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Conserved domains on  [gi|992389486|ref|WP_061076476|]
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MULTISPECIES: serine endoprotease DegP [Citrobacter]

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;
2-475 0e+00

serine endoprotease DegP;


:

Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 871.78  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486   2 KKTTLAMSALALSLGLALSPLSATAAETASATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSP 81
Cdd:PRK10942   1 KKTTLALSALALSLGLALSPLSATAAETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRQFQQFFGDNSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  82 FCQEGSPFQSSPFCQGGAQGGNGGGQQqKFMALGSGVIIDAAKGYVVTNNHVVDNATVIKVQLSDGRKFDAKIVGKDPRS 161
Cdd:PRK10942  81 FCQEGSPFQSSPFCQGGQGGNGGGQQQ-KFMALGSGVIIDADKGYVVTNNHVVDNATKIKVQLSDGRKFDAKVVGKDPRS 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 162 DIALIQIQDPKNLTAIKLADSDTLRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAQNYENFIQTDAAINRGNSGGAL 241
Cdd:PRK10942 160 DIALIQLQNPKNLTAIKMADSDALRVGDYTVAIGNPYGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGGAL 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 242 VNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEFGQVKRGELGIMGTELSSELAKAMKVDAQRGAFVSQVM 321
Cdd:PRK10942 240 VNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVL 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 322 PNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDGKPVTVNLELQQSSQTQVDSSSIFSGIEGA 401
Cdd:PRK10942 320 PNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSSQNQVDSSNIFNGIEGA 399

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486 402 EMSNKGQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKPSVLALNIQRGDSNIYLLMQ 475
Cdd:PRK10942 400 ELSNKGGDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKPSVLALNIQRGDSSIYLLMQ 473
 
Name Accession Description Interval E-value
PRK10942 PRK10942
serine endoprotease DegP;
2-475 0e+00

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 871.78  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486   2 KKTTLAMSALALSLGLALSPLSATAAETASATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSP 81
Cdd:PRK10942   1 KKTTLALSALALSLGLALSPLSATAAETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRQFQQFFGDNSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  82 FCQEGSPFQSSPFCQGGAQGGNGGGQQqKFMALGSGVIIDAAKGYVVTNNHVVDNATVIKVQLSDGRKFDAKIVGKDPRS 161
Cdd:PRK10942  81 FCQEGSPFQSSPFCQGGQGGNGGGQQQ-KFMALGSGVIIDADKGYVVTNNHVVDNATKIKVQLSDGRKFDAKVVGKDPRS 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 162 DIALIQIQDPKNLTAIKLADSDTLRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAQNYENFIQTDAAINRGNSGGAL 241
Cdd:PRK10942 160 DIALIQLQNPKNLTAIKMADSDALRVGDYTVAIGNPYGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGGAL 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 242 VNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEFGQVKRGELGIMGTELSSELAKAMKVDAQRGAFVSQVM 321
Cdd:PRK10942 240 VNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVL 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 322 PNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDGKPVTVNLELQQSSQTQVDSSSIFSGIEGA 401
Cdd:PRK10942 320 PNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSSQNQVDSSNIFNGIEGA 399

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486 402 EMSNKGQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKPSVLALNIQRGDSNIYLLMQ 475
Cdd:PRK10942 400 ELSNKGGDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKPSVLALNIQRGDSSIYLLMQ 473
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 39-474 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: 607.30  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486   39 PSLAPMLEKVMPSVVSINVEGS--TTVNTPRMPRNFQQFFGDDSPFCQEGSPFQsspfcqggaqggngggqqqKFMALGS 116
Cdd:TIGR02037   1 PSFAPLVEKVAPAVVNISVEGTvkRRNRPPALPPFFRQFFGDDMPDFPRQQREQ-------------------KVRGLGS 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  117 GVIIDAAkGYVVTNNHVVDNATVIKVQLSDGRKFDAKIVGKDPRSDIALIQIQDPKNLTAIKLADSDTLRVGDYTVAIGN 196
Cdd:TIGR02037  62 GVIISAD-GYVLTNNHVVDGADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIGN 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  197 PFGLGETVTSGIVSALGRSGLNAQNYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKN 276
Cdd:TIGR02037 141 PFGLGQTVTSGIVSALGRSGLGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAKN 220

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  277 LTSQMVEFGQVKRGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVG 356
Cdd:TIGR02037 221 VVDQLIEGGKVKRGWLGVTIQEVTSDLAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIG 300

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  357 TMPVGSKITLGLLRDGKPVTVNLELQQSSQTQVDSSSIFSGIEGA--------EMSNKGQDKGVVVNNVKANTPAAQIGL 428
Cdd:TIGR02037 301 TLKPGKKVTLGILRKGKEKTITVTLGASPEEQASSSNPFLGLTVAnlspeirkELRLKGDVKGVVVTKVVSGSPAARAGL 380

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*...
gi 992389486  429 KKGDVIVGANQQPVKNIAELRKILD--SKPSVLALNIQRGDSNIYLLM 474
Cdd:TIGR02037 381 QPGDVILSVNQQPVSSVAELRKVLAraKKGGRVALLILRGGATIFVTL 428
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 113-386 1.68e-141

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: 406.84  E-value: 1.68e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 113 ALGSGVIIDAaKGYVVTNNHVVDNATVIKVQLSDGRKFDAKIVGKDPRSDIALIQIqDPKNLTAIKLADSDTLRVGDYTV 192
Cdd:COG0265    1 GLGSGVIISP-DGYILTNNHVVEGADEITVTLADGREYPAKVVGRDPLTDLAVLKI-DAKDLPAAPLGDSDKLRVGDWVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 193 AIGNPFGLGETVTSGIVSALGRSG--LNAQNYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIP 270
Cdd:COG0265   79 AIGNPFGLGQTVTAGIVSALGRSIgsSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIISRSGGSQGIGFAIP 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 271 SNMVKNLTSQMVEFGQVKRGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAA 350
Cdd:COG0265  159 INLAKRVVEQLIETGRVRRGWLGVTIQPVTPELAEALGLPEPEGVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARD 238

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 992389486 351 LRAQVGTMPVGSKITLGLLRDGKPVTVNLELQQSSQ 386
Cdd:COG0265  239 LQRLLASLKPGDTVTLTVLRGGKELTVTVTLGERPE 274
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 289-379 1.88e-39

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: 137.61  E-value: 1.88e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 289 RGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGL 368
Cdd:cd10839    1 RGWLGVQIQELTPDLAESFGLKEPKGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATTKPGTKVELKI 80

                         90
                 ....*....|.
gi 992389486 369 LRDGKPVTVNL 379
Cdd:cd10839   81 LRDGKEKTLTV 91
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 115-251 2.99e-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: 2.99e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  115 GSGVIIDAaKGYVVTNNHVVDNAT-----VIKVQLSDGRKFDAKIVGKDPRSDIALIQI-QDPKNLTAIKLADSDTLRVG 188
Cdd:pfam13365   1 GTGFVVSS-DGLVLTNAHVVDDAEeaaveLVSVVLADGREYPATVVARDPDLDLALLRVsGDGRGLPPLPLGDSEPLVGG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486  189 DYTVAIGNPFGLGE-TVTSGIVSALGRSGlNAQNYENFIQTDAAINRGNSGGALVNLNGELIGI 251
Cdd:pfam13365  80 ERVYAVGYPLGGEKlSLSEGIVSGVDEGR-DGGDDGRVIQTDAALSPGSSGGPVFDADGRVVGI 142
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 309-372 6.62e-12

