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Conserved domains on  [gi|1927672041|emb|CAA0357320|]
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Periplasmic pH-dependent serine endoprotease DegQ [Klebsiella oxytoca]

Protein Classification

serine endoprotease DegQ( domain architecture ID 11484587)

serine endoprotease DegQ could degrade transiently denatured and unfolded proteins which accumulate in the periplasm following stress conditions

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10139 PRK10139
serine endoprotease DegQ;
1-455 0e+00

serine endoprotease DegQ;


:

Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 805.71  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041   1 MNKPTLLLSALALSIGLSLSALPPAAASLPTQVPGQGALPSLAPMLEKVLPAVVSVQVEGTASPAQDMPEELKKYFGDNA 80
Cdd:PRK10139    1 MKKQTQLLSALALSVGLTLSASFQAVASIPGQVAGQAPLPSLAPMLEKVLPAVVSVRVEGTASQGQKIPEEFKKFFGDDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  81 PQEQAQPFEGLGSGVIIDAAKGYVLTNNHVINQAQKISVQLNDGREFDAKLVGSDEQSDIALLQILKPSNLTQIAIADSD 160
Cdd:PRK10139   81 PDQPAQPFEGLGSGVIIDAAKGYVLTNNHVINQAQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIADSD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 161 KLRVGDFAVAVGNPFGLGQTATSGIVSALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSV 240
Cdd:PRK10139  161 KLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 241 GIGFAIPSNMAKILSQQLIQFGEIKRGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGK 320
Cdd:PRK10139  241 GIGFAIPSNMARTLAQQLIDFGEIKRGLLGIKGTEMSADIAKAFNLDVQRGAFVSEVLPNSGSAKAGVKAGDIITSLNGK 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 321 PLNSFAELRSRIATTEPGTKVKLGLLREGKPVEVEVTLDKSTSSSASAELIAPALQGASLSDGQMKDGTKGVIIDNVDKG 400
Cdd:PRK10139  321 PLNSFAELRSRIATTEPGTKVKLGLLRNGKPLEVEVTLDTSTSSSASAEMITPALQGATLSDGQLKDGTKGIKIDEVVKG 400

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1927672041 401 SPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKPTVIALNVVRGSESIYLLLR 455
Cdd:PRK10139  401 SPAAQAGLQKDDVIIGVNRDRVNSIAEMRKVLAAKPAIIALQIVRGNESIYLLLR 455
 
Name Accession Description Interval E-value
PRK10139 PRK10139
serine endoprotease DegQ;
1-455 0e+00

serine endoprotease DegQ;


Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 805.71  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041   1 MNKPTLLLSALALSIGLSLSALPPAAASLPTQVPGQGALPSLAPMLEKVLPAVVSVQVEGTASPAQDMPEELKKYFGDNA 80
Cdd:PRK10139    1 MKKQTQLLSALALSVGLTLSASFQAVASIPGQVAGQAPLPSLAPMLEKVLPAVVSVRVEGTASQGQKIPEEFKKFFGDDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  81 PQEQAQPFEGLGSGVIIDAAKGYVLTNNHVINQAQKISVQLNDGREFDAKLVGSDEQSDIALLQILKPSNLTQIAIADSD 160
Cdd:PRK10139   81 PDQPAQPFEGLGSGVIIDAAKGYVLTNNHVINQAQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIADSD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 161 KLRVGDFAVAVGNPFGLGQTATSGIVSALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSV 240
Cdd:PRK10139  161 KLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 241 GIGFAIPSNMAKILSQQLIQFGEIKRGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGK 320
Cdd:PRK10139  241 GIGFAIPSNMARTLAQQLIDFGEIKRGLLGIKGTEMSADIAKAFNLDVQRGAFVSEVLPNSGSAKAGVKAGDIITSLNGK 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 321 PLNSFAELRSRIATTEPGTKVKLGLLREGKPVEVEVTLDKSTSSSASAELIAPALQGASLSDGQMKDGTKGVIIDNVDKG 400
Cdd:PRK10139  321 PLNSFAELRSRIATTEPGTKVKLGLLRNGKPLEVEVTLDTSTSSSASAEMITPALQGATLSDGQLKDGTKGIKIDEVVKG 400

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1927672041 401 SPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKPTVIALNVVRGSESIYLLLR 455
Cdd:PRK10139  401 SPAAQAGLQKDDVIIGVNRDRVNSIAEMRKVLAAKPAIIALQIVRGNESIYLLLR 455
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 40-454 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: 570.70  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  40 PSLAPMLEKVLPAVVSVQVEGTA---SPAQDMPEELKKYFGDNAP----QEQAQPFEGLGSGVIIDAAkGYVLTNNHVIN 112
Cdd:TIGR02037   1 PSFAPLVEKVAPAVVNISVEGTVkrrNRPPALPPFFRQFFGDDMPdfprQQREQKVRGLGSGVIISAD-GYVLTNNHVVD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 113 QAQKISVQLNDGREFDAKLVGSDEQSDIALLQILKPSNLTQIAIADSDKLRVGDFAVAVGNPFGLGQTATSGIVSALGRS 192
Cdd:TIGR02037  80 GADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSALGRS 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 193 GLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIPSNMAKILSQQLIQFGEIKRGLLGIK 272
Cdd:TIGR02037 160 GLGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAKNVVDQLIEGGKVKRGWLGVT 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 273 GMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREGKPV 352
Cdd:TIGR02037 240 IQEVTSDLAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKGKEK 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 353 EVEVTLDKSTSSSASAELIAPALQGASLSD-----GQMKDGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAE 427
Cdd:TIGR02037 320 TITVTLGASPEEQASSSNPFLGLTVANLSPeirkeLRLKGDVKGVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAE 399

