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Conserved domains on  [gi|42573533|ref|NP_974863|]
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Trypsin family protein with PDZ domain-containing protein [Arabidopsis thaliana]

Protein Classification

S1C family serine protease( domain architecture ID 11415729)

S1C family serine protease containing a C-terminal PDZ domain, similar to the Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins

CATH:  2.40.10.10|2.30.42.10
EC:  3.4.21.-
Gene Ontology:  GO:0006508|GO:0004252|GO:0005515
MEROPS:  S1C
PubMed:  12408815|30712672|11158544|11283303|9383148
SCOP:  4001790

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 153-434 4.00e-96

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: 289.74  E-value: 4.00e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 153 GNGSGVVWDGQGYIVTNYHVIGNAlsrnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDAPEtlLKPIKV 232
Cdd:COG0265   1 GLGSGVIISPDGYILTNNHVVEGA-----------DEITVTLADG--REYPAKVVGRDPLTDLAVLKIDAKD--LPAAPL 65

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 233 GQSNSLKVGQQCLAIGNPFGFDHTLTVGVISGLNRDIFSQTGVTIGGGIQTDAAINPGNSGGPLLDSKGNLIGINTAIFT 312
Cdd:COG0265  66 GDSDKLRVGDWVLAIGNPFGLGQTVTAGIVSALGRSIGSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIIS 145

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 313 Q--------------TVLKIVPQLIQFSKVLRA--GINI-ELAPDPV-ANQLNVRNGALVLQVPGKSLAEKAGLHPtsrg 374
Cdd:COG0265 146 RsggsqgigfaipinLAKRVVEQLIETGRVRRGwlGVTIqPVTPELAeALGLPEPEGVLVARVEPGSPAAKAGLRP---- 221

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 375 fagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKISLEEKSS 434
Cdd:COG0265 222 -------GDVILAVDGKPVTSARDLQRLLASLKPGDTVTLTVLRGGKELTVTVTLGERPE 274
 
Name Accession Description Interval E-value
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 153-434 4.00e-96

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: 289.74  E-value: 4.00e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 153 GNGSGVVWDGQGYIVTNYHVIGNAlsrnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDAPEtlLKPIKV 232
Cdd:COG0265   1 GLGSGVIISPDGYILTNNHVVEGA-----------DEITVTLADG--REYPAKVVGRDPLTDLAVLKIDAKD--LPAAPL 65

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 233 GQSNSLKVGQQCLAIGNPFGFDHTLTVGVISGLNRDIFSQTGVTIGGGIQTDAAINPGNSGGPLLDSKGNLIGINTAIFT 312
Cdd:COG0265  66 GDSDKLRVGDWVLAIGNPFGLGQTVTAGIVSALGRSIGSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIIS 145

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 313 Q--------------TVLKIVPQLIQFSKVLRA--GINI-ELAPDPV-ANQLNVRNGALVLQVPGKSLAEKAGLHPtsrg 374
Cdd:COG0265 146 RsggsqgigfaipinLAKRVVEQLIETGRVRRGwlGVTIqPVTPELAeALGLPEPEGVLVARVEPGSPAAKAGLRP---- 221

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 375 fagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKISLEEKSS 434
Cdd:COG0265 222 -------GDVILAVDGKPVTSARDLQRLLASLKPGDTVTLTVLRGGKELTVTVTLGERPE 274
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 119-431 3.23e-74

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: 238.66  E-value: 3.23e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   119 IVQLFEKNTYSVVNIFDVTLR---------------------PQLKMTGVVEIPEGNGSGVVWDGQGYIVTNYHVIGNAl 177
Cdd:TIGR02037   3 FAPLVEKVAPAVVNISVEGTVkrrnrppalppffrqffgddmPDFPRQQREQKVRGLGSGVIISADGYVLTNNHVVDGA- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   178 srnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDAPETLlKPIKVGQSNSLKVGQQCLAIGNPFGFDHTL 257
Cdd:TIGR02037  82 ----------DEITVTLSDG--REFKAKLVGKDPRTDIAVLKIDAKKNL-PVIKLGDSDKLRVGDWVLAIGNPFGLGQTV 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   258 TVGVISGLNRDIfsQTGVTIGGGIQTDAAINPGNSGGPLLDSKGNLIGINTAIFTQT--------------VLKIVPQLI 323
Cdd:TIGR02037 149 TSGIVSALGRSG--LGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSggnvgigfaipsnmAKNVVDQLI 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   324 QFSKVLRA--GINI-ELAPDPV-ANQLNVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAEL 399
Cdd:TIGR02037 227 EGGKVKRGwlGVTIqEVTSDLAkSLGLEKQRGALVAQVLPGSPAEKAGLKA-----------GDVITSVNGKPISSFADL 295

                         330       340       350
                  ....*....|....*....|....*....|..
gi 42573533   400 MKILDEYSVGDKVTLKIKRGNEDLELKISLEE 431
Cdd:TIGR02037 296 RRAIGTLKPGKKVTLGILRKGKEKTITVTLGA 327
HhoA_HhoB_HtrA NF041521
HhoA/HhoB/HtrA family serine endopeptidase; Members of this family include the paralogous ...
 153-427 8.70e-60

HhoA/HhoB/HtrA family serine endopeptidase; Members of this family include the paralogous serine proteases HhoA, HhoB, and HtrA of the model cyanobacterial isolate Synechocystis sp. PCC 6803. They resemble the paralogous trio of serine proteases DegQ, DegP, and DegS of Escherichia coli.


