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Conserved domains on  [gi|696302157|ref|WP_032877670|]
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MULTISPECIES: RidA family protein [unclassified Acinetobacter]

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

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List of domain hits

 Name Accession Description Interval E-value
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 10-137 2.14e-17

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: 72.52  E-value: 2.14e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696302157  10 EIMNPDElydPRPNG-YSHITVVPpnlRTIHIAGQGGEN-KNGELSEYFDQQVQQVFYNIQHALASVHAQITDIAVLRIL 87
Cdd:COG0251    4 ELINPPA---PAPIGpYSQAVRVG---NLVFVSGQVPLDpDTGELGGDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVY 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 696302157  88 IVNHSAekhqalIQIMQKLWKKH---AFPACTLIPVPRLALeGMQIEVEATAY 137
Cdd:COG0251   78 LTDMAD------FAAVNEVYAEYfgeGRPARTAVGVAALPK-GALVEIEAIAA 123
 
Name Accession Description Interval E-value
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 10-137 2.14e-17

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: 72.52  E-value: 2.14e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696302157  10 EIMNPDElydPRPNG-YSHITVVPpnlRTIHIAGQGGEN-KNGELSEYFDQQVQQVFYNIQHALASVHAQITDIAVLRIL 87
Cdd:COG0251    4 ELINPPA---PAPIGpYSQAVRVG---NLVFVSGQVPLDpDTGELGGDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVY 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 696302157  88 IVNHSAekhqalIQIMQKLWKKH---AFPACTLIPVPRLALeGMQIEVEATAY 137
Cdd:COG0251   78 LTDMAD------FAAVNEVYAEYfgeGRPARTAVGVAALPK-GALVEIEAIAA 123
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 23-137 1.94e-12

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: 59.62  E-value: 1.94e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696302157   23 NGYSHitVVPPNlRTIHIAGQGGEN-KNGEL-SEYFDQQVQQVFYNIQHALASVHAQITDIAVLRILIVNHSAEKHQAli 100
Cdd:pfam01042   7 GPYSQ--AVKAG-NLVYVSGQIPLDpDTGKLvEGDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMNDFAEVN-- 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 696302157  101 QIMQKLWKKHAFPACTLIPVPRLALeGMQIEVEATAY 137
Cdd:pfam01042  82 EVYAEYFDADKAPARSAVGVAALPL-GALVEIEAIAV 117
YjgF_YER057c_UK114_like_4 cd06152
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 38-137 5.69e-10

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: 53.08  E-value: 5.69e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696302157  38 IHIAGQGGEN-KNGELSEYFDQQVQQVFYNIQHALASVHAQ-ITDIAVLRILIVNHSAEKHqalIQIMQKLWKK----HA 111
Cdd:cd06152   13 IEISGQGGWDpDTGKIPEDLEEEIDQAFDNVELALKAAGGKgWEQVYKVNSYHVDIKNEEA---FGLMVENFKKwmpnHQ 89

                         90       100
                 ....*....|....*....|....*.
gi 696302157 112 fPACTLIPVPRLALEGMQIEVEATAY 137
Cdd:cd06152   90 -PIWTCVGVTALGLPGMRVEIEVDAI 114
 
Name Accession Description Interval E-value
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 10-137 2.14e-17

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: 72.52  E-value: 2.14e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696302157  10 EIMNPDElydPRPNG-YSHITVVPpnlRTIHIAGQGGEN-KNGELSEYFDQQVQQVFYNIQHALASVHAQITDIAVLRIL 87
Cdd:COG0251    4 ELINPPA---PAPIGpYSQAVRVG---NLVFVSGQVPLDpDTGELGGDIEAQTRQVLENILAVLAAAGGSLDDVVKVTVY 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 696302157  88 IVNHSAekhqalIQIMQKLWKKH---AFPACTLIPVPRLALeGMQIEVEATAY 137
Cdd:COG0251   78 LTDMAD------FAAVNEVYAEYfgeGRPARTAVGVAALPK-GALVEIEAIAA 123
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 23-137 1.94e-12