                         410       420
                  ....*....|....*....|....*....
gi 1927672041 428 LRKVLE--SKPTVIALNVVRGSESIYLLL 454
Cdd:TIGR02037 400 LRKVLAraKKGGRVALLILRGGATIFVTL 428
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 90-360 2.92e-138

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: 397.60  E-value: 2.92e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  90 GLGSGVIIDAaKGYVLTNNHVINQAQKISVQLNDGREFDAKLVGSDEQSDIALLQIlKPSNLTQIAIADSDKLRVGDFAV 169
Cdd:COG0265     1 GLGSGVIISP-DGYILTNNHVVEGADEITVTLADGREYPAKVVGRDPLTDLAVLKI-DAKDLPAAPLGDSDKLRVGDWVL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 170 AVGNPFGLGQTATSGIVSALGRSG--LNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIP 247
Cdd:COG0265    79 AIGNPFGLGQTVTAGIVSALGRSIgsSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIISRSGGSQGIGFAIP 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 248 SNMAKILSQQLIQFGEIKRGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAE 327
Cdd:COG0265   159 INLAKRVVEQLIETGRVRRGWLGVTIQPVTPELAEALGLPEPEGVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARD 238

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1927672041 328 LRSRIATTEPGTKVKLGLLREGKPVEVEVTLDK 360
Cdd:COG0265   239 LQRLLASLKPGDTVTLTVLRGGKELTVTVTLGE 271
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 266-356 1.39e-37

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: 132.22  E-value: 1.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 266 RGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGL 345
Cdd:cd10839     1 RGWLGVQIQELTPDLAESFGLKEPKGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATTKPGTKVELKI 80

                          90
                  ....*....|.
gi 1927672041 346 LREGKPVEVEV 356
Cdd:cd10839    81 LRDGKEKTLTV 91
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 92-228 3.16e-33

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


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 122.14  E-value: 3.16e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  92 GSGVIIDAaKGYVLTNNHVINQAQKISVQLN-----DGREFDAKLVGSDEQSDIALLQILKP-SNLTQIAIADSDKLRVG 165
Cdd:pfam13365   1 GTGFVVSS-DGLVLTNAHVVDDAEEAAVELVsvvlaDGREYPATVVARDPDLDLALLRVSGDgRGLPPLPLGDSEPLVGG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1927672041 166 DFAVAVGNPFGLG-QTATSGIVSALGRSGLNLEGlENFIQTDASINRGNSGGALLNLNGELIGI 228
Cdd:pfam13365  80 ERVYAVGYPLGGEkLSLSEGIVSGVDEGRDGGDD-GRVIQTDAALSPGSSGGPVFDADGRVVGI 142
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 283-349 2.63e-10

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: 56.62  E-value: 2.63e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1927672041  283 AMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREG 349
Cdd:smart00228  19 VGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
GspC_delta NF041515
type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are ...
 299-357 8.64e-03

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: 37.93  E-value: 8.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1927672041 299 PNSGSAKAGVKSGDVIVSLNGKPLNS-------FAELRSriattepGTKVKLGLLREGKPVEVEVT 357
Cdd:NF041515  250 PGSLLGKLGLQNGDVLQSINGFDMTSpdkaleaYARLRS-------ADHLTVSVERRGKPVTLDYN 308
 
Name Accession Description Interval E-value
PRK10139 PRK10139
serine endoprotease DegQ;
1-455 0e+00

serine endoprotease DegQ;


Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 805.71  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041   1 MNKPTLLLSALALSIGLSLSALPPAAASLPTQVPGQGALPSLAPMLEKVLPAVVSVQVEGTASPAQDMPEELKKYFGDNA 80
Cdd:PRK10139    1 MKKQTQLLSALALSVGLTLSASFQAVASIPGQVAGQAPLPSLAPMLEKVLPAVVSVRVEGTASQGQKIPEEFKKFFGDDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  81 PQEQAQPFEGLGSGVIIDAAKGYVLTNNHVINQAQKISVQLNDGREFDAKLVGSDEQSDIALLQILKPSNLTQIAIADSD 160
Cdd:PRK10139   81 PDQPAQPFEGLGSGVIIDAAKGYVLTNNHVINQAQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIADSD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 161 KLRVGDFAVAVGNPFGLGQTATSGIVSALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSV 240
Cdd:PRK10139  161 KLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 241 GIGFAIPSNMAKILSQQLIQFGEIKRGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGK 320
Cdd:PRK10139  241 GIGFAIPSNMARTLAQQLIDFGEIKRGLLGIKGTEMSADIAKAFNLDVQRGAFVSEVLPNSGSAKAGVKAGDIITSLNGK 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 321 PLNSFAELRSRIATTEPGTKVKLGLLREGKPVEVEVTLDKSTSSSASAELIAPALQGASLSDGQMKDGTKGVIIDNVDKG 400
Cdd:PRK10139  321 PLNSFAELRSRIATTEPGTKVKLGLLRNGKPLEVEVTLDTSTSSSASAEMITPALQGATLSDGQLKDGTKGIKIDEVVKG 400

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1927672041 401 SPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKPTVIALNVVRGSESIYLLLR 455
Cdd:PRK10139  401 SPAAQAGLQKDDVIIGVNRDRVNSIAEMRKVLAAKPAIIALQIVRGNESIYLLLR 455
PRK10942 PRK10942
serine endoprotease DegP;
15-455 0e+00