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: 61.24  E-value: 6.62e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486   309 VDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDG 372
Cdd:smart00228  22 KDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
GspC_delta NF041515
type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are ...
 322-378 8.71e-06

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


Pssm-ID: 469401 [Multi-domain]  Cd Length: 310  Bit Score: 47.56  E-value: 8.71e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486 322 PNSSASKAGIKAGDVITSLNGKPISS-------FAALRAqvgtmpvGSKITLGLLRDGKPVTVN 378
Cdd:NF041515 250 PGSLLGKLGLQNGDVLQSINGFDMTSpdkaleaYARLRS-------ADHLTVSVERRGKPVTLD 306
 
Name Accession Description Interval E-value
PRK10942 PRK10942
serine endoprotease DegP;
2-475 0e+00

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 871.78  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486   2 KKTTLAMSALALSLGLALSPLSATAAETASATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSP 81
Cdd:PRK10942   1 KKTTLALSALALSLGLALSPLSATAAETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRQFQQFFGDNSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  82 FCQEGSPFQSSPFCQGGAQGGNGGGQQqKFMALGSGVIIDAAKGYVVTNNHVVDNATVIKVQLSDGRKFDAKIVGKDPRS 161
Cdd:PRK10942  81 FCQEGSPFQSSPFCQGGQGGNGGGQQQ-KFMALGSGVIIDADKGYVVTNNHVVDNATKIKVQLSDGRKFDAKVVGKDPRS 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 162 DIALIQIQDPKNLTAIKLADSDTLRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAQNYENFIQTDAAINRGNSGGAL 241
Cdd:PRK10942 160 DIALIQLQNPKNLTAIKMADSDALRVGDYTVAIGNPYGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGGAL 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 242 VNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEFGQVKRGELGIMGTELSSELAKAMKVDAQRGAFVSQVM 321
Cdd:PRK10942 240 VNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVL 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 322 PNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDGKPVTVNLELQQSSQTQVDSSSIFSGIEGA 401
Cdd:PRK10942 320 PNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSSQNQVDSSNIFNGIEGA 399

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486 402 EMSNKGQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKPSVLALNIQRGDSNIYLLMQ 475
Cdd:PRK10942 400 ELSNKGGDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKPSVLALNIQRGDSSIYLLMQ 473
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 39-474 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: 607.30  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486   39 PSLAPMLEKVMPSVVSINVEGS--TTVNTPRMPRNFQQFFGDDSPFCQEGSPFQsspfcqggaqggngggqqqKFMALGS 116
Cdd:TIGR02037   1 PSFAPLVEKVAPAVVNISVEGTvkRRNRPPALPPFFRQFFGDDMPDFPRQQREQ-------------------KVRGLGS 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  117 GVIIDAAkGYVVTNNHVVDNATVIKVQLSDGRKFDAKIVGKDPRSDIALIQIQDPKNLTAIKLADSDTLRVGDYTVAIGN 196
Cdd:TIGR02037  62 GVIISAD-GYVLTNNHVVDGADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIGN 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  197 PFGLGETVTSGIVSALGRSGLNAQNYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKN 276
Cdd:TIGR02037 141 PFGLGQTVTSGIVSALGRSGLGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAKN 220

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  277 LTSQMVEFGQVKRGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVG 356
Cdd:TIGR02037 221 VVDQLIEGGKVKRGWLGVTIQEVTSDLAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIG 300

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  357 TMPVGSKITLGLLRDGKPVTVNLELQQSSQTQVDSSSIFSGIEGA--------EMSNKGQDKGVVVNNVKANTPAAQIGL 428
Cdd:TIGR02037 301 TLKPGKKVTLGILRKGKEKTITVTLGASPEEQASSSNPFLGLTVAnlspeirkELRLKGDVKGVVVTKVVSGSPAARAGL 380

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*...
gi 992389486  429 KKGDVIVGANQQPVKNIAELRKILD--SKPSVLALNIQRGDSNIYLLM 474
Cdd:TIGR02037 381 QPGDVILSVNQQPVSSVAELRKVLAraKKGGRVALLILRGGATIFVTL 428
PRK10139 PRK10139
serine endoprotease DegQ;
38-475 0e+00

serine endoprotease DegQ;


Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 534.91  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  38 MPSLAPMLEKVMPSVVSINVEGsTTVNTPRMPRNFQQFFGDDSPfCQEGSPFQsspfcqggaqggngggqqqkfmALGSG 117
Cdd:PRK10139  39 LPSLAPMLEKVLPAVVSVRVEG-TASQGQKIPEEFKKFFGDDLP-DQPAQPFE----------------------GLGSG 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 118 VIIDAAKGYVVTNNHVVDNATVIKVQLSDGRKFDAKIVGKDPRSDIALIQIQDPKNLTAIKLADSDTLRVGDYTVAIGNP 197
Cdd:PRK10139  95 VIIDAAKGYVLTNNHVINQAQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIADSDKLRVGDFAVAVGNP 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 198 FGLGETVTSGIVSALGRSGLNAQNYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNL 277
Cdd:PRK10139 175 FGLGQTATSGIISALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIPSNMARTL 254

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 278 TSQMVEFGQVKRGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGT 357
Cdd:PRK10139 255 AQQLIDFGEIKRGLLGIKGTEMSADIAKAFNLDVQRGAFVSEVLPNSGSAKAGVKAGDIITSLNGKPLNSFAELRSRIAT 334

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 358 MPVGSKITLGLLRDGKPVTVNLELQQSSQTQVDSSSIFSGIEGAEMSN---KGQDKGVVVNNVKANTPAAQIGLKKGDVI 434
Cdd:PRK10139 335 TEPGTKVKLGLLRNGKPLEVEVTLDTSTSSSASAEMITPALQGATLSDgqlKDGTKGIKIDEVVKGSPAAQAGLQKDDVI 414

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|.
gi 992389486 435 VGANQQPVKNIAELRKILDSKPSVLALNIQRGDSNIYLLMQ 475
Cdd:PRK10139 415 IGVNRDRVNSIAEMRKVLAAKPAIIALQIVRGNESIYLLLR 455
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 113-386 1.68e-141

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: 406.84  E-value: 1.68e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 113 ALGSGVIIDAaKGYVVTNNHVVDNATVIKVQLSDGRKFDAKIVGKDPRSDIALIQIqDPKNLTAIKLADSDTLRVGDYTV 192
Cdd:COG0265    1 GLGSGVIISP-DGYILTNNHVVEGADEITVTLADGREYPAKVVGRDPLTDLAVLKI-DAKDLPAAPLGDSDKLRVGDWVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 193 AIGNPFGLGETVTSGIVSALGRSG--LNAQNYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIP 270
Cdd:COG0265   79 AIGNPFGLGQTVTAGIVSALGRSIgsSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIISRSGGSQGIGFAIP 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 271 SNMVKNLTSQMVEFGQVKRGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAA 350
Cdd:COG0265  159 INLAKRVVEQLIETGRVRRGWLGVTIQPVTPELAEALGLPEPEGVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARD 238

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 992389486 351 LRAQVGTMPVGSKITLGLLRDGKPVTVNLELQQSSQ 386
Cdd:COG0265  239 LQRLLASLKPGDTVTLTVLRGGKELTVTVTLGERPE 274
PRK10898 PRK10898
serine endoprotease DegS;
114-383 2.22e-76

serine endoprotease DegS;


