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Conserved domains on  [gi|1706894929|emb|VUX46589|]
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Membrane-bound serine protease (ClpP class) [Candidatus Defluviicoccus seviourii]

Protein Classification

NfeD family protein( domain architecture ID 11437047)

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 Bacillus subtilis membrane protein NfeD1b

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
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 23-466 5.59e-159

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


:

Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 456.24  E-value: 5.59e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929  23 LFLLTALAGWTGPASAGEPSRAAVVQLTITGPIGPATSDYVERGLGQAAADGAALVILRLDTPGGLDTSMREIIKAILAA 102
Cdd:COG1030     5 LLLLLALLLALAAPASAAAAAKKVYVIPIDGAIGPATADYLERALEEAEEEGADAVVLELDTPGGLVDSAREIVDAILAS 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 103 PLPVAGFVAPrGAHAASAGTFILYACHVAAMAPGTNLGAATPVAIGGPEGQPspkppereassprdepslpdVREKAASD 182
Cdd:COG1030    85 PVPVIVYVAS-GARAASAGAYILLASHIAAMAPGTNIGAATPVQIGGGIDEA--------------------MEEKVIND 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 183 AAAYIRSLAQLRGRNAAWAEKAVIEAASLSASDALAIGVVDLIAEDTDALLRALDgrtvtvagqqqrieTGRLTLTAIEP 262
Cdd:COG1030   144 AVAYIRSLAELRGRNADWAEAMVRESVSLTAEEALELGVIDLIAEDLDELLATLG--------------TAGAEIVEYEP 209

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 263 DWRARFLGIITNPNVAAILLLVGVYGVLFEFYSPGLVGPGVIGAICLVLALYAfHILPVSWGGVSLILLGIALLVAEAFV 342
Cdd:COG1030   210 TWRERLLSFLTNPNVAYILLLIGILGLIFELYTPGFGVPGVIGAIALLLAFYG-LYLPANYAGLLLFLLGIILLILELFV 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 343 PSFGVLGLGGITAFVIGAILLIEDDAPGFGVAWQLIGGSAVAFALTFGLLSTLVMRARARPVVTGREQLIGQTARVLDWS 422
Cdd:COG1030   289 PGFGILGIGGIIALVLGLLLLFDTDVPGLGVSALLIVAIALVIAIFLAFVLGKVLRARKRKPVTGAEELIGKEGVALTDL 368

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*
gi 1706894929 423 AGEGWVQLAGERWRARGPSA-LAPGMHVRVTGVDGLTLAVEAISP 466
Cdd:COG1030   369 RPSGKVRIDGERWDAVSEGEfIEKGEKVRVVGVEGLRLVVRPVEE 413
 
Name Accession Description Interval E-value
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 23-466 5.59e-159

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


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 456.24  E-value: 5.59e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929  23 LFLLTALAGWTGPASAGEPSRAAVVQLTITGPIGPATSDYVERGLGQAAADGAALVILRLDTPGGLDTSMREIIKAILAA 102
Cdd:COG1030     5 LLLLLALLLALAAPASAAAAAKKVYVIPIDGAIGPATADYLERALEEAEEEGADAVVLELDTPGGLVDSAREIVDAILAS 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 103 PLPVAGFVAPrGAHAASAGTFILYACHVAAMAPGTNLGAATPVAIGGPEGQPspkppereassprdepslpdVREKAASD 182
Cdd:COG1030    85 PVPVIVYVAS-GARAASAGAYILLASHIAAMAPGTNIGAATPVQIGGGIDEA--------------------MEEKVIND 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 183 AAAYIRSLAQLRGRNAAWAEKAVIEAASLSASDALAIGVVDLIAEDTDALLRALDgrtvtvagqqqrieTGRLTLTAIEP 262
Cdd:COG1030   144 AVAYIRSLAELRGRNADWAEAMVRESVSLTAEEALELGVIDLIAEDLDELLATLG--------------TAGAEIVEYEP 209