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 592.12  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  15 IGLSLSALPPAAASLPTQVPGQgALPSLAPMLEKVLPAVVSVQVEG-TASPAQDMPEELKKYFGDNAP------------ 81
Cdd:PRK10942   14 LGLALSPLSATAAETSSATTAQ-QMPSLAPMLEKVMPSVVSINVEGsTTVNTPRMPRQFQQFFGDNSPfcqegspfqssp 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  82 ----------QEQAQPFEGLGSGVIIDAAKGYVLTNNHVINQAQKISVQLNDGREFDAKLVGSDEQSDIALLQILKPSNL 151
Cdd:PRK10942   93 fcqggqggngGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATKIKVQLSDGRKFDAKVVGKDPRSDIALIQLQNPKNL 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 152 TQIAIADSDKLRVGDFAVAVGNPFGLGQTATSGIVSALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTA 231
Cdd:PRK10942  173 TAIKMADSDALRVGDYTVAIGNPYGLGETVTSGIVSALGRSGLNVENYENFIQTDAAINRGNSGGALVNLNGELIGINTA 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 232 ILAPGGGSVGIGFAIPSNMAKILSQQLIQFGEIKRGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSG 311
Cdd:PRK10942  253 ILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAG 332

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 312 DVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREGKPVEVEVTLDKSTSSSASAELIAPALQGASLSDgqmKDGTKG 391
Cdd:PRK10942  333 DVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSSQNQVDSSNIFNGIEGAELSN---KGGDKG 409

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1927672041 392 VIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKPTVIALNVVRGSESIYLLLR 455
Cdd:PRK10942  410 VVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKPSVLALNIQRGDSSIYLLMQ 473
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 40-454 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: 570.70  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  40 PSLAPMLEKVLPAVVSVQVEGTA---SPAQDMPEELKKYFGDNAP----QEQAQPFEGLGSGVIIDAAkGYVLTNNHVIN 112
Cdd:TIGR02037   1 PSFAPLVEKVAPAVVNISVEGTVkrrNRPPALPPFFRQFFGDDMPdfprQQREQKVRGLGSGVIISAD-GYVLTNNHVVD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 113 QAQKISVQLNDGREFDAKLVGSDEQSDIALLQILKPSNLTQIAIADSDKLRVGDFAVAVGNPFGLGQTATSGIVSALGRS 192
Cdd:TIGR02037  80 GADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSALGRS 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 193 GLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIPSNMAKILSQQLIQFGEIKRGLLGIK 272
Cdd:TIGR02037 160 GLGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAKNVVDQLIEGGKVKRGWLGVT 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 273 GMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREGKPV 352
Cdd:TIGR02037 240 IQEVTSDLAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKGKEK 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 353 EVEVTLDKSTSSSASAELIAPALQGASLSD-----GQMKDGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAE 427
Cdd:TIGR02037 320 TITVTLGASPEEQASSSNPFLGLTVANLSPeirkeLRLKGDVKGVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAE 399

                         410       420
                  ....*....|....*....|....*....
gi 1927672041 428 LRKVLE--SKPTVIALNVVRGSESIYLLL 454
Cdd:TIGR02037 400 LRKVLAraKKGGRVALLILRGGATIFVTL 428
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 90-360 2.92e-138

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: 397.60  E-value: 2.92e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  90 GLGSGVIIDAaKGYVLTNNHVINQAQKISVQLNDGREFDAKLVGSDEQSDIALLQIlKPSNLTQIAIADSDKLRVGDFAV 169
Cdd:COG0265     1 GLGSGVIISP-DGYILTNNHVVEGADEITVTLADGREYPAKVVGRDPLTDLAVLKI-DAKDLPAAPLGDSDKLRVGDWVL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 170 AVGNPFGLGQTATSGIVSALGRSG--LNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIP 247
Cdd:COG0265    79 AIGNPFGLGQTVTAGIVSALGRSIgsSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIISRSGGSQGIGFAIP 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 248 SNMAKILSQQLIQFGEIKRGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAE 327
Cdd:COG0265   159 INLAKRVVEQLIETGRVRRGWLGVTIQPVTPELAEALGLPEPEGVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARD 238

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1927672041 328 LRSRIATTEPGTKVKLGLLREGKPVEVEVTLDK 360
Cdd:COG0265   239 LQRLLASLKPGDTVTLTVLRGGKELTVTVTLGE 271
protease_degS TIGR02038
periplasmic serine pepetdase DegS; This family consists of the periplasmic serine protease ...
 28-362 1.02e-81

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: 256.29  E-value: 1.02e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  28 SLPTQVPGQGALP-SLAPMLEKVLPAVVSVQVEGTaspaqdmpeelkkyfgDNAPQEQAQpFEGLGSGVIIDAaKGYVLT 106
Cdd:TIGR02038  32 NSLLQNRGNNTVEiSFNKAVRRAAPAVVNIYNRSI----------------SQNSLNQLS-IQGLGSGVIMSK-EGYILT 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 107 NNHVINQAQKISVQLNDGREFDAKLVGSDEQSDIALLQIlKPSNLTQIAIADSDKLRVGDFAVAVGNPFGLGQTATSGIV 186
Cdd:TIGR02038  94 NYHVIKKADQIVVALQDGRKFEAELVGSDPLTDLAVLKI-EGDNLPTIPVNLDRPPHVGDVVLAIGNPYNLGQTITQGII 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 187 SALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGG--GSVGIGFAIPSNMAKILSQQLIQFGEI 264
Cdd:TIGR02038 173 SATGRNGLSSVGRQNFIQTDAAINAGNSGGALINTNGELVGINTASFQKGGdeGGEGINFAIPIKLAHKIMGKIIRDGRV 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 265 KRGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLG 344
Cdd:TIGR02038 253 IRGYIGVSGEDINSVVAQGLGLPDLRGIVITGVDPNGPAARAGILVRDVILKYDGKDVIGAEELMDRIAETRPGSKVMVT 332

                         330
                  ....*....|....*...
gi 1927672041 345 LLREGKPVEVEVTLDKST 362
Cdd:TIGR02038 333 VLRQGKQLELPVTIDEKP 350
PRK10898 PRK10898
serine endoprotease DegS;
91-359 1.19e-80

serine endoprotease DegS;


Pssm-ID: 182820 [Multi-domain]  Cd Length: 353  Bit Score: 253.39  E-value: 1.19e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  91 LGSGVIIDAaKGYVLTNNHVINQAQKISVQLNDGREFDAKLVGSDEQSDIALLQIlKPSNLTQIAIADSDKLRVGDFAVA 170
Cdd:PRK10898   79 LGSGVIMDQ-RGYILTNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKI-NATNLPVIPINPKRVPHIGDVVLA 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 171 VGNPFGLGQTATSGIVSALGRSGLNLEGLENFIQTDASINRGNSGGALLNLNGELIGINTAIL---APGGGSVGIGFAIP 247
Cdd:PRK10898  157 IGNPYNLGQTITQGIISATGRIGLSPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFdksNDGETPEGIGFAIP 236

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 248 SNMAKILSQQLIQFGEIKRGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAE 327
Cdd:PRK10898  237 TQLATKIMDKLIRDGRVIRGYIGIGGREIAPLHAQGGGIDQLQGIVVNEVSPDGPAAKAGIQVNDLIISVNNKPAISALE 316

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1927672041 328 LRSRIATTEPGTKVKLGLLREGKPVEVEVTLD 359
Cdd:PRK10898  317 TMDQVAEIRPGSVIPVVVMRDDKQLTLQVTIQ 348
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 266-356 1.39e-37

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: 132.22  E-value: 1.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 266 RGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGL 345
Cdd:cd10839     1 RGWLGVQIQELTPDLAESFGLKEPKGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATTKPGTKVELKI 80

                          90
                  ....*....|.
gi 1927672041 346 LREGKPVEVEV 356
Cdd:cd10839    81 LRDGKEKTLTV 91
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 92-228 3.16e-33

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


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 122.14  E-value: 3.16e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  92 GSGVIIDAaKGYVLTNNHVINQAQKISVQLN-----DGREFDAKLVGSDEQSDIALLQILKP-SNLTQIAIADSDKLRVG 165
Cdd:pfam13365   1 GTGFVVSS-DGLVLTNAHVVDDAEEAAVELVsvvlaDGREYPATVVARDPDLDLALLRVSGDgRGLPPLPLGDSEPLVGG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1927672041 166 DFAVAVGNPFGLG-QTATSGIVSALGRSGLNLEGlENFIQTDASINRGNSGGALLNLNGELIGI 228
Cdd:pfam13365  80 ERVYAVGYPLGGEkLSLSEGIVSGVDEGRDGGDD-GRVIQTDAALSPGSSGGPVFDADGRVVGI 142
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 373-455 2.10e-29

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: 110.02  E-value: 2.10e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 373 PALQGASLSDGQMKDGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKPTVIALNVVRGSESIYL 452
Cdd:cd23084     1 LALEGATVSNVTDEDGGKGVVVTEVDPGSPAAQSGLKKGDVIIGVNRQPVKSIAELRKVLKSKPSAVLLQIKRGDSSRYL 80


                  ...
gi 1927672041 453 LLR 455
Cdd:cd23084    81 ALP 83
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 266-356 2.16e-22

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: 90.82  E-value: 2.16e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 266 RGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGL 345
Cdd:cd06779     1 RPYLGIEMENISPLLAKELGLPVNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTKKPGDSLNLTI 80

                          90
                  ....*....|.
gi 1927672041 346 LREGKPVEVEV 356
Cdd:cd06779    81 LRDGKTLTVTV 91
Trypsin pfam00089
Trypsin;
94-252 6.61e-20

Trypsin;


Pssm-ID: 459667 [Multi-domain]  Cd Length: 219  Bit Score: 87.88  E-value: 6.61e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041  94 GVIIDaaKGYVLTNNHVINQAQKISV-------QLNDGREFDAKL---------VGSDEQSDIALLQILKPSNLTQ---- 153
Cdd:pfam00089  29 GSLIS--ENWVLTAAHCVSGASDVKVvlgahniVLREGGEQKFDVekiivhpnyNPDTLDNDIALLKLESPVTLGDtvrp 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 154 IAIADSD---KLRVGDFAVAVGNPFGLG-----QTATSGIVS-ALGRSGLNLEGLENFIQTDA---SINRGNSGGALLNL 221
Cdd:pfam00089 107 ICLPDASsdlPVGTTCTVSGWGNTKTLGpsdtlQEVTVPVVSrETCRSAYGGTVTDTMICAGAggkDACQGDSGGPLVCS 186

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1927672041 222 NGELIGINTAILAPGGGSVgIGFAIPSNMAK 252
Cdd:pfam00089 187 DGELIGIVSWGYGCASGNY-PGVYTPVSSYL 216
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 266-358 9.31e-16

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: 72.43  E-value: 9.31e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 266 RGLLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGL 345
Cdd:cd06777     1 RGYLGITLSEIPPAMARGGGIDQLQGALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVLELMDLVAEIRPGTVIPVVV 80

                          90
                  ....*....|...
gi 1927672041 346 LREGKPVEVEVTL 358
Cdd:cd06777    81 LRDGKQLTLEVTI 93
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 287-358 3.13e-15

