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Conserved domains on  [gi|1174937583|ref|WP_081610803|]
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nodulation protein NfeD [Thioalkalivibrio sp. ALJ7]

Protein Classification

nodulation protein NfeD( domain architecture ID 11437047)

nodulation protein NfeD (nodulation formation efficiency D) similar to Bacillus subtilis YqeZ, is a ClpP class membrane-bound serine protease which may be involved in setting up flotillin raft-like structures

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 ...
 22-509 4.38e-167

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


:

Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 478.97  E-value: 4.38e-167
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583  22 WSACLLLGAGSLVAASMADTSDRHGLLLTVEDAIGPATGDYIRRGIERAEAEDAEIMILMLDTPGGLDSSMRSIIKNILQ 101
Cdd:COG1030     4 LLLLLLALLLALAAPASAAAAAKKVYVIPIDGAIGPATADYLERALEEAEEEGADAVVLELDTPGGLVDSAREIVDAILA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 102 SDVPVVTYVYpSGSRAASAGTYMLYGSHVAAMAPATNLGSATPVQMGGGGlpgmdppepdedarddtetdeadgeardde 181
Cdd:COG1030    84 SPVPVIVYVA-SGARAASAGAYILLASHIAAMAPGTNIGAATPVQIGGGI------------------------------ 132

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 182 tdaadepadengaangevepaseeelleddpaprrgDDAMERKVLEDAVSYIRGLAERYGRNADWAEETVRDGSNLTATA 261
Cdd:COG1030   133 ------------------------------------DEAMEEKVINDAVAYIRSLAELRGRNADWAEAMVRESVSLTAEE 176

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 262 ALEQNVIDFVADNLDDLLaqidghtvrmhdgeRTLSTEGLRIERMDPDWRTQLLSVITNPNIAYILMLLGIYGIIFELSN 341
Cdd:COG1030   177 ALELGVIDLIAEDLDELL--------------ATLGTAGAEIVEYEPTWRERLLSFLTNPNVAYILLLIGILGLIFELYT 242

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 342 PGAIYPGVIGSIALILAFFALqVMPVNYAGLALMLLGMIFMIAEAFVPSFGALGIGGIVAFTTGSIILWDD--PNLNVAL 419
Cdd:COG1030   243 PGFGVPGVIGAIALLLAFYGL-YLPANYAGLLLFLLGIILLILELFVPGFGILGIGGIIALVLGLLLLFDTdvPGLGVSA 321

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 420 PLVIGTAIAIGILSVWVLGRLFSLRGKKPATGYEEMIGMIGEAREDFERSGRVWVHSEQWNAETSV-PVRQGQKVRVTAI 498
Cdd:COG1030   322 LLIVAIALVIAIFLAFVLGKVLRARKRKPVTGAEELIGKEGVALTDLRPSGKVRIDGERWDAVSEGeFIEKGEKVRVVGV 401

                         490
                  ....*....|.
gi 1174937583 499 EGLKLQVEPAT 509
Cdd:COG1030   402 EGLRLVVRPVE 412
PHA03169 super family cl27451
hypothetical protein; Provisional
 148-219 6.76e-05

hypothetical protein; Provisional


The actual alignment was detected with superfamily member PHA03169:

Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 45.35  E-value: 6.76e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174937583 148 GGGGLPGMDPPEPDEDARDDTETDEADGEARDDETDAA---DEPADENGAANGEVEPASEEellEDDPAPRRGDD 219
Cdd:PHA03169   93 SGSGSESVGSPTPSPSGSAEELASGLSPENTSGSSPESpasHSPPPSPPSHPGPHEPAPPE---SHNPSPNQQPS 164
 
Name Accession Description Interval E-value
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 22-509 4.38e-167

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


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 478.97  E-value: 4.38e-167
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583  22 WSACLLLGAGSLVAASMADTSDRHGLLLTVEDAIGPATGDYIRRGIERAEAEDAEIMILMLDTPGGLDSSMRSIIKNILQ 101
Cdd:COG1030     4 LLLLLLALLLALAAPASAAAAAKKVYVIPIDGAIGPATADYLERALEEAEEEGADAVVLELDTPGGLVDSAREIVDAILA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 102 SDVPVVTYVYpSGSRAASAGTYMLYGSHVAAMAPATNLGSATPVQMGGGGlpgmdppepdedarddtetdeadgeardde 181
Cdd:COG1030    84 SPVPVIVYVA-SGARAASAGAYILLASHIAAMAPGTNIGAATPVQIGGGI------------------------------ 132

