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Conserved domains on  [gi|488978433|ref|WP_002889286|]
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MULTISPECIES: serine endoprotease DegP [Klebsiella]

Protein Classification

Do/DegQ family serine endoprotease( domain architecture ID 11485116)

Do/DegQ family serine endoprotease such as serine endoprotease DegP, a regulated protease and chaperone that functions as a protein quality control factor in the bacterial envelope, involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10942 PRK10942
serine endoprotease DegP;
2-477 0e+00

serine endoprotease DegP;


:

Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 846.74  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433   2 KKTTLAMSALALSLGLALSPLSASAAETASSAtNAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDNS 81
Cdd:PRK10942   1 KKTTLALSALALSLGLALSPLSATAAETSSAT-TAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRQFQQFFGDNS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  82 PFCQDGSPFQSSPFCQGGGQGGQPDGGQqqKFMALGSGVIIDAAKGYVVTNNHVVDNATTIKVQLSDGRRFDAKVVGKDP 161
Cdd:PRK10942  80 PFCQEGSPFQSSPFCQGGQGGNGGGQQQ--KFMALGSGVIIDADKGYVVTNNHVVDNATKIKVQLSDGRKFDAKVVGKDP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 162 RSDIALIQIQDPKNLTAIKLADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGG 241
Cdd:PRK10942 158 RSDIALIQLQNPKNLTAIKMADSDALRVGDYTVAIGNPYGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGG 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 242 ALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTEQMVKYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQ 321
Cdd:PRK10942 238 ALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQ 317

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 322 VMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVELGLLRDGKPVTVTVELQQSNQTQVDSSTIFNGIE 401
Cdd:PRK10942 318 VLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSSQNQVDSSNIFNGIE 397

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488978433 402 GAEMSNKGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAKPSVLALNIQRGDASIYLLLQ 477
Cdd:PRK10942 398 GAELSNKGGDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKPSVLALNIQRGDSSIYLLMQ 473
 
Name Accession Description Interval E-value
PRK10942 PRK10942
serine endoprotease DegP;
2-477 0e+00

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 846.74  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433   2 KKTTLAMSALALSLGLALSPLSASAAETASSAtNAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDNS 81
Cdd:PRK10942   1 KKTTLALSALALSLGLALSPLSATAAETSSAT-TAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRQFQQFFGDNS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  82 PFCQDGSPFQSSPFCQGGGQGGQPDGGQqqKFMALGSGVIIDAAKGYVVTNNHVVDNATTIKVQLSDGRRFDAKVVGKDP 161
Cdd:PRK10942  80 PFCQEGSPFQSSPFCQGGQGGNGGGQQQ--KFMALGSGVIIDADKGYVVTNNHVVDNATKIKVQLSDGRKFDAKVVGKDP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 162 RSDIALIQIQDPKNLTAIKLADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGG 241
Cdd:PRK10942 158 RSDIALIQLQNPKNLTAIKMADSDALRVGDYTVAIGNPYGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGG 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 242 ALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTEQMVKYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQ 321
Cdd:PRK10942 238 ALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQ 317

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 322 VMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVELGLLRDGKPVTVTVELQQSNQTQVDSSTIFNGIE 401
Cdd:PRK10942 318 VLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSSQNQVDSSNIFNGIE 397

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488978433 402 GAEMSNKGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAKPSVLALNIQRGDASIYLLLQ 477
Cdd:PRK10942 398 GAELSNKGGDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKPSVLALNIQRGDSSIYLLMQ 473
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 40-476 0e+00

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: 584.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433   40 PSLAPMLEKVMPSVVSINVEGS--TTVNTPRMPRNFQQFFGDNSPFCQDGSPFQsspfcqgggqggqpdggqqqKFMALG 117
Cdd:TIGR02037   1 PSFAPLVEKVAPAVVNISVEGTvkRRNRPPALPPFFRQFFGDDMPDFPRQQREQ--------------------KVRGLG 60

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  118 SGVIIDAAkGYVVTNNHVVDNATTIKVQLSDGRRFDAKVVGKDPRSDIALIQIQDPKNLTAIKLADSDALRVGDYTVAIG 197
Cdd:TIGR02037  61 SGVIISAD-GYVLTNNHVVDGADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIG 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  198 NPFGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVK 277
Cdd:TIGR02037 140 NPFGLGQTVTSGIVSALGRSGLGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAK 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  278 NLTEQMVKYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQV 357
Cdd:TIGR02037 220 NVVDQLIEGGKVKRGWLGVTIQEVTSDLAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAI 299

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  358 GTMPIGSKVELGLLRDGKPVTVTVELQQSNQTQVDSSTIFNGIEGA--------EMSNKGQDKGVVVNNVKAGTPAAQIG 429
Cdd:TIGR02037 300 GTLKPGKKVTLGILRKGKEKTITVTLGASPEEQASSSNPFLGLTVAnlspeirkELRLKGDVKGVVVTKVVSGSPAARAG 379

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*....
gi 488978433  430 LKKGDVIVGANQQPVKNIADLRKIFDA--KPSVLALNIQRGDASIYLLL 476
Cdd:TIGR02037 380 LQPGDVILSVNQQPVSSVAELRKVLARakKGGRVALLILRGGATIFVTL 428
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 115-385 7.15e-134

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440035 [Multi-domain]  Cd Length: 274  Bit Score: 387.20  E-value: 7.15e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 115 ALGSGVIIDAaKGYVVTNNHVVDNATTIKVQLSDGRRFDAKVVGKDPRSDIALIQIqDPKNLTAIKLADSDALRVGDYTV 194
Cdd:COG0265    1 GLGSGVIISP-DGYILTNNHVVEGADEITVTLADGREYPAKVVGRDPLTDLAVLKI-DAKDLPAAPLGDSDKLRVGDWVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 195 AIGNPFGLGETVTSGIVSALGRSG--LNVENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIP 272
Cdd:COG0265   79 AIGNPFGLGQTVTAGIVSALGRSIgsSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIISRSGGSQGIGFAIP 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 273 SNMVKNLTEQMVKYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAA 352
Cdd:COG0265  159 INLAKRVVEQLIETGRVRRGWLGVTIQPVTPELAEALGLPEPEGVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARD 238

