NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|515743613|ref|WP_017176213|]
View 

MULTISPECIES: NfeD family protein [Staphylococcus]

Protein Classification

NfeD family protein( domain architecture ID 1002096)

NfeD (nodulation formation efficiency D) family protein containing only the C-terminal soluble OB-fold NfeD (NfeDC) domain, may interact with other spatially proximal membrane proteins and regulate their activities

CATH:  2.40.50.140
PubMed:  20012272
SCOP:  4001808

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NfeD super family cl34070
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 19-234 4.32e-28

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


The actual alignment was detected with superfamily member COG1030:

Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 109.95  E-value: 4.32e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515743613  19 SWLGDMSNIIVNPIVLLILTCIIFLGFLYQLYSKRINILGILASLALLILFLGFLIngDVNLISILLFFIGIILVIIELF 98
Cdd:COG1030  210 TWRERLLSFLTNPNVAYILLLIGILGLIFELYTPGFGVPGVIGAIALLLAFYGLYL--PANYAGLLLFLLGIILLILELF 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515743613  99 IVG-AVIGIIGIVLIIVSMIMLGDNI-----LVMLFNVIVALILSIIEWVILVKVFNRKipffdkviLNDSTSTEAGyrs 172
Cdd:COG1030  288 VPGfGILGIGGIIALVLGLLLLFDTDvpglgVSALLIVAIALVIAIFLAFVLGKVLRAR--------KRKPVTGAEE--- 356

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 515743613 173 hddrsyLVGKTAYTTTDLRPAGIITLDDKRIDAVSDGTFILRNKKVKILEVEGSRVVVREIK 234
Cdd:COG1030  357 ------LIGKEGVALTDLRPSGKVRIDGERWDAVSEGEFIEKGEKVRVVGVEGLRLVVRPVE 412
 
Name Accession Description Interval E-value
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 19-234 4.32e-28

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


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 109.95  E-value: 4.32e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515743613  19 SWLGDMSNIIVNPIVLLILTCIIFLGFLYQLYSKRINILGILASLALLILFLGFLIngDVNLISILLFFIGIILVIIELF 98
Cdd:COG1030  210 TWRERLLSFLTNPNVAYILLLIGILGLIFELYTPGFGVPGVIGAIALLLAFYGLYL--PANYAGLLLFLLGIILLILELF 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515743613  99 IVG-AVIGIIGIVLIIVSMIMLGDNI-----LVMLFNVIVALILSIIEWVILVKVFNRKipffdkviLNDSTSTEAGyrs 172
Cdd:COG1030  288 VPGfGILGIGGIIALVLGLLLLFDTDvpglgVSALLIVAIALVIAIFLAFVLGKVLRAR--------KRKPVTGAEE--- 356

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 515743613 173 hddrsyLVGKTAYTTTDLRPAGIITLDDKRIDAVSDGTFILRNKKVKILEVEGSRVVVREIK 234
Cdd:COG1030  357 ------LIGKEGVALTDLRPSGKVRIDGERWDAVSEGEFIEKGEKVRVVGVEGLRLVVRPVE 412
NfeD pfam01957
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ...
 132-232 2.99e-10

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: 55.28  E-value: 2.99e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515743613  132 VALILSIIEWVILVKVFNRKIPFFDKVILNDSTSTeagyrshddrsyLVGKTAYTTTDLRPA-GIITLDDKRIDAVSDGT 210
Cdd:pfam01957   1 VFAVVSLVLLLLLRPLALKRLRKKSPGSLTNRDEA------------LIGRTGVVLEDIRPDgGRVKIDGEEWTARSDGD 68

                          90       100
                  ....*....|....*....|..
gi 515743613  211 FILRNKKVKILEVEGSRVVVRE 232
Cdd:pfam01957  69 FIPAGTRVRVVAVEGLTLIVEP 90
 
Name Accession Description Interval E-value
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 19-234 4.32e-28

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


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 109.95  E-value: 4.32e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515743613  19 SWLGDMSNIIVNPIVLLILTCIIFLGFLYQLYSKRINILGILASLALLILFLGFLIngDVNLISILLFFIGIILVIIELF 98
Cdd:COG1030  210 TWRERLLSFLTNPNVAYILLLIGILGLIFELYTPGFGVPGVIGAIALLLAFYGLYL--PANYAGLLLFLLGIILLILELF 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515743613  99 IVG-AVIGIIGIVLIIVSMIMLGDNI-----LVMLFNVIVALILSIIEWVILVKVFNRKipffdkviLNDSTSTEAGyrs 172
Cdd:COG1030  288 VPGfGILGIGGIIALVLGLLLLFDTDvpglgVSALLIVAIALVIAIFLAFVLGKVLRAR--------KRKPVTGAEE--- 356

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 515743613 173 hddrsyLVGKTAYTTTDLRPAGIITLDDKRIDAVSDGTFILRNKKVKILEVEGSRVVVREIK 234
Cdd:COG1030  357 ------LIGKEGVALTDLRPSGKVRIDGERWDAVSEGEFIEKGEKVRVVGVEGLRLVVRPVE 412
NfeD pfam01957
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ...
 132-232 2.99e-10

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: 55.28  E-value: 2.99e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515743613  132 VALILSIIEWVILVKVFNRKIPFFDKVILNDSTSTeagyrshddrsyLVGKTAYTTTDLRPA-GIITLDDKRIDAVSDGT 210
Cdd:pfam01957   1 VFAVVSLVLLLLLRPLALKRLRKKSPGSLTNRDEA------------LIGRTGVVLEDIRPDgGRVKIDGEEWTARSDGD 68

                          90       100
                  ....*....|....*....|..
gi 515743613  211 FILRNKKVKILEVEGSRVVVRE 232
Cdd:pfam01957  69 FIPAGTRVRVVAVEGLTLIVEP 90
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH