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Conserved domains on  [gi|495775919|ref|WP_008500498|]
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MULTISPECIES: RidA family protein [Enterobacterales]

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 ...
 10-113 1.89e-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: 147.30  E-value: 1.89e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919  10 ARWSDVVIHNQTLYYTGVPANL-DADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAMNKAWDAWVVAGH 88
Cdd:cd06150    1 ARMSQAVVHNGTVYLAGQVADDtSADITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMADFAAMNAVWDAWVPPGH 80

                         90       100
                 ....*....|....*....|....*
gi 495775919  89 APVRCTVQATLMKPEYKVEIKIIAA 113
Cdd:cd06150   81 APARACVEAKLADPGYLVEIVVTAA 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 ...
 10-113 1.89e-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: 147.30  E-value: 1.89e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919  10 ARWSDVVIHNQTLYYTGVPANL-DADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAMNKAWDAWVVAGH 88
Cdd:cd06150    1 ARMSQAVVHNGTVYLAGQVADDtSADITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMADFAAMNAVWDAWVPPGH 80

                         90       100
                 ....*....|....*....|....*
gi 495775919  89 APVRCTVQATLMKPEYKVEIKIIAA 113
Cdd:cd06150   81 APARACVEAKLADPGYLVEIVVTAA 105
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 4-113 1.81e-33

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: 112.39  E-value: 1.81e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919    4 VRIDAEARWSDVVIHNQTLYYTG-VPANLD------ADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAM 76
Cdd:pfam01042   1 NAPAAAGPYSQAVKAGNLVYVSGqIPLDPDtgklveGDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMNDFAEV 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 495775919   77 NKAWDAWVVAGHAPVRCTVQATLMKPEYKVEIKIIAA 113
Cdd:pfam01042  81 NEVYAEYFDADKAPARSAVGVAALPLGALVEIEAIAV 117
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 1-114 1.12e-24

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: 90.24  E-value: 1.12e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919   1 MTIVRIDAEA-----RWSDVVIHNQTLYYTGVPA------NLDADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLAN 69
Cdd:COG0251    1 MTRELINPPApapigPYSQAVRVGNLVFVSGQVPldpdtgELGGDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLTD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 495775919  70 KDDFAAMNKAWDAWvVAGHAPVRCTVQATLMKPEYKVEIKIIAAV 114
Cdd:COG0251   81 MADFAAVNEVYAEY-FGEGRPARTAVGVAALPKGALVEIEAIAAL 124
TIGR00004 TIGR00004
reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of ...
 12-114 1.18e-10

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: 54.22  E-value: 1.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919   12 WSDVVIHNQTLYYTG----VPANLD---ADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAMNKAWDAWv 84
Cdd:TIGR00004  16 YSQAVKVGNTVYVSGqiplDPSTGElvgGDIAEQAEQVLENLKAILEAAGLSLDDVVKTTVFLTDLNDFAEVNEVYGQY- 94

                          90       100       110
                  ....*....|....*....|....*....|
gi 495775919   85 VAGHAPVRCTVQATLMKPEYKVEIKIIAAV 114
Cdd:TIGR00004  95 FDEHYPARSAVQVAALPKGVLVEIEAIAVK 124
PRK11401 PRK11401
enamine/imine deaminase;
33-112 4.25e-05

enamine/imine deaminase;


Pssm-ID: 105214  Cd Length: 129  Bit Score: 40.05  E-value: 4.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919  33 ADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAMNKAWDAWVVAGHA--PVRCTVQATLMKPEYKVEIKI 110
Cdd:PRK11401  44 ADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQAtyPTRSCVQVARLPKDVKLEIEA 123


                 ..
gi 495775919 111 IA 112
Cdd:PRK11401 124 IA 125
 
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 ...
 10-113 1.89e-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: 147.30  E-value: 1.89e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919  10 ARWSDVVIHNQTLYYTGVPANL-DADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAMNKAWDAWVVAGH 88
Cdd:cd06150    1 ARMSQAVVHNGTVYLAGQVADDtSADITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMADFAAMNAVWDAWVPPGH 80

                         90       100
                 ....*....|....*....|....*
gi 495775919  89 APVRCTVQATLMKPEYKVEIKIIAA 113
Cdd:cd06150   81 APARACVEAKLADPGYLVEIVVTAA 105
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 4-113 1.81e-33

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: 112.39  E-value: 1.81e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919    4 VRIDAEARWSDVVIHNQTLYYTG-VPANLD------ADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAM 76
Cdd:pfam01042   1 NAPAAAGPYSQAVKAGNLVYVSGqIPLDPDtgklveGDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMNDFAEV 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 495775919   77 NKAWDAWVVAGHAPVRCTVQATLMKPEYKVEIKIIAA 113
Cdd:pfam01042  81 NEVYAEYFDADKAPARSAVGVAALPLGALVEIEAIAV 117
YjgF_YER057c_UK114_family cd00448
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 12-112 6.71e-26

