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Conserved domains on  [gi|446610507|ref|WP_000687853|]
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MULTISPECIES: RidA family protein [Bacillus]

Protein Classification

RidA family protein( domain architecture ID 10115181)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YjgF_YER057c_UK114_like_1 cd02199
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 9-150 2.91e-72

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: 100006  Cd Length: 142  Bit Score: 213.09  E-value: 2.91e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507   9 ELGIILTNTSPAKALYVPVKQLGNSLFVSGQAPFIDGTPAYTGKVGGERTLEEAQEAARICIINTLAAVKEYIGDLDRIV 88
Cdd:cd02199    1 ELGLELPPAPAPVGNYVPAVRTGNLLYVSGQLPRVDGKLVYTGKVGADLSVEEGQEAARLCALNALAALKAALGDLDRVK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446610507  89 NVVKLQAFVNCEIEFNQQHIVINAASKLLHDIFGVEGQHARTAIGVNQLPMNITVEIDSIFE 150
Cdd:cd02199   81 RVVRLTGFVNSAPDFTEQPKVANGASDLLVEVFGEAGRHARSAVGVASLPLNAAVEVEAIVE 142
 
Name Accession Description Interval E-value
YjgF_YER057c_UK114_like_1 cd02199
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 9-150 2.91e-72

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: 100006  Cd Length: 142  Bit Score: 213.09  E-value: 2.91e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507   9 ELGIILTNTSPAKALYVPVKQLGNSLFVSGQAPFIDGTPAYTGKVGGERTLEEAQEAARICIINTLAAVKEYIGDLDRIV 88
Cdd:cd02199    1 ELGLELPPAPAPVGNYVPAVRTGNLLYVSGQLPRVDGKLVYTGKVGADLSVEEGQEAARLCALNALAALKAALGDLDRVK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446610507  89 NVVKLQAFVNCEIEFNQQHIVINAASKLLHDIFGVEGQHARTAIGVNQLPMNITVEIDSIFE 150
Cdd:cd02199   81 RVVRLTGFVNSAPDFTEQPKVANGASDLLVEVFGEAGRHARSAVGVASLPLNAAVEVEAIVE 142
YjgF_endoribonc pfam14588
YjgF/chorismate_mutase-like, putative endoribonuclease; YjgF_Endoribonuc is a putative ...
 4-140 2.96e-28

YjgF/chorismate_mutase-like, putative endoribonuclease; YjgF_Endoribonuc is a putative endoribonuclease. The structure is of beta-alpha-beta-alpha-beta(2) domains common both to bacterial chorismate mutase and to members of the YjgF family. These proteins form trimers with a three-fold symmetry with three closely-packed beta-sheets. The YjgF family is a large, widely distributed family of proteins of unknown biochemical function that are highly conserved among eubacteria, archaea and eukaryotes.


Pssm-ID: 405301  Cd Length: 148  Bit Score: 101.94  E-value: 2.96e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507    4 EQRMEELGIILTNTSPAKALYVPVKQLGNSLFVSGQAPFIDGTPAYTGKVGGERTLEEAQEAARICIINTLAAVKEYIGD 83
Cdd:pfam14588   1 ESRLMAAGLELPEPAAALGAYEPWAIVANFITTSFQFPFDGEKLLHQGLLGADVSTQDGIAAARLAALNAIAQLAEAAGE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 446610507   84 LDRIVNVVKLQAFVNCEIEFNQQHIVINAASKLLHDIFGVEGQHARTAIGVNQLPMN 140
Cdd:pfam14588  81 LANIKQIIRLDGHLGCHQDCDDHPKALDAASDLLLDIFGEAGRHARTALGHHVMPLG 137
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 12-151 1.08e-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: 94.47  E-value: 1.08e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507  12 IILTNTSPAKALYVPVKQLGNSLFVSGQAPFIDGTpaytGKVGGErtleeAQEAARICIINTLAAVKEYIGDLDRivnVV 91
Cdd:COG0251    5 LINPPAPAPIGPYSQAVRVGNLVFVSGQVPLDPDT----GELGGD-----IEAQTRQVLENILAVLAAAGGSLDD---VV 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507  92 KLQAFVNCEIEFNqqhivinAASKLLHDIFGvEGQHARTAIGVNQLPMNITVEIDSIFEI 151
Cdd:COG0251   73 KVTVYLTDMADFA-------AVNEVYAEYFG-EGRPARTAVGVAALPKGALVEIEAIAAL 124
TIGR00004 TIGR00004
reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of ...
 12-148 3.63e-06

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: 43.44  E-value: 3.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507   12 IILTNTSPAK-ALYVPVKQLGNSLFVSGQAPFidgTPAyTGK-VGGErtleeAQEAARICIINTLAAVKEYIGDLDRIVN 89
Cdd:TIGR00004   3 IISTDKAPAAiGPYSQAVKVGNTVYVSGQIPL---DPS-TGElVGGD-----IAEQAEQVLENLKAILEAAGLSLDDVVK 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446610507   90 VVKLQAFVNCEIEFNqqhivinaaskllhdifGVEGQH------ARTAIGVNQLPMNITVEIDSI 148
Cdd:TIGR00004  74 TTVFLTDLNDFAEVN-----------------EVYGQYfdehypARSAVQVAALPKGVLVEIEAI 121
 
Name Accession Description Interval E-value
YjgF_YER057c_UK114_like_1 cd02199
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 9-150 2.91e-72

