NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1002259351|ref|XP_015634005|]
View 

protease Do-like 8, chloroplastic isoform X1 [Oryza sativa Japonica Group]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 150-443 4.44e-108

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: 320.56  E-value: 4.44e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 150 GNGSGVVWDDSGHIVTNYHVVGNAlskkpkpgevvARVNILAADGiqKNFEGKLVGADRSKDLAVLKVDAPTdlLKPINV 229
Cdd:COG0265     1 GLGSGVIISPDGYILTNNHVVEGA-----------DEITVTLADG--REYPAKVVGRDPLTDLAVLKIDAKD--LPAAPL 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 230 GQSSALRVGQQCLAIGNPFGFDHALTVGVISGLNRDIFSQAGVTIGGGIQTDAAINPGNSGGPLLDSKGHMIGINTAIFT 309
Cdd:COG0265    66 GDSDKLRVGDWVLAIGNPFGLGQTVTAGIVSALGRSIGSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIIS 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 310 QTGTSAGVGFAIPSSTVLKIAPQLIQFGKVRRAGLNVEFAP--DPIA--YQLNVRTGSLILQVPGGSAAAKAGLVPtsrg 385
Cdd:COG0265   146 RSGGSQGIGFAIPINLAKRVVEQLIETGRVRRGWLGVTIQPvtPELAeaLGLPEPEGVLVARVEPGSPAAKAGLRP---- 221

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002259351 386 fagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPLEEA 443
Cdd:COG0265   222 -------GDVILAVDGKPVTSARDLQRLLASLKPGDTVTLTVLRGGKELTVTVTLGER 272
 
Name Accession Description Interval E-value
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 150-443 4.44e-108

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: 320.56  E-value: 4.44e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 150 GNGSGVVWDDSGHIVTNYHVVGNAlskkpkpgevvARVNILAADGiqKNFEGKLVGADRSKDLAVLKVDAPTdlLKPINV 229
Cdd:COG0265     1 GLGSGVIISPDGYILTNNHVVEGA-----------DEITVTLADG--REYPAKVVGRDPLTDLAVLKIDAKD--LPAAPL 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 230 GQSSALRVGQQCLAIGNPFGFDHALTVGVISGLNRDIFSQAGVTIGGGIQTDAAINPGNSGGPLLDSKGHMIGINTAIFT 309
Cdd:COG0265    66 GDSDKLRVGDWVLAIGNPFGLGQTVTAGIVSALGRSIGSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIIS 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 310 QTGTSAGVGFAIPSSTVLKIAPQLIQFGKVRRAGLNVEFAP--DPIA--YQLNVRTGSLILQVPGGSAAAKAGLVPtsrg 385
Cdd:COG0265   146 RSGGSQGIGFAIPINLAKRVVEQLIETGRVRRGWLGVTIQPvtPELAeaLGLPEPEGVLVARVEPGSPAAKAGLRP---- 221

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002259351 386 fagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPLEEA 443
Cdd:COG0265   222 -------GDVILAVDGKPVTSARDLQRLLASLKPGDTVTLTVLRGGKELTVTVTLGER 272
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 149-444 3.40e-86

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: 269.86  E-value: 3.40e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 149 EGNGSGVVWDDSGHIVTNYHVVGNAlskkpkpgevvARVNILAADGIQknFEGKLVGADRSKDLAVLKVDAPTDLlKPIN 228
Cdd:TIGR02037  57 RGLGSGVIISADGYVLTNNHVVDGA-----------DEITVTLSDGRE--FKAKLVGKDPRTDIAVLKIDAKKNL-PVIK 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 229 VGQSSALRVGQQCLAIGNPFGFDHALTVGVISGLNRDIFSQAgvTIGGGIQTDAAINPGNSGGPLLDSKGHMIGINTAIF 308
Cdd:TIGR02037 123 LGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSALGRSGLGIG--DYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAIL 200

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 309 TQTGTSAGVGFAIPSSTVLKIAPQLIQFGKVRRAGLNVEFapDPI------AYQLNVRTGSLILQVPGGSAAAKAGLVPt 382
Cdd:TIGR02037 201 SPSGGNVGIGFAIPSNMAKNVVDQLIEGGKVKRGWLGVTI--QEVtsdlakSLGLEKQRGALVAQVLPGSPAEKAGLKA- 277

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002259351 383 srgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPLEEAS 444
Cdd:TIGR02037 278 ----------GDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKGKEKTITVTLGASP 329
HhoA_HhoB_HtrA NF041521
HhoA/HhoB/HtrA family serine endopeptidase; Members of this family include the paralogous ...
 150-437 4.51e-69

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: 222.35  E-value: 4.51e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 150 GNGSGVVWDDSGHIVTNYHVVGNAlskkpkpgevvARVNILAADGiqKNFEGKLVGADRSKDLAVLKVDAPTdlLKPINV 229
Cdd:NF041521   56 GTGSGFIISSDGIILTNAHVVDGA-----------DTVTVTLKDG--RTFEGKVLGTDPVTDVAVVKIEAKN--LPTVPL 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 230 GQSSALRVGQQCLAIGNPFGFDHALTVGVISGLNRDIfSQAGVTIG--GGIQTDAAINPGNSGGPLLDSKGHMIGINTAI 307
Cdd:NF041521  121 GNSDQLQPGEWAIAIGNPLGLDNTVTLGIISATGRSS-SQVGVPDKrvDFIQTDAAINPGNSGGPLLNARGEVIGINTAI 199

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 308 FtqtGTSAGVGFAIPSSTVLKIAPQLIQFGKVRRAGLNVEFA---PDpIAYQLN----------VRTGSLILQVPGGSAA 374
Cdd:NF041521  200 R---AGAQGLGFAIPINTAQRIADQLIAGGKVEHPYLGIQMVtltPE-LKQEINsdpnsgftvpEDEGVLIVRVVPNSPA 275

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002259351 375 AKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVT 437
Cdd:NF041521  276 ARAGLRA-----------GDVIQKINGQPVTTAEQVQQIVENSQVGQTLQLEVQRNGQTQTLT 327
PRK10942 PRK10942
serine endoprotease DegP;
152-444 1.99e-52

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 183.04  E-value: 1.99e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 152 GSGVVWD-DSGHIVTNYHVVGNAlskkpkpgevvARVNILAADGiqKNFEGKLVGADRSKDLAVLKVDAPTDLlKPINVG 230
Cdd:PRK10942  113 GSGVIIDaDKGYVVTNNHVVDNA-----------TKIKVQLSDG--RKFDAKVVGKDPRSDIALIQLQNPKNL-TAIKMA 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 231 QSSALRVGQQCLAIGNPFGFDHALTVGVISGLNRdifsqAGVTIGGG---IQTDAAINPGNSGGPLLDSKGHMIGINTAI 307
Cdd:PRK10942  179 DSDALRVGDYTVAIGNPYGLGETVTSGIVSALGR-----SGLNVENYenfIQTDAAINRGNSGGALVNLNGELIGINTAI 253

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 308 FTQTGTSAGVGFAIPSSTVLKIAPQLIQFGKVRRA-------GLNVEFAPdpiAYQLNVRTGSLILQVPGGSAAAKAGlv 380
Cdd:PRK10942  254 LAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGelgimgtELNSELAK---AMKVDAQRGAFVSQVLPNSSAAKAG-- 328

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002259351 381 ptsrgfagnIVLGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPLEEAS 444
Cdd:PRK10942  329 ---------IKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSS 383
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 339-440 6.19e-46

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: 154.27  E-value: 6.19e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 339 VRRAGLNVEFAPDPIAYQLNVRTGSLILQVPGGSAAAKAGLVPTSRGFAGNIVLGDVIVAVDGKPIKGKSDLSRVLDDYG 418
Cdd:cd00990     1 VVRPGLGISFAPDQVARQLGVRSGVLVLDVPPGGPAAKAGLRGTKRDEFGRIVLGDVIVAVDGKPVKNESDLYRALDEYK 80

                          90       100
                  ....*....|....*....|..
gi 1002259351 419 VGDKVSLTIQRGAETLEVTLPL 440
Cdd:cd00990    81 VGDVVTLKVLRGGTKVDLKVTL 102
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 152-303 3.15e-31

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


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 116.75  E-value: 3.15e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 152 GSGVVWDDSGHIVTNYHVVGNAlskkpkPGEVVARVNILAADGIQknFEGKLVGADRSKDLAVLKVDAPTDLLKPINVGQ 231
Cdd:pfam13365   1 GTGFVVSSDGLVLTNAHVVDDA------EEAAVELVSVVLADGRE--YPATVVARDPDLDLALLRVSGDGRGLPPLPLGD 72

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002259351 232 SSALRVGQQCLAIGNPFGFDH-ALTVGVISGLNRdifSQAGVTIGGGIQTDAAINPGNSGGPLLDSKGHMIGI 303
Cdd:pfam13365  73 SEPLVGGERVYAVGYPLGGEKlSLSEGIVSGVDE---GRDGGDDGRVIQTDAALSPGSSGGPVFDADGRVVGI 142
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 353-430 1.00e-07

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: 49.30  E-value: 1.00e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002259351  353 IAYQLNVRTGSLILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRG 430
Cdd:smart00228  18 LVGGKDEGGGVVVSSVVPGSPAAKAGLRV-----------GDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRG 84
MarP_fam_protase NF033740
MarP family serine protease; The founding member of this family of membrane-spanning serine ...
 152-330 2.39e-07

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: 52.50  E-value: 2.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 152 GSGVVWDDsGHIVTNYHVVGNalskkpkpgevVARVNILAADGIQknFEGKLVGADRSKDLAVLKVdaPTDLLKPINVGQ 231
Cdd:NF033740  213 GSGFVVAP-DRVMTNAHVVAG-----------TDEVTVETVGGGT--LDARVVYYDPDRDIAVLAV--PGLGLPPLPFAD 276

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 232 SSALRvGQQCLAIGNPFG--FDHA----LTVGVISGLN--------RDIFSQAGVtigggiqtdaaINPGNSGGPLLDSK 297
Cdd:NF033740  277 EPAET-GDDAIVLGYPEGgpFTATparvRERIALSGPDiygsgtvtREVYTLRGT-----------VRPGNSGGPLLDPD 344

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1002259351 298 GHMIGIntaIFTQTGTSAGVGFAIPSSTVLKIA 330
Cdd:NF033740  345 GRVLGV---VFAAAVDDSDTGYALTADEVRPDL 374
 
Name Accession Description Interval E-value
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 150-443 4.44e-108

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: 320.56  E-value: 4.44e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 150 GNGSGVVWDDSGHIVTNYHVVGNAlskkpkpgevvARVNILAADGiqKNFEGKLVGADRSKDLAVLKVDAPTdlLKPINV 229
Cdd:COG0265     1 GLGSGVIISPDGYILTNNHVVEGA-----------DEITVTLADG--REYPAKVVGRDPLTDLAVLKIDAKD--LPAAPL 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 230 GQSSALRVGQQCLAIGNPFGFDHALTVGVISGLNRDIFSQAGVTIGGGIQTDAAINPGNSGGPLLDSKGHMIGINTAIFT 309
Cdd:COG0265    66 GDSDKLRVGDWVLAIGNPFGLGQTVTAGIVSALGRSIGSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIIS 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 310 QTGTSAGVGFAIPSSTVLKIAPQLIQFGKVRRAGLNVEFAP--DPIA--YQLNVRTGSLILQVPGGSAAAKAGLVPtsrg 385
Cdd:COG0265   146 RSGGSQGIGFAIPINLAKRVVEQLIETGRVRRGWLGVTIQPvtPELAeaLGLPEPEGVLVARVEPGSPAAKAGLRP---- 221