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 263 DWRARFLGIITNPNVAAILLLVGVYGVLFEFYSPGLVGPGVIGAICLVLALYAfHILPVSWGGVSLILLGIALLVAEAFV 342
Cdd:COG1030   210 TWRERLLSFLTNPNVAYILLLIGILGLIFELYTPGFGVPGVIGAIALLLAFYG-LYLPANYAGLLLFLLGIILLILELFV 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 343 PSFGVLGLGGITAFVIGAILLIEDDAPGFGVAWQLIGGSAVAFALTFGLLSTLVMRARARPVVTGREQLIGQTARVLDWS 422
Cdd:COG1030   289 PGFGILGIGGIIALVLGLLLLFDTDVPGLGVSALLIVAIALVIAIFLAFVLGKVLRARKRKPVTGAEELIGKEGVALTDL 368

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*
gi 1706894929 423 AGEGWVQLAGERWRARGPSA-LAPGMHVRVTGVDGLTLAVEAISP 466
Cdd:COG1030   369 RPSGKVRIDGERWDAVSEGEfIEKGEKVRVVGVEGLRLVVRPVEE 413
Clp_protease_NfeD_1 cd07020
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 46-250 1.78e-91

Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control.


Pssm-ID: 132931 [Multi-domain]  Cd Length: 187  Bit Score: 275.59  E-value: 1.78e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929  46 VVQLTITGPIGPATSDYVERGLGQAAADGAALVILRLDTPGGLDTSMREIIKAILAAPLPVAGFVAPRGAHAASAGTFIL 125
Cdd:cd07020     1 VYVLEINGAITPATADYLERAIDQAEEGGADALIIELDTPGGLLDSTREIVQAILASPVPVVVYVYPSGARAASAGTYIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 126 YACHVAAMAPGTNLGAATPVAIGGPEGQPspkppereassprdepslPDVREKAASDAAAYIRSLAQLRGRNAAWAEKAV 205
Cdd:cd07020    81 LAAHIAAMAPGTNIGAAHPVAIGGGGGSD------------------PVMEKKILNDAVAYIRSLAELRGRNAEWAEKAV 142

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1706894929 206 IEAASLSASDALAIGVVDLIAEDTDALLRALDGRTVTVAGQQQRI 250
Cdd:cd07020   143 RESLSLTAEEALKLGVIDLIAADLNELLKKLDGRTVKVAGKEVTL 187
NfeD pfam01957
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ...
 381-462 2.29e-11

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: 59.90  E-value: 2.29e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 381 SAVAFALTFGLLSTLVMRARARPVVTGREQLIGQTARVLDW-SAGEGWVQLAGERWRARGPS-ALAPGMHVRVTGVDGLT 458
Cdd:pfam01957   6 SLVLLLLLRPLALKRLRKKSPGSLTNRDEALIGRTGVVLEDiRPDGGRVKIDGEEWTARSDGdFIPAGTRVRVVAVEGLT 85


                  ....
gi 1706894929 459 LAVE 462
Cdd:pfam01957  86 LIVE 89
 
Name Accession Description Interval E-value
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 23-466 5.59e-159

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


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 456.24  E-value: 5.59e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929  23 LFLLTALAGWTGPASAGEPSRAAVVQLTITGPIGPATSDYVERGLGQAAADGAALVILRLDTPGGLDTSMREIIKAILAA 102
Cdd:COG1030     5 LLLLLALLLALAAPASAAAAAKKVYVIPIDGAIGPATADYLERALEEAEEEGADAVVLELDTPGGLVDSAREIVDAILAS 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 103 PLPVAGFVAPrGAHAASAGTFILYACHVAAMAPGTNLGAATPVAIGGPEGQPspkppereassprdepslpdVREKAASD 182
Cdd:COG1030    85 PVPVIVYVAS-GARAASAGAYILLASHIAAMAPGTNIGAATPVQIGGGIDEA--------------------MEEKVIND 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 183 AAAYIRSLAQLRGRNAAWAEKAVIEAASLSASDALAIGVVDLIAEDTDALLRALDgrtvtvagqqqrieTGRLTLTAIEP 262
Cdd:COG1030   144 AVAYIRSLAELRGRNADWAEAMVRESVSLTAEEALELGVIDLIAEDLDELLATLG--------------TAGAEIVEYEP 209

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 263 DWRARFLGIITNPNVAAILLLVGVYGVLFEFYSPGLVGPGVIGAICLVLALYAfHILPVSWGGVSLILLGIALLVAEAFV 342
Cdd:COG1030   210 TWRERLLSFLTNPNVAYILLLIGILGLIFELYTPGFGVPGVIGAIALLLAFYG-LYLPANYAGLLLFLLGIILLILELFV 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 343 PSFGVLGLGGITAFVIGAILLIEDDAPGFGVAWQLIGGSAVAFALTFGLLSTLVMRARARPVVTGREQLIGQTARVLDWS 422
Cdd:COG1030   289 PGFGILGIGGIIALVLGLLLLFDTDVPGLGVSALLIVAIALVIAIFLAFVLGKVLRARKRKPVTGAEELIGKEGVALTDL 368