Pssm-ID: 182820 [Multi-domain]  Cd Length: 353  Bit Score: 242.99  E-value: 2.22e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 114 LGSGVIIDAaKGYVVTNNHVVDNATVIKVQLSDGRKFDAKIVGKDPRSDIALIQIqDPKNLTAIKLADSDTLRVGDYTVA 193
Cdd:PRK10898  79 LGSGVIMDQ-RGYILTNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKI-NATNLPVIPINPKRVPHIGDVVLA 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 194 IGNPFGLGETVTSGIVSALGRSGLNAQNYENFIQTDAAINRGNSGGALVNLNGELIGINTaiLAPDGGNI-----GIGFA 268
Cdd:PRK10898 157 IGNPYNLGQTITQGIISATGRIGLSPTGRQNFLQTDASINHGNSGGALVNSLGELMGINT--LSFDKSNDgetpeGIGFA 234

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 269 IPSNMVKNLTSQMVEFGQVKRGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSF 348
Cdd:PRK10898 235 IPTQLATKIMDKLIRDGRVIRGYIGIGGREIAPLHAQGGGIDQLQGIVVNEVSPDGPAAKAGIQVNDLIISVNNKPAISA 314

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 992389486 349 AALRAQVGTMPVGSKITLGLLRDGKPVTVNLELQQ 383
Cdd:PRK10898 315 LETMDQVAEIRPGSVIPVVVMRDDKQLTLQVTIQE 349
protease_degS TIGR02038
periplasmic serine pepetdase DegS; This family consists of the periplasmic serine protease ...
 114-377 2.90e-74

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: 237.42  E-value: 2.90e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  114 LGSGVIIDAaKGYVVTNNHVVDNATVIKVQLSDGRKFDAKIVGKDPRSDIALIQIQdPKNLTAIKLADSDTLRVGDYTVA 193
Cdd:TIGR02038  79 LGSGVIMSK-EGYILTNYHVIKKADQIVVALQDGRKFEAELVGSDPLTDLAVLKIE-GDNLPTIPVNLDRPPHVGDVVLA 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  194 IGNPFGLGETVTSGIVSALGRSGLNAQNYENFIQTDAAINRGNSGGALVNLNGELIGINTAIL--APDGGNIGIGFAIPS 271
Cdd:TIGR02038 157 IGNPYNLGQTITQGIISATGRNGLSSVGRQNFIQTDAAINAGNSGGALINTNGELVGINTASFqkGGDEGGEGINFAIPI 236

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  272 NMVKNLTSQMVEFGQVKRGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAAL 351
Cdd:TIGR02038 237 KLAHKIMGKIIRDGRVIRGYIGVSGEDINSVVAQGLGLPDLRGIVITGVDPNGPAARAGILVRDVILKYDGKDVIGAEEL 316

                         250       260       270
                  ....*....|....*....|....*....|
gi 992389486  352 RAQVGTMPVGSKITLGLLRDGK----PVTV 377
Cdd:TIGR02038 317 MDRIAETRPGSKVMVTVLRQGKqlelPVTI 346
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 289-379 1.88e-39

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: 137.61  E-value: 1.88e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 289 RGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGL 368
Cdd:cd10839    1 RGWLGVQIQELTPDLAESFGLKEPKGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATTKPGTKVELKI 80

                         90
                 ....*....|.
gi 992389486 369 LRDGKPVTVNL 379
Cdd:cd10839   81 LRDGKEKTLTV 91
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 115-251 2.99e-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: 2.99e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  115 GSGVIIDAaKGYVVTNNHVVDNAT-----VIKVQLSDGRKFDAKIVGKDPRSDIALIQI-QDPKNLTAIKLADSDTLRVG 188
Cdd:pfam13365   1 GTGFVVSS-DGLVLTNAHVVDDAEeaaveLVSVVLADGREYPATVVARDPDLDLALLRVsGDGRGLPPLPLGDSEPLVGG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486  189 DYTVAIGNPFGLGE-TVTSGIVSALGRSGlNAQNYENFIQTDAAINRGNSGGALVNLNGELIGI 251
Cdd:pfam13365  80 ERVYAVGYPLGGEKlSLSEGIVSGVDEGR-DGGDDGRVIQTDAALSPGSSGGPVFDADGRVVGI 142
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 396-475 3.80e-32

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: 117.73  E-value: 3.80e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 396 SGIEGAEMSN---KGQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKPSVLALNIQRGDSNIYL 472
Cdd:cd23084    1 LALEGATVSNvtdEDGGKGVVVTEVDPGSPAAQSGLKKGDVIIGVNRQPVKSIAELRKVLKSKPSAVLLQIKRGDSSRYL 80


                 ...
gi 992389486 473 LMQ 475
Cdd:cd23084   81 ALP 83
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 289-379 1.26e-26

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: 102.76  E-value: 1.26e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 289 RGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGL 368
Cdd:cd06779    1 RPYLGIEMENISPLLAKELGLPVNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTKKPGDSLNLTI 80

                         90
                 ....*....|.
gi 992389486 369 LRDGKPVTVNL 379
Cdd:cd06779   81 LRDGKTLTVTV 91
Trypsin pfam00089
Trypsin;
117-276 9.81e-24

Trypsin;


Pssm-ID: 459667 [Multi-domain]  Cd Length: 219  Bit Score: 99.05  E-value: 9.81e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  117 GVIIDaaKGYVVTNNHVVDNATVIKVQLS---------DGRKFDAKIV-------GKDPRSDIALIQIQDPKNLT----A 176
Cdd:pfam00089  29 GSLIS--ENWVLTAAHCVSGASDVKVVLGahnivlregGEQKFDVEKIivhpnynPDTLDNDIALLKLESPVTLGdtvrP 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  177 IKLAD-SDTLRVGD--YTVAIGNPFGLG------ETVTSGIVSALGRSGLNAQNYENFIQTDA---AINRGNSGGALVNL 244
Cdd:pfam00089 107 ICLPDaSSDLPVGTtcTVSGWGNTKTLGpsdtlqEVTVPVVSRETCRSAYGGTVTDTMICAGAggkDACQGDSGGPLVCS 186

                         170       180       190
                  ....*....|....*....|....*....|..
gi 992389486  245 NGELIGINTAILAPDGGNIgIGFAIPSNMVKN 276
Cdd:pfam00089 187 DGELIGIVSWGYGCASGNY-PGVYTPVSSYLD 217
SdrC COG3480
Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];
305-384 1.20e-15

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


Pssm-ID: 442703 [Multi-domain]  Cd Length: 344  Bit Score: 77.93  E-value: 1.20e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 305 KAMKVDAQRGAFVSQVMPNSSASKAgIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDGKPVTVNLELQQS 384
Cdd:COG3480  130 RAAGYPVTEGVYVASVLEGSPADGV-LQPGDVITAVDGKPVTTAEDLRDALAAKKPGDTVTLTVTRDGKEKTVTVTLVKL 208
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 292-377 3.26e-15

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: 71.20  E-value: 3.26e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 292 LGIMGTELSSELAK--------AMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSK 363
Cdd:cd10838    4 LGIQMTTLTPELAQqnnrnpnsPVRIPEVDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRIVEQAGVGEE 83

                         90
                 ....*....|....
gi 992389486 364 ITLGLLRDGKPVTV 377
Cdd:cd10838   84 LELTVLRGDRRQTL 97
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 317-389 5.80e-15

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 75.89  E-value: 5.80e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 992389486 317 VSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPvGSKITLGLLRDGKPVTVNLELQQSSQTQV 389
Cdd:COG0750  132 VGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDDLVDIIRASP-GKPLTLTVERDGEELTLTVTPRLVEEDGV 203
PDZ_2 pfam13180
PDZ domain;
309-381 6.52e-15