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002259351 386 fagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPLEEA 443
Cdd:COG0265   222 -------GDVILAVDGKPVTSARDLQRLLASLKPGDTVTLTVLRGGKELTVTVTLGER 272
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 149-444 3.40e-86

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: 269.86  E-value: 3.40e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 149 EGNGSGVVWDDSGHIVTNYHVVGNAlskkpkpgevvARVNILAADGIQknFEGKLVGADRSKDLAVLKVDAPTDLlKPIN 228
Cdd:TIGR02037  57 RGLGSGVIISADGYVLTNNHVVDGA-----------DEITVTLSDGRE--FKAKLVGKDPRTDIAVLKIDAKKNL-PVIK 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 229 VGQSSALRVGQQCLAIGNPFGFDHALTVGVISGLNRDIFSQAgvTIGGGIQTDAAINPGNSGGPLLDSKGHMIGINTAIF 308
Cdd:TIGR02037 123 LGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSALGRSGLGIG--DYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAIL 200

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 309 TQTGTSAGVGFAIPSSTVLKIAPQLIQFGKVRRAGLNVEFapDPI------AYQLNVRTGSLILQVPGGSAAAKAGLVPt 382
Cdd:TIGR02037 201 SPSGGNVGIGFAIPSNMAKNVVDQLIEGGKVKRGWLGVTI--QEVtsdlakSLGLEKQRGALVAQVLPGSPAEKAGLKA- 277

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002259351 383 srgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPLEEAS 444
Cdd:TIGR02037 278 ----------GDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKGKEKTITVTLGASP 329
HhoA_HhoB_HtrA NF041521
HhoA/HhoB/HtrA family serine endopeptidase; Members of this family include the paralogous ...
 150-437 4.51e-69

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: 222.35  E-value: 4.51e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 150 GNGSGVVWDDSGHIVTNYHVVGNAlskkpkpgevvARVNILAADGiqKNFEGKLVGADRSKDLAVLKVDAPTdlLKPINV 229
Cdd:NF041521   56 GTGSGFIISSDGIILTNAHVVDGA-----------DTVTVTLKDG--RTFEGKVLGTDPVTDVAVVKIEAKN--LPTVPL 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 230 GQSSALRVGQQCLAIGNPFGFDHALTVGVISGLNRDIfSQAGVTIG--GGIQTDAAINPGNSGGPLLDSKGHMIGINTAI 307
Cdd:NF041521  121 GNSDQLQPGEWAIAIGNPLGLDNTVTLGIISATGRSS-SQVGVPDKrvDFIQTDAAINPGNSGGPLLNARGEVIGINTAI 199

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 308 FtqtGTSAGVGFAIPSSTVLKIAPQLIQFGKVRRAGLNVEFA---PDpIAYQLN----------VRTGSLILQVPGGSAA 374
Cdd:NF041521  200 R---AGAQGLGFAIPINTAQRIADQLIAGGKVEHPYLGIQMVtltPE-LKQEINsdpnsgftvpEDEGVLIVRVVPNSPA 275

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002259351 375 AKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVT 437
Cdd:NF041521  276 ARAGLRA-----------GDVIQKINGQPVTTAEQVQQIVENSQVGQTLQLEVQRNGQTQTLT 327
PRK10942 PRK10942
serine endoprotease DegP;
152-444 1.99e-52

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 183.04  E-value: 1.99e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 152 GSGVVWD-DSGHIVTNYHVVGNAlskkpkpgevvARVNILAADGiqKNFEGKLVGADRSKDLAVLKVDAPTDLlKPINVG 230
Cdd:PRK10942  113 GSGVIIDaDKGYVVTNNHVVDNA-----------TKIKVQLSDG--RKFDAKVVGKDPRSDIALIQLQNPKNL-TAIKMA 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 231 QSSALRVGQQCLAIGNPFGFDHALTVGVISGLNRdifsqAGVTIGGG---IQTDAAINPGNSGGPLLDSKGHMIGINTAI 307
Cdd:PRK10942  179 DSDALRVGDYTVAIGNPYGLGETVTSGIVSALGR-----SGLNVENYenfIQTDAAINRGNSGGALVNLNGELIGINTAI 253