Pssm-ID: 469406 [Multi-domain]  Cd Length: 334  Bit Score: 198.08  E-value: 8.70e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  153 GNGSGVVWDGQGYIVTNYHVIGNAlsrnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDAPEtlLKPIKV 232
Cdd:NF041521  56 GTGSGFIISSDGIILTNAHVVDGA-----------DTVTVTLKDG--RTFEGKVLGTDPVTDVAVVKIEAKN--LPTVPL 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  233 GQSNSLKVGQQCLAIGNPFGFDHTLTVGVISGLNRDIfSQTGVTIG--GGIQTDAAINPGNSGGPLLDSKGNLIGINTAI 310
Cdd:NF041521 121 GNSDQLQPGEWAIAIGNPLGLDNTVTLGIISATGRSS-SQVGVPDKrvDFIQTDAAINPGNSGGPLLNARGEVIGINTAI 199

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  311 FT-----------QTVLKIVPQLIQFSKVLRAGINI-----------ELAPDPVAN-QLNVRNGALVLQVPGKSLAEKAG 367
Cdd:NF041521 200 RAgaqglgfaipiNTAQRIADQLIAGGKVEHPYLGIqmvtltpelkqEINSDPNSGfTVPEDEGVLIVRVVPNSPAARAG 279

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  368 LHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKI 427
Cdd:NF041521 280 LRA-----------GDVIQKINGQPVTTAEQVQQIVENSQVGQTLQLEVQRNGQTQTLTV 328
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 328-429 1.30e-45

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: 153.12  E-value: 1.30e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 328 VLRAGINIELAPDPVANQLNVRNGALVLQVPGKSLAEKAGLHPTSRGFAGNIVLGDIIVAVDDKPVKNKAELMKILDEYS 407
Cdd:cd00990   1 VVRPGLGISFAPDQVARQLGVRSGVLVLDVPPGGPAAKAGLRGTKRDEFGRIVLGDVIVAVDGKPVKNESDLYRALDEYK 80

                        90       100
                ....*....|....*....|..
gi 42573533 408 VGDKVTLKIKRGNEDLELKISL 429
Cdd:cd00990  81 VGDVVTLKVLRGGTKVDLKVTL 102
PRK10139 PRK10139
serine endoprotease DegQ;
152-434 1.05e-41

serine endoprotease DegQ;


Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 153.56  E-value: 1.05e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  152 EGNGSGVVWDG-QGYIVTNYHVIGNAlsrnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDAPETLLKpI 230
Cdd:PRK10139  89 EGLGSGVIIDAaKGYVLTNNHVINQA-----------QKISIQLNDG--REFDAKLIGSDDQSDIALLQIQNPSKLTQ-I 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  231 KVGQSNSLKVGQQCLAIGNPFGFDHTLTVGVISGLNRDIFSQTGVTigGGIQTDAAINPGNSGGPLLDSKGNLIGINTAI 310
Cdd:PRK10139 155 AIADSDKLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLNLEGLE--NFIQTDASINRGNSGGALLNLNGELIGINTAI 232

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  311 F--------------TQTVLKIVPQLIQFSKVLRAGINI---ELAPDPV-ANQLNVRNGALVLQVPGKSLAEKAGlhpts 372
Cdd:PRK10139 233 LapgggsvgigfaipSNMARTLAQQLIDFGEIKRGLLGIkgtEMSADIAkAFNLDVQRGAFVSEVLPNSGSAKAG----- 307

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 42573533  373 rgfagnIVLGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKISLEEKSS 434
Cdd:PRK10139 308 ------VKAGDIITSLNGKPLNSFAELRSRIATTEPGTKVKLGLLRNGKPLEVEVTLDTSTS 363
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 155-306 1.92e-33

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


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 122.53  E-value: 1.92e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   155 GSGVVWDGQGYIVTNYHVIGNAlsrnpsPGDVVGRVNILASDGVQknFEGKLVGADRAKDLAVLKVDAPETLLKPIKVGQ 234
Cdd:pfam13365   1 GTGFVVSSDGLVLTNAHVVDDA------EEAAVELVSVVLADGRE--YPATVVARDPDLDLALLRVSGDGRGLPPLPLGD 72

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42573533   235 SNSLKVGQQCLAIGNPFGFDH-TLTVGVISGLNRDIFSQTGvtiGGGIQTDAAINPGNSGGPLLDSKGNLIGI 306
Cdd:pfam13365  73 SEPLVGGERVYAVGYPLGGEKlSLSEGIVSGVDEGRDGGDD---GRVIQTDAALSPGSSGGPVFDADGRVVGI 142
MarP_fam_protase NF033740
MarP family serine protease; The founding member of this family of membrane-spanning serine ...
 155-306 2.89e-06

MarP family serine protease; The founding member of this family of membrane-spanning serine proteases, which is restricted to Actinobacteria, is the acid resistance periplasmic serine protease MarP of Mycobacterium tuberculosis. Recent work shows that MarP is required to cleave and activate the peptidoglycan hydrolase RipA, and loss of RipA activity creates a defect in progeny separation during cell division. Therefore, the requirement for MarP in order to survive acidic conditions may be a consequence of peptidoglycan hydrolysis requirements, explaining why MarP family members are distributed more broadly in the Actinobacteria than the subset of species capable of surviving intracellularly as pathogens.


Pssm-ID: 468161 [Multi-domain]  Cd Length: 390  Bit Score: 49.03  E-value: 2.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  155 GSGVVWDgQGYIVTNYHVIgnALSRNPSPGDVVGRVnilasdgvqknFEGKLVGADRAKDLAVLKVdaPETLLKPIKVGQ 234
Cdd:NF033740 213 GSGFVVA-PDRVMTNAHVV--AGTDEVTVETVGGGT-----------LDARVVYYDPDRDIAVLAV--PGLGLPPLPFAD 276

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  235 SNSlKVGQQCLAIGNPFGFDHTLT------VGVISGLnrDIFSQTGV-----TIGGGIQtdaainPGNSGGPLLDSKGNL 303
Cdd:NF033740 277 EPA-ETGDDAIVLGYPEGGPFTATparvreRIALSGP--DIYGSGTVtrevyTLRGTVR------PGNSGGPLLDPDGRV 347


                 ...
gi 42573533  304 IGI 306
Cdd:NF033740 348 LGV 350
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 342-420 1.14e-05

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: 43.52  E-value: 1.14e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 42573533    342 VANQLNVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGN 420
Cdd:smart00228  18 LVGGKDEGGGVVVSSVVPGSPAAKAGLRV-----------GDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
 
Name Accession Description Interval E-value
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 153-434 4.00e-96

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: 289.74  E-value: 4.00e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 153 GNGSGVVWDGQGYIVTNYHVIGNAlsrnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDAPEtlLKPIKV 232
Cdd:COG0265   1 GLGSGVIISPDGYILTNNHVVEGA-----------DEITVTLADG--REYPAKVVGRDPLTDLAVLKIDAKD--LPAAPL 65

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 233 GQSNSLKVGQQCLAIGNPFGFDHTLTVGVISGLNRDIFSQTGVTIGGGIQTDAAINPGNSGGPLLDSKGNLIGINTAIFT 312
Cdd:COG0265  66 GDSDKLRVGDWVLAIGNPFGLGQTVTAGIVSALGRSIGSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIIS 145

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 313 Q--------------TVLKIVPQLIQFSKVLRA--GINI-ELAPDPV-ANQLNVRNGALVLQVPGKSLAEKAGLHPtsrg 374
Cdd:COG0265 146 RsggsqgigfaipinLAKRVVEQLIETGRVRRGwlGVTIqPVTPELAeALGLPEPEGVLVARVEPGSPAAKAGLRP---- 221

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 375 fagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKISLEEKSS 434
Cdd:COG0265 222 -------GDVILAVDGKPVTSARDLQRLLASLKPGDTVTLTVLRGGKELTVTVTLGERPE 274
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 119-431 3.23e-74

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: 238.66  E-value: 3.23e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   119 IVQLFEKNTYSVVNIFDVTLR---------------------PQLKMTGVVEIPEGNGSGVVWDGQGYIVTNYHVIGNAl 177
Cdd:TIGR02037   3 FAPLVEKVAPAVVNISVEGTVkrrnrppalppffrqffgddmPDFPRQQREQKVRGLGSGVIISADGYVLTNNHVVDGA- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   178 srnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDAPETLlKPIKVGQSNSLKVGQQCLAIGNPFGFDHTL 257
Cdd:TIGR02037  82 ----------DEITVTLSDG--REFKAKLVGKDPRTDIAVLKIDAKKNL-PVIKLGDSDKLRVGDWVLAIGNPFGLGQTV 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   258 TVGVISGLNRDIfsQTGVTIGGGIQTDAAINPGNSGGPLLDSKGNLIGINTAIFTQT--------------VLKIVPQLI 323
Cdd:TIGR02037 149 TSGIVSALGRSG--LGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSggnvgigfaipsnmAKNVVDQLI 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   324 QFSKVLRA--GINI-ELAPDPV-ANQLNVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAEL 399
Cdd:TIGR02037 227 EGGKVKRGwlGVTIqEVTSDLAkSLGLEKQRGALVAQVLPGSPAEKAGLKA-----------GDVITSVNGKPISSFADL 295

                         330       340       350
                  ....*....|....*....|....*....|..
gi 42573533   400 MKILDEYSVGDKVTLKIKRGNEDLELKISLEE 431
Cdd:TIGR02037 296 RRAIGTLKPGKKVTLGILRKGKEKTITVTLGA 327
HhoA_HhoB_HtrA NF041521
HhoA/HhoB/HtrA family serine endopeptidase; Members of this family include the paralogous ...
 153-427 8.70e-60

HhoA/HhoB/HtrA family serine endopeptidase; Members of this family include the paralogous serine proteases HhoA, HhoB, and HtrA of the model cyanobacterial isolate Synechocystis sp. PCC 6803. They resemble the paralogous trio of serine proteases DegQ, DegP, and DegS of Escherichia coli.