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: 93.01  E-value: 6.71e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919  12 WSDVVIHNQTLYYTGVPANLDA------DAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAMNKAWDAWVV 85
Cdd:cd00448    1 YSQAVRVGNLVFVSGQIPLDPDgelvpgDIEAQTRQALENLEAVLEAAGGSLDDVVKVTVYLTDMADFAAVNEVYDEFFG 80

                         90       100
                 ....*....|....*....|....*..
gi 495775919  86 AGHAPVRCTVQATLMKPEYKVEIKIIA 112
Cdd:cd00448   81 EGPPPARTAVGVAALPPGALVEIEAIA 107
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 1-114 1.12e-24

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: 90.24  E-value: 1.12e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919   1 MTIVRIDAEA-----RWSDVVIHNQTLYYTGVPA------NLDADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLAN 69
Cdd:COG0251    1 MTRELINPPApapigPYSQAVRVGNLVFVSGQVPldpdtgELGGDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLTD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 495775919  70 KDDFAAMNKAWDAWvVAGHAPVRCTVQATLMKPEYKVEIKIIAAV 114
Cdd:COG0251   81 MADFAAVNEVYAEY-FGEGRPARTAVGVAALPKGALVEIEAIAAL 124
TIGR00004 TIGR00004
reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of ...
 12-114 1.18e-10

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: 54.22  E-value: 1.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919   12 WSDVVIHNQTLYYTG----VPANLD---ADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAMNKAWDAWv 84
Cdd:TIGR00004  16 YSQAVKVGNTVYVSGqiplDPSTGElvgGDIAEQAEQVLENLKAILEAAGLSLDDVVKTTVFLTDLNDFAEVNEVYGQY- 94

                          90       100       110
                  ....*....|....*....|....*....|
gi 495775919   85 VAGHAPVRCTVQATLMKPEYKVEIKIIAAV 114
Cdd:TIGR00004  95 FDEHYPARSAVQVAALPKGVLVEIEAIAVK 124
YjgF_YER057c_UK114_like_6 cd06154
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 34-112 3.76e-10

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: 52.94  E-value: 3.76e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919  34 DAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAMNKAWdAWVVAGHAPVRCTVQATLM-KPEYKVEIKIIA 112
Cdd:cd06154   41 DAYEQTRQCLEIIEAALAEAGASLEDVVRTRMYVTDIADFEAVGRAH-GEVFGDIRPAATMVVVSLLvDPEMLVEIEVTA 119
PRK11401 PRK11401
enamine/imine deaminase;
33-112 4.25e-05

enamine/imine deaminase;


Pssm-ID: 105214  Cd Length: 129  Bit Score: 40.05  E-value: 4.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919  33 ADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAMNKAWDAWVVAGHA--PVRCTVQATLMKPEYKVEIKI 110
Cdd:PRK11401  44 ADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFDEHQAtyPTRSCVQVARLPKDVKLEIEA 123


                 ..
gi 495775919 111 IA 112
Cdd:PRK11401 124 IA 125
YjgF_YER057c_UK114_like_3 cd06151
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 20-112 1.04e-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: 38.84  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919  20 QTLYYTG-VPANLDADA-----------FEQTANTLAQIDAVLEKQGSDKSRI------LDATIFLANKDDFAAMNKAWD 81
Cdd:cd06151   12 ATIYLSGtVPAVVNASApkgsparygdtETQTISVLKRIETILQSQGLTMGDVvkmrvfLVADPALDGKMDFAGFMKAYR 91

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 495775919  82 AWVvaGHA-----PVRCTVQ-ATLMKPEYKVEIKIIA 112
Cdd:cd06151   92 QFF--GTAeqpnkPARSTLQvAGLVNPGWLVEIEVVA 126
YjgH_like cd02198
YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, ...
 11-114 2.41e-04

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: 37.63  E-value: 2.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919  11 RWSDVVIHNQTLYYTGV----PANLDADAFE-QTANTLAQIDAVLEKQGSDKSRILDATIFLAN-KDDFAAMNKAWDAWV 84
Cdd:cd02198    2 GYSPAVRVGDTLFVSGQvgsdADGSVAEDFEaQFRLAFQNLGAVLEAAGCSFDDVVELTTFHVDmAAHLPAFAAVKDEYF 81

                         90       100       110
                 ....*....|....*....|....*....|
gi 495775919  85 VAGHAPVRCTVQATLMKPEYKVEIKIIAAV 114
Cdd:cd02198   82 KEPYPAWTAVGVAWLARPGLLVEIKVVAVR 111
eu_AANH_C_1 cd06155
A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine ...
 30-113 3.66e-04

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: 36.85  E-value: 3.66e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495775919  30 NLDADAFEQTANTLAQIDAVLEKQGSDKSRILDATIFLANKDDFAAMNKAWDAWVVAGHAPVRCTVQATLMkPEYKVEIK 109
Cdd:cd06155   19 ESDETVEEQMESIFSKLREILQSNGLSLSDILYVTLYLRDMSDFAEVNSVYGTFFDKPNPPSRVCVECGLP-EGCDVQLS 97


                 ....
gi 495775919 110 IIAA 113
Cdd:cd06155   98 CVAA 101
 
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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