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: 71.13  E-value: 3.13e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1927672041 287 DVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREGKPVEVEVTL 358
Cdd:cd06781    27 NVNKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILYSHKVGDTVKVTIYRDGKEKTLNIKL 98
PDZ_2 pfam13180
PDZ domain;
287-358 4.57e-15

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 69.99  E-value: 4.57e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1927672041 287 DVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREGKPVEVEVTL 358
Cdd:pfam13180   3 DLEGGVVVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALYGHKPGDTVTLQVYRDGKLLTVEVKL 74
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 294-359 1.89e-13

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 71.27  E-value: 1.89e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1927672041 294 VSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTePGTKVKLGLLREGKPVEVEVTLD 359
Cdd:COG0750   132 VGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDDLVDIIRAS-PGKPLTLTVERDGEELTLTVTPR 196
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 267-357 1.74e-12

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: 63.49  E-value: 1.74e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 267 GLLGIKGMEMSADIAK--------AMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPG 338
Cdd:cd10838     2 PYLGIQMTTLTPELAQqnnrnpnsPVRIPEVDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRIVEQAGVG 81

                          90
                  ....*....|....*....
gi 1927672041 339 TKVKLGLLREGKPVEVEVT 357
Cdd:cd10838    82 EELELTVLRGDRRQTLAVK 100
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 294-395 2.14e-12

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: 67.97  E-value: 2.14e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 294 VSEVLPNSGSAKAGVKSGDVIVSLNGKPLN--SFAELRSRIAtTEPGTKVKLGLLREG--KPVEVEVTLDKSTSSSASAE 369
Cdd:COG0793    75 VVSVIPGSPAEKAGIKPGDIILAIDGKSVAglTLDDAVKLLR-GKAGTKVTLTIKRPGegEPITVTLTRAEIKLPSVEAK 153

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1927672041 370 LIA--------PALQGASLSD------GQMKDGTKGVIID 395
Cdd:COG0793   154 LLEgkigyiriPSFGENTAEEfkralkELKKQGAKGLILD 193
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 294-364 2.40e-11

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: 59.51  E-value: 2.40e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1927672041 294 VSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIAtTEPGTKVKLGLLREGKPVEVEVTLDKSTSS 364
Cdd:cd23081     3 VGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRIVR-ENPGKPLTLKIERDGKILTVTVTPELVEVE 72
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 266-358 4.45e-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: 59.51  E-value: 4.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 266 RGLLGIkgmEMSAD-IAKAMNldVQRGAFVSEVLPNSGSAKAGVKS-----------GDVIVSLNGKPLNSFAELRSRIA 333
Cdd:cd00990     3 RPGLGI---SFAPDqVARQLG--VRSGVLVLDVPPGGPAAKAGLRGtkrdefgrivlGDVIVAVDGKPVKNESDLYRALD 77

                          90       100
                  ....*....|....*....|....*
gi 1927672041 334 TTEPGTKVKLGLLREGKPVEVEVTL 358
Cdd:cd00990    78 EYKVGDVVTLKVLRGGTKVDLKVTL 102
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 258-346 5.98e-11

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 58.45  E-value: 5.98e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 258 LIQFGEIKRGLLGIKGmemsadiaKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEP 337
Cdd:pfam00595   1 QVTLEKDGRGGLGFSL--------KGGSDQGDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGS 72


                  ....*....
gi 1927672041 338 GTKVKLGLL 346
Cdd:pfam00595  73 GGKVTLTIL 81
cpPDZ1_MamE-like cd23087
circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease ...
 268-351 8.85e-11

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: 58.35  E-value: 8.85e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 268 LLGIKGMEMSADIAKAMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLR 347
Cdd:cd23087     3 LLGAALTPMQQRLGQQTNLPAGRGVFVSGVTPNTPAAAAGLRPGDVILKVDGRPVHQPEEVSAIMAEMPNGRSVRLGVLR 82


                  ....
gi 1927672041 348 EGKP 351
Cdd:cd23087    83 DGDV 86
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 283-349 2.63e-10

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: 56.62  E-value: 2.63e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1927672041  283 AMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREG 349
Cdd:smart00228  19 VGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 387-454 1.15e-09

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: 54.99  E-value: 1.15e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 387 DGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESK--PTVIALNVVRGSESIYLLL 454
Cdd:cd06779    22 PVNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTKkpGDSLNLTILRDGKTLTVTV 91
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 385-435 1.68e-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: 54.95  E-value: 1.68e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1927672041 385 MKDGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESK 435
Cdd:cd06781    25 PSNVNKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILYSH 75
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 269-337 1.72e-09

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: 54.81  E-value: 1.72e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1927672041 269 LGIKGMEMSADIAKAMNL------DVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEP 337
Cdd:cd06785     4 IGIRMLTLTPSLLEELKQrnpdfpDVSSGVYVHKVIPGSPAQRAGLKDGDVIISINGKPVKSSSDVYEAVKSGSS 78
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 377-443 1.95e-09

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 54.21  E-value: 1.95e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1927672041 377 GASLSDGQmKDGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKPT--VIALNV 443
Cdd:pfam00595  13 GFSLKGGS-DQGDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSggKVTLTI 80
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 387-445 1.08e-08

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


Pssm-ID: 467630 [Multi-domain]  Cd Length: 91  Bit Score: 52.10  E-value: 1.08e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1927672041 387 DGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKP--TVIALNVVR 445
Cdd:cd10839    22 KEPKGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATTKpgTKVELKILR 82
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 293-358 1.37e-08