Pssm-ID: 469406 [Multi-domain]  Cd Length: 334  Bit Score: 198.08  E-value: 8.70e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  153 GNGSGVVWDGQGYIVTNYHVIGNAlsrnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDAPEtlLKPIKV 232
Cdd:NF041521  56 GTGSGFIISSDGIILTNAHVVDGA-----------DTVTVTLKDG--RTFEGKVLGTDPVTDVAVVKIEAKN--LPTVPL 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  233 GQSNSLKVGQQCLAIGNPFGFDHTLTVGVISGLNRDIfSQTGVTIG--GGIQTDAAINPGNSGGPLLDSKGNLIGINTAI 310
Cdd:NF041521 121 GNSDQLQPGEWAIAIGNPLGLDNTVTLGIISATGRSS-SQVGVPDKrvDFIQTDAAINPGNSGGPLLNARGEVIGINTAI 199

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  311 FT-----------QTVLKIVPQLIQFSKVLRAGINI-----------ELAPDPVAN-QLNVRNGALVLQVPGKSLAEKAG 367
Cdd:NF041521 200 RAgaqglgfaipiNTAQRIADQLIAGGKVEHPYLGIqmvtltpelkqEINSDPNSGfTVPEDEGVLIVRVVPNSPAARAG 279

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  368 LHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKI 427
Cdd:NF041521 280 LRA-----------GDVIQKINGQPVTTAEQVQQIVENSQVGQTLQLEVQRNGQTQTLTV 328
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 328-429 1.30e-45

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: 153.12  E-value: 1.30e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 328 VLRAGINIELAPDPVANQLNVRNGALVLQVPGKSLAEKAGLHPTSRGFAGNIVLGDIIVAVDDKPVKNKAELMKILDEYS 407
Cdd:cd00990   1 VVRPGLGISFAPDQVARQLGVRSGVLVLDVPPGGPAAKAGLRGTKRDEFGRIVLGDVIVAVDGKPVKNESDLYRALDEYK 80

                        90       100
                ....*....|....*....|..
gi 42573533 408 VGDKVTLKIKRGNEDLELKISL 429
Cdd:cd00990  81 VGDVVTLKVLRGGTKVDLKVTL 102
PRK10139 PRK10139
serine endoprotease DegQ;
152-434 1.05e-41

serine endoprotease DegQ;


Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 153.56  E-value: 1.05e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  152 EGNGSGVVWDG-QGYIVTNYHVIGNAlsrnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDAPETLLKpI 230
Cdd:PRK10139  89 EGLGSGVIIDAaKGYVLTNNHVINQA-----------QKISIQLNDG--REFDAKLIGSDDQSDIALLQIQNPSKLTQ-I 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  231 KVGQSNSLKVGQQCLAIGNPFGFDHTLTVGVISGLNRDIFSQTGVTigGGIQTDAAINPGNSGGPLLDSKGNLIGINTAI 310
Cdd:PRK10139 155 AIADSDKLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLNLEGLE--NFIQTDASINRGNSGGALLNLNGELIGINTAI 232

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  311 F--------------TQTVLKIVPQLIQFSKVLRAGINI---ELAPDPV-ANQLNVRNGALVLQVPGKSLAEKAGlhpts 372
Cdd:PRK10139 233 LapgggsvgigfaipSNMARTLAQQLIDFGEIKRGLLGIkgtEMSADIAkAFNLDVQRGAFVSEVLPNSGSAKAG----- 307

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 42573533  373 rgfagnIVLGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKISLEEKSS 434
Cdd:PRK10139 308 ------VKAGDIITSLNGKPLNSFAELRSRIATTEPGTKVKLGLLRNGKPLEVEVTLDTSTS 363
PRK10942 PRK10942
serine endoprotease DegP;
155-433 3.49e-41

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 152.23  E-value: 3.49e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  155 GSGVVWD-GQGYIVTNYHVIGNAlsrnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDAPETLlKPIKVG 233
Cdd:PRK10942 113 GSGVIIDaDKGYVVTNNHVVDNA-----------TKIKVQLSDG--RKFDAKVVGKDPRSDIALIQLQNPKNL-TAIKMA 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  234 QSNSLKVGQQCLAIGNPFGFDHTLTVGVISGLNRdifsqTGVTIGGG---IQTDAAINPGNSGGPLLDSKGNLIGINTAI 310
Cdd:PRK10942 179 DSDALRVGDYTVAIGNPYGLGETVTSGIVSALGR-----SGLNVENYenfIQTDAAINRGNSGGALVNLNGELIGINTAI 253

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  311 F--------------TQTVLKIVPQLIQFSKVLRAGINI---ELAPDPV-ANQLNVRNGALVLQVPGKSLAEKAGlhpts 372
Cdd:PRK10942 254 LapdggnigigfaipSNMVKNLTSQMVEYGQVKRGELGImgtELNSELAkAMKVDAQRGAFVSQVLPNSSAAKAG----- 328

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42573533  373 rgfagnIVLGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKISLEEKS 433
Cdd:PRK10942 329 ------IKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSS 383
PRK10898 PRK10898
serine endoprotease DegS;
155-431 4.01e-41

serine endoprotease DegS;


Pssm-ID: 182820 [Multi-domain]  Cd Length: 353  Bit Score: 149.38  E-value: 4.01e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  155 GSGVVWDGQGYIVTNYHVIGNAlsrnpspgdvvGRVNILASDGvqKNFEGKLVGADRAKDLAVLKVDApeTLLKPIKVGQ 234
Cdd:PRK10898  80 GSGVIMDQRGYILTNKHVINDA-----------DQIIVALQDG--RVFEALLVGSDSLTDLAVLKINA--TNLPVIPINP 144