                        250       260       270
                 ....*....|....*....|....*....|...
gi 488978433 353 LRAQVGTMPIGSKVELGLLRDGKPVTVTVELQQ 385
Cdd:COG0265  239 LQRLLASLKPGDTVTLTVLRGGKELTVTVTLGE 271
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 117-253 3.14e-34

Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 125.23  E-value: 3.14e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  117 GSGVIIDAaKGYVVTNNHVVDNATTI-----KVQLSDGRRFDAKVVGKDPRSDIALIQI-QDPKNLTAIKLADSDALRVG 190
Cdd:pfam13365   1 GTGFVVSS-DGLVLTNAHVVDDAEEAavelvSVVLADGREYPATVVARDPDLDLALLRVsGDGRGLPPLPLGDSEPLVGG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488978433  191 DYTVAIGNPFGLGE-TVTSGIVSALGRSGlNVENYENFIQTDAAINRGNSGGALVNLNGELIGI 253
Cdd:pfam13365  80 ERVYAVGYPLGGEKlSLSEGIVSGVDEGR-DGGDDGRVIQTDAALSPGSSGGPVFDADGRVVGI 142
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 291-381 8.57e-31

circularly permuted first PDZ domain (PDZ1) 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 1 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 identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for 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 1 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: 467630 [Multi-domain]  Cd Length: 91  Bit Score: 114.12  E-value: 8.57e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 291 RGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVELGL 370
Cdd:cd10839    1 RGWLGVQIQELTPDLAESFGLKEPKGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATTKPGTKVELKI 80

                         90
                 ....*....|.
gi 488978433 371 LRDGKPVTVTV 381
Cdd:cd10839   81 LRDGKEKTLTV 91
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 406-469 1.23e-08

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: 52.00  E-value: 1.23e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488978433   406 SNKGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLR--KIFDAKPSVLALNIQRGD 469
Cdd:smart00228  20 GGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEavDLLKKAGGKVTLTVLRGG 85
 
Name Accession Description Interval E-value
PRK10942 PRK10942
serine endoprotease DegP;
2-477 0e+00

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 846.74  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433   2 KKTTLAMSALALSLGLALSPLSASAAETASSAtNAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDNS 81
Cdd:PRK10942   1 KKTTLALSALALSLGLALSPLSATAAETSSAT-TAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRQFQQFFGDNS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  82 PFCQDGSPFQSSPFCQGGGQGGQPDGGQqqKFMALGSGVIIDAAKGYVVTNNHVVDNATTIKVQLSDGRRFDAKVVGKDP 161
Cdd:PRK10942  80 PFCQEGSPFQSSPFCQGGQGGNGGGQQQ--KFMALGSGVIIDADKGYVVTNNHVVDNATKIKVQLSDGRKFDAKVVGKDP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 162 RSDIALIQIQDPKNLTAIKLADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGG 241
Cdd:PRK10942 158 RSDIALIQLQNPKNLTAIKMADSDALRVGDYTVAIGNPYGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGG 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 242 ALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTEQMVKYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQ 321
Cdd:PRK10942 238 ALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQ 317

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 322 VMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVELGLLRDGKPVTVTVELQQSNQTQVDSSTIFNGIE 401
Cdd:PRK10942 318 VLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSSQNQVDSSNIFNGIE 397

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488978433 402 GAEMSNKGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAKPSVLALNIQRGDASIYLLLQ 477
Cdd:PRK10942 398 GAELSNKGGDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKPSVLALNIQRGDSSIYLLMQ 473
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 40-476 0e+00

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: 584.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433   40 PSLAPMLEKVMPSVVSINVEGS--TTVNTPRMPRNFQQFFGDNSPFCQDGSPFQsspfcqgggqggqpdggqqqKFMALG 117
Cdd:TIGR02037   1 PSFAPLVEKVAPAVVNISVEGTvkRRNRPPALPPFFRQFFGDDMPDFPRQQREQ--------------------KVRGLG 60

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  118 SGVIIDAAkGYVVTNNHVVDNATTIKVQLSDGRRFDAKVVGKDPRSDIALIQIQDPKNLTAIKLADSDALRVGDYTVAIG 197
Cdd:TIGR02037  61 SGVIISAD-GYVLTNNHVVDGADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIG 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  198 NPFGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVK 277
Cdd:TIGR02037 140 NPFGLGQTVTSGIVSALGRSGLGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAK 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  278 NLTEQMVKYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQV 357
Cdd:TIGR02037 220 NVVDQLIEGGKVKRGWLGVTIQEVTSDLAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAI 299

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  358 GTMPIGSKVELGLLRDGKPVTVTVELQQSNQTQVDSSTIFNGIEGA--------EMSNKGQDKGVVVNNVKAGTPAAQIG 429
Cdd:TIGR02037 300 GTLKPGKKVTLGILRKGKEKTITVTLGASPEEQASSSNPFLGLTVAnlspeirkELRLKGDVKGVVVTKVVSGSPAARAG 379

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*....
gi 488978433  430 LKKGDVIVGANQQPVKNIADLRKIFDA--KPSVLALNIQRGDASIYLLL 476
Cdd:TIGR02037 380 LQPGDVILSVNQQPVSSVAELRKVLARakKGGRVALLILRGGATIFVTL 428
PRK10139 PRK10139
serine endoprotease DegQ;
39-477 0e+00

serine endoprotease DegQ;


Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 516.04  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  39 MPSLAPMLEKVMPSVVSINVEGsTTVNTPRMPRNFQQFFGDNSPfCQDGSPFQsspfcqgggqggqpdggqqqkfmALGS 118
Cdd:PRK10139  39 LPSLAPMLEKVLPAVVSVRVEG-TASQGQKIPEEFKKFFGDDLP-DQPAQPFE-----------------------GLGS 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 119 GVIIDAAKGYVVTNNHVVDNATTIKVQLSDGRRFDAKVVGKDPRSDIALIQIQDPKNLTAIKLADSDALRVGDYTVAIGN 198
Cdd:PRK10139  94 GVIIDAAKGYVLTNNHVINQAQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIADSDKLRVGDFAVAVGN 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 199 PFGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKN 278
Cdd:PRK10139 174 PFGLGQTATSGIISALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIPSNMART 253

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 279 LTEQMVKYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVG 358
Cdd:PRK10139 254 LAQQLIDFGEIKRGLLGIKGTEMSADIAKAFNLDVQRGAFVSEVLPNSGSAKAGVKAGDIITSLNGKPLNSFAELRSRIA 333

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 359 TMPIGSKVELGLLRDGKPVTVTVELQQSNQTQVDSSTIFNGIEGAEMSN---KGQDKGVVVNNVKAGTPAAQIGLKKGDV 435
Cdd:PRK10139 334 TTEPGTKVKLGLLRNGKPLEVEVTLDTSTSSSASAEMITPALQGATLSDgqlKDGTKGIKIDEVVKGSPAAQAGLQKDDV 413

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|..
gi 488978433 436 IVGANQQPVKNIADLRKIFDAKPSVLALNIQRGDASIYLLLQ 477
Cdd:PRK10139 414 IIGVNRDRVNSIAEMRKVLAAKPAIIALQIVRGNESIYLLLR 455
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 115-385 7.15e-134

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440035 [Multi-domain]  Cd Length: 274  Bit Score: 387.20  E-value: 7.15e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 115 ALGSGVIIDAaKGYVVTNNHVVDNATTIKVQLSDGRRFDAKVVGKDPRSDIALIQIqDPKNLTAIKLADSDALRVGDYTV 194
Cdd:COG0265    1 GLGSGVIISP-DGYILTNNHVVEGADEITVTLADGREYPAKVVGRDPLTDLAVLKI-DAKDLPAAPLGDSDKLRVGDWVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 195 AIGNPFGLGETVTSGIVSALGRSG--LNVENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIP 272
Cdd:COG0265   79 AIGNPFGLGQTVTAGIVSALGRSIgsSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIISRSGGSQGIGFAIP 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 273 SNMVKNLTEQMVKYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAA 352
Cdd:COG0265  159 INLAKRVVEQLIETGRVRRGWLGVTIQPVTPELAEALGLPEPEGVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARD 238

                        250       260       270
                 ....*....|....*....|....*....|...
gi 488978433 353 LRAQVGTMPIGSKVELGLLRDGKPVTVTVELQQ 385
Cdd:COG0265  239 LQRLLASLKPGDTVTLTVLRGGKELTVTVTLGE 271
protease_degS TIGR02038
periplasmic serine pepetdase DegS; This family consists of the periplasmic serine protease ...
 116-385 5.32e-69

periplasmic serine pepetdase DegS; This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E). [Protein fate, Degradation of proteins, peptides, and glycopeptides, Regulatory functions, Protein interactions]


Pssm-ID: 273939 [Multi-domain]  Cd Length: 351  Bit Score: 223.93  E-value: 5.32e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  116 LGSGVIIDAaKGYVVTNNHVVDNATTIKVQLSDGRRFDAKVVGKDPRSDIALIQIQdPKNLTAIKLADSDALRVGDYTVA 195
Cdd:TIGR02038  79 LGSGVIMSK-EGYILTNYHVIKKADQIVVALQDGRKFEAELVGSDPLTDLAVLKIE-GDNLPTIPVNLDRPPHVGDVVLA 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  196 IGNPFGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGGALVNLNGELIGINTAIL--APDGGNIGIGFAIPS 273
Cdd:TIGR02038 157 IGNPYNLGQTITQGIISATGRNGLSSVGRQNFIQTDAAINAGNSGGALINTNGELVGINTASFqkGGDEGGEGINFAIPI 236

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  274 NMVKNLTEQMVKYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAAL 353
Cdd:TIGR02038 237 KLAHKIMGKIIRDGRVIRGYIGVSGEDINSVVAQGLGLPDLRGIVITGVDPNGPAARAGILVRDVILKYDGKDVIGAEEL 316

                         250       260       270
                  ....*....|....*....|....*....|..
gi 488978433  354 RAQVGTMPIGSKVELGLLRDGKPVTVTVELQQ 385
Cdd:TIGR02038 317 MDRIAETRPGSKVMVTVLRQGKQLELPVTIDE 348
PRK10898 PRK10898
serine endoprotease DegS;
116-385 1.48e-67

serine endoprotease DegS;


Pssm-ID: 182820 [Multi-domain]  Cd Length: 353  Bit Score: 220.26  E-value: 1.48e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 116 LGSGVIIDAaKGYVVTNNHVVDNATTIKVQLSDGRRFDAKVVGKDPRSDIALIQIqDPKNLTAIKLADSDALRVGDYTVA 195
Cdd:PRK10898  79 LGSGVIMDQ-RGYILTNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKI-NATNLPVIPINPKRVPHIGDVVLA 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 196 IGNPFGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGGALVNLNGELIGINTaiLAPDGGNI-----GIGFA 270
Cdd:PRK10898 157 IGNPYNLGQTITQGIISATGRIGLSPTGRQNFLQTDASINHGNSGGALVNSLGELMGINT--LSFDKSNDgetpeGIGFA 234

