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Conserved domains on  [gi|1308809926|gb|PKN48009|]
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hypothetical protein CVU59_00700 [Deltaproteobacteria bacterium HGW-Deltaproteobacteria-17]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
GspC_delta super family cl49484
type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are ...
 4-293 6.50e-62

type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are GspC (general secretion protein C), a component of type II secretion systems (T2SS), of a form found prmarily in deltaproteobacteria. This HMM is designed to be complementary to other HMMs that identify GspC rather that to separate a distinct subtype.


The actual alignment was detected with superfamily member NF041515:

Pssm-ID: 469401 [Multi-domain]  Cd Length: 310  Bit Score: 198.17  E-value: 6.50e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926   4 ATLVLLQGLGAGVIAAdIVAWKLYSAPRLETsrRPVAMVDTAPKKPEYVADLRGLLRRNIFCATCEPisLDDLAGTATAA 83
Cdd:NF041515   10 VLLALAAYFQASGVNA-LVAAALLPLPPAAA--APAAPPAAPPAAARRAKDADAILARNIFDSVTGP--LDPEPEEPAAP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926  84 GEPPAAASLEGAE-------LVGTMVSANTKDSLATVvltAHTEAKFVLLSEGDALGDATVVAIESKRVVFTQGGQEKVL 156
Cdd:NF041515   85 EEPPDGDDPAEPPpcsgrvrLVATVVSDDPEWSFAAI---ADGGGKTRLYRVGDEVDGATVVAIGWDRVWLRNGGRRCQL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926 157 NLMGE---PKNSPMVATTTPPPGAANPKGD-----DGRIQQVGPYKYEVDKAVITDFMKNMASASSGARVMPDA-NG--- 224
Cdd:NF041515  162 DLFDGappPAPAPPAAPAPAPPPPARAGGAlppeiASGIKKVSDTEYEIDRSLVDKVLENQAELMRQARIVPEFeNGkvv 241

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1308809926 225 GFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQTINMDYSIR 293
Cdd:NF041515  242 GFKLFGIRPGSLLGKLGLQNGDVLQSINGFDMTSPDKALEAYARLRSADHLTVSVERRGKPVTLDYNIR 310
 
Name Accession Description Interval E-value
GspC_delta NF041515
type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are ...
 4-293 6.50e-62

type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are GspC (general secretion protein C), a component of type II secretion systems (T2SS), of a form found prmarily in deltaproteobacteria. This HMM is designed to be complementary to other HMMs that identify GspC rather that to separate a distinct subtype.


Pssm-ID: 469401 [Multi-domain]  Cd Length: 310  Bit Score: 198.17  E-value: 6.50e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926   4 ATLVLLQGLGAGVIAAdIVAWKLYSAPRLETsrRPVAMVDTAPKKPEYVADLRGLLRRNIFCATCEPisLDDLAGTATAA 83
Cdd:NF041515   10 VLLALAAYFQASGVNA-LVAAALLPLPPAAA--APAAPPAAPPAAARRAKDADAILARNIFDSVTGP--LDPEPEEPAAP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926  84 GEPPAAASLEGAE-------LVGTMVSANTKDSLATVvltAHTEAKFVLLSEGDALGDATVVAIESKRVVFTQGGQEKVL 156
Cdd:NF041515   85 EEPPDGDDPAEPPpcsgrvrLVATVVSDDPEWSFAAI---ADGGGKTRLYRVGDEVDGATVVAIGWDRVWLRNGGRRCQL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926 157 NLMGE---PKNSPMVATTTPPPGAANPKGD-----DGRIQQVGPYKYEVDKAVITDFMKNMASASSGARVMPDA-NG--- 224
Cdd:NF041515  162 DLFDGappPAPAPPAAPAPAPPPPARAGGAlppeiASGIKKVSDTEYEIDRSLVDKVLENQAELMRQARIVPEFeNGkvv 241

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1308809926 225 GFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQTINMDYSIR 293
Cdd:NF041515  242 GFKLFGIRPGSLLGKLGLQNGDVLQSINGFDMTSPDKALEAYARLRSADHLTVSVERRGKPVTLDYNIR 310
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 86-293 3.16e-36

Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 128.94  E-value: 3.16e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926  86 PPAAASLEGAELVGTMVSANTKDSLATVvltAHTEAKFVLLSEGDAL-GDATVVAIESKRVVFTQGGQEKVLNLMGEPKN 164
Cdd:COG3031    17 TDAPETRLNLTLLGVVASSDPERSFAII---AEGGGKQKSYRVGDEIpGGATLVAVYRDRVILSNNGRLETLMLDGEDYA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926 165 SPMVAtttPPPGAANPKGDDGRIQQVGPYKYEVDKAVItdfMKNMASASSGARVMP-DANG---GFKVSFVRSFSVFYKL 240
Cdd:COG3031    94 APAAA---AAAPASSPAASSAAASAGGQEELEVSRDEL---LANPNELLDYIRLSPvREDGklvGYRVNPGRPGSLFSKL 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1308809926 241 GIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQTINMDYSIR 293
Cdd:COG3031   168 GLQPGDVITSINGQDLTDPAQALELLQQLRDASEVTLTVERNGQPVTLTYNLR 220
typeII_sec_gspC TIGR01713
type II secretion system protein C; This model represents GspC, protein C of the main terminal ...
 83-288 3.85e-11

type II secretion system protein C; This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 273770 [Multi-domain]  Cd Length: 259  Bit Score: 62.15  E-value: 3.85e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926  83 AGEPPAAASLEGAELVGTMVSAnTKDSLATVVLTAHTEAKFVLLSEGD-----ALGDAT------VVAIESKRVVFTQGG 151
Cdd:TIGR01713  59 FNEKSVSEVKTSPVSVNAPVSP-LSLKLTGIVASSDRIRSIAIIEEGSeqvslGINESFegykakIAKIEPDRVIFEYNG 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926 152 QEKVLNLmgepKNSPMVATTTPppgAANPKGDDGRIQQVGPYKYEVDKAVITDFMKNmasassgarvmpDANGGFKVSFV 231
Cdd:TIGR01713 138 RYEPLEL----KNTKGEKSNNS---SEIVVSRRIIEELTKDPQKMFDYIRLSPVMKN------------DKLEGYRLNPG 198

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1308809926 232 RSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQT--INM 288
Cdd:TIGR01713 199 KDPSLFYKSGLQDGDIAVALNGLDLRDPEQAFQALQMLREETNLTLTVERDGQRedIYV 257
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 206-289 2.87e-04

circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and YyxA and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis HtrA/YkdA, HtrB/YvtA and YyxA/YycK, and related domains. HtrA-type serine proteases participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. HtrA, HtrB, and YyxA have a single transmembrane domain at the N-terminus and a PDZ domain at the C-terminus. Expression of htrA and htrB genes is induced both by heat shock and by secretion stress (by a common) mechanism; yyxA is neither heat shock nor secretion stress inducible. HtrA and HtrB may have overlapping cellular functions; YyxA may have a cellular function distinct from the other two proteases or have the same function but under different conditions. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This BsHtrA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467622 [Multi-domain]  Cd Length: 98  Bit Score: 39.16  E-value: 2.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926 206 MKNMASASSGAR----VMPDANGGFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNR 281
Cdd:cd06781     8 MVDLSDVPEYEQqslkLPSNVNKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILYSHKVGDTVKVTIYR 87


                  ....*...
gi 1308809926 282 GGQTINMD 289
Cdd:cd06781    88 DGKEKTLN 95
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 219-283 1.53e-03

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.


Pssm-ID: 214570 [Multi-domain]  Cd Length: 85  Bit Score: 36.97  E-value: 1.53e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1308809926  219 MPDANGGFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGG 283
Cdd:smart00228  21 GKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
PRK10942 PRK10942
serine endoprotease DegP;
216-289 5.86e-03

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 37.82  E-value: 5.86e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1308809926 216 ARVMP-DANGGFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQTINMD 289
Cdd:PRK10942  302 AKAMKvDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVN 376
 
Name Accession Description Interval E-value
GspC_delta NF041515
type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are ...
 4-293 6.50e-62

type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are GspC (general secretion protein C), a component of type II secretion systems (T2SS), of a form found prmarily in deltaproteobacteria. This HMM is designed to be complementary to other HMMs that identify GspC rather that to separate a distinct subtype.