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: 51.72  E-value: 1.37e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1927672041 293 FVSEVLPNSGSAKAGVKSGDVIVSLNGKPLN--SFAELRSRIaTTEPGTKVKLGLLREGKPVEVEVTL 358
Cdd:cd06782    17 VVVSPIPGGPAEKAGIKPGDVIVAVDGESVRgmSLDEVVKLL-RGPKGTKVKLTIRRGGEGEPRDVTL 83
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
291-374 3.43e-08

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


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 55.60  E-value: 3.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 291 GAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSfAELRSRIATTEPGTKVKLGLLREGKPVEVEVTLDKSTSSSASAEL 370
Cdd:COG3975   495 GLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVTA-DNLDDALAAYKPGDPIELLVFRRDELRTVTVTLAAAPADTYKLER 573


                  ....
gi 1927672041 371 IAPA 374
Cdd:COG3975   574 VEGA 577
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 377-447 6.74e-08

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


Pssm-ID: 214570 [Multi-domain]  Cd Length: 85  Bit Score: 49.68  E-value: 6.74e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1927672041  377 GASLSDGqmKDGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSI--AELRKVLESKPTVIALNVVRGS 447
Cdd:smart00228  15 GFSLVGG--KDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLthLEAVDLLKKAGGKVTLTVLRGG 85
PDZ_2 pfam13180
PDZ domain;
385-452 9.43e-08

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 49.19  E-value: 9.43e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 385 MKDGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKP--TVIALNVVRGSESIYL 452
Cdd:pfam13180   1 FVDLEGGVVVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALYGHKpgDTVTLQVYRDGKLLTV 70
cpPDZ_AtDEGP14-like cd23085
circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) ...
 266-328 1.27e-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: 49.38  E-value: 1.27e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1927672041 266 RGLLGIKGMEMSADIAK------AMNLDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAEL 328
Cdd:cd23085     1 RPWLGMKMLELNEHIIAqlkerdPMFPDVKAGVLVPQVIPGSPAERAGLRPGDVIVEFDGKPVDSTKQI 69
Peptidase_M50 pfam02163
Peptidase family M50;
293-361 1.46e-07

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 52.88  E-value: 1.46e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1927672041 293 FVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIAtTEPGTKVKLGLLREGKPVEVEVTLDKS 361
Cdd:pfam02163  96 VIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQDLVEALA-KSPGKPITLTVERGGQTLTVTITPKSS 163
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 267-351 1.89e-07

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: 48.39  E-value: 1.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 267 GLLGIKGMEMSADiakamnlDVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRsRIATTEPgTKVKLGLL 346
Cdd:cd23084     2 ALEGATVSNVTDE-------DGGKGVVVTEVDPGSPAAQSGLKKGDVIIGVNRQPVKSIAELR-KVLKSKP-SAVLLQIK 72


                  ....*
gi 1927672041 347 REGKP 351
Cdd:cd23084    73 RGDSS 77
cpPDZ_BsYlbL-like cd23080
circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ ...
 291-358 8.30e-07

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: 46.72  E-value: 8.30e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1927672041 291 GAFVSEVLPNSgSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREGKPVEVEVTL 358
Cdd:cd23080     1 GVYVLSVVENM-PAKGILEAGDKITAIDGQNFQSSEKLIDYISSKKAGDKVKVKYERDEKEKEAELKL 67
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 393-452 9.39e-07

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 50.47  E-value: 9.39e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1927672041 393 IIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKP-TVIALNVVRGSESIYL 452
Cdd:COG0750   131 VVGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDDLVDIIRASPgKPLTLTVERDGEELTL 191
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 393-445 2.59e-06

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 44.44  E-value: 2.59e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1927672041 393 IIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESK-PTVIALNVVR 445
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLQGSaGESVTLTVRR 54
cpPDZ1_EcRseP-like cd23082
circularly permuted PDZ domain 1 (PDZ-N) of Escherichia coli Regulator of sigma-E protease ...
 294-359 2.77e-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: 45.44  E-value: 2.77e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1927672041 294 VSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREGKPVEVEVTLD 359
Cdd:cd23082     3 IGEIAPNSIAAQAGIEPGDEIKAVDGIEVPDWDSVRLQLVDKLGAGSVQITVQPFGSGAEREVTLD 68
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 294-359 3.21e-06

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


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 48.05  E-value: 3.21e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1927672041 294 VSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREGKPVEVEVTLD 359
Cdd:COG3031   155 VNPGRPGSLFSKLGLQPGDVITSINGQDLTDPAQALELLQQLRDASEVTLTVERNGQPVTLTYNLR 220
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 293-347 4.63e-06

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 43.67  E-value: 4.63e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1927672041 293 FVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEpGTKVKLGLLR 347
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLQGSA-GESVTLTVRR 54
Peptidase_M50 pfam02163
Peptidase family M50;
392-452 1.73e-05

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 46.33  E-value: 1.73e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1927672041 392 VIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKP-TVIALNVVRGSESIYL 452
Cdd:pfam02163  95 PVIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQDLVEALAKSPgKPITLTVERGGQTLTV 156
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 387-452 2.05e-05

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: 43.26  E-value: 2.05e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1927672041 387 DGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKPTvIALNVVRGSESIYL 452
Cdd:cd06785    28 DVSSGVYVHKVIPGSPAQRAGLKDGDVIISINGKPVKSSSDVYEAVKSGSS-LLVVVRRGNEDLLL 92
PDZ7_GRIP1-2-like cd06685
PDZ domain 7 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related ...
 377-433 2.20e-05

PDZ domain 7 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-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 GRIP family PDZ7 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: 467173 [Multi-domain]  Cd Length: 85  Bit Score: 42.63  E-value: 2.20e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1927672041 377 GASLSDGQMkdgTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRS---------IAELRKVLE 433
Cdd:cd06685    18 GFSVSDGLY---EKGVYVNAIRPGGPADLSGLQPYDRILQVNHVRTRDfdcclvvplIAESGDKLE 80
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
386-446 2.57e-05