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: 59.62  E-value: 1.94e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696302157   23 NGYSHitVVPPNlRTIHIAGQGGEN-KNGEL-SEYFDQQVQQVFYNIQHALASVHAQITDIAVLRILIVNHSAEKHQAli 100
Cdd:pfam01042   7 GPYSQ--AVKAG-NLVYVSGQIPLDpDTGKLvEGDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMNDFAEVN-- 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 696302157  101 QIMQKLWKKHAFPACTLIPVPRLALeGMQIEVEATAY 137
Cdd:pfam01042  82 EVYAEYFDADKAPARSAVGVAALPL-GALVEIEAIAV 117
YjgF_YER057c_UK114_like_4 cd06152
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 38-137 5.69e-10

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: 53.08  E-value: 5.69e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696302157  38 IHIAGQGGEN-KNGELSEYFDQQVQQVFYNIQHALASVHAQ-ITDIAVLRILIVNHSAEKHqalIQIMQKLWKK----HA 111
Cdd:cd06152   13 IEISGQGGWDpDTGKIPEDLEEEIDQAFDNVELALKAAGGKgWEQVYKVNSYHVDIKNEEA---FGLMVENFKKwmpnHQ 89

                         90       100
                 ....*....|....*....|....*.
gi 696302157 112 fPACTLIPVPRLALEGMQIEVEATAY 137
Cdd:cd06152   90 -PIWTCVGVTALGLPGMRVEIEVDAI 114
YjgF_YER057c_UK114_like_6 cd06154
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 24-136 5.81e-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: 53.33  E-value: 5.81e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696302157  24 GYSHITVVPPnlrTIHIAGQGGENKNG-ELSEYFDQQVQQVFYNIQHALASVHAQITDIAVLRILIVNhsAEKHQALIQI 102
Cdd:cd06154   12 GYSRAVRVGN---WVFVSGTTGYDYDGmVMPGDAYEQTRQCLEIIEAALAEAGASLEDVVRTRMYVTD--IADFEAVGRA 86

                         90       100       110
                 ....*....|....*....|....*....|....
gi 696302157 103 MQKLWKKHAfPACTLIPVPRLALEGMQIEVEATA 136
Cdd:cd06154   87 HGEVFGDIR-PAATMVVVSLLVDPEMLVEIEVTA 119
YjgH_like cd02198
YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, ...
 37-137 2.31e-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: 43.40  E-value: 2.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696302157  37 TIHIAGQGGENKNGELSEYFDQQVQQVFYNIQHALASVHAQITDIAVLRILIVNHSAEKHqALIQIMQKLWkKHAFPACT 116
Cdd:cd02198   12 TLFVSGQVGSDADGSVAEDFEAQFRLAFQNLGAVLEAAGCSFDDVVELTTFHVDMAAHLP-AFAAVKDEYF-KEPYPAWT 89

                         90       100
                 ....*....|....*....|.
gi 696302157 117 LIPVPRLALEGMQIEVEATAY 137
Cdd:cd02198   90 AVGVAWLARPGLLVEIKVVAV 110
YjgF_YER057c_UK114_like_3 cd06151
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 31-136 5.51e-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: 100008  Cd Length: 126  Bit Score: 40.00  E-value: 5.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696302157  31 VPPNLRTIHIAGQGGENKN-----GELSEYFDQQVQ--QVFYNIQHALASVHAQITDIAVLRILIVNHSAEKHQALIQIM 103
Cdd:cd06151    7 VPAGAATIYLSGTVPAVVNasapkGSPARYGDTETQtiSVLKRIETILQSQGLTMGDVVKMRVFLVADPALDGKMDFAGF 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 696302157 104 QKLWKKH-------AFPACTLIPVPRLALEGMQIEVEATA 136
Cdd:cd06151   87 MKAYRQFfgtaeqpNKPARSTLQVAGLVNPGWLVEIEVVA 126
 
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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