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 69.61  E-value: 6.52e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 992389486  309 VDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDGKPVTVNLEL 381
Cdd:pfam13180   2 VDLEGGVVVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALYGHKPGDTVTLQVYRDGKLLTVEVKL 74
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 408-472 7.56e-15

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: 69.63  E-value: 7.56e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 992389486 408 QDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSK--PSVLALNIQRGDSNIYL 472
Cdd:cd06779   23 VNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTKkpGDSLNLTILRDGKTLTV 89
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 292-381 2.03e-14

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: 68.82  E-value: 2.03e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 292 LGIMGTELS---SELAKAMKV--DAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITL 366
Cdd:cd06781    4 LGISMVDLSdvpEYEQQSLKLpsNVNKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILYSHKVGDTVKV 83

                         90
                 ....*....|....*
gi 992389486 367 GLLRDGKPVTVNLEL 381
Cdd:cd06781   84 TIYRDGKEKTLNIKL 98
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 289-381 3.65e-14

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: 67.80  E-value: 3.65e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 289 RGELGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGL 368
Cdd:cd06777    1 RGYLGITLSEIPPAMARGGGIDQLQGALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVLELMDLVAEIRPGTVIPVVV 80

                         90
                 ....*....|...
gi 992389486 369 LRDGKPVTVNLEL 381
Cdd:cd06777   81 LRDGKQLTLEVTI 93
cpPDZ1_MamE-like cd23087
circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease ...
 292-379 2.20e-13

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: 65.67  E-value: 2.20e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 292 LGIMGTELSSELAKAMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRD 371
Cdd:cd23087    4 LGAALTPMQQRLGQQTNLPAGRGVFVSGVTPNTPAAAAGLRPGDVILKVDGRPVHQPEEVSAIMAEMPNGRSVRLGVLRD 83


                 ....*...
gi 992389486 372 GKPVTVNL 379
Cdd:cd23087   84 GDVRNMSL 91
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 317-394 2.44e-13

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: 65.29  E-value: 2.44e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 992389486 317 VSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPvGSKITLGLLRDGKPVTVNLELQQSSQTQVDSSSI 394
Cdd:cd23081    3 VGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRIVRENP-GKPLTLKIERDGKILTVTVTPELVEVEGKGVGRI 79
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 286-369 5.51e-13

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 64.22  E-value: 5.51e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  286 QVKRGELGIMGTELSSelakaMKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKIT 365
Cdd:pfam00595   3 TLEKDGRGGLGFSLKG-----GSDQGDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSGGKVT 77


                  ....
gi 992389486  366 LGLL 369
Cdd:pfam00595  78 LTIL 81
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 309-372 6.62e-12

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: 61.24  E-value: 6.62e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486   309 VDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDG 372
Cdd:smart00228  22 KDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 287-381 3.32e-11

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: 59.90  E-value: 3.32e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 287 VKRGELGImgTELSSELAKAMKVDaqRGAFVSQVMPNSSASKAGIKA-----------GDVITSLNGKPISSFAALRAQV 355
Cdd:cd00990    1 VVRPGLGI--SFAPDQVARQLGVR--SGVLVLDVPPGGPAAKAGLRGtkrdefgrivlGDVIVAVDGKPVKNESDLYRAL 76

                         90       100
                 ....*....|....*....|....*.
gi 992389486 356 GTMPVGSKITLGLLRDGKPVTVNLEL 381
Cdd:cd00990   77 DEYKVGDVVTLKVLRGGTKVDLKVTL 102
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 283-379 1.80e-10

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: 62.19  E-value: 1.80e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 283 EFGQVKRGELGIMGTELSSElakamkvdaQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISS------FAALRAqvg 356
Cdd:COG0793   50 DFQESTSGEFGGLGAELGEE---------DGKVVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGltlddaVKLLRG--- 117

                         90       100
                 ....*....|....*....|....*
gi 992389486 357 tmPVGSKITLGLLRDG--KPVTVNL 379
Cdd:COG0793  118 --KAGTKVTLTIKRPGegEPITVTL 140
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 397-464 9.19e-10

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 54.98  E-value: 9.19e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486  397 GIEGAEMSNKGqDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKPS--VLALNIQ 464
Cdd:pfam00595  13 GFSLKGGSDQG-DPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSggKVTLTIL 81
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 292-347 9.31e-10

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: 55.58  E-value: 9.31e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 992389486 292 LGIMGTELSSELAKAMKV------DAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISS 347
Cdd:cd06785    4 IGIRMLTLTPSLLEELKQrnpdfpDVSSGVYVHKVIPGSPAQRAGLKDGDVIISINGKPVKS 65
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
307-383 1.29e-09

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


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 60.22  E-value: 1.29e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 992389486 307 MKVDAQRG-AFVSQVMPNSSASKAGIKAGDVITSLNGKPISSfAALRAQVGTMPVGSKITLGLLRDGKPVTVNLELQQ 383
Cdd:COG3975  487 LRVSADGGgLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVTA-DNLDDALAAYKPGDPIELLVFRRDELRTVTVTLAA 563
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 409-455 2.52e-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: 54.18  E-value: 2.52e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 992389486 409 DKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSK 455
Cdd:cd06781   29 NKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILYSH 75
Peptidase_M50 pfam02163
Peptidase family M50;
316-389 2.82e-09

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 58.27  E-value: 2.82e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486  316 FVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPvGSKITLGLLRDGKPVTVNLELQQSSQTQV 389
Cdd:pfam02163  96 VIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQDLVEALAKSP-GKPITLTVERGGQTLTVTITPKSSEESKF 168
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 316-382 3.19e-09

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: 53.64  E-value: 3.19e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 992389486 316 FVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAqVGTM--PVGSKITLGLLRDGKPVTVNLELQ 382
Cdd:cd06782   17 VVVSPIPGGPAEKAGIKPGDVIVAVDGESVRGMSLDEV-VKLLrgPKGTKVKLTIRRGGEGEPRDVTLT 84
PDZ_2 pfam13180
PDZ domain;
406-472 3.84e-09

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 53.04  E-value: 3.84e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 992389486  406 KGQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAEL-RKILDSKP-SVLALNIQRGDSNIYL 472
Cdd:pfam13180   2 VDLEGGVVVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLeSALYGHKPgDTVTLQVYRDGKLLTV 70
eMpr COG3591
V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, ...
 113-281 6.18e-09

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


Pssm-ID: 442810 [Multi-domain]  Cd Length: 194  Bit Score: 55.84  E-value: 6.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 113 ALGSGVIIdaAKGYVVTNNHVVDN------ATVIKV----QLSDGRKFDAK--------IVGKDPRSDIALIQIQDPKNL 174
Cdd:COG3591   12 GVCTGTLI--GPNLVLTAGHCVYDgagggwATNIVFvpgyNGGPYGTATATrfrvppgwVASGDAGYDYALLRLDEPLGD 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 175 T--AIKLADSDTLRVGDYTVAIGNPFGLGETVTsgivsaLGRSGLNAQNYENFIQTDAAINRGNSGGALVNLN---GELI 249
Cdd:COG3591   90 TtgWLGLAFNDAPLAGEPVTIIGYPGDRPKDLS------LDCSGRVTGVQGNRLSYDCDTTGGSSGSPVLDDSdggGRVV 163