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 308 FTQTGTSAGVGFAIPSSTVLKIAPQLIQFGKVRRA-------GLNVEFAPdpiAYQLNVRTGSLILQVPGGSAAAKAGlv 380
Cdd:PRK10942  254 LAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGelgimgtELNSELAK---AMKVDAQRGAFVSQVLPNSSAAKAG-- 328

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002259351 381 ptsrgfagnIVLGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPLEEAS 444
Cdd:PRK10942  329 ---------IKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNVELQQSS 383
PRK10139 PRK10139
serine endoprotease DegQ;
149-444 7.00e-52

serine endoprotease DegQ;


Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 180.91  E-value: 7.00e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 149 EGNGSGVVWDDS-GHIVTNYHVVGNAlskkpkpgevvARVNILAADGiqKNFEGKLVGADRSKDLAVLKVDAPTDLLKpI 227
Cdd:PRK10139   89 EGLGSGVIIDAAkGYVLTNNHVINQA-----------QKISIQLNDG--REFDAKLIGSDDQSDIALLQIQNPSKLTQ-I 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 228 NVGQSSALRVGQQCLAIGNPFGFDHALTVGVISGLNRDIFSQAGVTigGGIQTDAAINPGNSGGPLLDSKGHMIGINTAI 307
Cdd:PRK10139  155 AIADSDKLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLNLEGLE--NFIQTDASINRGNSGGALLNLNGELIGINTAI 232

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 308 FTQTGTSAGVGFAIPSSTVLKIAPQLIQFGKVRRAGLNV---EFAPD-PIAYQLNVRTGSLILQVPGGSAAAKAGlvpts 383
Cdd:PRK10139  233 LAPGGGSVGIGFAIPSNMARTLAQQLIDFGEIKRGLLGIkgtEMSADiAKAFNLDVQRGAFVSEVLPNSGSAKAG----- 307

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002259351 384 rgfagnIVLGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPLEEAS 444
Cdd:PRK10139  308 ------VKAGDIITSLNGKPLNSFAELRSRIATTEPGTKVKLGLLRNGKPLEVEVTLDTST 362
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 339-440 6.19e-46

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: 154.27  E-value: 6.19e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 339 VRRAGLNVEFAPDPIAYQLNVRTGSLILQVPGGSAAAKAGLVPTSRGFAGNIVLGDVIVAVDGKPIKGKSDLSRVLDDYG 418
Cdd:cd00990     1 VVRPGLGISFAPDQVARQLGVRSGVLVLDVPPGGPAAKAGLRGTKRDEFGRIVLGDVIVAVDGKPVKNESDLYRALDEYK 80

                          90       100
                  ....*....|....*....|..
gi 1002259351 419 VGDKVSLTIQRGAETLEVTLPL 440
Cdd:cd00990    81 VGDVVTLKVLRGGTKVDLKVTL 102
PRK10898 PRK10898
serine endoprotease DegS;
127-403 1.86e-37

serine endoprotease DegS;


Pssm-ID: 182820 [Multi-domain]  Cd Length: 353  Bit Score: 139.75  E-value: 1.86e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 127 VVNIFDATLRP----QLNVTGVveipegnGSGVVWDDSGHIVTNYHVVGNAlskkpkpgevvARVNILAADGiqKNFEGK 202
Cdd:PRK10898   58 VVNVYNRSLNStshnQLEIRTL-------GSGVIMDQRGYILTNKHVINDA-----------DQIIVALQDG--RVFEAL 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 203 LVGADRSKDLAVLKVDAPTDLLKPINVGQSSalRVGQQCLAIGNPFGFDHALTVGVISGLNRDIFSQAGVTigGGIQTDA 282
Cdd:PRK10898  118 LVGSDSLTDLAVLKINATNLPVIPINPKRVP--HIGDVVLAIGNPYNLGQTITQGIISATGRIGLSPTGRQ--NFLQTDA 193

