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Conserved domains on  [gi|15598695|ref|NP_252189|]
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hypothetical protein PA3499 [Pseudomonas aeruginosa PAO1]

Protein Classification

RidA family protein( domain architecture ID 10087367)

RidA (reactive intermediate/imine deaminase A) family protein similar to 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

EC:  3.5.-.-
Gene Ontology:  GO:0016787
PubMed:  22094463|25975565

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YjgF_YER057c_UK114_family cd00448
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 20-132 7.77e-21

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: 81.07  E-value: 7.77e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695  20 WSNALLVGEELVMSGMTAH-PATRQAAErgaalDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAIGRAR 98
Cdd:cd00448   1 YSQAVRVGNLVFVSGQIPLdPDGELVPG-----DIEAQTRQALENLEAVLEAAGGSLDDVVKVTVYLTDMADFAAVNEVY 75

                        90       100       110
                ....*....|....*....|....*....|....
gi 15598695  99 QEFFAGQGtFPASTLVEVSGLvFPELLVEIDAWA 132
Cdd:cd00448  76 DEFFGEGP-PPARTAVGVAAL-PPGALVEIEAIA 107
 
Name Accession Description Interval E-value
YjgF_YER057c_UK114_family cd00448
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 20-132 7.77e-21

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: 81.07  E-value: 7.77e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695  20 WSNALLVGEELVMSGMTAH-PATRQAAErgaalDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAIGRAR 98
Cdd:cd00448   1 YSQAVRVGNLVFVSGQIPLdPDGELVPG-----DIEAQTRQALENLEAVLEAAGGSLDDVVKVTVYLTDMADFAAVNEVY 75

                        90       100       110
                ....*....|....*....|....*....|....
gi 15598695  99 QEFFAGQGtFPASTLVEVSGLvFPELLVEIDAWA 132
Cdd:cd00448  76 DEFFGEGP-PPARTAVGVAAL-PPGALVEIEAIA 107
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 16-135 1.60e-20

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: 80.99  E-value: 1.60e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695  16 PDASWSNALLVGEELVMSGMTAH-PATRQAAErgaalDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAI 94
Cdd:COG0251  13 PIGPYSQAVRVGNLVFVSGQVPLdPDTGELGG-----DIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLTDMADFAAV 87

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 15598695  95 GRARQEFFAGQgtFPASTLVEVSGLVFpELLVEIDAWARLD 135
Cdd:COG0251  88 NEVYAEYFGEG--RPARTAVGVAALPK-GALVEIEAIAALP 125
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 16-132 7.65e-11

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: 55.77  E-value: 7.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695    16 PDASWSNALLVGEELVMSGmtaHPATRQAAERGAALDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAIG 95
Cdd:pfam01042   5 AAGPYSQAVKAGNLVYVSG---QIPLDPDTGKLVEGDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMNDFAEVN 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 15598695    96 RARQEFFAGqGTFPASTLVEVSGLVfPELLVEIDAWA 132
Cdd:pfam01042  82 EVYAEYFDA-DKAPARSAVGVAALP-LGALVEIEAIA 116
PRK11401 PRK11401
enamine/imine deaminase;
26-132 6.53e-08

enamine/imine deaminase;


Pssm-ID: 105214  Cd Length: 129  Bit Score: 48.14  E-value: 6.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695   26 VGEELVMSGMTahPATRQAAErgAALDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAIGRARQEFF-AG 104
Cdd:PRK11401  23 LGSMVFTSGQI--PVCPQTGE--IPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFdEH 98

                         90       100
                 ....*....|....*....|....*...
gi 15598695  105 QGTFPASTLVEVSGLVfPELLVEIDAWA 132
Cdd:PRK11401  99 QATYPTRSCVQVARLP-KDVKLEIEAIA 125
 
Name Accession Description Interval E-value
YjgF_YER057c_UK114_family cd00448
YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, ...
 20-132 7.77e-21

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: 81.07  E-value: 7.77e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695  20 WSNALLVGEELVMSGMTAH-PATRQAAErgaalDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAIGRAR 98
Cdd:cd00448   1 YSQAVRVGNLVFVSGQIPLdPDGELVPG-----DIEAQTRQALENLEAVLEAAGGSLDDVVKVTVYLTDMADFAAVNEVY 75

                        90       100       110
                ....*....|....*....|....*....|....
gi 15598695  99 QEFFAGQGtFPASTLVEVSGLvFPELLVEIDAWA 132
Cdd:cd00448  76 DEFFGEGP-PPARTAVGVAAL-PPGALVEIEAIA 107
RidA COG0251
Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 ...
 16-135 1.60e-20

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: 80.99  E-value: 1.60e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695  16 PDASWSNALLVGEELVMSGMTAH-PATRQAAErgaalDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAI 94
Cdd:COG0251  13 PIGPYSQAVRVGNLVFVSGQVPLdPDTGELGG-----DIEAQTRQVLENILAVLAAAGGSLDDVVKVTVYLTDMADFAAV 87

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 15598695  95 GRARQEFFAGQgtFPASTLVEVSGLVFpELLVEIDAWARLD 135
Cdd:COG0251  88 NEVYAEYFGEG--RPARTAVGVAALPK-GALVEIEAIAALP 125
YjgF_YER057c_UK114_like_6 cd06154
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 18-132 4.67e-18

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: 74.51  E-value: 4.67e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695  18 ASWSNALLVGEELVMSGMTA-HPATRQAAErgaalDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAIGR 96
Cdd:cd06154  11 AGYSRAVRVGNWVFVSGTTGyDYDGMVMPG-----DAYEQTRQCLEIIEAALAEAGASLEDVVRTRMYVTDIADFEAVGR 85

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 15598695  97 ARQEFFAGQGtfPASTLVEVSGLVFPELLVEIDAWA 132
Cdd:cd06154  86 AHGEVFGDIR--PAATMVVVSLLVDPEMLVEIEVTA 119
Ribonuc_L-PSP pfam01042
Endoribonuclease L-PSP; Endoribonuclease active on single-stranded mRNA. Inhibits protein ...
 16-132 7.65e-11

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: 55.77  E-value: 7.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695    16 PDASWSNALLVGEELVMSGmtaHPATRQAAERGAALDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAIG 95
Cdd:pfam01042   5 AAGPYSQAVKAGNLVYVSG---QIPLDPDTGKLVEGDVAEQTRQVLENIKAVLAAAGASLSDVVKVTIFLADMNDFAEVN 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 15598695    96 RARQEFFAGqGTFPASTLVEVSGLVfPELLVEIDAWA 132
Cdd:pfam01042  82 EVYAEYFDA-DKAPARSAVGVAALP-LGALVEIEAIA 116
YjgH_like cd02198
YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, ...
 21-134 7.88e-10

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: 52.65  E-value: 7.88e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695  21 SNALLVGEELVMSGMTAHPATRQAAErgaalDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADK-DAIGRARQ 99
Cdd:cd02198   4 SPAVRVGDTLFVSGQVGSDADGSVAE-----DFEAQFRLAFQNLGAVLEAAGCSFDDVVELTTFHVDMAAHlPAFAAVKD 78

                        90       100       110
                ....*....|....*....|....*....|....*
gi 15598695 100 EFFAGQgtFPASTLVEVSGLVFPELLVEIDAWARL 134
Cdd:cd02198  79 EYFKEP--YPAWTAVGVAWLARPGLLVEIKVVAVR 111
YjgF_YER057c_UK114_like_3 cd06151
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 33-132 1.05e-09

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: 52.71  E-value: 1.05e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695  33 SGMTAHP--ATRQAAERGAALDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYV------TRIADKDAIGRARQEFF-- 102
Cdd:cd06151  17 SGTVPAVvnASAPKGSPARYGDTETQTISVLKRIETILQSQGLTMGDVVKMRVFLvadpalDGKMDFAGFMKAYRQFFgt 96

                        90       100       110
                ....*....|....*....|....*....|
gi 15598695 103 AGQGTFPASTLVEVSGLVFPELLVEIDAWA 132
Cdd:cd06151  97 AEQPNKPARSTLQVAGLVNPGWLVEIEVVA 126
PRK11401 PRK11401
enamine/imine deaminase;
26-132 6.53e-08

enamine/imine deaminase;


Pssm-ID: 105214  Cd Length: 129  Bit Score: 48.14  E-value: 6.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695   26 VGEELVMSGMTahPATRQAAErgAALDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAIGRARQEFF-AG 104
Cdd:PRK11401  23 LGSMVFTSGQI--PVCPQTGE--IPADVQDQARLSLENVKAIVVAAGLSVGDIIKMTVFITDLNDFATINEVYKQFFdEH 98

                         90       100
                 ....*....|....*....|....*...
gi 15598695  105 QGTFPASTLVEVSGLVfPELLVEIDAWA 132
Cdd:PRK11401  99 QATYPTRSCVQVARLP-KDVKLEIEAIA 125
YjgF_YER057c_UK114_like_2 cd06150
This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in ...
 43-132 2.29e-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: 45.99  E-value: 2.29e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598695  43 QAAErGAALDAHAQALVVLGKVKALLEAAGGHVGNLYKLNVYVTRIADKDAIGRARQEFFAGQGTfPASTLVEVsGLVFP 122
Cdd:cd06150  18 QVAD-DTSADITGQTRQVLAKIDALLAEAGSDKSRILSATIWLADMADFAAMNAVWDAWVPPGHA-PARACVEA-KLADP 94

                        90
                ....*....|
gi 15598695 123 ELLVEIDAWA 132
Cdd:cd06150  95 GYLVEIVVTA 104
 
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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