGGD-ETGNYAPDMAAQVGTALKRIIKLLGEAGASPEHIVRLTWYLT 79
Cdd:COG0251    3 RELINPPAPAPIGPYSQAVRV---GNLVFVSGQVPLDpDTGELGGDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLT 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 517269154  80 SRSEYEaagaGIGAAWKETLGRNFPPSTLLYIGGLVDDrAKVEIEVTAFVP 130
Cdd:COG0251   80 DMADFA----AVNEVYAEYFGEGRPARTAVGVAALPKG-ALVEIEAIAALP 125
YjgF_YER057c_UK114_family cd00448
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 15-127 1.90e-22

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: 84.92  E-value: 1.90e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154  15 FSHGVVVegpGRWVVLAGQTGGDETGNYAP-DMAAQVGTALKRIIKLLGEAGASPEHIVRLTWYLTSRSEYEaagaGIGA 93
Cdd:cd00448    1 YSQAVRV---GNLVFVSGQIPLDPDGELVPgDIEAQTRQALENLEAVLEAAGGSLDDVVKVTVYLTDMADFA----AVNE 73

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 517269154  94 AWKETLG-RNFPPSTLLYIGGLVDDrAKVEIEVTA 127
Cdd:cd00448   74 VYDEFFGeGPPPARTAVGVAALPPG-ALVEIEAIA 107
YjgF_YER057c_UK114_like_6 cd06154
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 3-127 6.14e-22

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: 83.76  E-value: 6.14e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154   3 ILQPAEWKKPRGFSHGVVVegpGRWVVLAGQTG-GDETGNYAPDMAAQVGTALKRIIKLLGEAGASPEHIVRLTWYLTSR 81
Cdd:cd06154    1 ISSGSPWEEQAGYSRAVRV---GNWVFVSGTTGyDYDGMVMPGDAYEQTRQCLEIIEAALAEAGASLEDVVRTRMYVTDI 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 517269154  82 SEYEAAGAGIgaawKETLGRNFPPSTLLYIGGLVDDRAKVEIEVTA 127
Cdd:cd06154   78 ADFEAVGRAH----GEVFGDIRPAATMVVVSLLVDPEMLVEIEVTA 119
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 14-127 9.12e-14

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: 62.70  E-value: 9.12e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154   14 GFSHGVVVegpGRWVVLAGQTGGDE-TGNYAP-DMAAQVGTALKRIIKLLGEAGASPEHIVRLTWYLTSRSEYEaagaGI 91
Cdd:pfam01042   8 PYSQAVKA---GNLVYVSGQIPLDPdTGKLVEgDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMNDFA----EV 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 517269154   92 GAAWKETLGRNFPPSTLLYIGGLVDDRAKVEIEVTA 127
Cdd:pfam01042  81 NEVYAEYFDADKAPARSAVGVAALPLGALVEIEAIA 116
YjgH_like cd02198
YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, ...
 14-127 1.86e-08

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: 48.80  E-value: 1.86e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154  14 GFSHGVVVegpGRWVVLAGQTGGDETGNYAPDMAAQVGTALKRIIKLLGEAGASPEHIVRLTWYLT-SRSEYEAAGAGIG 92
Cdd:cd02198    2 GYSPAVRV---GDTLFVSGQVGSDADGSVAEDFEAQFRLAFQNLGAVLEAAGCSFDDVVELTTFHVdMAAHLPAFAAVKD 78

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 517269154  93 AAWKETlgrnFPPSTLLYIGGLVDDRAKVEIEVTA 127
Cdd:cd02198   79 EYFKEP----YPAWTAVGVAWLARPGLLVEIKVVA 109
YjgF_YER057c_UK114_like_2 cd06150
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 28-127 8.44e-07

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: 44.45  E-value: 8.44e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154  28 VVLAGQTGGDETGnyapDMAAQVGTALKRIIKLLGEAGASPEHIVRLTWYLTSRSEYEaagaGIGAAWKETLGRNFPPST 107
Cdd:cd06150   13 VYLAGQVADDTSA----DITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMADFA----AMNAVWDAWVPPGHAPAR 84

                         90       100
                 ....*....|....*....|
gi 517269154 108 LLYIGGLVDDRAKVEIEVTA 127
Cdd:cd06150   85 ACVEAKLADPGYLVEIVVTA 104
YjgF_YER057c_UK114_like_4 cd06152
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 14-128 3.27e-03

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: 100009  Cd Length: 114  Bit Score: 34.97  E-value: 3.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517269154  14 GFSHGVVVegpGRWVVLAGQTGGD-ETGNYAPDMAAQVGTALKRIIKLLGEAGASP-EHIVRLTWYLTSRSEyEAAGAGI 91
Cdd:cd06152    2 HYSQAVRI---GDRIEISGQGGWDpDTGKIPEDLEEEIDQAFDNVELALKAAGGKGwEQVYKVNSYHVDIKN-EEAFGLM 77

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 517269154  92 GAAWKETLGRNFPPSTLLYIGGLVDDRAKVEIEVTAF 128
Cdd:cd06152   78 VENFKKWMPNHQPIWTCVGVTALGLPGMRVEIEVDAI 114
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH