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Conserved domains on  [gi|1820367846|ref|WP_165458546|]
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1,2-phenylacetyl-CoA epoxidase subunit PaaD [Raoultella ornithinolytica]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PA_CoA_Oxy4 super family cl27483
phenylacetate-CoA oxygenase, PaaJ subunit; Phenylacetate-CoA oxygenase is comprised of a five ...
 22-165 9.68e-78

phenylacetate-CoA oxygenase, PaaJ subunit; Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA. [Energy metabolism, Other]


The actual alignment was detected with superfamily member TIGR02159:

Pssm-ID: 131214  Cd Length: 146  Bit Score: 227.75  E-value: 9.68e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820367846  22 IPDPEVPVLTITDLGMVRSVAPHGEGWVIGFTPTYSGCPATEHLLGEIRATMARHGYTPVHVVLQLDPPWTTDWMNQDAR 101
Cdd:TIGR02159   1 VPDPEIPVVSVTDLGMVREVDVDGGGVVVKFTPTYSGCPALEVIRQDIRDAVRALGVEVVEVSTSLDPPWTTDWITEDAR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1820367846 102 ERLRQYGISPPQGHACHAG--LQQEVVCPRCGSVHTTPISEFGSTACKALYRCDSCREPFDYFKCI 165
Cdd:TIGR02159  81 EKLREYGIAPPAGHYVVGVspEPPSVQCPRCGSADTTITSIFGPTACKALYRCRACKEPFEYFKPI 146
 
Name Accession Description Interval E-value
PA_CoA_Oxy4 TIGR02159
phenylacetate-CoA oxygenase, PaaJ subunit; Phenylacetate-CoA oxygenase is comprised of a five ...
 22-165 9.68e-78

phenylacetate-CoA oxygenase, PaaJ subunit; Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA. [Energy metabolism, Other]


Pssm-ID: 131214  Cd Length: 146  Bit Score: 227.75  E-value: 9.68e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820367846  22 IPDPEVPVLTITDLGMVRSVAPHGEGWVIGFTPTYSGCPATEHLLGEIRATMARHGYTPVHVVLQLDPPWTTDWMNQDAR 101
Cdd:TIGR02159   1 VPDPEIPVVSVTDLGMVREVDVDGGGVVVKFTPTYSGCPALEVIRQDIRDAVRALGVEVVEVSTSLDPPWTTDWITEDAR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1820367846 102 ERLRQYGISPPQGHACHAG--LQQEVVCPRCGSVHTTPISEFGSTACKALYRCDSCREPFDYFKCI 165
Cdd:TIGR02159  81 EKLREYGIAPPAGHYVVGVspEPPSVQCPRCGSADTTITSIFGPTACKALYRCRACKEPFEYFKPI 146
PaaD COG2151
Metal-sulfur cluster biosynthetic enzyme [Posttranslational modification, protein turnover, ...
 14-104 8.59e-32

Metal-sulfur cluster biosynthetic enzyme [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441754  Cd Length: 102  Bit Score: 109.81  E-value: 8.59e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820367846  14 AIWALLSEIPDPEVPVlTITDLGMVRSVAPHGEGWV-IGFTPTYSGCPATEHLLGEIRATMAR-HGYTPVHVVLQLDPPW 91
Cdd:COG2151    11 EVWEALKTVYDPEIPV-NIVDLGLIYDVEVDDDGRVkVTMTLTTPGCPAADVIPDDVEEALEEvPGVEDVEVELVWDPPW 89

                          90
                  ....*....|...
gi 1820367846  92 TTDWMNQDARERL 104
Cdd:COG2151    90 TPDRMSEEARLKL 102
FeS_assembly_P pfam01883
Iron-sulfur cluster assembly protein; This family has an alpha/beta topology, with 13 ...
 14-71 5.12e-07

Iron-sulfur cluster assembly protein; This family has an alpha/beta topology, with 13 conserved hydrophobic residues at its core and a putative active site containing a highly conserved cysteine. Members of this family are involved in a range of physiological functions. The family includes PaaJ (PhaH) from Pseudomonas putida. PaaJ forms a complex with PaaG (PhaF), PaaI (PhaG) and PaaK (PhaI), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid. It also includes PaaD from Escherichia coli, a member of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation. Furthermore, several members of this family are shown to be involved in iron-sulfur (FeS) cluster assembly. Iron-sulfur (FeS) clusters are inorganic co-factors that are are able to transfer electrons and act as catalysts. They are involved in diverse cellular processes including cellular respiration, DNA replication and repair, antibiotic resistance, and dinitrogen fixation. The biogenesis of such clusters from elemental iron and sulfur is an enzymatic process that requires a set of specialized proteins. Proteins containing this domain include the chloroplast protein HCF101 (high chlorophyll fluorescence 101), which has been described as an essential and specific factor for assembly of [4Fe-4S]-cluster-containing protein complexes such as the membrane complex Photosystem I (PSI) and the heterodimeric FTR (ferredoxin-thioredoxin reductase) complex and is involved in the assembly of [4Fe-4S] clusters and their transfer to apoproteins. The mature HCF101 protein contains this domain at the N-terminal as well as eight cysteine residues along the sequence. All cysteine residues are conserved among higher plants, but of the two cysteine residues located in this domain only Cys128 is highly conserved and is present in the highly conserved P-loop domain of the plant HCF101 (CKGGVGKS). SufT protein from Staphylococcus aureus is composed of this domain solely and is shown to be involved in the maturation of FeS proteins. Given all this data, it is hypothesized that this domain might play a role in FeS cluster assembly.