                        170       180       190
                 ....*....|....*....|....*....|..
gi 992389486 250 GINTAIlAPDGGNIGIgfAIPSNMVKNLTSQM 281
Cdd:COG3591  164 GVHSAG-GADRANTGV--RLTSAIVAALRAWA 192
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 404-467 7.05e-09

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: 52.77  E-value: 7.05e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 992389486   404 SNKGQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNI--AELRKILDSKPSVLALNIQRGD 467
Cdd:smart00228  20 GGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLthLEAVDLLKKAGGKVTLTVLRGG 85
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 322-382 1.03e-08

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


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 55.37  E-value: 1.03e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 992389486 322 PNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDGKPVTVNLELQ 382
Cdd:COG3031  160 PGSLFSKLGLQPGDVITSINGQDLTDPAQALELLQQLRDASEVTLTVERNGQPVTLTYNLR 220
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 316-370 1.37e-08

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 50.99  E-value: 1.37e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 992389486  316 FVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTmPVGSKITLGLLR 370
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLQG-SAGESVTLTVRR 54
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 375-467 1.67e-08

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: 52.32  E-value: 1.67e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 375 VTVNLELQQSSQTQVDSSSIFSgiegaemsnkgQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDS 454
Cdd:cd10838    9 TTLTPELAQQNNRNPNSPVRIP-----------EVDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRIVEQ 77

                         90
                 ....*....|....*
gi 992389486 455 KP--SVLALNIQRGD 467
Cdd:cd10838   78 AGvgEELELTVLRGD 92
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 413-467 4.23e-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: 55.09  E-value: 4.23e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 992389486 413 VVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKIL-DSKPSVLALNIQRGD 467
Cdd:COG0750  131 VVGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDDLVDIIrASPGKPLTLTVERDG 186
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 407-468 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 992389486 407 GQDKGVVVNNVKANTPAAQIGLKK-----------GDVIVGANQQPVKNIAELRKILDSKPS--VLALNIQRGDS 468
Cdd:cd00990   20 GVRSGVLVLDVPPGGPAAKAGLRGtkrdefgrivlGDVIVAVDGKPVKNESDLYRALDEYKVgdVVTLKVLRGGT 94
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 412-474 3.31e-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: 47.96  E-value: 3.31e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486 412 VVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKP-SVLALNIQRGDSNIYLLM 474
Cdd:cd23081    1 PVVGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRIVRENPgKPLTLKIERDGKILTVTV 64
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 413-465 5.11e-07

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 46.37  E-value: 5.11e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 992389486  413 VVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSK-PSVLALNIQR 465
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLQGSaGESVTLTVRR 54
cpPDZ_RseP_YlbL-like cd10824
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), ...
 317-381 5.47e-07

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), Bacillus subtilis YlbL protease, 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), Bacillus subtilis YlbL, and related domains, including archaeal and chloroplast PDZ domains. RseP participates in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. 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 beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP-YlbL 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: 467636 [Multi-domain]  Cd Length: 82  Bit Score: 47.18  E-value: 5.47e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 992389486 317 VSQVMPNSSASKAGiKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDGKPVTVNLEL 381
Cdd:cd10824    3 VLSVKPNSPAAKAL-HAGDLITEIDGQPTKSWQTFIDYIHDKKVGESVKITYKHGNKNEEASLKL 66
cpPDZ_AtDEGP14-like cd23085
circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) ...
 310-356 7.49e-07

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: 47.46  E-value: 7.49e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 992389486 310 DAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVG 356
Cdd:cd23085   28 DVKAGVLVPQVIPGSPAERAGLRPGDVIVEFDGKPVDSTKQIIDALG 74
cpPDZ2_EcRseP-like cd23083
circularly permuted PDZ domain 2 (PDZ-C) of Escherichia coli Regulator of sigma-E protease ...
 317-379 1.32e-06

circularly permuted PDZ domain 2 (PDZ-C) 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-sigmaE) 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 it 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: 467640 [Multi-domain]  Cd Length: 85  Bit Score: 46.35  E-value: 1.32e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 992389486 317 VSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPvGSKITLGLLRDGKPVTVNL 379
Cdd:cd23083    3 LANVQPNSAAEKAGLQAGDRIVKVDGQPLTQWQTFVMAVRDNP-GKPLALEIERQGSPLSLTL 64
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 411-466 1.39e-06

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: 46.34  E-value: 1.39e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 992389486 411 GVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKpSVLALNIQRG 466
Cdd:cd06785   32 GVYVHKVIPGSPAQRAGLKDGDVIISINGKPVKSSSDVYEAVKSG-SSLLVVVRRG 86
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 382-469 1.74e-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: 49.87  E-value: 1.74e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 382 QQSSQTQVDSSSIFSGIeGAEMSNKgqDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVK--NIAELRKILDSKP-SV 458
Cdd:COG0793   46 EEYEDFQESTSGEFGGL-GAELGEE--DGKVVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAglTLDDAVKLLRGKAgTK 122

                         90
                 ....*....|.
gi 992389486 459 LALNIQRGDSN 469
Cdd:COG0793  123 VTLTIKRPGEG 133
cpPDZ1_ScNma111-like cd06786
circularly permuted first PDZ domain (PDZ1) of Saccharomyces cerevisiae pro-apoptotic serine ...
 317-380 3.40e-06

circularly permuted first PDZ domain (PDZ1) of Saccharomyces cerevisiae pro-apoptotic serine protease Nma111p and related domains; First PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the HtrA-type protease Saccharomyces cerevisiae Nma111p (also known as Ynm3p), and related domains. Nma111p is a nuclear serine protease which mediates apoptosis through proteolysis of the apoptotic inhibitor Bir1p. Nma111p is composed of 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. 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 ScNma111-like PDZ1 domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation places both beta-strands A and B on the C-terminus.


Pssm-ID: 467625 [Multi-domain]  Cd Length: 89  Bit Score: 45.26  E-value: 3.40e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486 317 VSQVMPNSSASKAgIKAGDVITSLNGKPISSFAALRAQVGTMpVGSKITLGLLRDGKPVTVNLE 380
Cdd:cd06786   27 AETVLPEGPADGK-LEEGDVLISVNGELITQFIRLEEILDEN-VGKTVELVVQRGGEEITVTIT 88
PLN00049 PLN00049
carboxyl-terminal processing protease; Provisional
 322-379 4.12e-06

carboxyl-terminal processing protease; Provisional


Pssm-ID: 177681 [Multi-domain]  Cd Length: 389  Bit Score: 48.96  E-value: 4.12e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 992389486 322 PNSSASKAGIKAGDVITSLNGKP---ISSFAALRAQVGtmPVGSKITLGLLRDGKPVTVNL 379
Cdd:PLN00049 111 PGGPAARAGIRPGDVILAIDGTStegLSLYEAADRLQG--PEGSSVELTLRRGPETRLVTL 169
PRK10779 PRK10779
sigma E protease regulator RseP;
307-379 4.49e-06

sigma E protease regulator RseP;


Pssm-ID: 182723 [Multi-domain]  Cd Length: 449  Bit Score: 48.91  E-value: 4.49e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 992389486 307 MKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPvGSKITLGLLRDGKPVTVNL 379
Cdd:PRK10779 215 RPRGPQIEPVLAEVQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRDNP-GKPLALEIERQGSPLSLTL 286
GspC_delta NF041515
type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are ...
 322-378 8.71e-06