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


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 46.74  E-value: 2.57e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1927672041 386 KDGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSiAELRKVLESKPT--VIALNVVRG 446
Cdd:COG3975   490 SADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVTA-DNLDDALAAYKPgdPIELLVFRR 551
PDZ2_L-delphilin-like cd06744
PDZ domain 2 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 ...
 392-424 2.61e-05

PDZ domain 2 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of delphilin (also known as glutamate receptor, ionotropic, delta 2-interacting protein 1, L-delphilin). Delphilin, a postsynaptic protein which it is selectively expressed at cerebellar Purkinje cells, links the glutamate receptor delta 2 subunit (GluRdelta2) with the actin cytoskeleton and various signaling molecules. Two alternatively spliced isoforms of delphilin have been characterized: L-delphilin has two PDZ domains, PDZ1 and PDZ2, and S-delphilin has a single PDZ domain (PDZ2). These two isoforms are differently palmitoylated and may be involved in controlling GluRdelta2 signaling in Purkinje cells. 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 delphilin-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F


Pssm-ID: 467226 [Multi-domain]  Cd Length: 75  Bit Score: 42.26  E-value: 2.61e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1927672041 392 VIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRS 424
Cdd:cd06744    21 VYIESVDPGSAAERAGLKPGDRILFLNGLDVRN 53
cpPDZ1_ScNma111-like cd06786
circularly permuted first PDZ domain (PDZ1) of Saccharomyces cerevisiae pro-apoptotic serine ...
 294-357 2.81e-05

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: 42.56  E-value: 2.81e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1927672041 294 VSEVLPNSGSAKAgVKSGDVIVSLNGKPLNSFAELRSrIATTEPGTKVKLGLLREGKPVEVEVT 357
Cdd:cd06786    27 AETVLPEGPADGK-LEEGDVLISVNGELITQFIRLEE-ILDENVGKTVELVVQRGGEEITVTIT 88
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 389-446 2.83e-05

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: 43.08  E-value: 2.83e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 389 TKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKPT--VIALNVVRG 446
Cdd:cd10838    32 VDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRIVEQAGVgeELELTVLRG 91
cpPDZ2_EcRseP-like cd23083
circularly permuted PDZ domain 2 (PDZ-C) of Escherichia coli Regulator of sigma-E protease ...
 294-369 3.00e-05

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: 42.50  E-value: 3.00e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1927672041 294 VSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIaTTEPGTKVKLGLLREGKPVEVEVTLDKSTSSSASAE 369
Cdd:cd23083     3 LANVQPNSAAEKAGLQAGDRIVKVDGQPLTQWQTFVMAV-RDNPGKPLALEIERQGSPLSLTLIPDSKELNQGKAI 77
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 390-448 3.08e-05

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: 42.56  E-value: 3.08e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1927672041 390 KGVIIDNVDKGSPAAQAGLH---KD--------DIIIGLNRERVRSIAELRKVLESKPT--VIALNVVRGSE 448
Cdd:cd00990    23 SGVLVLDVPPGGPAAKAGLRgtkRDefgrivlgDVIVAVDGKPVKNESDLYRALDEYKVgdVVTLKVLRGGT 94
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 384-449 3.87e-05

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: 45.63  E-value: 3.87e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1927672041 384 QMKDGtkGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVR--SIAELRKVLESKP-TVIALNVVRGSES 449
Cdd:COG0793    67 GEEDG--KVVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAglTLDDAVKLLRGKAgTKVTLTIKRPGEG 133
PDZ_NHERF-like cd06768
PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related ...
 388-422 5.25e-05

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: 41.27  E-value: 5.25e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1927672041 388 GTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERV 422
Cdd:cd06768    21 GRPGHFIREVDPGSPAERAGLKDGDRLVEVNGENV 55
PRK10779 PRK10779
sigma E protease regulator RseP;
294-359 7.25e-05

sigma E protease regulator RseP;


Pssm-ID: 182723 [Multi-domain]  Cd Length: 449  Bit Score: 45.06  E-value: 7.25e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1927672041 294 VSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTePGTKVKLGLLREGKPVEVEVTLD 359
Cdd:PRK10779  225 LAEVQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRDN-PGKPLALEIERQGSPLSLTLTPD 289
cpPDZ_AtDEGP14-like cd23085
circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) ...
 387-448 2.56e-04

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: 40.14  E-value: 2.56e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1927672041 387 DGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKPTVIALNVVRGSE 448
Cdd:cd23085    28 DVKAGVLVPQVIPGSPAERAGLRPGDVIVEFDGKPVDSTKQIIDALGDKVGKPFKVVVKRAN 89
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 387-445 3.46e-04

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: 39.68  E-value: 3.46e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1927672041 387 DGTKGVIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAEL-RKVLESKP-TVIALNVVR 445
Cdd:cd06777    22 DQLQGALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVLELmDLVAEIRPgTVIPVVVLR 82
PDZ_PDZD11-like cd06752
PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic ...
 287-319 5.39e-04

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: 38.83  E-value: 5.39e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1927672041 287 DVQRGAFVSEVLPNSGSAKAGVKSGDVIVSLNG 319
Cdd:cd06752    22 ASGLGIFISKVIPDSDAHRLGLKEGDQILSVNG 54
cpPDZ2_MamE-like cd23086
circularly permuted PDZ domain 2 of Magnetospirillum magneticum magnetosome formation protease ...
 290-350 5.49e-04