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 271 IPSNMVKNLTEQMVKYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSF 350
Cdd:PRK10898 235 IPTQLATKIMDKLIRDGRVIRGYIGIGGREIAPLHAQGGGIDQLQGIVVNEVSPDGPAAKAGIQVNDLIISVNNKPAISA 314

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 488978433 351 AALRAQVGTMPIGSKVELGLLRDGKPVTVTVELQQ 385
Cdd:PRK10898 315 LETMDQVAEIRPGSVIPVVVMRDDKQLTLQVTIQE 349
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 117-253 3.14e-34

Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 125.23  E-value: 3.14e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  117 GSGVIIDAaKGYVVTNNHVVDNATTI-----KVQLSDGRRFDAKVVGKDPRSDIALIQI-QDPKNLTAIKLADSDALRVG 190
Cdd:pfam13365   1 GTGFVVSS-DGLVLTNAHVVDDAEEAavelvSVVLADGREYPATVVARDPDLDLALLRVsGDGRGLPPLPLGDSEPLVGG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488978433  191 DYTVAIGNPFGLGE-TVTSGIVSALGRSGlNVENYENFIQTDAAINRGNSGGALVNLNGELIGI 253
Cdd:pfam13365  80 ERVYAVGYPLGGEKlSLSEGIVSGVDEGR-DGGDDGRVIQTDAALSPGSSGGPVFDADGRVVGI 142
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 291-381 8.57e-31

circularly permuted first PDZ domain (PDZ1) 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 1 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 identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for 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 1 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: 467630 [Multi-domain]  Cd Length: 91  Bit Score: 114.12  E-value: 8.57e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 291 RGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVELGL 370
Cdd:cd10839    1 RGWLGVQIQELTPDLAESFGLKEPKGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATTKPGTKVELKI 80

                         90
                 ....*....|.
gi 488978433 371 LRDGKPVTVTV 381
Cdd:cd10839   81 LRDGKEKTLTV 91
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 398-477 2.36e-30

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: 112.72  E-value: 2.36e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 398 NGIEGAEMSN---KGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAKPSVLALNIQRGDASIYL 474
Cdd:cd23084    1 LALEGATVSNvtdEDGGKGVVVTEVDPGSPAAQSGLKKGDVIIGVNRQPVKSIAELRKVLKSKPSAVLLQIKRGDSSRYL 80


                 ...
gi 488978433 475 LLQ 477
Cdd:cd23084   81 ALP 83
Trypsin pfam00089
Trypsin;
119-278 1.35e-23

Trypsin;


Pssm-ID: 459667 [Multi-domain]  Cd Length: 219  Bit Score: 98.67  E-value: 1.35e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  119 GVIIDaaKGYVVTNNHVVDNATTIKVQLS---------DGRRFDAKVV-------GKDPRSDIALIQIQDPKNLT----A 178
Cdd:pfam00089  29 GSLIS--ENWVLTAAHCVSGASDVKVVLGahnivlregGEQKFDVEKIivhpnynPDTLDNDIALLKLESPVTLGdtvrP 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  179 IKLADSDAL---RVGDYTVAIGNPFGLG------ETVTSGIVSALGRSGLNVENYENFIQTDA---AINRGNSGGALVNL 246
Cdd:pfam00089 107 ICLPDASSDlpvGTTCTVSGWGNTKTLGpsdtlqEVTVPVVSRETCRSAYGGTVTDTMICAGAggkDACQGDSGGPLVCS 186

                         170       180       190
                  ....*....|....*....|....*....|..
gi 488978433  247 NGELIGINTAILAPDGGNIgIGFAIPSNMVKN 278
Cdd:pfam00089 187 DGELIGIVSWGYGCASGNY-PGVYTPVSSYLD 217
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 291-381 2.39e-19

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Deg/HtrA-type serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. Typically, these proteases have an N-terminal serine protease domain and at least one C-terminal PDZ domain that recognizes substrates, and in some cases activates the protease function. An exception is yeast Nma11p which has two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. HtrA-type proteases include the human HtrA1-4 and MBTPS2, tricorn protease, DegS, DegP and C-terminal processing peptidase, cyanobacterial serine proteases Hhoa, HhoB, and HtrA, and yeast Nma11p. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-termini 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 Deg/HtrA family PDZ domain is a circularly permuted PDZ domain which places beta-strand A at the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467621 [Multi-domain]  Cd Length: 91  Bit Score: 82.73  E-value: 2.39e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 291 RGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVELGL 370
Cdd:cd06779    1 RPYLGIEMENISPLLAKELGLPVNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTKKPGDSLNLTI 80

                         90
                 ....*....|.
gi 488978433 371 LRDGKPVTVTV 381
Cdd:cd06779   81 LRDGKTLTVTV 91
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 410-476 2.92e-14

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Deg/HtrA-type serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. Typically, these proteases have an N-terminal serine protease domain and at least one C-terminal PDZ domain that recognizes substrates, and in some cases activates the protease function. An exception is yeast Nma11p which has two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. HtrA-type proteases include the human HtrA1-4 and MBTPS2, tricorn protease, DegS, DegP and C-terminal processing peptidase, cyanobacterial serine proteases Hhoa, HhoB, and HtrA, and yeast Nma11p. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-termini 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 Deg/HtrA family PDZ domain is a circularly permuted PDZ domain which places beta-strand A at the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467621 [Multi-domain]  Cd Length: 91  Bit Score: 68.09  E-value: 2.92e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488978433 410 QDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAK--PSVLALNIQRGDASIYLLL 476
Cdd:cd06779   23 VNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTKkpGDSLNLTILRDGKTLTVTV 91
SdrC COG3480
Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];
307-386 8.09e-12

Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];


