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Conserved domains on  [gi|1654098627|gb|TKY78975|]
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NfeD family protein [Enterobacter hormaechei]

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 ...
 24-149 3.76e-38

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


:

Pssm-ID: 441193  Cd Length: 143  Bit Score: 126.47  E-value: 3.76e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1654098627  24 EMLGGNGYLLWSGVAAVITGLVVWLLpVGWEWQGALFAVLTLLAAWLWWRWLNKRVKAQKPvdaHLNQRGQQIVGRRFTL 103
Cdd:COG1585    20 ELLTPGFFLLWFGLGALAVGLLALLG-LSLWLQLLVFAVLSLLLLLLWRRLLKRRLRSDAP---LLNTRVDALIGRTATV 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1654098627 104 DNALINGRGHMRVGDSSWPVVADDDLSAGTRVEVIAVEGITLRVKA 149
Cdd:COG1585    96 VEPIDNGRGRVKLGGEEWRARSEDDLPAGTRVRVVAVEGNTLIVEP 141
 
Name Accession Description Interval E-value
YbbJ COG1585
Membrane protein implicated in regulation of membrane protease activity [Posttranslational ...
 24-149 3.76e-38

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


Pssm-ID: 441193  Cd Length: 143  Bit Score: 126.47  E-value: 3.76e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1654098627  24 EMLGGNGYLLWSGVAAVITGLVVWLLpVGWEWQGALFAVLTLLAAWLWWRWLNKRVKAQKPvdaHLNQRGQQIVGRRFTL 103
Cdd:COG1585    20 ELLTPGFFLLWFGLGALAVGLLALLG-LSLWLQLLVFAVLSLLLLLLWRRLLKRRLRSDAP---LLNTRVDALIGRTATV 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1654098627 104 DNALINGRGHMRVGDSSWPVVADDDLSAGTRVEVIAVEGITLRVKA 149
Cdd:COG1585    96 VEPIDNGRGRVKLGGEEWRARSEDDLPAGTRVRVVAVEGNTLIVEP 141
NfeD pfam01957
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ...
 59-148 8.07e-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: 72.99  E-value: 8.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1654098627  59 LFAVLTLLAAWLWWRWLNKRVKaqKPVDAHLNQRGQQIVGRRFTLDNALINGRGHMRVGDSSWPVVADDD-LSAGTRVEV 137
Cdd:pfam01957   1 VFAVVSLVLLLLLRPLALKRLR--KKSPGSLTNRDEALIGRTGVVLEDIRPDGGRVKIDGEEWTARSDGDfIPAGTRVRV 78

                          90
                  ....*....|.
gi 1654098627 138 IAVEGITLRVK 148
Cdd:pfam01957  79 VAVEGLTLIVE 89
 
Name Accession Description Interval E-value
YbbJ COG1585
Membrane protein implicated in regulation of membrane protease activity [Posttranslational ...
 24-149 3.76e-38

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


Pssm-ID: 441193  Cd Length: 143  Bit Score: 126.47  E-value: 3.76e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1654098627  24 EMLGGNGYLLWSGVAAVITGLVVWLLpVGWEWQGALFAVLTLLAAWLWWRWLNKRVKAQKPvdaHLNQRGQQIVGRRFTL 103
Cdd:COG1585    20 ELLTPGFFLLWFGLGALAVGLLALLG-LSLWLQLLVFAVLSLLLLLLWRRLLKRRLRSDAP---LLNTRVDALIGRTATV 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1654098627 104 DNALINGRGHMRVGDSSWPVVADDDLSAGTRVEVIAVEGITLRVKA 149
Cdd:COG1585    96 VEPIDNGRGRVKLGGEEWRARSEDDLPAGTRVRVVAVEGNTLIVEP 141
NfeD pfam01957
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ...
 59-148 8.07e-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: 72.99  E-value: 8.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1654098627  59 LFAVLTLLAAWLWWRWLNKRVKaqKPVDAHLNQRGQQIVGRRFTLDNALINGRGHMRVGDSSWPVVADDD-LSAGTRVEV 137
Cdd:pfam01957   1 VFAVVSLVLLLLLRPLALKRLR--KKSPGSLTNRDEALIGRTGVVLEDIRPDGGRVKIDGEEWTARSDGDfIPAGTRVRV 78

                          90
                  ....*....|.
gi 1654098627 138 IAVEGITLRVK 148
Cdd:pfam01957  79 VAVEGLTLIVE 89
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 35-148 1.05e-07

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


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 49.47  E-value: 1.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1654098627  35 SGVAAVITGLV------VWLLPVGWEWQGALFAVLTLLAAWLWWRWLnkRVKAQKPVDAHLNQRGQQIVgrrfTLDNalI 108
Cdd:COG1030   297 GGIIALVLGLLllfdtdVPGLGVSALLIVAIALVIAIFLAFVLGKVL--RARKRKPVTGAEELIGKEGV----ALTD--L 368

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1654098627 109 NGRGHMRVGDSSWPVVADDD-LSAGTRVEVIAVEGITLRVK 148
Cdd:COG1030   369 RPSGKVRIDGERWDAVSEGEfIEKGEKVRVVGVEGLRLVVR 409
 
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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