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


Pssm-ID: 469401 [Multi-domain]  Cd Length: 310  Bit Score: 47.56  E-value: 8.71e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486 322 PNSSASKAGIKAGDVITSLNGKPISS-------FAALRAqvgtmpvGSKITLGLLRDGKPVTVN 378
Cdd:NF041515 250 PGSLLGKLGLQNGDVLQSINGFDMTSpdkaleaYARLRS-------ADHLTVSVERRGKPVTLD 306
cpPDZ1_EcRseP-like cd23082
circularly permuted PDZ domain 1 (PDZ-N) of Escherichia coli Regulator of sigma-E protease ...
 317-387 9.86e-06

circularly permuted PDZ domain 1 (PDZ-N) 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-sigmaE) 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 it 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: 467639 [Multi-domain]  Cd Length: 89  Bit Score: 43.90  E-value: 9.86e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 992389486 317 VSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDGKPVTVNLELQQSSQT 387
Cdd:cd23082    3 IGEIAPNSIAAQAGIEPGDEIKAVDGIEVPDWDSVRLQLVDKLGAGSVQITVQPFGSGAEREVTLDLRDWT 73
Peptidase_M50 pfam02163
Peptidase family M50;
412-474 1.99e-05

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 46.33  E-value: 1.99e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 992389486  412 VVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKPSV-LALNIQRGDSNIYLLM 474
Cdd:pfam02163  95 PVIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQDLVEALAKSPGKpITLTVERGGQTLTVTI 158
cpPDZ_BsYlbL-like cd23080
circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ ...
 314-383 2.01e-05

circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis YlbL and related domains. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. Deletion of both proteases leads to accumulation of the cell division inhibitor YneA. 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 YlbL 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: 467637 [Multi-domain]  Cd Length: 83  Bit Score: 42.87  E-value: 2.01e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 314 GAFVSQVMPNSSAsKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDGKPVTVNLELQQ 383
Cdd:cd23080    1 GVYVLSVVENMPA-KGILEAGDKITAIDGQNFQSSEKLIDYISSKKAGDKVKVKYERDEKEKEAELKLKQ 69
cpPDZ_AtDEGP14-like cd23085
circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) ...
 409-473 2.67e-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: 42.83  E-value: 2.67e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 992389486 409 DKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKPSV-LALNIQRGDSNIYLL 473
Cdd:cd23085   30 KAGVLVPQVIPGSPAERAGLRPGDVIVEFDGKPVDSTKQIIDALGDKVGKpFKVVVKRANKVQVTL 95
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 385-470 4.01e-05

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


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 44.59  E-value: 4.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 385 SQTQVDSSSIFSGIEGAEMSNKGQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILD--SKPSVLALN 462
Cdd:COG3031  126 DELLANPNELLDYIRLSPVREDGKLVGYRVNPGRPGSLFSKLGLQPGDVITSINGQDLTDPAQALELLQqlRDASEVTLT 205


                 ....*...
gi 992389486 463 IQRGDSNI 470
Cdd:COG3031  206 VERNGQPV 213
PDZ_PDZD11-like cd06752
PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic ...
 310-342 5.82e-05

PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZD11, and related domains. PDZD11 (also known as ATPase-interacting PDZ protein, plasma membrane calcium ATPase-interacting single-PDZ protein, PMCA-interacting single-PDZ protein, PISP) is involved in the dynamic assembly of apical junctions (AJs). It is recruited by PLEKHA7 to AJs to promote the efficient junctional recruitment and stabilization of nectins, and the efficient early phases of assembly of AJs in epithelial cells. The PDZD11 PDZ domain binds nectin-1 and nectin-3. PDZD11 also binds to a PDZ binding motif located in the C-terminal tail of the human sodium-dependent multivitamin transporter, to the cytoplasmic tail of the Menkes copper ATPase ATP7A, and to the cytoplasmic tail of all plasma membrane Ca2+-ATPase b-splice variants. 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 PDZD11-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: 467234 [Multi-domain]  Cd Length: 83  Bit Score: 41.53  E-value: 5.82e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 992389486 310 DAQRGAFVSQVMPNSSASKAGIKAGDVITSLNG 342
Cdd:cd06752   22 ASGLGIFISKVIPDSDAHRLGLKEGDQILSVNG 54
PDZ_tamalin_CYTIP-like cd06713
PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains; PDZ ...
 316-348 6.65e-05

PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of tamalin, cytohesin-1-interacting protein, and related domains. Tamalin (trafficking regulator and scaffold protein tamalin, also known as general receptor for phosphoinositides 1-associated scaffold protein, GRASP) functions to link receptors, including group 1 metabotropic glutamate receptors (mGluRs), to neuronal proteins. The tamalin PDZ domain binds the C-terminal domains of group I mGluRs; it also binds potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2), neurotrophin-3 (NT3) TrkCT1-truncated receptor, SAP90/PSD-95-associated protein, and tamalin itself. CYTIP (cytohesin-1-interacting protein, also known as Pleckstrin homology Sec7 and coiled-coil domain-binding protein) sequesters cytohesin-1 in the cytoplasm, limiting its interaction with beta2 integrins; cytohesin-1 binds the CYTIP coiled coil domain. The CYTIP PDZ domain can bind the C-terminal peptide of protocadherin alpha-1 (PCDHA1), indicating a possible interaction between the two. 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 tamalin-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: 467197 [Multi-domain]  Cd Length: 91  Bit Score: 41.45  E-value: 6.65e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 992389486 316 FVSQVMPNSSASKAGIKAGDVITSLNGKPISSF 348
Cdd:cd06713   38 YVCRVHEDSPAYLAGLTAGDVILSVNGVSVEGA 70
cpPDZ2_MamE-like cd23086
circularly permuted PDZ domain 2 of Magnetospirillum magneticum magnetosome formation protease ...
 313-373 6.67e-05

circularly permuted PDZ domain 2 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 2 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. 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 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: 467633 [Multi-domain]  Cd Length: 96  Bit Score: 41.85  E-value: 6.67e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 992389486 313 RGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKITLGLLRDGK 373
Cdd:cd23086   30 KGAQVAEVLAGSRAAVAGLQANDLILEVNNRPVTSPARLDAAIKGATAGQQILLKVHRNGQ 90
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 395-444 7.92e-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: 41.31  E-value: 7.92e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 992389486 395 FSGIeGAEMSnKGQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKN 444
Cdd:cd06782    1 FGGI-GIEIG-KDDDGYLVVVSPIPGGPAEKAGIKPGDVIVAVDGESVRG 48
cpPDZ1_MamE-like cd23087
circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease ...
 410-457 1.54e-04

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: 40.63  E-value: 1.54e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 992389486 410 KGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKPS 457
Cdd:cd23087   25 RGVFVSGVTPNTPAAAAGLRPGDVILKVDGRPVHQPEEVSAIMAEMPN 72
PDZ1_harmonin cd06737
PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic ...
 314-348 1.61e-04

PDZ domain 1 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 1 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 PDZ1 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: 467219 [Multi-domain]  Cd Length: 85  Bit Score: 40.32  E-value: 1.61e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 992389486 314 GAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSF 348
Cdd:cd06737   28 GLFVSHVSPGSQADNKGLRVGDEIVRINGYSISQC 62
PDZ_ARHGEF11-12-like cd23069
PDZ domain of ARHGEF11, ARHGEF12, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 307-369 2.97e-04

