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Conserved domains on  [gi|145698226|ref|NP_415021|]
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NfeD-like family protein YbbJ [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

NfeD family protein( domain architecture ID 10003982)

NfeD (nodulation formation efficiency D) family protein containing only the C-terminal soluble OB-fold NfeD (NfeDC) domain, may function by associating with neighboring slipin clusters; similar to Escherichia coli inner membrane protein YbbJ

CATH:  2.40.50.140
Gene Ontology:  GO:0016020
PubMed:  20012272|18687870
SCOP:  4001808

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbbJ COG1585
Membrane protein implicated in regulation of membrane protease activity [Posttranslational ...
 5-151 7.56e-40

Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones];


:

Pssm-ID: 441193  Cd Length: 143  Bit Score: 131.09  E-value: 7.56e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145698226   5 MVVHPHIFWLSLGGLLLAAEMLGGNGYLLWSGVAAVITGLVVWLVpLGWEWQGVMFAILTLLAAWLWWKWLSRRVREQKh 84
Cdd:COG1585    1 MSALPWLIWLILGLLLLIAELLTPGFFLLWFGLGALAVGLLALLG-LSLWLQLLVFAVLSLLLLLLWRRLLKRRLRSDA- 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 145698226  85 sdSHLNQRGQQLIGRRFVLESPLVNGRGHMRVGDSSWPVSASEDLGAGTHVEVIAIEGITLHIRAVS 151
Cdd:COG1585   79 --PLLNTRVDALIGRTATVVEPIDNGRGRVKLGGEEWRARSEDDLPAGTRVRVVAVEGNTLIVEPVE 143
 
Name Accession Description Interval E-value
YbbJ COG1585
Membrane protein implicated in regulation of membrane protease activity [Posttranslational ...
 5-151 7.56e-40

Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441193  Cd Length: 143  Bit Score: 131.09  E-value: 7.56e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145698226   5 MVVHPHIFWLSLGGLLLAAEMLGGNGYLLWSGVAAVITGLVVWLVpLGWEWQGVMFAILTLLAAWLWWKWLSRRVREQKh 84
Cdd:COG1585    1 MSALPWLIWLILGLLLLIAELLTPGFFLLWFGLGALAVGLLALLG-LSLWLQLLVFAVLSLLLLLLWRRLLKRRLRSDA- 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 145698226  85 sdSHLNQRGQQLIGRRFVLESPLVNGRGHMRVGDSSWPVSASEDLGAGTHVEVIAIEGITLHIRAVS 151
Cdd:COG1585   79 --PLLNTRVDALIGRTATVVEPIDNGRGRVKLGGEEWRARSEDDLPAGTRVRVVAVEGNTLIVEPVE 143
NfeD pfam01957
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ...
 60-148 2.88e-18

NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout prokaryotes and are frequently associated with genes encoding stomatin-like proteins (slipins). There appear to be three major groups: an ancestral group with only an N-terminal serine protease domain and this C-terminal beta sheet-rich domain which is structurally very similar to the OB-fold domain, associated with its neighbouring slipin cluster; a second major group with an additional middle, membrane-spanning domain, associated in some species with eoslipin and in others with yqfA; a final 'artificial' group which unites truncated forms lacking the protease region and associated with their ancestral gene partner, either yqfA or eoslipin. This NefD, C-terminal, domain appears to be the major one for relating to the associated protein. NfeD homologs are clearly reliant on their conserved gene neighbour which is assumed to be necessary for function, either through direct physical interaction or by functioning in the same pathway, possibly involve with lipid-rafts.


Pssm-ID: 460395  Cd Length: 90  Bit Score: 74.15  E-value: 2.88e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145698226   60 FAILTLLAAWLWWKWLSRRVReqKHSDSHLNQRGQQLIGRRFVLESPLVNGRGHMRVGDSSWPV-SASEDLGAGTHVEVI 138
Cdd:pfam01957   2 FAVVSLVLLLLLRPLALKRLR--KKSPGSLTNRDEALIGRTGVVLEDIRPDGGRVKIDGEEWTArSDGDFIPAGTRVRVV 79