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  235 SNSLKVGQQCLAIGNPFGFDHTLTVGVISGLNRDIFSQTGVTigGGIQTDAAINPGNSGGPLLDSKGNLIGINT------ 308
Cdd:PRK10898 145 KRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLSPTGRQ--NFLQTDASINHGNSGGALVNSLGELMGINTlsfdks 222

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  309 -----------AIFTQTVLKIVPQLIQFSKVLRAGINI---ELAP--DPVANQLNVRnGALVLQVPGKSLAEKAGLHPts 372
Cdd:PRK10898 223 ndgetpegigfAIPTQLATKIMDKLIRDGRVIRGYIGIggrEIAPlhAQGGGIDQLQ-GIVVNEVSPDGPAAKAGIQV-- 299

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 42573533  373 rgfagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKISLEE 431
Cdd:PRK10898 300 ---------NDLIISVNNKPAISALETMDQVAEIRPGSVIPVVVMRDDKQLTLQVTIQE 349
protease_degS TIGR02038
periplasmic serine pepetdase DegS; This family consists of the periplasmic serine protease ...
 129-432 6.56e-41

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: 148.82  E-value: 6.56e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   129 SVVNIFDVTL----RPQLKMTGVveipegnGSGVVWDGQGYIVTNYHVIGNAlsrnpspgdvvGRVNILASDGvqKNFEG 204
Cdd:TIGR02038  57 AVVNIYNRSIsqnsLNQLSIQGL-------GSGVIMSKEGYILTNYHVIKKA-----------DQIVVALQDG--RKFEA 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   205 KLVGADRAKDLAVLKVDApeTLLKPIKVGQSNSLKVGQQCLAIGNPFGFDHTLTVGVISGLNRDIFSQTGVTigGGIQTD 284
Cdd:TIGR02038 117 ELVGSDPLTDLAVLKIEG--DNLPTIPVNLDRPPHVGDVVLAIGNPYNLGQTITQGIISATGRNGLSSVGRQ--NFIQTD 192

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   285 AAINPGNSGGPLLDSKGNLIGINTAIFTQT----------------VLKIVPQLIQFSKVLRAGINIELAP-DPVANQ-- 345
Cdd:TIGR02038 193 AAINAGNSGGALINTNGELVGINTASFQKGgdeggeginfaipiklAHKIMGKIIRDGRVIRGYIGVSGEDiNSVVAQgl 272

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   346 -LNVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLE 424
Cdd:TIGR02038 273 gLPDLRGIVITGVDPNGPAARAGILV-----------RDVILKYDGKDVIGAEELMDRIAETRPGSKVMVTVLRQGKQLE 341


                  ....*...
gi 42573533   425 LKISLEEK 432
Cdd:TIGR02038 342 LPVTIDEK 349
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 155-306 1.92e-33

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


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 122.53  E-value: 1.92e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   155 GSGVVWDGQGYIVTNYHVIGNAlsrnpsPGDVVGRVNILASDGVQknFEGKLVGADRAKDLAVLKVDAPETLLKPIKVGQ 234
Cdd:pfam13365   1 GTGFVVSSDGLVLTNAHVVDDA------EEAAVELVSVVLADGRE--YPATVVARDPDLDLALLRVSGDGRGLPPLPLGD 72

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42573533   235 SNSLKVGQQCLAIGNPFGFDH-TLTVGVISGLNRDIFSQTGvtiGGGIQTDAAINPGNSGGPLLDSKGNLIGI 306
Cdd:pfam13365  73 SEPLVGGERVYAVGYPLGGEKlSLSEGIVSGVDEGRDGGDD---GRVIQTDAALSPGSSGGPVFDADGRVVGI 142
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 330-427 5.45e-16

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: 72.71  E-value: 5.45e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 330 RAGINIELAPDPVANQLN--VRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEYS 407
Cdd:cd06779   3 YLGIEMENISPLLAKELGlpVNRGVLVAEVIPGSPAAKAGLKE-----------GDVILSVNGKPVTSFNDLRAALDTKK 71

                        90       100
                ....*....|....*....|
gi 42573533 408 VGDKVTLKIKRGNEDLELKI 427
Cdd:cd06779  72 PGDSLNLTILRDGKTLTVTV 91
Trypsin pfam00089
Trypsin;
162-311 2.56e-15

Trypsin;


Pssm-ID: 459667 [Multi-domain]  Cd Length: 219  Bit Score: 74.79  E-value: 2.56e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   162 GQGYIVTNYHVIGNAlsrnPSPGDVVGRVNILASDG------VQKNFEGKLVGADRA-KDLAVLKVDAPETLLKPIKVG- 233
Cdd:pfam00089  33 SENWVLTAAHCVSGA----SDVKVVLGAHNIVLREGgeqkfdVEKIIVHPNYNPDTLdNDIALLKLESPVTLGDTVRPIc 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   234 ---QSNSLKVGQQCLAIG----NPFGFDHTLTVGVISGLNRD-IFSQTGVTIGGG-IQTDA---AINPGNSGGPLLDSKG 301
Cdd:pfam00089 109 lpdASSDLPVGTTCTVSGwgntKTLGPSDTLQEVTVPVVSREtCRSAYGGTVTDTmICAGAggkDACQGDSGGPLVCSDG 188

                         170
                  ....*....|
gi 42573533   302 NLIGINTAIF 311
Cdd:pfam00089 189 ELIGIVSWGY 198
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 346-427 8.84e-13