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: 100006  Cd Length: 142  Bit Score: 213.09  E-value: 2.91e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507   9 ELGIILTNTSPAKALYVPVKQLGNSLFVSGQAPFIDGTPAYTGKVGGERTLEEAQEAARICIINTLAAVKEYIGDLDRIV 88
Cdd:cd02199    1 ELGLELPPAPAPVGNYVPAVRTGNLLYVSGQLPRVDGKLVYTGKVGADLSVEEGQEAARLCALNALAALKAALGDLDRVK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446610507  89 NVVKLQAFVNCEIEFNQQHIVINAASKLLHDIFGVEGQHARTAIGVNQLPMNITVEIDSIFE 150
Cdd:cd02199   81 RVVRLTGFVNSAPDFTEQPKVANGASDLLVEVFGEAGRHARSAVGVASLPLNAAVEVEAIVE 142
YjgF_endoribonc pfam14588
YjgF/chorismate_mutase-like, putative endoribonuclease; YjgF_Endoribonuc is a putative ...
 4-140 2.96e-28

YjgF/chorismate_mutase-like, putative endoribonuclease; YjgF_Endoribonuc is a putative endoribonuclease. The structure is of beta-alpha-beta-alpha-beta(2) domains common both to bacterial chorismate mutase and to members of the YjgF family. These proteins form trimers with a three-fold symmetry with three closely-packed beta-sheets. The YjgF family is a large, widely distributed family of proteins of unknown biochemical function that are highly conserved among eubacteria, archaea and eukaryotes.


Pssm-ID: 405301  Cd Length: 148  Bit Score: 101.94  E-value: 2.96e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507    4 EQRMEELGIILTNTSPAKALYVPVKQLGNSLFVSGQAPFIDGTPAYTGKVGGERTLEEAQEAARICIINTLAAVKEYIGD 83
Cdd:pfam14588   1 ESRLMAAGLELPEPAAALGAYEPWAIVANFITTSFQFPFDGEKLLHQGLLGADVSTQDGIAAARLAALNAIAQLAEAAGE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 446610507   84 LDRIVNVVKLQAFVNCEIEFNQQHIVINAASKLLHDIFGVEGQHARTAIGVNQLPMN 140
Cdd:pfam14588  81 LANIKQIIRLDGHLGCHQDCDDHPKALDAASDLLLDIFGEAGRHARTALGHHVMPLG 137
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 12-151 1.08e-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: 94.47  E-value: 1.08e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507  12 IILTNTSPAKALYVPVKQLGNSLFVSGQAPFIDGTpaytGKVGGErtleeAQEAARICIINTLAAVKEYIGDLDRivnVV 91
Cdd:COG0251    5 LINPPAPAPIGPYSQAVRVGNLVFVSGQVPLDPDT----GELGGD-----IEAQTRQVLENILAVLAAAGGSLDD---VV 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507  92 KLQAFVNCEIEFNqqhivinAASKLLHDIFGvEGQHARTAIGVNQLPMNITVEIDSIFEI 151
Cdd:COG0251   73 KVTVYLTDMADFA-------AVNEVYAEYFG-EGRPARTAVGVAALPKGALVEIEAIAAL 124
YjgF_YER057c_UK114_family cd00448
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 24-146 2.44e-20

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: 80.30  E-value: 2.44e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507  24 YVPVKQLGNSLFVSGQAPFIDGTPAYTGkvggertleEAQEAARICIINTLAAVKEYIGDLDrivNVVKLQAFVNCEIEF 103
Cdd:cd00448    1 YSQAVRVGNLVFVSGQIPLDPDGELVPG---------DIEAQTRQALENLEAVLEAAGGSLD---DVVKVTVYLTDMADF 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 446610507 104 NqqhiVINAASKLLhdiFGVEGQHARTAIGVNQLPMNITVEID 146
Cdd:cd00448   69 A----AVNEVYDEF---FGEGPPPARTAVGVAALPPGALVEIE 104
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 24-148 1.54e-10

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: 55.00  E-value: 1.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507   24 YVPVKQLGNSLFVSGQAPFIDgtpaYTGKVGGErTLEEAQEAARICIINTLAAVKeyiGDLDrivNVVKLQAFVNCEIEF 103
Cdd:pfam01042   9 YSQAVKAGNLVYVSGQIPLDP----DTGKLVEG-DVAEQTRQVLENIKAVLAAAG---ASLS---DVVKVTIFLADMNDF 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 446610507  104 NQQHIVINAASKLLHdifgvegQHARTAIGVNQLPMNITVEIDSI 148
Cdd:pfam01042  78 AEVNEVYAEYFDADK-------APARSAVGVAALPLGALVEIEAI 115
TIGR00004 TIGR00004
reactive intermediate/imine deaminase; This protein was described initially as an inhibitor of ...
 12-148 3.63e-06

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: 43.44  E-value: 3.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446610507   12 IILTNTSPAK-ALYVPVKQLGNSLFVSGQAPFidgTPAyTGK-VGGErtleeAQEAARICIINTLAAVKEYIGDLDRIVN 89
Cdd:TIGR00004   3 IISTDKAPAAiGPYSQAVKVGNTVYVSGQIPL---DPS-TGElVGGD-----IAEQAEQVLENLKAILEAAGLSLDDVVK 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446610507   90 VVKLQAFVNCEIEFNqqhivinaaskllhdifGVEGQH------ARTAIGVNQLPMNITVEIDSI 148
Cdd:TIGR00004  74 TTVFLTDLNDFAEVN-----------------EVYGQYfdehypARSAVQVAALPKGVLVEIEAI 121
 
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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