PDZ domain of ARHGEF11, ARHGEF12, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ARHGEF11, ARHGEF12, and related domains. This subfamily includes the GEFs (guanine exchange factors) ARHGEF11 (Rho guanine nucleotide exchange factor 11, known as PDZ-RhoGEF) and ARHGEF12 (Rho guanine nucleotide exchange factor 12, also known as leukemia-associated RhoGEF). GEFs activate Rho GTPases by promoting GTP binding. ARHGEF11/12 are regulators of G protein signaling (RGS) domain-containing GEFs; the RGS domain mediates their binding to and activation of Galpha (and Gq also in the case of ARHGEF12), in response to G-protein coupled receptor activation. ARHGEF11 and 12 are involved in serum-signaling, and regulate Yes-Associated Protein (YAP1)-dependent transcription. The ARHGEF12 PDZ domain binds plexin-B1 and the receptor tyrosine kinase insulin-like growth factor receptor (IGF-R1) beta-subunit. ARHGEF12 also interacts with glutamate receptor delta-1(GluD1), a postsynaptic organizer of inhibitory synapses in cortical pyramidal neurons. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ARHGEF11-12-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: 467282 [Multi-domain]  Cd Length: 76  Bit Score: 39.30  E-value: 2.97e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 992389486 307 MKVDAQRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAqVGTMPVGSKITLGLL 369
Cdd:cd23069   15 LTVSGDNPVFVQSVKEGGAAYRAGVQEGDRIIKVNGTLVTHSNHLEV-VKLIKSGSYVALTLL 76
PDZ_PDLIM-like cd06753
PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 317-354 5.04e-04

PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). 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 PDLIM-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: 467235 [Multi-domain]  Cd Length: 79  Bit Score: 38.67  E-value: 5.04e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 992389486 317 VSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQ 354
Cdd:cd06753   26 ISRVTPGGKAAQANLRPGDVILAINGESTEGMTHLEAQ 63
PDZ_ZASP52-like cd23068
PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), ...
 316-346 6.92e-04

PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. 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 Zasp52-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: 467281 [Multi-domain]  Cd Length: 82  Bit Score: 38.28  E-value: 6.92e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 992389486 316 FVSQVMPNSSASKAGIKAGDVITSLNGKPIS 346
Cdd:cd23068   28 SIQKVNPGSPADKAGLRRGDVILRINGTDTS 58
cpPDZ_RseP_YlbL-like cd10824
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), ...
 412-469 8.54e-04

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), Bacillus subtilis YlbL protease, 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), Bacillus subtilis YlbL, and related domains, including archaeal and chloroplast PDZ domains. RseP participates in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. 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 beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP-YlbL 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: 467636 [Multi-domain]  Cd Length: 82  Bit Score: 38.32  E-value: 8.54e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 992389486 412 VVVNNVKANTPAAQIgLKKGDVIVGANQQPVKNIAELRKILDSKP--SVLALNIQRGDSN 469
Cdd:cd10824    1 VVVLSVKPNSPAAKA-LHAGDLITEIDGQPTKSWQTFIDYIHDKKvgESVKITYKHGNKN 59
PDZ_SYNPO2-like cd10820
PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related ...
 406-464 8.82e-04

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: 38.06  E-value: 8.82e-04
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                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 992389486 406 KGQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNI--AELRKILDSKPSVLALNIQ 464
Cdd:cd10820   18 SEQKKPLQVAKIRKKSKAALAGLCEGDELLSINGKPCADLshSEAMDLIDSSGDTLQLLIK 78
PDZ_NHERF-like cd06768
PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related ...
 313-345 9.15e-04

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. 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 NHERF-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: 467249 [Multi-domain]  Cd Length: 80  Bit Score: 37.80  E-value: 9.15e-04
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gi 992389486 313 RGAFVSQVMPNSSASKAGIKAGDVITSLNGKPI 345
Cdd:cd06768   23 PGHFIREVDPGSPAERAGLKDGDRLVEVNGENV 55
PDZ3_Scribble-like cd06702
PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...
 314-346 9.59e-04

PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. 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 Scribble-like 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: 467186 [Multi-domain]  Cd Length: 89  Bit Score: 38.39  E-value: 9.59e-04
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                 ....*....|....*....|....*....|...
gi 992389486 314 GAFVSQVMPNSSASKAGIKAGDVITSLNGKPIS 346
Cdd:cd06702   33 GIFISKVIPDGAAAKSGLRIGDRILSVNGKDLR 65
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 405-464 1.52e-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: 37.52  E-value: 1.52e-03
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gi 992389486 405 NKGQDKGVVVNNVKANTPAAQIG-LKKGDVIVGANQQPVKNI--AELRKILDSKPSVLALNIQ 464
Cdd:cd00136   19 GKDGGGGIFVSRVEPGGPAARDGrLRVGDRILEVNGVSLEGLthEEAVELLKSAGGEVTLTVR 81
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 314-345 2.13e-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: 2.13e-03
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gi 992389486 314 GAFVSQVMPNSSASKAG-IKAGDVITSLNGKPI 345
Cdd:cd00136   25 GIFVSRVEPGGPAARDGrLRVGDRILEVNGVSL 57
PDZ1_FL-whirlin cd06740
PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 ...
 314-346 2.61e-03

PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. 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 whirlin family PDZ1 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: 467222 [Multi-domain]  Cd Length: 82  Bit Score: 36.96  E-value: 2.61e-03
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gi 992389486 314 GAFVSQVMPNSSASKAGIKAGDVITSLNGKPIS 346
Cdd:cd06740   28 GIYVSLVEPGSLAEKEGLRVGDQILRVNDVSFE 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 ...
 314-342 3.33e-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: 36.39  E-value: 3.33e-03
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gi 992389486 314 GAFVSQVMPNSSASKAGIKAGDVITSLNG 342
Cdd:cd06729   24 GIFVAGVQEGSPAEKQGLQEGDQILKVNG 52
PDZ_MAST cd06705
PDZ domain of the microtubule-associated serine-threonine (MAST) protein kinase family; PDZ ...
 317-345 3.39e-03

PDZ domain of the microtubule-associated serine-threonine (MAST) protein kinase family; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MAST family kinases, including MAST1-4. These MAST proteins contain a DUF1908 domain, a serine/threonine kinase domain, a AGC-kinase C-terminal domain, and a PDZ domain; MAST family member MASTL is a shorter protein lacking the PDZ domain. The PDZ domain gives the MAST family the capacity to scaffold its own kinase activity. These kinases are implicated in the inhibition of neurite outgrowth and regeneration in cultured cells. Their binding partners include microtubules, beta2-syntrophin, TNF receptor-associated factor 6 (TRAF6), cAMP-regulated phosphoprotein (ARPP-16), and PTEN. This family also includes Caenorhabditis elegans KIN-4 MAST kinase, a key longevity factor acting through binding PTEN phosphatase, and Drosophila Drop out which regulates dynein-dependent transport during embryonic development. 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 MAST-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: 467189 [Multi-domain]  Cd Length: 93  Bit Score: 36.84  E-value: 3.39e-03
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gi 992389486 317 VSQVMPNSSASKAGIKAGDVITSLNGKPI 345
Cdd:cd06705   37 VTAVEEGSPAYEAGLRPGDLITHVNGEPV 65
PDZ3_ZO1-like_domain cd06729
PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ ...
 407-467 3.43e-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: 36.39  E-value: 3.43e-03
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gi 992389486 407 GQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILdskpsvLALNIQRGD 467
Cdd:cd06729   20 GNDVGIFVAGVQEGSPAEKQGLQEGDQILKVNGVDFRNLTREEAVL------FLLDLPKGE 74
PRK10779 PRK10779
sigma E protease regulator RseP;
317-474 3.64e-03

sigma E protease regulator RseP;