Pssm-ID: 442703 [Multi-domain]  Cd Length: 344  Bit Score: 66.37  E-value: 8.09e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 307 KAMKVDAQRGAFVSQVMPGSAAAKAGIKAgDVITSLNGKAISSFAALRAQVGTMPIGSKVELGLLRDGKPVTVTVELQQS 386
Cdd:COG3480  130 RAAGYPVTEGVYVASVLEGSPADGVLQPG-DVITAVDGKPVTTAEDLRDALAAKKPGDTVTLTVTRDGKEKTVTVTLVKL 208
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 377-469 1.73e-10

circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB, and HtrA and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the cyanobacterial Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB and HtrA, and related domains. These three proteases are functionally overlapping, and are involved in a number of key physiological responses, ranging from protection against light and heat stresses to phototaxis. HhoA assembles into trimers, mediated by its protease domain and further into a hexamer by a novel interaction between the PDZ domains of opposing trimers. 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 HhoA-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: 467629 [Multi-domain]  Cd Length: 104  Bit Score: 57.71  E-value: 1.73e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 377 VTVTVELQQSNQTQVDSSTIFNgiegaemsnkgQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFD- 455
Cdd:cd10838    9 TTLTPELAQQNNRNPNSPVRIP-----------EVDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRIVEq 77

                         90
                 ....*....|....*
gi 488978433 456 AKPS-VLALNIQRGD 469
Cdd:cd10838   78 AGVGeELELTVLRGD 92
eMpr COG3591
V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, ...
 115-283 1.46e-09

V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442810 [Multi-domain]  Cd Length: 194  Bit Score: 57.38  E-value: 1.46e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 115 ALGSGVIIdaAKGYVVTNNHVVDN------ATTIKVQLS-DGRRF------DAKVVGK-----DPRSDIALIQIQDPKNL 176
Cdd:COG3591   12 GVCTGTLI--GPNLVLTAGHCVYDgagggwATNIVFVPGyNGGPYgtatatRFRVPPGwvasgDAGYDYALLRLDEPLGD 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 177 T--AIKLADSDALRVGDYTVAIGNPFGLGETVTsgivsaLGRSGLNVENYENFIQTDAAINRGNSGGALVNLN---GELI 251
Cdd:COG3591   90 TtgWLGLAFNDAPLAGEPVTIIGYPGDRPKDLS------LDCSGRVTGVQGNRLSYDCDTTGGSSGSPVLDDSdggGRVV 163

                        170       180       190
                 ....*....|....*....|....*....|..
gi 488978433 252 GINTAIlAPDGGNIGIgfAIPSNMVKNLTEQM 283
Cdd:COG3591  164 GVHSAG-GADRANTGV--RLTSAIVAALRAWA 192
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 399-466 3.29e-09

PDZ domain; PDZ domains are found in diverse signaling proteins.


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 53.44  E-value: 3.29e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  399 GIEGAEMSNKGqDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAKPS--VLALNIQ 466
Cdd:pfam00595  13 GFSLKGGSDQG-DPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSggKVTLTIL 81
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 294-381 4.30e-09

circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB, and HtrA and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the cyanobacterial Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB and HtrA, and related domains. These three proteases are functionally overlapping, and are involved in a number of key physiological responses, ranging from protection against light and heat stresses to phototaxis. HhoA assembles into trimers, mediated by its protease domain and further into a hexamer by a novel interaction between the PDZ domains of opposing trimers. 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 HhoA-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: 467629 [Multi-domain]  Cd Length: 104  Bit Score: 53.86  E-value: 4.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 294 LGIMGTELNSELAK--------AMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSK 365
Cdd:cd10838    4 LGIQMTTLTPELAQqnnrnpnsPVRIPEVDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRIVEQAGVGEE 83

                         90
                 ....*....|....*.
gi 488978433 366 VELGLLRDGKPVTVTV 381
Cdd:cd10838   84 LELTVLRGDRRQTLAV 99
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 403-453 6.78e-09

circularly permuted first PDZ domain (PDZ1) 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 1 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 identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for 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 1 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: 467630 [Multi-domain]  Cd Length: 91  Bit Score: 52.87  E-value: 6.78e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488978433 403 AEMSNKGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKI 453
Cdd:cd10839   16 AESFGLKEPKGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNR 66
PDZ_2 pfam13180
PDZ domain;
311-383 8.02e-09

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 52.27  E-value: 8.02e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488978433  311 VDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVELGLLRDGKPVTVTVEL 383
Cdd:pfam13180   2 VDLEGGVVVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALYGHKPGDTVTLQVYRDGKLLTVEVKL 74
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 411-453 8.48e-09

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: 53.02  E-value: 8.48e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 488978433 411 DKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKI 453
Cdd:cd06781   29 NKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQI 71
PDZ_2 pfam13180
PDZ domain;
408-469 1.23e-08

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 51.50  E-value: 1.23e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488978433  408 KGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADL-RKIFDAKP-SVLALNIQRGD 469
Cdd:pfam13180   2 VDLEGGVVVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLeSALYGHKPgDTVTLQVYRDG 65
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 406-469 1.23e-08

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: 52.00  E-value: 1.23e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488978433   406 SNKGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLR--KIFDAKPSVLALNIQRGD 469
Cdd:smart00228  20 GGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEavDLLKKAGGKVTLTVLRGG 85
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 291-383 2.12e-08

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: 51.62  E-value: 2.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 291 RGELGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVELGL 370
Cdd:cd06777    1 RGYLGITLSEIPPAMARGGGIDQLQGALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVLELMDLVAEIRPGTVIPVVV 80

                         90
                 ....*....|...
gi 488978433 371 LRDGKPVTVTVEL 383
Cdd:cd06777   81 LRDGKQLTLEVTI 93
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 415-474 6.72e-08

Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, protein turnover, chaperones, Transcription];