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: 63.65  E-value: 8.84e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 346 LNVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLEL 425
Cdd:cd10839  21 LKEPKGALVAQVLPDSPAAKAGLKA-----------GDVILSLNGKPITSSADLRNRVATTKPGTKVELKILRDGKEKTL 89


                ..
gi 42573533 426 KI 427
Cdd:cd10839  90 TV 91
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 345-429 8.90e-12

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: 61.11  E-value: 8.90e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 345 QLNVRNGALVLQVPGKSLAEKAGLHptsrgfagnivLGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLE 424
Cdd:cd06781  25 PSNVNKGVYVAQVQSNSPAEKAGLK-----------KGDVITKLDGKKVESSSDLRQILYSHKVGDTVKVTIYRDGKEKT 93


                ....*
gi 42573533 425 LKISL 429
Cdd:cd06781  94 LNIKL 98
PDZ_2 pfam13180
PDZ domain;
347-429 2.97e-10

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 56.13  E-value: 2.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   347 NVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELK 426
Cdd:pfam13180   3 DLEGGVVVVSVKSSGPAAKAGLKA-----------GDVILSIDGRKINDLTDLESALYGHKPGDTVTLQVYRDGKLLTVE 71


                  ...
gi 42573533   427 ISL 429
Cdd:pfam13180  72 VKL 74
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 346-429 2.26e-09

circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB, and HtrA and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the cyanobacterial Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB and HtrA, and related domains. These three proteases are functionally overlapping, and are involved in a number of key physiological responses, ranging from protection against light and heat stresses to phototaxis. HhoA assembles into trimers, mediated by its protease domain and further into a hexamer by a novel interaction between the PDZ domains of opposing trimers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This HhoA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467629 [Multi-domain]  Cd Length: 104  Bit Score: 54.63  E-value: 2.26e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 346 LNVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGneDLEL 425
Cdd:cd10838  29 IPEVDGVLIMQVLPNSPAARAGLRR-----------GDVIQAVDGQPVTTADDVQRIVEQAGVGEELELTVLRG--DRRQ 95


                ....
gi 42573533 426 KISL 429
Cdd:cd10838  96 TLAV 99
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
330-431 1.90e-08

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


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 56.37  E-value: 1.90e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 330 RAGINIELAPDPVANQ-----LNVRNGALVLQ--VPGkSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVkNKAELMKI 402
Cdd:COG3975 468 PFGLKLVYEDAPSLKPslglrVSADGGGLVVTsvLWG-SPAYKAGLSA-----------GDELLAIDGLRV-TADNLDDA 534

                        90       100
                ....*....|....*....|....*....
gi 42573533 403 LDEYSVGDKVTLKIKRGNEDLELKISLEE 431
Cdd:COG3975 535 LAAYKPGDPIELLVFRRDELRTVTVTLAA 563
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 352-432 2.16e-08

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 55.48  E-value: 2.16e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 352 ALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEYSvGDKVTLKIKRGNEDLELKISLEE 431
Cdd:COG0750 130 PVVGEVVPGSPAAKAGLQP-----------GDRIVAINGQPVTSWDDLVDIIRASP-GKPLTLTVERDGEELTLTVTPRL 197


                .
gi 42573533 432 K 432
Cdd:COG0750 198 V 198
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 347-431 7.16e-08

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: 50.19  E-value: 7.16e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 347 NVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILdeySVGDKVTLKIKRGNEDLELK 426
Cdd:cd06785  28 DVSSGVYVHKVIPGSPAQRAGLKD-----------GDVIISINGKPVKSSSDVYEAV---KSGSSLLVVVRRGNEDLLLT 93


                ....*
gi 42573533 427 ISLEE 431
Cdd:cd06785  94 VTPEE 98
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 330-429 4.43e-07

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: 47.77  E-value: 4.43e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 330 RAGINIELAPDPVANQLNVR----NGALVLQVPGKSLAEKAGLHptsrgfagnivLGDIIVAVDDKPVKNKAELMKILDE 405
Cdd:cd06777   1 RGYLGITLSEIPPAMARGGGidqlQGALVKGVSPDSPAAKAGIQ-----------VGDIILQFDNKPVISVLELMDLVAE 69

                        90       100
                ....*....|....*....|....
gi 42573533 406 YSVGDKVTLKIKRGNEDLELKISL 429
Cdd:cd06777  70 IRPGTVIPVVVLRDGKQLTLEVTI 93
cpPDZ_AtDEGP14-like cd23085
circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) ...
 347-431 8.98e-07

circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Arabidopsis thaliana putative protease DEGP14 and related domains. DEGP14 is a putative protease belonging to the HtrA family of housekeeping proteases. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This AtDEGP14-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467632 [Multi-domain]  Cd Length: 101  Bit Score: 47.07  E-value: 8.98e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 347 NVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDeYSVGDKVTLKIKRGNEDLE-L 425
Cdd:cd23085  28 DVKAGVLVPQVIPGSPAERAGLRP-----------GDVIVEFDGKPVDSTKQIIDALG-DKVGKPFKVVVKRANKVQVtL 95


                ....*.
gi 42573533 426 KISLEE 431
Cdd:cd23085  96 TVTPEE 101
cpPDZ_BsYlbL-like cd23080
circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ ...
 375-429 1.76e-06