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*
gi 1706894929 423 AGEGWVQLAGERWRARGPSA-LAPGMHVRVTGVDGLTLAVEAISP 466
Cdd:COG1030   369 RPSGKVRIDGERWDAVSEGEfIEKGEKVRVVGVEGLRLVVRPVEE 413
Clp_protease_NfeD_1 cd07020
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 46-250 1.78e-91

Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control.


Pssm-ID: 132931 [Multi-domain]  Cd Length: 187  Bit Score: 275.59  E-value: 1.78e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929  46 VVQLTITGPIGPATSDYVERGLGQAAADGAALVILRLDTPGGLDTSMREIIKAILAAPLPVAGFVAPRGAHAASAGTFIL 125
Cdd:cd07020     1 VYVLEINGAITPATADYLERAIDQAEEGGADALIIELDTPGGLLDSTREIVQAILASPVPVVVYVYPSGARAASAGTYIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 126 YACHVAAMAPGTNLGAATPVAIGGPEGQPspkppereassprdepslPDVREKAASDAAAYIRSLAQLRGRNAAWAEKAV 205
Cdd:cd07020    81 LAAHIAAMAPGTNIGAAHPVAIGGGGGSD------------------PVMEKKILNDAVAYIRSLAELRGRNAEWAEKAV 142

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1706894929 206 IEAASLSASDALAIGVVDLIAEDTDALLRALDGRTVTVAGQQQRI 250
Cdd:cd07020   143 RESLSLTAEEALKLGVIDLIAADLNELLKKLDGRTVKVAGKEVTL 187
Clp_protease_NfeD_like cd07021
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 46-234 9.41e-30

Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control.


Pssm-ID: 132932 [Multi-domain]  Cd Length: 178  Bit Score: 114.22  E-value: 9.41e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929  46 VVQLTITGPIGPATSDYVERGLGQAAADGAALVILRLDTPGGLDTSMREIIKAILAAPLPVAGFVAPRgahAASAGTFIL 125
Cdd:cd07021     1 VYVIPIEGEIDPGLAAFVERALKEAKEEGADAVVLDIDTPGGRVDSALEIVDLILNSPIPTIAYVNDR---AASAGALIA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 126 YACHVAAMAPGTNLGAATPVaigGPEGQPSpkppereassprdepslpdVREKAASDAAAYIRSLAQLRGRNAAWAEKAV 205
Cdd:cd07021    78 LAADEIYMAPGATIGAAEPI---PGDGNGA-------------------ADEKVQSYWRAKMRAAAEKKGRDPDIAEAMV 135

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1706894929 206 IEAA-------------SLSASDALAIGVVDLIAEDTDALLR 234
Cdd:cd07021   136 DKDIevpgvgikggellTLTADEALKVGYAEGIAGSLDELLV 177
Clp_protease_NfeD cd07015
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 51-234 2.06e-28

Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control.


Pssm-ID: 132926  Cd Length: 172  Bit Score: 110.56  E-value: 2.06e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929  51 ITGPIGPATSDYVERGLGQAAADGAALVILRLDTPGGLDTSMREIIKAILAAPLPVAGFVAPRGAHAASAGTFILYACHV 130
Cdd:cd07015     6 IKGQITSYTYDQFDRYITIAEQDNAEAIIIELDTPGGRADAAGNIVQRIQQSKIPVIIYVYPPGASAASAGTYIALGSHL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 131 AAMAPGTNLGAATPVAIGGPEGQPSPKPPereassprdepslpdvreKAASDAAAYIRSLAQLRGRNAAWAEKAVIEAAS 210
Cdd:cd07015    86 IAMAPGTSIGACRPILGYSQNGSIIEAPP------------------KITNYFIAYIKSLAQESGRNATIAEEFITKDLS 147

                         170       180
                  ....*....|....*....|....
gi 1706894929 211 LSASDALAIGVVDLIAEDTDALLR 234
Cdd:cd07015   148 LTPEEALKYGVIEVVARDINELLK 171
YbbJ COG1585
Membrane protein implicated in regulation of membrane protease activity [Posttranslational ...
 329-465 4.04e-19