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 283 AINPGNSGGPLLDSKGHMIGINTAIFTQT---GTSAGVGFAIPSSTVLKIAPQLIQFGKVRRA--GLNVEFAPdPIAYQ- 356
Cdd:PRK10898  194 SINHGNSGGALVNSLGELMGINTLSFDKSndgETPEGIGFAIPTQLATKIMDKLIRDGRVIRGyiGIGGREIA-PLHAQg 272

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1002259351 357 --LNVRTGSLILQVPGGSAAAKAGlvptsrgfagnIVLGDVIVAVDGKP 403
Cdd:PRK10898  273 ggIDQLQGIVVNEVSPDGPAAKAG-----------IQVNDLIISVNNKP 310
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 152-303 3.15e-31

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


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 116.75  E-value: 3.15e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 152 GSGVVWDDSGHIVTNYHVVGNAlskkpkPGEVVARVNILAADGIQknFEGKLVGADRSKDLAVLKVDAPTDLLKPINVGQ 231
Cdd:pfam13365   1 GTGFVVSSDGLVLTNAHVVDDA------EEAAVELVSVVLADGRE--YPATVVARDPDLDLALLRVSGDGRGLPPLPLGD 72

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002259351 232 SSALRVGQQCLAIGNPFGFDH-ALTVGVISGLNRdifSQAGVTIGGGIQTDAAINPGNSGGPLLDSKGHMIGI 303
Cdd:pfam13365  73 SEPLVGGERVYAVGYPLGGEKlSLSEGIVSGVDE---GRDGGDDGRVIQTDAALSPGSSGGPVFDADGRVVGI 142
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 340-438 2.33e-17

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: 76.95  E-value: 2.33e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 340 RRAGLNVEF--APDPIAYQLNVRTGSLILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDY 417
Cdd:cd06779     2 PYLGIEMENisPLLAKELGLPVNRGVLVAEVIPGSPAAKAGLKE-----------GDVILSVNGKPVTSFNDLRAALDTK 70

                          90       100
                  ....*....|....*....|.
gi 1002259351 418 GVGDKVSLTIQRGAETLEVTL 438
Cdd:cd06779    71 KPGDSLNLTILRDGKTLTVTV 91
Trypsin pfam00089
Trypsin;
159-328 4.38e-15

Trypsin;


Pssm-ID: 459667 [Multi-domain]  Cd Length: 219  Bit Score: 74.02  E-value: 4.38e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 159 DSGHIVTNYHVVGNALSKKPKPGEVVARVNilaaDGIQKNFEGK------LVGADR-SKDLAVLKVDAP---TDLLKPIN 228
Cdd:pfam00089  33 SENWVLTAAHCVSGASDVKVVLGAHNIVLR----EGGEQKFDVEkiivhpNYNPDTlDNDIALLKLESPvtlGDTVRPIC 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 229 VGQSSA-LRVGQQCLAIG----NPFGFDHALTVGVISGLNRD-IFSQAGVTIGGG-IQTDA---AINPGNSGGPLLDSKG 298
Cdd:pfam00089 109 LPDASSdLPVGTTCTVSGwgntKTLGPSDTLQEVTVPVVSREtCRSAYGGTVTDTmICAGAggkDACQGDSGGPLVCSDG 188

                         170       180       190
                  ....*....|....*....|....*....|
gi 1002259351 299 HMIGINTAIFtQTGTSAGVGFAIPSSTVLK 328
Cdd:pfam00089 189 ELIGIVSWGY-GCASGNYPGVYTPVSSYLD 217
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
341-443 3.13e-12