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: 45.56  E-value: 1.76e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 42573533 375 FAGNIVLGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKISL 429
Cdd:cd23080  13 AKGILEAGDKITAIDGQNFQSSEKLIDYISSKKAGDKVKVKYERDEKEKEAELKL 67
MarP_fam_protase NF033740
MarP family serine protease; The founding member of this family of membrane-spanning serine ...
 155-306 2.89e-06

MarP family serine protease; The founding member of this family of membrane-spanning serine proteases, which is restricted to Actinobacteria, is the acid resistance periplasmic serine protease MarP of Mycobacterium tuberculosis. Recent work shows that MarP is required to cleave and activate the peptidoglycan hydrolase RipA, and loss of RipA activity creates a defect in progeny separation during cell division. Therefore, the requirement for MarP in order to survive acidic conditions may be a consequence of peptidoglycan hydrolysis requirements, explaining why MarP family members are distributed more broadly in the Actinobacteria than the subset of species capable of surviving intracellularly as pathogens.


Pssm-ID: 468161 [Multi-domain]  Cd Length: 390  Bit Score: 49.03  E-value: 2.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  155 GSGVVWDgQGYIVTNYHVIgnALSRNPSPGDVVGRVnilasdgvqknFEGKLVGADRAKDLAVLKVdaPETLLKPIKVGQ 234
Cdd:NF033740 213 GSGFVVA-PDRVMTNAHVV--AGTDEVTVETVGGGT-----------LDARVVYYDPDRDIAVLAV--PGLGLPPLPFAD 276

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533  235 SNSlKVGQQCLAIGNPFGFDHTLT------VGVISGLnrDIFSQTGV-----TIGGGIQtdaainPGNSGGPLLDSKGNL 303
Cdd:NF033740 277 EPA-ETGDDAIVLGYPEGGPFTATparvreRIALSGP--DIYGSGTVtrevyTLRGTVR------PGNSGGPLLDPDGRV 347


                 ...
gi 42573533  304 IGI 306
Cdd:NF033740 348 LGV 350
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 345-429 3.36e-06

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


Pssm-ID: 440556 [Multi-domain]  Cd Length: 341  Bit Score: 48.71  E-value: 3.36e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 345 QLNVRNGALVLQ--VPGkSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNkaelMKILDEYS-----VGDKVTLKIK 417
Cdd:COG0793  65 ELGEEDGKVVVVsvIPG-SPAEKAGIKP-----------GDIILAIDGKSVAG----LTLDDAVKllrgkAGTKVTLTIK 128

                        90
                ....*....|..
gi 42573533 418 RGNEDLELKISL 429
Cdd:COG0793 129 RPGEGEPITVTL 140
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 363-430 4.65e-06

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: 44.78  E-value: 4.65e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42573533 363 AEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNK-----AELMKildeYSVGDKVTLKIKRGNEDLELKISLE 430
Cdd:cd06782  27 AEKAGIKP-----------GDVIVAVDGESVRGMsldevVKLLR----GPKGTKVKLTIRRGGEGEPRDVTLT 84
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 336-430 1.11e-05

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


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 46.13  E-value: 1.11e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 336 ELAPDP--VANQLNV----RNGALV-LQV-PGK--SLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDE 405
Cdd:COG3031 127 ELLANPneLLDYIRLspvrEDGKLVgYRVnPGRpgSLFSKLGLQP-----------GDVITSINGQDLTDPAQALELLQQ 195

                        90       100
                ....*....|....*....|....*
gi 42573533 406 YSVGDKVTLKIKRGNEDLELKISLE 430
Cdd:COG3031 196 LRDASEVTLTVERNGQPVTLTYNLR 220
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 342-420 1.14e-05

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: 43.52  E-value: 1.14e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 42573533    342 VANQLNVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGN 420
Cdd:smart00228  18 LVGGKDEGGGVVVSSVVPGSPAAKAGLRV-----------GDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 349-421 1.41e-05

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: 43.00  E-value: 1.41e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42573533 349 RNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDeySVGDKVTLKIKRGNE 421
Cdd:cd23084  17 GKGVVVTEVDPGSPAAQSGLKK-----------GDVIIGVNRQPVKSIAELRKVLK--SKPSAVLLQIKRGDS 76
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 361-418 1.13e-04

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 39.82  E-value: 1.13e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 42573533   361 SLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEySVGDKVTLKIKR 418
Cdd:pfam17820   9 SPAERAGLRV-----------GDVILAVNGKPVRSLEDVARLLQG-SAGESVTLTVRR 54
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 361-432 1.26e-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: 40.25  E-value: 1.26e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 42573533 361 SLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEySVGDKVTLKIKRGNEDLELKISLEEK 432
Cdd:cd23081  10 SPAAEAGLKP-----------GDRILKIDGQKVRTWEDIVRIVRE-NPGKPLTLKIERDGKILTVTVTPELV 69
cpPDZ1_ScNma111-like cd06786
circularly permuted first PDZ domain (PDZ1) of Saccharomyces cerevisiae pro-apoptotic serine ...
 382-427 2.46e-04

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: 39.87  E-value: 2.46e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 42573533 382 GDIIVAVDDKPVKNKAELMKILDEySVGDKVTLKIKRGNEDLELKI 427
Cdd:cd06786  43 GDVLISVNGELITQFIRLEEILDE-NVGKTVELVVQRGGEEITVTI 87
eMpr COG3591
V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, ...
 146-309 3.00e-04