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


Pssm-ID: 441193  Cd Length: 143  Bit Score: 83.71  E-value: 4.04e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 329 ILLGIALLVAEAFVPSFGVLGLGgITAFVIGAILLIeddapGFGVAWQLIGGSAVAFALTFGLLSTL--VMRARARPVVT 406
Cdd:COG1585    10 LILGLLLLIAELLTPGFFLLWFG-LGALAVGLLALL-----GLSLWLQLLVFAVLSLLLLLLWRRLLkrRLRSDAPLLNT 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 407 GREQLIGQTARVL-DWSAGEGWVQLAGERWRARGPSALAPGMHVRVTGVDGLTLAVEAIS 465
Cdd:COG1585    84 RVDALIGRTATVVePIDNGRGRVKLGGEEWRARSEDDLPAGTRVRVVAVEGNTLIVEPVE 143
Clp_protease_like cd00394
Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ...
 51-225 5.73e-14

Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. Another family included in this class of enzymes is the signal peptide peptidase A (SppA; S49) which is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Mutagenesis studies suggest that the catalytic center of SppA comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain. Others, including sohB peptidase, protein C, protein 1510-N and archaeal signal peptide peptidase, do not contain the amino-terminal domain. The third family included in this hierarchy is nodulation formation efficiency D (NfeD) which is a membrane-bound Clp-class protease and only found in bacteria and archaea. Majority of the NfeD genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named stomatin operon partner protein (STOPP). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 from Pyrococcus horikoshii has been shown to possess serine protease activity having a Ser-Lys catalytic dyad.


Pssm-ID: 132923 [Multi-domain]  Cd Length: 161  Bit Score: 69.34  E-value: 5.73e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929  51 ITGPIGPATSDYVERGLGQAAADGAAL-VILRLDTPGGLDTSMREIIKAILAAPLPVAGFVaprGAHAASAGTFILYACH 129
Cdd:cd00394     4 INGVIEDVSADQLAAQIRFAEADNSVKaIVLEVNTPGGRVDAGMNIVDALQASRKPVIAYV---GGQAASAGYYIATAAN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 130 VAAMAPGTNLGAATPVAIGGPEGQPSpkppEREASsprdepslpdvrEKAASDAAAYIRSLAQLRGRNAAWAEKAVIE-A 208
Cdd:cd00394    81 KIVMAPGTRVGSHGPIGGYGGNGNPT----AQEAD------------QRIILYFIARFISLVAENRGQTTEKLEEDIEkD 144

                         170
                  ....*....|....*..
gi 1706894929 209 ASLSASDALAIGVVDLI 225
Cdd:cd00394   145 LVLTAQEALEYGLVDAL 161
NfeD pfam01957
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ...
 381-462 2.29e-11

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: 59.90  E-value: 2.29e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929 381 SAVAFALTFGLLSTLVMRARARPVVTGREQLIGQTARVLDW-SAGEGWVQLAGERWRARGPS-ALAPGMHVRVTGVDGLT 458
Cdd:pfam01957   6 SLVLLLLLRPLALKRLRKKSPGSLTNRDEALIGRTGVVLEDiRPDGGRVKIDGEEWTARSDGdFIPAGTRVRVVAVEGLT 85


                  ....
gi 1706894929 459 LAVE 462
Cdd:pfam01957  86 LIVE 89
SppA COG0616
Periplasmic serine protease, ClpP class [Posttranslational modification, protein turnover, ...
 35-140 7.40e-03

Periplasmic serine protease, ClpP class [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440381 [Multi-domain]  Cd Length: 215  Bit Score: 37.85  E-value: 7.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706894929  35 PASAGEPSRAAVVQLTITGPI--------GPATSDYVERGLGQAAADGAAL-VILRLDTPGGLDTSMREIIKAIL---AA 102
Cdd:COG0616     1 AKARPPKVKPSIAVIDLEGTIvdgggppsGEIGLEDILAALRKAAEDPDVKaVVLRINSPGGSVAASEEIRDALRrlrAK 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1706894929 103 PLPVAGFVaprGAHAASAGTFILYACHVAAMAPGTNLG 140
Cdd:COG0616    81 GKPVVASM---GDVAASGGYYIASAADKIYANPTTITG 115
 
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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