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 182 tdaadepadengaangevepaseeelleddpaprrgDDAMERKVLEDAVSYIRGLAERYGRNADWAEETVRDGSNLTATA 261
Cdd:COG1030   133 ------------------------------------DEAMEEKVINDAVAYIRSLAELRGRNADWAEAMVRESVSLTAEE 176

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 262 ALEQNVIDFVADNLDDLLaqidghtvrmhdgeRTLSTEGLRIERMDPDWRTQLLSVITNPNIAYILMLLGIYGIIFELSN 341
Cdd:COG1030   177 ALELGVIDLIAEDLDELL--------------ATLGTAGAEIVEYEPTWRERLLSFLTNPNVAYILLLIGILGLIFELYT 242

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 342 PGAIYPGVIGSIALILAFFALqVMPVNYAGLALMLLGMIFMIAEAFVPSFGALGIGGIVAFTTGSIILWDD--PNLNVAL 419
Cdd:COG1030   243 PGFGVPGVIGAIALLLAFYGL-YLPANYAGLLLFLLGIILLILELFVPGFGILGIGGIIALVLGLLLLFDTdvPGLGVSA 321

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 420 PLVIGTAIAIGILSVWVLGRLFSLRGKKPATGYEEMIGMIGEAREDFERSGRVWVHSEQWNAETSV-PVRQGQKVRVTAI 498
Cdd:COG1030   322 LLIVAIALVIAIFLAFVLGKVLRARKRKPVTGAEELIGKEGVALTDLRPSGKVRIDGERWDAVSEGeFIEKGEKVRVVGV 401

                         490
                  ....*....|.
gi 1174937583 499 EGLKLQVEPAT 509
Cdd:COG1030   402 EGLRLVVRPVE 412
Clp_protease_NfeD_1 cd07020
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 47-296 1.60e-87

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: 267.11  E-value: 1.60e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583  47 LLLTVEDAIGPATGDYIRRGIERAEAEDAEIMILMLDTPGGLDSSMRSIIKNILQSDVPVVTYVYPSGSRAASAGTYMLY 126
Cdd:cd07020     2 YVLEINGAITPATADYLERAIDQAEEGGADALIIELDTPGGLLDSTREIVQAILASPVPVVVYVYPSGARAASAGTYILL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 127 GSHVAAMAPATNLGSATPVQMGGGGLpgmdppepdedarddtetdeadgearddetdaadepadengaangevepaseee 206
Cdd:cd07020    82 AAHIAAMAPGTNIGAAHPVAIGGGGG------------------------------------------------------ 107

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 207 lleddpaprrGDDAMERKVLEDAVSYIRGLAERYGRNADWAEETVRDGSNLTATAALEQNVIDFVADNLDDLLAQIDGHT 286
Cdd:cd07020   108 ----------SDPVMEKKILNDAVAYIRSLAELRGRNAEWAEKAVRESLSLTAEEALKLGVIDLIAADLNELLKKLDGRT 177

                         250
                  ....*....|
gi 1174937583 287 VRMHDGERTL 296
Cdd:cd07020   178 VKVAGKEVTL 187
NfeD pfam01957
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ...
 425-507 2.23e-13

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: 65.68  E-value: 2.23e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 425 TAIAIGILSVWVLGRLFSLRGKKPATGY-----EEMIGMIGEAREDFERS-GRVWVHSEQWNAETSVP-VRQGQKVRVTA 497
Cdd:pfam01957   1 VFAVVSLVLLLLLRPLALKRLRKKSPGSltnrdEALIGRTGVVLEDIRPDgGRVKIDGEEWTARSDGDfIPAGTRVRVVA 80

                          90
                  ....*....|
gi 1174937583 498 IEGLKLQVEP 507
Cdd:pfam01957  81 VEGLTLIVEP 90
PHA03169 PHA03169
hypothetical protein; Provisional
 148-219 6.76e-05

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 45.35  E-value: 6.76e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174937583 148 GGGGLPGMDPPEPDEDARDDTETDEADGEARDDETDAA---DEPADENGAANGEVEPASEEellEDDPAPRRGDD 219
Cdd:PHA03169   93 SGSGSESVGSPTPSPSGSAEELASGLSPENTSGSSPESpasHSPPPSPPSHPGPHEPAPPE---SHNPSPNQQPS 164
CobT2 COG4547
Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; ...
 156-222 3.60e-03

Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; Cobalamin biosynthesis cobaltochelatase CobT subunit is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 443611 [Multi-domain]  Cd Length: 608  Bit Score: 40.16  E-value: 3.60e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1174937583 156 DPPEPDEDARDDTETDEADGEARDDETDAADEPA---------DENGAANGEVEPASEEELLEDDPAPrRGDDAME 222
Cdd:COG4547   214 DEDEEDEDDEDDSGEQEEDEEDGEDEDEESDEGAeaedaeasgDDAEEGESEAAEAESDEMAEEAEGE-DSEEPGE 288
 
Name Accession Description Interval E-value
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 22-509 4.38e-167

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


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 478.97  E-value: 4.38e-167
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583  22 WSACLLLGAGSLVAASMADTSDRHGLLLTVEDAIGPATGDYIRRGIERAEAEDAEIMILMLDTPGGLDSSMRSIIKNILQ 101
Cdd:COG1030     4 LLLLLLALLLALAAPASAAAAAKKVYVIPIDGAIGPATADYLERALEEAEEEGADAVVLELDTPGGLVDSAREIVDAILA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 102 SDVPVVTYVYpSGSRAASAGTYMLYGSHVAAMAPATNLGSATPVQMGGGGlpgmdppepdedarddtetdeadgeardde 181
Cdd:COG1030    84 SPVPVIVYVA-SGARAASAGAYILLASHIAAMAPGTNIGAATPVQIGGGI------------------------------ 132

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 182 tdaadepadengaangevepaseeelleddpaprrgDDAMERKVLEDAVSYIRGLAERYGRNADWAEETVRDGSNLTATA 261
Cdd:COG1030   133 ------------------------------------DEAMEEKVINDAVAYIRSLAELRGRNADWAEAMVRESVSLTAEE 176

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 262 ALEQNVIDFVADNLDDLLaqidghtvrmhdgeRTLSTEGLRIERMDPDWRTQLLSVITNPNIAYILMLLGIYGIIFELSN 341
Cdd:COG1030   177 ALELGVIDLIAEDLDELL--------------ATLGTAGAEIVEYEPTWRERLLSFLTNPNVAYILLLIGILGLIFELYT 242

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 342 PGAIYPGVIGSIALILAFFALqVMPVNYAGLALMLLGMIFMIAEAFVPSFGALGIGGIVAFTTGSIILWDD--PNLNVAL 419
Cdd:COG1030   243 PGFGVPGVIGAIALLLAFYGL-YLPANYAGLLLFLLGIILLILELFVPGFGILGIGGIIALVLGLLLLFDTdvPGLGVSA 321

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 420 PLVIGTAIAIGILSVWVLGRLFSLRGKKPATGYEEMIGMIGEAREDFERSGRVWVHSEQWNAETSV-PVRQGQKVRVTAI 498
Cdd:COG1030   322 LLIVAIALVIAIFLAFVLGKVLRARKRKPVTGAEELIGKEGVALTDLRPSGKVRIDGERWDAVSEGeFIEKGEKVRVVGV 401

                         490
                  ....*....|.
gi 1174937583 499 EGLKLQVEPAT 509
Cdd:COG1030   402 EGLRLVVRPVE 412
Clp_protease_NfeD_1 cd07020
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 47-296 1.60e-87

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: 267.11  E-value: 1.60e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583  47 LLLTVEDAIGPATGDYIRRGIERAEAEDAEIMILMLDTPGGLDSSMRSIIKNILQSDVPVVTYVYPSGSRAASAGTYMLY 126
Cdd:cd07020     2 YVLEINGAITPATADYLERAIDQAEEGGADALIIELDTPGGLLDSTREIVQAILASPVPVVVYVYPSGARAASAGTYILL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 127 GSHVAAMAPATNLGSATPVQMGGGGLpgmdppepdedarddtetdeadgearddetdaadepadengaangevepaseee 206
Cdd:cd07020    82 AAHIAAMAPGTNIGAAHPVAIGGGGG------------------------------------------------------ 107

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 207 lleddpaprrGDDAMERKVLEDAVSYIRGLAERYGRNADWAEETVRDGSNLTATAALEQNVIDFVADNLDDLLAQIDGHT 286
Cdd:cd07020   108 ----------SDPVMEKKILNDAVAYIRSLAELRGRNAEWAEKAVRESLSLTAEEALKLGVIDLIAADLNELLKKLDGRT 177

                         250
                  ....*....|
gi 1174937583 287 VRMHDGERTL 296
Cdd:cd07020   178 VKVAGKEVTL 187
Clp_protease_NfeD cd07015
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 51-279 4.22e-26

