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Conserved domains on  [gi|2564918218|ref|WP_306120130|]
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MULTISPECIES: RidA family protein [unclassified Roseitalea]

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 ...
 9-149 2.74e-57

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: 175.34  E-value: 2.74e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564918218   9 LGINLPDPASPSFNYVPVTVHRGVAYVSGQVPKVDGEVRVFGKVGAEVDLETAQGEARVCVLQGLACLRAELGSLDRIER 88
Cdd:cd02199     2 LGLELPPAPAPVGNYVPAVRTGNLLYVSGQLPRVDGKLVYTGKVGADLSVEEGQEAARLCALNALAALKAALGDLDRVKR 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2564918218  89 ILKINGYVASAPGFNGQPSVLDAASDLLGEIFGAAGRHARAAVGVAELPRDCAVEIEMTVA 149
Cdd:cd02199    82 VVRLTGFVNSAPDFTEQPKVANGASDLLVEVFGEAGRHARSAVGVASLPLNAAVEVEAIVE 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 ...
 9-149 2.74e-57

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: 175.34  E-value: 2.74e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564918218   9 LGINLPDPASPSFNYVPVTVHRGVAYVSGQVPKVDGEVRVFGKVGAEVDLETAQGEARVCVLQGLACLRAELGSLDRIER 88
Cdd:cd02199     2 LGLELPPAPAPVGNYVPAVRTGNLLYVSGQLPRVDGKLVYTGKVGADLSVEEGQEAARLCALNALAALKAALGDLDRVKR 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2564918218  89 ILKINGYVASAPGFNGQPSVLDAASDLLGEIFGAAGRHARAAVGVAELPRDCAVEIEMTVA 149
Cdd:cd02199    82 VVRLTGFVNSAPDFTEQPKVANGASDLLVEVFGEAGRHARSAVGVASLPLNAAVEVEAIVE 142
YjgF_endoribonc pfam14588
YjgF/chorismate_mutase-like, putative endoribonuclease; YjgF_Endoribonuc is a putative ...
 3-123 2.70e-20

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: 81.14  E-value: 2.70e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564918218   3 EERLKSLGINLPDPASPSFNYVPVTVHRGVAYVSGQVPKVDGEVRVFGKVGAEVDLETAQGEARVCVLQGLACLRAELGS 82
Cdd:pfam14588   1 ESRLMAAGLELPEPAAALGAYEPWAIVANFITTSFQFPFDGEKLLHQGLLGADVSTQDGIAAARLAALNAIAQLAEAAGE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2564918218  83 LDRIERILKINGYVASAPGFNGQPSVLDAASDLLGEIFGAA 123
Cdd:pfam14588  81 LANIKQIIRLDGHLGCHQDCDDHPKALDAASDLLLDIFGEA 121
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 14-151 3.45e-18

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: 75.21  E-value: 3.45e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564918218  14 PDPASPSFNYVPVTVHRGVAYVSGQVPKVDGEvrvfGKVGAEVdletaQGEARVCVLQGLACLRAELGSLDRIeriLKIN 93
Cdd:COG0251     8 PPAPAPIGPYSQAVRVGNLVFVSGQVPLDPDT----GELGGDI-----EAQTRQVLENILAVLAAAGGSLDDV---VKVT 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2564918218  94 GYVASAPGFNGqpsvldaASDLLGEIFGAAGRHARAaVGVAELPRDCAVEIEMTVAVR 151
Cdd:COG0251    76 VYLTDMADFAA-------VNEVYAEYFGEGRPARTA-VGVAALPKGALVEIEAIAALP 125
 