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: 39.16  E-value: 5.49e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1927672041 290 RGAFVSEVLPNSGSAKAGVKSGDVIVSLNGKPLNSFAELRSRIATTEPGTKVKLGLLREGK 350
Cdd:cd23086    30 KGAQVAEVLAGSRAAVAGLQANDLILEVNNRPVTSPARLDAAIKGATAGQQILLKVHRNGQ 90
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 392-436 6.10e-04

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


Pssm-ID: 467638 [Multi-domain]  Cd Length: 83  Bit Score: 38.71  E-value: 6.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1927672041 392 VIIDNVDKGSPAAQAGLHKDDIIIGLNRERVRSIAELRKVLESKP 436
Cdd:cd23081     1 PVVGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRIVRENP 45
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 377-444 7.33e-04

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: 38.29  E-value: 7.33e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1927672041 377 GASLSDGqmKDGTKGVIIDNVDKGSPAAQAG-LHKDDIIIGLNRERVRSI--AELRKVLESKPTVIALNVV 444
Cdd:cd00136    13 GFSIRGG--KDGGGGIFVSRVEPGGPAARDGrLRVGDRILEVNGVSLEGLthEEAVELLKSAGGEVTLTVR 81
PLN00049 PLN00049
carboxyl-terminal processing protease; Provisional
 299-360 1.54e-03

carboxyl-terminal processing protease; Provisional


Pssm-ID: 177681 [Multi-domain]  Cd Length: 389  Bit Score: 40.49  E-value: 1.54e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1927672041 299 PNSGSAKAGVKSGDVIVSLNGKPLN--SFAELRSRIATTEpGTKVKLGLLREGKPVEVEVTLDK 360
Cdd:PLN00049  111 PGGPAARAGIRPGDVILAIDGTSTEglSLYEAADRLQGPE-GSSVELTLRRGPETRLVTLTREK 173
DUF3394 pfam11874
Domain of unknown function (DUF3394); This domain is functionally uncharacterized. This domain ...
 325-423 1.85e-03

Domain of unknown function (DUF3394); This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with pfam06808.


Pssm-ID: 432151  Cd Length: 179  Bit Score: 39.07  E-value: 1.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1927672041 325 FAELRSRIATTEPGTKVKLGLLR---EGKPVEVEVTLDKSTSSSASAELiapalQGASLSDgqMKDGTKgVIIDNVDKGS 401
Cdd:pfam11874  61 PSELVQVAEQAPAGSRLRLRVSGenlEGEEVTKTVLLPLGDGGDGAERL-----RAAGLTL--LDEGGK-VLVDNVEFGS 132

                          90       100
                  ....*....|....*....|..
gi 1927672041 402 PAAQAGLHKDDIIIGLNRERVR 423
Cdd:pfam11874 133 PAEKAGIDFDFEIVEVKVPADR 154
PDZ_RapGEF2_RapGEF6-like cd06755
PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange ...
 291-319 1.92e-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: 37.24  E-value: 1.92e-03
                          10        20
                  ....*....|....*....|....*....
gi 1927672041 291 GAFVSEVLPNSGSAKAGVKSGDVIVSLNG 319
Cdd:cd06755    27 GIFVSKVEKGSKAAEAGLKRGDQILEVNG 55
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 287-322 3.62e-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: 36.37  E-value: 3.62e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1927672041 287 DVQRGAFVSEVLPNSGSAKAG-VKSGDVIVSLNGKPL 322
Cdd:cd00136    21 DGGGGIFVSRVEPGGPAARDGrLRVGDRILEVNGVSL 57
PDZ_rhophilin-like cd06712
PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 294-321 6.86e-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: 6.86e-03
                          10        20
                  ....*....|....*....|....*...
gi 1927672041 294 VSEVLPNSGSAKAGVKSGDVIVSLNGKP 321
Cdd:cd06712    25 VASVDPGSCAAEAGLKEGDYIVSVGGVD 52
PDZ_PDLIM-like cd06753
PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 294-319 8.20e-03

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: 35.20  E-value: 8.20e-03
                          10        20
                  ....*....|....*....|....*.
gi 1927672041 294 VSEVLPNSGSAKAGVKSGDVIVSLNG 319
Cdd:cd06753    26 ISRVTPGGKAAQANLRPGDVILAING 51
GspC_delta NF041515
type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are ...
 299-357 8.64e-03

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: 37.93  E-value: 8.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1927672041 299 PNSGSAKAGVKSGDVIVSLNGKPLNS-------FAELRSriattepGTKVKLGLLREGKPVEVEVT 357
Cdd:NF041515  250 PGSLLGKLGLQNGDVLQSINGFDMTSpdkaleaYARLRS-------ADHLTVSVERRGKPVTLDYN 308
PDZ_SHANK1_3-like cd06746
PDZ domain of SH3 and multiple ankyrin repeat domains protein 1 (SHANK1), SHANK2, SHANK3, and ...
 394-424 8.76e-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: 8.76e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1927672041 394 IDNVDKGSPAAQAGLHKDDIIIGLNRERVRS 424
Cdd:cd06746    46 LESVDPGGVADKAGLKKGDFLLEINGEDVVK 76
PDZ2-PDZRN4-like cd06716
PDZ domain 2 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related ...
 290-328 9.35e-03

PDZ domain 2 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. 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 PDZRN4-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467200 [Multi-domain]  Cd Length: 88  Bit Score: 35.33  E-value: 9.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1927672041 290 RGAFVSEVLPNSGSAKAG-VKSGDVIVSLNGKPLNSFAEL 328
Cdd:cd06716    31 TGIYVSEVDPNSIAAKDGrIREGDQILQINGVDVQNREEA 70
 
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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