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: 104.40  E-value: 4.22e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583  51 VEDAIGPATGDYIRRGIERAEAEDAEIMILMLDTPGGLDSSMRSIIKNILQSDVPVVTYVYPSGSRAASAGTYMLYGSHV 130
Cdd:cd07015     6 IKGQITSYTYDQFDRYITIAEQDNAEAIIIELDTPGGRADAAGNIVQRIQQSKIPVIIYVYPPGASAASAGTYIALGSHL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 131 AAMAPATNLGSATPVqmgggglpgmdppepdedarddtetdeaDGEARDDETDAADEpadengaangevepaseeelled 210
Cdd:cd07015    86 IAMAPGTSIGACRPI----------------------------LGYSQNGSIIEAPP----------------------- 114

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1174937583 211 dpaprrgddamerKVLEDAVSYIRGLAERYGRNADWAEETVRDGSNLTATAALEQNVIDFVADNLDDLL 279
Cdd:cd07015   115 -------------KITNYFIAYIKSLAQESGRNATIAEEFITKDLSLTPEEALKYGVIEVVARDINELL 170
Clp_protease_NfeD_like cd07021
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 47-281 1.05e-20

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: 89.57  E-value: 1.05e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583  47 LLLTVEDAIGPATGDYIRRGIERAEAEDAEIMILMLDTPGGLDSSMRSIIKNILQSDVPVVTYVYPsgsRAASAGTYMLY 126
Cdd:cd07021     2 YVIPIEGEIDPGLAAFVERALKEAKEEGADAVVLDIDTPGGRVDSALEIVDLILNSPIPTIAYVND---RAASAGALIAL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 127 GSHVAAMAPATNLGSATPVQMGGGGlpgmdppepdedarddtetdeadgearddetdaadepadengaangevepaseee 206
Cdd:cd07021    79 AADEIYMAPGATIGAAEPIPGDGNG------------------------------------------------------- 103

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 207 lleddpaprrgddAMERKVLEDAVSYIRGLAERYGRNADWAEETVRDGS-------------NLTATAALEQNVIDFVAD 273
Cdd:cd07021   104 -------------AADEKVQSYWRAKMRAAAEKKGRDPDIAEAMVDKDIevpgvgikggellTLTADEALKVGYAEGIAG 170


                  ....*...
gi 1174937583 274 NLDDLLAQ 281
Cdd:cd07021   171 SLDELLVK 178
YbbJ COG1585
Membrane protein implicated in regulation of membrane protease activity [Posttranslational ...
 368-509 3.85e-17

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


Pssm-ID: 441193  Cd Length: 143  Bit Score: 78.32  E-value: 3.85e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 368 NYAGLALMLLGMIFMIAEAFVPSFGAL--GIGGIVAfttgSIILWddpnLNVALPLVIGTAIAIGILSVWVLGRLFSLRG 445
Cdd:COG1585     3 ALPWLIWLILGLLLLIAELLTPGFFLLwfGLGALAV----GLLAL----LGLSLWLQLLVFAVLSLLLLLLWRRLLKRRL 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1174937583 446 KKPA----TGYEEMIGMIGEAREDF-ERSGRVWVHSEQWNAETSVPVRQGQKVRVTAIEGLKLQVEPAT 509
Cdd:COG1585    75 RSDApllnTRVDALIGRTATVVEPIdNGRGRVKLGGEEWRARSEDDLPAGTRVRVVAVEGNTLIVEPVE 143
NfeD pfam01957
NfeD-like C-terminal, partner-binding; NfeD-like proteins are widely distributed throughout ...
 425-507 2.23e-13

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: 65.68  E-value: 2.23e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 425 TAIAIGILSVWVLGRLFSLRGKKPATGY-----EEMIGMIGEAREDFERS-GRVWVHSEQWNAETSVP-VRQGQKVRVTA 497
Cdd:pfam01957   1 VFAVVSLVLLLLLRPLALKRLRKKSPGSltnrdEALIGRTGVVLEDIRPDgGRVKIDGEEWTARSDGDfIPAGTRVRVVA 80

                          90
                  ....*....|
gi 1174937583 498 IEGLKLQVEP 507
Cdd:pfam01957  81 VEGLTLIVEP 90
Clp_protease_like cd00394
Caseinolytic protease (ClpP) is an ATP-dependent protease; Clp protease (caseinolytic protease; ...
 48-151 1.44e-10