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 54.32  E-value: 6.72e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488978433 415 VVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAKP-SVLALNIQRGDASIYL 474
Cdd:COG0750  131 VVGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDDLVDIIRASPgKPLTLTVERDGEELTL 191
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 409-469 1.12e-07

circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Arabidopsis thaliana DEGP1 (also known as protease Do-like 1, chloroplastic, protein DEGRADATION OF PERIPLASMIC PROTEINS 1, DEGP PROTEASE 1 and DEG1), and related domains. DEGP1 is a serine protease that is required at high temperature and may be involved in the degradation of damaged proteins. This family also includes Arabidopsis protease DEGP8/Do-like 8 (chloroplastic), a probable serine protease. 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 AtDEGP-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: 467618 [Multi-domain]  Cd Length: 102  Bit Score: 49.88  E-value: 1.12e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488978433 409 GQDKGVVVNNVKAGTPAAQIGLKK-----------GDVIVGANQQPVKNIADLRKIFDAKPS--VLALNIQRGD 469
Cdd:cd00990   20 GVRSGVLVLDVPPGGPAAKAGLRGtkrdefgrivlGDVIVAVDGKPVKNESDLYRALDEYKVgdVVTLKVLRGG 93
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 414-476 5.99e-07

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in 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 beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.


Pssm-ID: 467638 [Multi-domain]  Cd Length: 83  Bit Score: 47.19  E-value: 5.99e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488978433 414 VVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAKP-SVLALNIQRGDASIYLLL 476
Cdd:cd23081    1 PVVGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRIVRENPgKPLTLKIERDGKILTVTV 64
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 413-468 6.66e-07

circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of HtrA family serine proteases including human HtrA1, HtrA2 (mitochondrial), HtrA3, and HtrA4, and related domains. These proteases are key enzymes associated with pregnancy. Their diverse biological functions include cell growth proliferation, migration and apoptosis. They are also implicated in disorders including Alzheimer's, Parkinson's, arthritis and cancer. HtrA1 (also known as high-temperature requirement A serine peptidase 1, L56, and serine protease 11) substrates include extracellular matrix proteins, proteoglycans, and insulin-like growth factor (IGF)-binding proteins. HtrA1 also inhibits signaling by members of the transforming growth factor beta (TGF-beta) family. 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 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 HtrA-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: 467624 [Multi-domain]  Cd Length: 98  Bit Score: 47.49  E-value: 6.66e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488978433 413 GVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAKpSVLALNIQRG 468
Cdd:cd06785   32 GVYVHKVIPGSPAQRAGLKDGDVIISINGKPVKSSSDVYEAVKSG-SSLLVVVRRG 86
cpPDZ1_MamE-like cd23087
circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease ...
 294-381 7.98e-07

circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease MamE and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Magnetospirillum magneticum MamE (also known as magnetochrome MamE and magnetosome serine protease MamE), and related domains. MamE is a serine protease required to produce magnetite crystals in the magnetotactic bacterium M. magneticum. It is involved in localization of some proteins (at least MamA, MamC, MamF, MamI and MamJ) to the magnetosome, and likely cleaves at least itself, MamO and MamP. MamE-PDZ1 may bind MamB. Its autoproteolysis is stimulated by exogenous substrates or peptides that bind to its PDZ domains. Peptide binding to either the first or the second PDZ domain of MamE can activate proteolysis; activation through PDZ2 is much weaker. 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 MamE-like PDZ domain 1 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: 467634 [Multi-domain]  Cd Length: 91  Bit Score: 47.18  E-value: 7.98e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 294 LGIMGTELNSELAKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVELGLLRD 373
Cdd:cd23087    4 LGAALTPMQQRLGQQTNLPAGRGVFVSGVTPNTPAAAAGLRPGDVILKVDGRPVHQPEEVSAIMAEMPNGRSVRLGVLRD 83


                 ....*...
gi 488978433 374 GKPVTVTV 381
Cdd:cd23087   84 GDVRNMSL 91
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 319-391 1.00e-06

Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, protein turnover, chaperones, Transcription];


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 50.47  E-value: 1.00e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488978433 319 VSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPiGSKVELGLLRDGKPVTVTVELQQSNQTQV 391
Cdd:COG0750  132 VGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDDLVDIIRASP-GKPLTLTVERDGEELTLTVTPRLVEEDGV 203
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 415-467 1.40e-06

PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 45.21  E-value: 1.40e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 488978433  415 VVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAK-PSVLALNIQR 467
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLQGSaGESVTLTVRR 54
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 294-383 4.88e-06

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: 44.93  E-value: 4.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 294 LGIMG---TELNSELAKAMKV--DAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVEL 368
Cdd:cd06781    4 LGISMvdlSDVPEYEQQSLKLpsNVNKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILYSHKVGDTVKV 83

                         90
                 ....*....|....*
gi 488978433 369 GLLRDGKPVTVTVEL 383
Cdd:cd06781   84 TIYRDGKEKTLNIKL 98
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 384-471 9.89e-06

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440556 [Multi-domain]  Cd Length: 341  Bit Score: 47.56  E-value: 9.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 384 QQSNQTQVDSSTIFNGIeGAEMSNKgqDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVK--NIADLRKIFDAKP-SV 460
Cdd:COG0793   46 EEYEDFQESTSGEFGGL-GAELGEE--DGKVVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAglTLDDAVKLLRGKAgTK 122

                         90
                 ....*....|.
gi 488978433 461 LALNIQRGDAS 471
Cdd:COG0793  123 VTLTIKRPGEG 133
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 288-371 1.42e-05

PDZ domain; PDZ domains are found in diverse signaling proteins.