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 ...
 9-149 2.74e-57

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: 175.34  E-value: 2.74e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564918218   9 LGINLPDPASPSFNYVPVTVHRGVAYVSGQVPKVDGEVRVFGKVGAEVDLETAQGEARVCVLQGLACLRAELGSLDRIER 88
Cdd:cd02199     2 LGLELPPAPAPVGNYVPAVRTGNLLYVSGQLPRVDGKLVYTGKVGADLSVEEGQEAARLCALNALAALKAALGDLDRVKR 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2564918218  89 ILKINGYVASAPGFNGQPSVLDAASDLLGEIFGAAGRHARAAVGVAELPRDCAVEIEMTVA 149
Cdd:cd02199    82 VVRLTGFVNSAPDFTEQPKVANGASDLLVEVFGEAGRHARSAVGVASLPLNAAVEVEAIVE 142
YjgF_endoribonc pfam14588
YjgF/chorismate_mutase-like, putative endoribonuclease; YjgF_Endoribonuc is a putative ...
 3-123 2.70e-20

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: 81.14  E-value: 2.70e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564918218   3 EERLKSLGINLPDPASPSFNYVPVTVHRGVAYVSGQVPKVDGEVRVFGKVGAEVDLETAQGEARVCVLQGLACLRAELGS 82
Cdd:pfam14588   1 ESRLMAAGLELPEPAAALGAYEPWAIVANFITTSFQFPFDGEKLLHQGLLGADVSTQDGIAAARLAALNAIAQLAEAAGE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2564918218  83 LDRIERILKINGYVASAPGFNGQPSVLDAASDLLGEIFGAA 123
Cdd:pfam14588  81 LANIKQIIRLDGHLGCHQDCDDHPKALDAASDLLLDIFGEA 121
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 14-151 3.45e-18

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: 75.21  E-value: 3.45e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564918218  14 PDPASPSFNYVPVTVHRGVAYVSGQVPKVDGEvrvfGKVGAEVdletaQGEARVCVLQGLACLRAELGSLDRIeriLKIN 93
Cdd:COG0251     8 PPAPAPIGPYSQAVRVGNLVFVSGQVPLDPDT----GELGGDI-----EAQTRQVLENILAVLAAAGGSLDDV---VKVT 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2564918218  94 GYVASAPGFNGqpsvldaASDLLGEIFGAAGRHARAaVGVAELPRDCAVEIEMTVAVR 151
Cdd:COG0251    76 VYLTDMADFAA-------VNEVYAEYFGEGRPARTA-VGVAALPKGALVEIEAIAALP 125
YjgF_YER057c_UK114_family cd00448
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 23-148 3.49e-14

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: 64.12  E-value: 3.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564918218  23 YVPVTVHRGVAYVSGQVPKVDGEvrvfgkvgaEVDLETAQGEARVCVLQGLACLRAELGSLDRIeriLKINGYVASApgf 102
Cdd:cd00448     1 YSQAVRVGNLVFVSGQIPLDPDG---------ELVPGDIEAQTRQALENLEAVLEAAGGSLDDV---VKVTVYLTDM--- 65

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2564918218 103 nGQPSVLDAASDllgEIFGAAGRHARAAVGVAELPRDCAVEIEMTV 148
Cdd:cd00448    66 -ADFAAVNEVYD---EFFGEGPPPARTAVGVAALPPGALVEIEAIA 107
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 14-149 3.80e-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: 53.84  E-value: 3.80e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564918218  14 PDPASPsfnYVPVTVHRGVAYVSGQVPKVDGEVRVFGkvgaevdlETAQGEARvcvlQGLACLRAELGSLD-RIERILKI 92
Cdd:pfam01042   3 PAAAGP---YSQAVKAGNLVYVSGQIPLDPDTGKLVE--------GDVAEQTR----QVLENIKAVLAAAGaSLSDVVKV 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2564918218  93 NGYVASAPGFNGQPSVLDAASDLLGeifgaagRHARAAVGVAELPRDCAVEIEMTVA 149
Cdd:pfam01042  68 TIFLADMNDFAEVNEVYAEYFDADK-------APARSAVGVAALPLGALVEIEAIAV 117
 
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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