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: 59.71  E-value: 1.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583  48 LLTVEDAIGPATGDYIRRGIERAEAED-AEIMILMLDTPGGLDSSMRSIIKNILQSDVPVVTYVYPSgsrAASAGTYMLY 126
Cdd:cd00394     1 VIFINGVIEDVSADQLAAQIRFAEADNsVKAIVLEVNTPGGRVDAGMNIVDALQASRKPVIAYVGGQ---AASAGYYIAT 77

                          90       100
                  ....*....|....*....|....*
gi 1174937583 127 GSHVAAMAPATNLGSATPVQMGGGG 151
Cdd:cd00394    78 AANKIVMAPGTRVGSHGPIGGYGGN 102
PHA03169 PHA03169
hypothetical protein; Provisional
 148-219 6.76e-05

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 45.35  E-value: 6.76e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174937583 148 GGGGLPGMDPPEPDEDARDDTETDEADGEARDDETDAA---DEPADENGAANGEVEPASEEellEDDPAPRRGDD 219
Cdd:PHA03169   93 SGSGSESVGSPTPSPSGSAEELASGLSPENTSGSSPESpasHSPPPSPPSHPGPHEPAPPE---SHNPSPNQQPS 164
GAAP_like cd10429
Golgi antiapoptotic protein; GAAP (or transmembrane BAX inhibitor motif containing 4) is a ...
 337-409 1.55e-04

Golgi antiapoptotic protein; GAAP (or transmembrane BAX inhibitor motif containing 4) is a regulator of apoptosis that is related to the BAX inhibitor (BI)-1 like family of small transmembrane proteins, which have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Human GAAP has been linked to the modulation of intracellular fluxes of Ca(2+), by suppressing influx from the extracellular medium and reducing release from intracellular stores. A viral homolog (vaccinia virus vGAAP) acts similar to its human counterpart in inhibiting apoptosis.


Pssm-ID: 198411  Cd Length: 233  Bit Score: 43.36  E-value: 1.55e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174937583 337 FELSNPGAIYPGVIGSIALILA--FFALQVmPVNyaglaLMLLGmIFMIAEAFvpsfgalGIGGIVAFTTGSIIL 409
Cdd:cd10429    61 FVQSHPWLFLISLIGSLILLIAlyWKRHSH-PVN-----LILLS-LFTLCEAY-------TVGLVVSFYDGKIVL 121
DUF6056 pfam19528
Family of unknown function (DUF6056); This family of integral membrane proteins is ...
 311-435 2.69e-03

Family of unknown function (DUF6056); This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 448 and 528 amino acids in length. There is a conserved NYL sequence motif.


Pssm-ID: 437360  Cd Length: 444  Bit Score: 40.33  E-value: 2.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174937583 311 RTQLLSVITNPNIAYILMLLGIYGIIFELSNPgAIYPGVIGSIALILAFFALQVMPVNYAGLALMLLGMIFMIAEAFVPS 390
Cdd:pfam19528 237 RADAEGTEENHLGLLLLVLARFLKITLNLREN-YLLLLLIFVVLLILLFLKKKNKKVFLLSLLFFLGGLATAYAMIASPE 315

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1174937583 391 FGA-LGIGGIVAFTTGSIILWDDPNLNVALPLVIGTAIAIgILSVW 435
Cdd:pfam19528 316 FPArAFFGAVIFLIIAILILLRDLAELESLLRKIAAILIV-VLTIL 360
CobT2 COG4547
Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; ...
 156-222 3.60e-03

Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; Cobalamin biosynthesis cobaltochelatase CobT subunit is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 443611 [Multi-domain]  Cd Length: 608  Bit Score: 40.16  E-value: 3.60e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1174937583 156 DPPEPDEDARDDTETDEADGEARDDETDAADEPA---------DENGAANGEVEPASEEELLEDDPAPrRGDDAME 222
Cdd:COG4547   214 DEDEEDEDDEDDSGEQEEDEEDGEDEDEESDEGAeaedaeasgDDAEEGESEAAEAESDEMAEEAEGE-DSEEPGE 288
PRK14891 PRK14891
50S ribosomal protein L24e/unknown domain fusion protein; Provisional
 159-206 4.90e-03

50S ribosomal protein L24e/unknown domain fusion protein; Provisional


Pssm-ID: 184885 [Multi-domain]  Cd Length: 131  Bit Score: 37.24  E-value: 4.90e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1174937583 159 EPDEDARDDTETDEADGEARDDETD-AADEPADENGAANGEVEPASEEE 206
Cdd:PRK14891   80 DADEDADEAAEADAADEADEEEETDeAVDETADEADAEAEEADEEEDEE 128
 
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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