Pssm-ID: 182723 [Multi-domain]  Cd Length: 449  Bit Score: 39.66  E-value: 3.64e-03
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gi 992389486 317 VSQVMPNSSASKAGIKAGDVITSLNGKPISSFAALRAQ-----------VGTMPVGSKITlgllrdgkpVTVNLELQQ-- 383
Cdd:PRK10779 130 VGEIAPNSIAAQAQIAPGTELKAVDGIETPDWDAVRLAlvskigdesttITVAPFGSDQR---------RDKTLDLRHwa 200

                         90       100       110       120       130       140       150       160
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gi 992389486 384 ---SSQTQVDSSSIFSgiegaemsnKGQDKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIAELRKILDSKPSV-L 459
Cdd:PRK10779 201 fepDKQDPVSSLGIRP---------RGPQIEPVLAEVQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRDNPGKpL 271

                        170
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gi 992389486 460 ALNIQRGDSNIYLLM 474
Cdd:PRK10779 272 ALEIERQGSPLSLTL 286
PDZ_TAX1BP3-like cd10822
PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic ...
 409-465 3.68e-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: 36.55  E-value: 3.68e-03
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gi 992389486 409 DKGVVVNNVKANTPAAQIGLKKGDVIVGANQQPVKNIA--ELRKILDSKPSVLALNIQR 465
Cdd:cd10822   36 DKGIYVTRVSEGGPAEKAGLQVGDKILQVNGWDMTMVThkQAVKRLTKKKPVLRMLVTR 94
PDZ_RapGEF2_RapGEF6-like cd06755
PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange ...
 314-342 3.84e-03

PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange factor 6, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Rap guanine nucleotide exchange factor 2 (RapGEF2, also named RA-GEF-1, PDZ-GEF1, CNrasGEF and nRapGEP) and Rap guanine nucleotide exchange factor 6 (RapGEF6, also named RA-GEF-2 and PDZ-GEF2). RapGEF2 and RapGEF6 constitute a subfamily of guanine nucleotide exchange factors (GEFs) for RAP small GTPases that is characterized by the possession of the PDZ and Ras/Rap-associating domains. They activate Rap small GTPases, by catalyzing the release of GDP from the inactive GDP-bound forms, thereby accelerating GTP loading to yield the active GTP-bound forms. The PDZ domain of RapGEF6 (also known as PDZ-GEF2) binds junctional adhesion molecule A (JAM-A). 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 RapGEF2 and RapGEF6 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: 467237 [Multi-domain]  Cd Length: 83  Bit Score: 36.47  E-value: 3.84e-03
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gi 992389486 314 GAFVSQVMPNSSASKAGIKAGDVITSLNG 342
Cdd:cd06755   27 GIFVSKVEKGSKAAEAGLKRGDQILEVNG 55
PDZ_RGS12-like cd06710
PDZ domain of regulator of G-protein signaling 12 (RGS12), and related domains; PDZ (PSD-95 ...
 312-346 4.52e-03

PDZ domain of regulator of G-protein signaling 12 (RGS12), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS12, and related domains. RGS12 downregulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. The RGS12 PDZ domain can bind selectively to C-terminal (A/S)-T-X-(L/V) motifs as found within both the CXCR2 IL-8 receptor, and the alternative 3' exon form of RGS12. 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 RGS12-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: 467194 [Multi-domain]  Cd Length: 76  Bit Score: 36.07  E-value: 4.52e-03
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gi 992389486 312 QRGAFVSQVMPNSSASKAGIKAGDVITSLNGKPIS 346
Cdd:cd06710   19 QAPCVLSCVVRGSPADVAGLKAGDQILAVNGINVS 53
cpPDZ_MBTPS2-like cd06775
circularly permuted PDZ domain of membrane-bound transcription factor site-2 protease (MBTPS2, ...
 313-347 6.87e-03

circularly permuted PDZ domain of membrane-bound transcription factor site-2 protease (MBTPS2, also known as S2P) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MBTPS2, also known as sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), and related domains. MBTPS2 is a zinc metalloprotease (MEROPS family M50A). In the Golgi, it catalyzes the second step in the proteolytic activation of sterol regulatory element-binding proteins (SREBPs), releasing the transcriptionally active N-terminal domain of SREBP, which then enters the nucleus and activates genes encoding the low density lipoprotein (LDL) receptor and enzymes for cholesterol and fatty acid biosynthesis. MBTPS2 also mediates the second step in the proteolytic activation of the cyclic AMP-dependent transcription factor ATF6. ATF6 is a membrane-bound transcription factor that activates genes in the endoplasmic reticulum (ER) stress response. 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. One permutation places beta-strand A on the C-terminus, another permutation places both beta-strands A and B on the C-terminus.


Pssm-ID: 467619 [Multi-domain]  Cd Length: 107  Bit Score: 36.06  E-value: 6.87e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 992389486 313 RGAFVSQVMPNSSAS-KAGIKAGDVITSLNGKPISS 347
Cdd:cd06775   35 SGVVVTEVVENSPVSgPRGLFVGDVITSINDCPVTS 70
PDZ_rhophilin-like cd06712
PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 317-344 7.25e-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: 35.25  E-value: 7.25e-03
                         10        20
                 ....*....|....*....|....*...
gi 992389486 317 VSQVMPNSSASKAGIKAGDVITSLNGKP 344
Cdd:cd06712   25 VASVDPGSCAAEAGLKEGDYIVSVGGVD 52
PDZ1_PDZD7-like cd10833
PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related ...
 314-342 7.28e-03

PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the first PDZ domain of the canonical isoform of PDZD7- isoform 1. 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 PDZD7-like family PDZ1 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: 467269 [Multi-domain]  Cd Length: 84  Bit Score: 35.49  E-value: 7.28e-03
                         10        20
                 ....*....|....*....|....*....
gi 992389486 314 GAFVSQVMPNSSASKAGIKAGDVITSLNG 342
Cdd:cd10833   27 GIFVSKVEEGSAAERAGLCVGDKITEVNG 55
PDZ_SHANK1_3-like cd06746
PDZ domain of SH3 and multiple ankyrin repeat domains protein 1 (SHANK1), SHANK2, SHANK3, and ...
 316-349 8.59e-03

PDZ domain of SH3 and multiple ankyrin repeat domains protein 1 (SHANK1), SHANK2, SHANK3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SHANK1, SHANK2, SHANK3, and related domains. SHANK family proteins, SHANK1 (also known as somatostatin receptor-interacting protein, SSTR-interacting protein, SSTRIP), SHANK2 (also known as cortactin-binding protein 1, proline-rich synapse-associated protein 1), and SHANK3 (proline-rich synapse-associated protein 2) are synaptic scaffolding proteins which are highly enriched in the post-synaptic densities of excitatory synapses. They have been implicated in synaptic transmission, synapse formation, synaptic plasticity, and cytoskeletal remodeling, and are regulators of Cav1 calcium current and CREB target expression. Many protein ligands have been identified for the Shank PDZ domain, such as GKAP (also known as SAPAP), betaPIX (a guanine nucleotide exchange factor used by Rho GTPase family members Rac1 and Cdc42), alpha-latrotoxin, neuroligin, group I metabotropic glutamate receptors (mGluRs), and L-type calcium channels. 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 SHANK-like family domain is a canonical PDZ domain containing 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.


Pssm-ID: 467228 [Multi-domain]  Cd Length: 101  Bit Score: 35.65  E-value: 8.59e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 992389486 316 FVSQVMPNSSASKAGIKAGDVITSLNGKPISSFA 349
Cdd:cd06746   45 YLESVDPGGVADKAGLKKGDFLLEINGEDVVKAS 78
 
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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