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


Pssm-ID: 442810 [Multi-domain]  Cd Length: 194  Bit Score: 41.59  E-value: 3.00e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 146 GVVEIPEGNGSG---VVwdGQGYIVTNYHVIgnalsrnPSPGDVVGRVNILASDGVQKNFEGKLVGA------------D 210
Cdd:COG3591   3 GRLETDGGGGVCtgtLI--GPNLVLTAGHCV-------YDGAGGGWATNIVFVPGYNGGPYGTATATrfrvppgwvasgD 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 211 RAKDLAVLKVDAP-ETLLKPIKVGQSNSLKVGQQCLAIGNPFGFDHTLTVGVisglNRDIFSQTGVTIGGGIQTDaainP 289
Cdd:COG3591  74 AGYDYALLRLDEPlGDTTGWLGLAFNDAPLAGEPVTIIGYPGDRPKDLSLDC----SGRVTGVQGNRLSYDCDTT----G 145

                       170       180
                ....*....|....*....|...
gi 42573533 290 GNSGGPLLDSKGN---LIGINTA 309
Cdd:COG3591 146 GSSGSPVLDDSDGggrVVGVHSA 168
Peptidase_M50 pfam02163
Peptidase family M50;
353-427 6.64e-04

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 41.32  E-value: 6.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 42573533   353 LVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMKILDEySVGDKVTLKIKRGNEDLELKI 427
Cdd:pfam02163  96 VIGGVAPGSPAAKAGLKP-----------GDVILSINGKKITSWQDLVEALAK-SPGKPITLTVERGGQTLTVTI 158
cpPDZ_RseP_YlbL-like cd10824
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), ...
 382-432 3.65e-03

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), Bacillus subtilis YlbL protease, and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), Bacillus subtilis YlbL, and related domains, including archaeal and chloroplast PDZ domains. RseP participates in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP-YlbL family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.


Pssm-ID: 467636 [Multi-domain]  Cd Length: 82  Bit Score: 36.40  E-value: 3.65e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 42573533 382 GDIIVAVDDKPVKNKAELMKILDEYSVGDKVTLKIKRGNEDLELKISLEEK 432
Cdd:cd10824  19 GDLITEIDGQPTKSWQTFIDYIHDKKVGESVKITYKHGNKNEEASLKLTAI 69
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 322-417 5.75e-03

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 35.72  E-value: 5.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533   322 LIQFSKVLRAGINIELapdpVANQLNVRNGALVLQVPGKSLAEKAGLHPtsrgfagnivlGDIIVAVDDKPVKNKAELMK 401
Cdd:pfam00595   1 QVTLEKDGRGGLGFSL----KGGSDQGDPGIFVSEVLPGGAAEAGGLKV-----------GDRILSINGQDVENMTHEEA 65

                          90
                  ....*....|....*.
gi 42573533   402 ILDEYSVGDKVTLKIK 417
Cdd:pfam00595  66 VLALKGSGGKVTLTIL 81
alphaLP-like cd21112
alpha-lytic protease (alpha-LP), a bacterial serine protease of the chymotrypsin family, and ...
 161-309 6.98e-03

alpha-lytic protease (alpha-LP), a bacterial serine protease of the chymotrypsin family, and similar proteins; This family represents the catalytic domain of alpha-lytic protease (alpha-LP) and its closely-related homologs. Alpha-lytic protease (EC 3.4.21.12; also called alpha-lytic endopeptidase), originally isolated from the myxobacterium Lysobacter enzymogenes, belongs to the MEROPS peptidase family S1, subfamily S1E (streptogrisin A subfamily). It is synthesized as a pro-enzyme, thus having two domains; the N-terminal pro-domain acts as a foldase, required transiently for the correct folding of the protease domain, and also acts as a potent inhibitor of the mature enzyme, while the C-terminal domain catalyzes the cleavage of peptide bonds. Members of the alpha-lytic protease subfamily include Nocardiopsis alba protease (NAPase), a secreted chymotrypsin from the alkaliphile Cellulomonas bogoriensis, streptogrisins (SPG-A, SPG-B, SPG-C, and SPG-D), and Thermobifida fusca protease A (TFPA). These serine proteases have characteristic kinetic stability, exhibited by their extremely slow unfolding kinetics. The active site, characteristic of serine proteases, contains the catalytic triad consisting of serine acting as a nucleophile, aspartate as an electrophile, and histidine as a base, all required for activity. This model represents the C-terminal catalytic domain of alpha-lytic proteases.


Pssm-ID: 411050  Cd Length: 188  Bit Score: 37.67  E-value: 6.98e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 161 DGQGYIVTNYH--VIGNALSRNPSPGDVVGRVnilasdgVQKNFEGKlvgadrakDLAVLKVDAPETLLKP--------- 229
Cdd:cd21112  25 SGTPYFLTAGHcgNGGGTVYADGALGVPIGTV-------VASSFPGN--------DYALVRVTNPGWTPPPevrtygggt 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42573533 230 IKVGQSNSLKVGQQ-CLAiGNPFGFdhtlTVGVISGLNRDIFSQTGvTIGGGIQTDAAINPGNSGGPLLdSKGNLIGINT 308
Cdd:cd21112  90 VPITGSAEPVVGAPvCKS-GRTTGW----TCGTVTAVNVTVNYPGG-TVTGLTRTNACAEPGDSGGPVF-SGTQALGITS 162


                .
gi 42573533 309 A 309
Cdd:cd21112 163 G 163
 
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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