Pssm-ID: 469401 [Multi-domain]  Cd Length: 310  Bit Score: 198.17  E-value: 6.50e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926   4 ATLVLLQGLGAGVIAAdIVAWKLYSAPRLETsrRPVAMVDTAPKKPEYVADLRGLLRRNIFCATCEPisLDDLAGTATAA 83
Cdd:NF041515   10 VLLALAAYFQASGVNA-LVAAALLPLPPAAA--APAAPPAAPPAAARRAKDADAILARNIFDSVTGP--LDPEPEEPAAP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926  84 GEPPAAASLEGAE-------LVGTMVSANTKDSLATVvltAHTEAKFVLLSEGDALGDATVVAIESKRVVFTQGGQEKVL 156
Cdd:NF041515   85 EEPPDGDDPAEPPpcsgrvrLVATVVSDDPEWSFAAI---ADGGGKTRLYRVGDEVDGATVVAIGWDRVWLRNGGRRCQL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926 157 NLMGE---PKNSPMVATTTPPPGAANPKGD-----DGRIQQVGPYKYEVDKAVITDFMKNMASASSGARVMPDA-NG--- 224
Cdd:NF041515  162 DLFDGappPAPAPPAAPAPAPPPPARAGGAlppeiASGIKKVSDTEYEIDRSLVDKVLENQAELMRQARIVPEFeNGkvv 241

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1308809926 225 GFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQTINMDYSIR 293
Cdd:NF041515  242 GFKLFGIRPGSLLGKLGLQNGDVLQSINGFDMTSPDKALEAYARLRSADHLTVSVERRGKPVTLDYNIR 310
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 86-293 3.16e-36

Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 128.94  E-value: 3.16e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926  86 PPAAASLEGAELVGTMVSANTKDSLATVvltAHTEAKFVLLSEGDAL-GDATVVAIESKRVVFTQGGQEKVLNLMGEPKN 164
Cdd:COG3031    17 TDAPETRLNLTLLGVVASSDPERSFAII---AEGGGKQKSYRVGDEIpGGATLVAVYRDRVILSNNGRLETLMLDGEDYA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926 165 SPMVAtttPPPGAANPKGDDGRIQQVGPYKYEVDKAVItdfMKNMASASSGARVMP-DANG---GFKVSFVRSFSVFYKL 240
Cdd:COG3031    94 APAAA---AAAPASSPAASSAAASAGGQEELEVSRDEL---LANPNELLDYIRLSPvREDGklvGYRVNPGRPGSLFSKL 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1308809926 241 GIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQTINMDYSIR 293
Cdd:COG3031   168 GLQPGDVITSINGQDLTDPAQALELLQQLRDASEVTLTVERNGQPVTLTYNLR 220
typeII_sec_gspC TIGR01713
type II secretion system protein C; This model represents GspC, protein C of the main terminal ...
 83-288 3.85e-11

type II secretion system protein C; This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 273770 [Multi-domain]  Cd Length: 259  Bit Score: 62.15  E-value: 3.85e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926  83 AGEPPAAASLEGAELVGTMVSAnTKDSLATVVLTAHTEAKFVLLSEGD-----ALGDAT------VVAIESKRVVFTQGG 151
Cdd:TIGR01713  59 FNEKSVSEVKTSPVSVNAPVSP-LSLKLTGIVASSDRIRSIAIIEEGSeqvslGINESFegykakIAKIEPDRVIFEYNG 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926 152 QEKVLNLmgepKNSPMVATTTPppgAANPKGDDGRIQQVGPYKYEVDKAVITDFMKNmasassgarvmpDANGGFKVSFV 231
Cdd:TIGR01713 138 RYEPLEL----KNTKGEKSNNS---SEIVVSRRIIEELTKDPQKMFDYIRLSPVMKN------------DKLEGYRLNPG 198

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1308809926 232 RSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQT--INM 288
Cdd:TIGR01713 199 KDPSLFYKSGLQDGDIAVALNGLDLRDPEQAFQALQMLREETNLTLTVERDGQRedIYV 257
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 206-289 2.87e-04

circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and YyxA and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis HtrA/YkdA, HtrB/YvtA and YyxA/YycK, and related domains. HtrA-type serine proteases participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. HtrA, HtrB, and YyxA have a single transmembrane domain at the N-terminus and a PDZ domain at the C-terminus. Expression of htrA and htrB genes is induced both by heat shock and by secretion stress (by a common) mechanism; yyxA is neither heat shock nor secretion stress inducible. HtrA and HtrB may have overlapping cellular functions; YyxA may have a cellular function distinct from the other two proteases or have the same function but under different conditions. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This BsHtrA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467622 [Multi-domain]  Cd Length: 98  Bit Score: 39.16  E-value: 2.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926 206 MKNMASASSGAR----VMPDANGGFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNR 281
Cdd:cd06781     8 MVDLSDVPEYEQqslkLPSNVNKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILYSHKVGDTVKVTIYR 87


                  ....*...
gi 1308809926 282 GGQTINMD 289
Cdd:cd06781    88 DGKEKTLN 95
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 219-283 1.53e-03

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.


Pssm-ID: 214570 [Multi-domain]  Cd Length: 85  Bit Score: 36.97  E-value: 1.53e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1308809926  219 MPDANGGFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGG 283
Cdd:smart00228  21 GKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 211-286 1.69e-03

circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine endoprotease DegP and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Escherichia coli DegP (also known as heat shock protein DegP and Protease Do), and related domains. DegP belongs to the HtrA family of housekeeping proteases. It acts as a protease, degrading transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions, and as a molecular chaperone at low temperatures. DegP has two PDZ domains in addition to the protease domain; its PDZ1 domain is responsible for the identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for the combining with other DegP monomers to form a stable oligomer structure. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegP family PDZ domain 2 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467631 [Multi-domain]  Cd Length: 83  Bit Score: 36.84  E-value: 1.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308809926 211 SASSGARVMP----DANGGFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDqTFALYTKLKDANhLTLSLNRGGQTI 286
Cdd:cd23084     1 LALEGATVSNvtdeDGGKGVVVTEVDPGSPAAQSGLKKGDVIIGVNRQPVKSIA-ELRKVLKSKPSA-VLLQIKRGDSSR 78
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 219-286 1.95e-03

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273938 [Multi-domain]  Cd Length: 428  Bit Score: 39.51  E-value: 1.95e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1308809926 219 MPDANGGFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQTI 286
Cdd:TIGR02037 357 LKGDVKGVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKKGGRVALLILRGGATI 424
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 224-292 4.22e-03

circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Escherichia coli DegS and related domains. DegS (also known as Site-1 protease DegS, S1P protease DegS, and Site-1-type intramembrane protease) participates in the activation of the sigma(E) extracytoplasmic stress response. Initially, there is an accumulation of misfolded membrane proteins (OMPs) in the periplasm which bind by their YXF motif to the DegS PDZ domain, activating DegS-catalyzed cleavage of the RseA periplasmic domain and making RseA a substrate for cleavage by another membrane protease RseP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegS family PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467620 [Multi-domain]  Cd Length: 93  Bit Score: 35.83  E-value: 4.22e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1308809926 224 GGFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQTINMDYSI 292
Cdd:cd06777    25 QGALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVLELMDLVAEIRPGTVIPVVVLRDGKQLTLEVTI 93
PRK10942 PRK10942
serine endoprotease DegP;
216-289 5.86e-03

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 37.82  E-value: 5.86e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1308809926 216 ARVMP-DANGGFKVSFVRSFSVFYKLGIRSGDVISSVNNIQLDSIDQTFALYTKLKDANHLTLSLNRGGQTINMD 289
Cdd:PRK10942  302 AKAMKvDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVN 376
 
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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