Pssm-ID: 460370  Cd Length: 73  Bit Score: 44.93  E-value: 5.12e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1820367846  14 AIWALLSEIPDPEVPVlTITDLGMVRSVAPHGEGWVIGFTPTYSGCPATEHLLGEIRA 71
Cdd:pfam01883   3 AVLAALRTVIDPETGV-DLVSLGLVRNIDIEGGKVSVDITLTYPACPAAEAIRADAEA 59
 
Name Accession Description Interval E-value
PA_CoA_Oxy4 TIGR02159
phenylacetate-CoA oxygenase, PaaJ subunit; Phenylacetate-CoA oxygenase is comprised of a five ...
 22-165 9.68e-78

phenylacetate-CoA oxygenase, PaaJ subunit; Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA. [Energy metabolism, Other]


Pssm-ID: 131214  Cd Length: 146  Bit Score: 227.75  E-value: 9.68e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820367846  22 IPDPEVPVLTITDLGMVRSVAPHGEGWVIGFTPTYSGCPATEHLLGEIRATMARHGYTPVHVVLQLDPPWTTDWMNQDAR 101
Cdd:TIGR02159   1 VPDPEIPVVSVTDLGMVREVDVDGGGVVVKFTPTYSGCPALEVIRQDIRDAVRALGVEVVEVSTSLDPPWTTDWITEDAR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1820367846 102 ERLRQYGISPPQGHACHAG--LQQEVVCPRCGSVHTTPISEFGSTACKALYRCDSCREPFDYFKCI 165
Cdd:TIGR02159  81 EKLREYGIAPPAGHYVVGVspEPPSVQCPRCGSADTTITSIFGPTACKALYRCRACKEPFEYFKPI 146
PaaD COG2151
Metal-sulfur cluster biosynthetic enzyme [Posttranslational modification, protein turnover, ...
 14-104 8.59e-32

Metal-sulfur cluster biosynthetic enzyme [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441754  Cd Length: 102  Bit Score: 109.81  E-value: 8.59e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820367846  14 AIWALLSEIPDPEVPVlTITDLGMVRSVAPHGEGWV-IGFTPTYSGCPATEHLLGEIRATMAR-HGYTPVHVVLQLDPPW 91
Cdd:COG2151    11 EVWEALKTVYDPEIPV-NIVDLGLIYDVEVDDDGRVkVTMTLTTPGCPAADVIPDDVEEALEEvPGVEDVEVELVWDPPW 89

                          90
                  ....*....|...
gi 1820367846  92 TTDWMNQDARERL 104
Cdd:COG2151    90 TPDRMSEEARLKL 102
FeS_assembly_P pfam01883
Iron-sulfur cluster assembly protein; This family has an alpha/beta topology, with 13 ...
 14-71 5.12e-07

Iron-sulfur cluster assembly protein; This family has an alpha/beta topology, with 13 conserved hydrophobic residues at its core and a putative active site containing a highly conserved cysteine. Members of this family are involved in a range of physiological functions. The family includes PaaJ (PhaH) from Pseudomonas putida. PaaJ forms a complex with PaaG (PhaF), PaaI (PhaG) and PaaK (PhaI), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid. It also includes PaaD from Escherichia coli, a member of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation. Furthermore, several members of this family are shown to be involved in iron-sulfur (FeS) cluster assembly. Iron-sulfur (FeS) clusters are inorganic co-factors that are are able to transfer electrons and act as catalysts. They are involved in diverse cellular processes including cellular respiration, DNA replication and repair, antibiotic resistance, and dinitrogen fixation. The biogenesis of such clusters from elemental iron and sulfur is an enzymatic process that requires a set of specialized proteins. Proteins containing this domain include the chloroplast protein HCF101 (high chlorophyll fluorescence 101), which has been described as an essential and specific factor for assembly of [4Fe-4S]-cluster-containing protein complexes such as the membrane complex Photosystem I (PSI) and the heterodimeric FTR (ferredoxin-thioredoxin reductase) complex and is involved in the assembly of [4Fe-4S] clusters and their transfer to apoproteins. The mature HCF101 protein contains this domain at the N-terminal as well as eight cysteine residues along the sequence. All cysteine residues are conserved among higher plants, but of the two cysteine residues located in this domain only Cys128 is highly conserved and is present in the highly conserved P-loop domain of the plant HCF101 (CKGGVGKS). SufT protein from Staphylococcus aureus is composed of this domain solely and is shown to be involved in the maturation of FeS proteins. Given all this data, it is hypothesized that this domain might play a role in FeS cluster assembly.


Pssm-ID: 460370  Cd Length: 73  Bit Score: 44.93  E-value: 5.12e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1820367846  14 AIWALLSEIPDPEVPVlTITDLGMVRSVAPHGEGWVIGFTPTYSGCPATEHLLGEIRA 71
Cdd:pfam01883   3 AVLAALRTVIDPETGV-DLVSLGLVRNIDIEGGKVSVDITLTYPACPAAEAIRADAEA 59
tRNA-synt_1f pfam01921
tRNA synthetases class I (K); This family includes only lysyl tRNA synthetases from ...
 124-155 6.84e-03

tRNA synthetases class I (K); This family includes only lysyl tRNA synthetases from prokaryotes.


Pssm-ID: 396483  Cd Length: 357  Bit Score: 36.08  E-value: 6.84e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1820367846 124 EVVCPRCGSVHTTPISEFgSTACKALYRCDSC 155
Cdd:pfam01921 172 LPICPKCGRVLTTPVVEY-DEGGTIRYRCDEC 202
 
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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