                          90
                  ....*....|
gi 145698226  139 AIEGITLHIR 148
Cdd:pfam01957  80 AVEGLTLIVE 89
cobS PRK00235
cobalamin synthase; Reviewed
 33-78 5.11e-03

cobalamin synthase; Reviewed


Pssm-ID: 234697  Cd Length: 249  Bit Score: 35.97  E-value: 5.11e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 145698226  33 LWSGVAAVITGLVVWLVPLGWeWQGVMFAILTLLAAWLWWKWLSRR 78
Cdd:PRK00235 176 GRQLLLALALGLALLLPLLGG-WAGLLALLVALVAAFLLGRLFVRR 220
 
Name Accession Description Interval E-value
YbbJ COG1585
Membrane protein implicated in regulation of membrane protease activity [Posttranslational ...
 5-151 7.56e-40

Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441193  Cd Length: 143  Bit Score: 131.09  E-value: 7.56e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145698226   5 MVVHPHIFWLSLGGLLLAAEMLGGNGYLLWSGVAAVITGLVVWLVpLGWEWQGVMFAILTLLAAWLWWKWLSRRVREQKh 84
Cdd:COG1585    1 MSALPWLIWLILGLLLLIAELLTPGFFLLWFGLGALAVGLLALLG-LSLWLQLLVFAVLSLLLLLLWRRLLKRRLRSDA- 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 145698226  85 sdSHLNQRGQQLIGRRFVLESPLVNGRGHMRVGDSSWPVSASEDLGAGTHVEVIAIEGITLHIRAVS 151
Cdd:COG1585   79 --PLLNTRVDALIGRTATVVEPIDNGRGRVKLGGEEWRARSEDDLPAGTRVRVVAVEGNTLIVEPVE 143
NfeD pfam01957
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ...
 60-148 2.88e-18

NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout prokaryotes and are frequently associated with genes encoding stomatin-like proteins (slipins). There appear to be three major groups: an ancestral group with only an N-terminal serine protease domain and this C-terminal beta sheet-rich domain which is structurally very similar to the OB-fold domain, associated with its neighbouring slipin cluster; a second major group with an additional middle, membrane-spanning domain, associated in some species with eoslipin and in others with yqfA; a final 'artificial' group which unites truncated forms lacking the protease region and associated with their ancestral gene partner, either yqfA or eoslipin. This NefD, C-terminal, domain appears to be the major one for relating to the associated protein. NfeD homologs are clearly reliant on their conserved gene neighbour which is assumed to be necessary for function, either through direct physical interaction or by functioning in the same pathway, possibly involve with lipid-rafts.


Pssm-ID: 460395  Cd Length: 90  Bit Score: 74.15  E-value: 2.88e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145698226   60 FAILTLLAAWLWWKWLSRRVReqKHSDSHLNQRGQQLIGRRFVLESPLVNGRGHMRVGDSSWPV-SASEDLGAGTHVEVI 138
Cdd:pfam01957   2 FAVVSLVLLLLLRPLALKRLR--KKSPGSLTNRDEALIGRTGVVLEDIRPDGGRVKIDGEEWTArSDGDFIPAGTRVRVV 79

                          90
                  ....*....|
gi 145698226  139 AIEGITLHIR 148
Cdd:pfam01957  80 AVEGLTLIVE 89
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 35-152 2.16e-07

Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 48.70  E-value: 2.16e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145698226  35 SGVAAVITGLV------VWLVPLGWEWQGVMFAILTLLAAWLWWKWLSRRVREQKHSDshlnqrgQQLIGRRFVLESPLv 108
Cdd:COG1030  297 GGIIALVLGLLllfdtdVPGLGVSALLIVAIALVIAIFLAFVLGKVLRARKRKPVTGA-------EELIGKEGVALTDL- 368

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 145698226 109 NGRGHMRVGDSSWP-VSASEDLGAGTHVEVIAIEGITLHIRAVSS 152
Cdd:COG1030  369 RPSGKVRIDGERWDaVSEGEFIEKGEKVRVVGVEGLRLVVRPVEE 413
cobS PRK00235
cobalamin synthase; Reviewed
 33-78 5.11e-03

cobalamin synthase; Reviewed


Pssm-ID: 234697  Cd Length: 249  Bit Score: 35.97  E-value: 5.11e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 145698226  33 LWSGVAAVITGLVVWLVPLGWeWQGVMFAILTLLAAWLWWKWLSRR 78
Cdd:PRK00235 176 GRQLLLALALGLALLLPLLGG-WAGLLALLVALVAAFLLGRLFVRR 220
 
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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