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 43.04  E-value: 1.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  288 QVKRGELGIMGTELnselaKAMKVDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVE 367
Cdd:pfam00595   3 TLEKDGRGGLGFSL-----KGGSDQGDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSGGKVT 77


                  ....
gi 488978433  368 LGLL 371
Cdd:pfam00595  78 LTIL 81
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 387-472 1.48e-05

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


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 46.13  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 387 NQTQVDSSTIFNGIEGAEMSNKGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFD--AKPSVLALN 464
Cdd:COG3031  126 DELLANPNELLDYIRLSPVREDGKLVGYRVNPGRPGSLFSKLGLQPGDVITSINGQDLTDPAQALELLQqlRDASEVTLT 205


                 ....*...
gi 488978433 465 IQRGDASI 472
Cdd:COG3031  206 VERNGQPV 213
cpPDZ_AtDEGP14-like cd23085
circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) ...
 411-457 2.48e-05

circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Arabidopsis thaliana putative protease DEGP14 and related domains. DEGP14 is a putative protease belonging to the HtrA family of housekeeping proteases. 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 AtDEGP14-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: 467632 [Multi-domain]  Cd Length: 101  Bit Score: 43.22  E-value: 2.48e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 488978433 411 DKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAK 457
Cdd:cd23085   30 KAGVLVPQVIPGSPAERAGLRPGDVIVEFDGKPVDSTKQIIDALGDK 76
Peptidase_M50 pfam02163
Peptidase family M50;
414-468 5.00e-05

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 45.18  E-value: 5.00e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 488978433  414 VVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAKPSV-LALNIQRG 468
Cdd:pfam02163  95 PVIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQDLVEALAKSPGKpITLTVERG 150
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 397-446 9.48e-05

circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CPP (also known as tail-specific protease, PRC protein, Protease Re, and Photosystem II D1 protein processing peptidase), and related domains. CPP belongs to the peptidase S41A family. It cleaves a C-terminal 11 residue peptide from the precursor form of penicillin-binding protein 3, and may have a role in protecting bacterium from thermal and osmotic stresses. In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II. 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 CPP-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: 467623 [Multi-domain]  Cd Length: 88  Bit Score: 40.93  E-value: 9.48e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 488978433 397 FNGIeGAEMSnKGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKN 446
Cdd:cd06782    1 FGGI-GIEIG-KDDDGYLVVVSPIPGGPAEKAGIKPGDVIVAVDGESVRG 48
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 337-384 1.99e-04

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


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 42.66  E-value: 1.99e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 488978433 337 DVITSLNGKAISSFAALRAQVGTMPIGSKVELGLLRDGKPVTVTVELQ 384
Cdd:COG3031  173 DVITSINGQDLTDPAQALELLQQLRDASEVTLTVERNGQPVTLTYNLR 220
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 337-383 3.42e-04

circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Arabidopsis thaliana DEGP1 (also known as protease Do-like 1, chloroplastic, protein DEGRADATION OF PERIPLASMIC PROTEINS 1, DEGP PROTEASE 1 and DEG1), and related domains. DEGP1 is a serine protease that is required at high temperature and may be involved in the degradation of damaged proteins. This family also includes Arabidopsis protease DEGP8/Do-like 8 (chloroplastic), a probable serine protease. 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 AtDEGP-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: 467618 [Multi-domain]  Cd Length: 102  Bit Score: 39.87  E-value: 3.42e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 488978433 337 DVITSLNGKAISSFAALRAQVGTMPIGSKVELGLLRDGKPVTVTVEL 383
Cdd:cd00990   56 DVIVAVDGKPVKNESDLYRALDEYKVGDVVTLKVLRGGTKVDLKVTL 102
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 319-396 6.95e-04

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in 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 beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.


Pssm-ID: 467638 [Multi-domain]  Cd Length: 83  Bit Score: 38.33  E-value: 6.95e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488978433 319 VSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPiGSKVELGLLRDGKPVTVTVELQQSNQTQVDSSTI 396
Cdd:cd23081    3 VGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRIVRENP-GKPLTLKIERDGKILTVTVTPELVEVEGKGVGRI 79
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 311-374 7.85e-04

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: 38.51  E-value: 7.85e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488978433   311 VDAQRGAFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPIGSKVELGLLRDG 374
Cdd:smart00228  22 KDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
309-391 1.74e-03

Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 40.96  E-value: 1.74e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433 309 MKVDAQRG-AFVSQVMPGSAAAKAGIKAGDVITSLNGKAISSfAALRAQVGTMPIGSKVELGLLRDGKPVTVTVELQQSN 387
Cdd:COG3975  487 LRVSADGGgLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVTA-DNLDDALAAYKPGDPIELLVFRRDELRTVTVTLAAAP 565


                 ....
gi 488978433 388 QTQV 391
Cdd:COG3975  566 ADTY 569
cpPDZ1_MamE-like cd23087
circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease ...
 412-459 2.08e-03

circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease MamE and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Magnetospirillum magneticum MamE (also known as magnetochrome MamE and magnetosome serine protease MamE), and related domains. MamE is a serine protease required to produce magnetite crystals in the magnetotactic bacterium M. magneticum. It is involved in localization of some proteins (at least MamA, MamC, MamF, MamI and MamJ) to the magnetosome, and likely cleaves at least itself, MamO and MamP. MamE-PDZ1 may bind MamB. Its autoproteolysis is stimulated by exogenous substrates or peptides that bind to its PDZ domains. Peptide binding to either the first or the second PDZ domain of MamE can activate proteolysis; activation through PDZ2 is much weaker. 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 MamE-like PDZ domain 1 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: 467634 [Multi-domain]  Cd Length: 91  Bit Score: 37.55  E-value: 2.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 488978433 412 KGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIADLRKIFDAKPS 459
Cdd:cd23087   25 RGVFVSGVTPNTPAAAAGLRPGDVILKVDGRPVHQPEEVSAIMAEMPN 72
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 407-447 2.20e-03

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467153 [Multi-domain]  Cd Length: 81  Bit Score: 37.14  E-value: 2.20e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 488978433 407 NKGQDKGVVVNNVKAGTPAAQIG-LKKGDVIVGANQQPVKNI 447
Cdd:cd00136   19 GKDGGGGIFVSRVEPGGPAARDGrLRVGDRILEVNGVSLEGL 60
PDZ3_ZO1-like_domain cd06729
PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ ...
 409-447 2.72e-03

PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467211 [Multi-domain]  Cd Length: 82  Bit Score: 36.78  E-value: 2.72e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 488978433 409 GQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNI 447
Cdd:cd06729   20 GNDVGIFVAGVQEGSPAEKQGLQEGDQILKVNGVDFRNL 58
PDZ2_harmonin cd06738
PDZ domain 2 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic ...
 406-463 2.92e-03

PDZ domain 2 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467220 [Multi-domain]  Cd Length: 82  Bit Score: 36.53  E-value: 2.92e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488978433 406 SNKGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNIadlrkifDAKPSVLAL 463
Cdd:cd06738   21 SGPTQKPGIFISNVKPGSLAEEVGLEVGDQIVEVNGTSFTNV-------DHKEAVMAL 71
PDZ_rhophilin-like cd06712
PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 411-445 4.16e-03

PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of rhophilin-1, rhophilin-2, and related domains. Rhophilin-1 (RHPN1, also known as GTP-Rho-binding protein 1) and rhophilin-2 (RHPN2, also known as GTP-Rho-binding protein 2) are Rho-GTP binding proteins involved in cytoskeletal dynamics. Rhophilin-2 inhibits RhoA's activity to induce F-actin stress fibers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This rhophilin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467196 [Multi-domain]  Cd Length: 78  Bit Score: 36.02  E-value: 4.16e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 488978433 411 DKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVK 445
Cdd:cd06712   20 DSPVQVASVDPGSCAAEAGLKEGDYIVSVGGVDCK 54
PDZ_RGS3-like cd06711
PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 ...
 414-444 4.65e-03

PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS3, and related domains. RGS3 down-regulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. It downregulates G-protein-mediated release of inositol phosphates and activation of MAP kinases. In Eph/ephrin signaling, RGS3 binds via its PDZ domain to the cytoplasmic C terminus of Eph receptor tyrosine kinase EphB. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RGS3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467195 [Multi-domain]  Cd Length: 77  Bit Score: 35.83  E-value: 4.65e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 488978433 414 VVVNNVKAGTPAAQIGLKKGDVIVGANQQPV 444
Cdd:cd06711   22 VRVQAVDPGGPAEQAGLQQGDTVLQINGQPV 52
Peptidase_M50 pfam02163
Peptidase family M50;
318-405 4.95e-03

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 39.01  E-value: 4.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978433  318 FVSQVMPGSAAAKAGIKAGDVITSLNGKAISSFAALRAQVGTMPiGSKVELGLLRDGKPVTVTVELQQSNQTQvdsstiF 397
Cdd:pfam02163  96 VIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQDLVEALAKSP-GKPITLTVERGGQTLTVTITPKSSEESK------F 168


                  ....*...
gi 488978433  398 NGIEGAEM 405
Cdd:pfam02163 169 IGIGPVYV 176
PDZ_SYNPO2-like cd10820
PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related ...
 408-466 4.98e-03

PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNPO2, SYNPO2L, and related domains. SYNPO2 (also known as genethonin-2, myopodin) is a cytoskeleton adaptor protein. It participates in chaperone-assisted selective autophagy (CASA), a mechanism for the disposal of misfolded and damaged proteins and provides a link between the CASA chaperone complex and a membrane-tethering and fusion machinery that generates autophagosome membranes. The SYNPO2 PPxY motif binds CASA cochaperone BCL2-associated athanogene 3 (BAG3) and the SYNPO2 PDZ domain binds vacuolar protein sorting 18 homolog (VPS18). There are three isoforms of SYNPO2, which possess an amino-terminal PDZ domain (SYNPO2a, b, c); the short isoform SYNPO2d, lacks the PDZ domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNPO2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467264 [Multi-domain]  Cd Length: 78  Bit Score: 35.75  E-value: 4.98e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488978433 408 KGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNI--ADLRKIFDAKPSVLALNIQ 466
Cdd:cd10820   18 SEQKKPLQVAKIRKKSKAALAGLCEGDELLSINGKPCADLshSEAMDLIDSSGDTLQLLIK 78
PDZ_TAX1BP3-like cd10822
PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic ...
 411-440 5.56e-03

PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of TAX1BP3, and related domains. TAX1BP3 (also known as glutaminase-interacting protein 3, tax interaction protein 1, TIP-1, tax-interacting protein 1) may regulate a number of protein-protein interactions by competing for PDZ domain binding sites. TAX1BP3 binds beta-catenin and may act as an inhibitor of the Wnt signaling pathway. It competes with LIN7A (also known as Lin-7A or LIN-7A) for inward rectifier potassium channel 4 (KCNJ4) binding, and thereby promotes KCNJ4 internalization. It may play a role in the Rho signaling pathway, and in the activation of CDC42 by the viral protein HPV16 E6. Binding partners of the TAX1BP3 PDZ domain include beta-catenin, KCNJ4, glutaminase liver isoform (GLS2), rho guanine nucleotide exchange factor 16 (ARHGEF16), rhotekin, and CDK5 regulatory subunit-associated protein 3 (also known as LAPZ). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This TAX1BP3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467265 [Multi-domain]  Cd Length: 94  Bit Score: 36.16  E-value: 5.56e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 488978433 411 DKGVVVNNVKAGTPAAQIGLKKGDVIVGAN 440
Cdd:cd10822   36 DKGIYVTRVSEGGPAEKAGLQVGDKILQVN 65
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
408-458 8.45e-03

Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 38.65  E-value: 8.45e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488978433 408 KGQDKGVVVNNVKAGTPAAQIGLKKGDVIVGANQQPVKNiADLRKIF-DAKP 458
Cdd:COG3975  490 SADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVTA-DNLDDALaAYKP 540
 
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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