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


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 68.31  E-value: 3.13e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 341 RAGLNVEFAPDP-IAYQLNVRTGS-----LILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGkSDLSRVL 414
Cdd:COG3975   468 PFGLKLVYEDAPsLKPSLGLRVSAdggglVVTSVLWGSPAYKAGLSA-----------GDELLAIDGLRVTA-DNLDDAL 535

                          90       100
                  ....*....|....*....|....*....
gi 1002259351 415 DDYGVGDKVSLTIQRGAETLEVTLPLEEA 443
Cdd:COG3975   536 AAYKPGDPIELLVFRRDELRTVTVTLAAA 564
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 354-438 3.50e-12

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: 62.11  E-value: 3.50e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 354 AYQLNVRTGSLILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAET 433
Cdd:cd10839    18 SFGLKEPKGALVAQVLPDSPAAKAGLKA-----------GDVILSLNGKPITSSADLRNRVATTKPGTKVELKILRDGKE 86


                  ....*
gi 1002259351 434 LEVTL 438
Cdd:cd10839    87 KTLTV 91
SdrC COG3480
Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];
359-443 7.48e-12

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


Pssm-ID: 442703 [Multi-domain]  Cd Length: 344  Bit Score: 66.37  E-value: 7.48e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 359 VRTGSLILQVPGGSAAAkaglvptsrgfaGNIVLGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTL 438
Cdd:COG3480   136 VTEGVYVASVLEGSPAD------------GVLQPGDVITAVDGKPVTTAEDLRDALAAKKPGDTVTLTVTRDGKEKTVTV 203


                  ....*
gi 1002259351 439 PLEEA 443
Cdd:COG3480   204 TLVKL 208
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 357-438 9.42e-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: 61.18  E-value: 9.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 357 LNVRTGSLILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEV 436
Cdd:cd10838    29 IPEVDGVLIMQVLPNSPAARAGLRR-----------GDVIQAVDGQPVTTADDVQRIVEQAGVGEELELTVLRGDRRQTL 97


                  ..
gi 1002259351 437 TL 438
Cdd:cd10838    98 AV 99
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 365-442 2.10e-10

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 62.03  E-value: 2.10e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002259351 365 ILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGvGDKVSLTIQRGAETLEVTLPLEE 442
Cdd:COG0750   132 VGEVVPGSPAAKAGLQP-----------GDRIVAINGQPVTSWDDLVDIIRASP-GKPLTLTVERDGEELTLTVTPRL 197
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 355-438 4.65e-10

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: 56.49  E-value: 4.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 355 YQLNVRTGSLILQVPGGSAAAKAGLVptsrgfagnivLGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQR-GAE- 432
Cdd:cd06781    24 LPSNVNKGVYVAQVQSNSPAEKAGLK-----------KGDVITKLDGKKVESSSDLRQILYSHKVGDTVKVTIYRdGKEk 92


                  ....*.
gi 1002259351 433 TLEVTL 438
Cdd:cd06781    93 TLNIKL 98
PDZ_2 pfam13180
PDZ domain;
358-440 5.70e-10

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 55.36  E-value: 5.70e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 358 NVRTGSLILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVT 437
Cdd:pfam13180   3 DLEGGVVVVSVKSSGPAAKAGLKA-----------GDVILSIDGRKINDLTDLESALYGHKPGDTVTLQVYRDGKLLTVE 71


                  ...
gi 1002259351 438 LPL 440
Cdd:pfam13180  72 VKL 74
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 325-442 3.70e-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: 53.66  E-value: 3.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 325 TVLKIAPQLIQFGKVRraglNVEFaPDpiayqlnVRTGSLILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPI 404
Cdd:cd06785     7 RMLTLTPSLLEELKQR----NPDF-PD-------VSSGVYVHKVIPGSPAQRAGLKD-----------GDVIISINGKPV 63

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1002259351 405 KGKSDLSRVLDDygvGDKVSLTIQRGAETLEVTLPLEE 442
Cdd:cd06785    64 KSSSDVYEAVKS---GSSLLVVVRRGNEDLLLTVTPEE 98
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 353-430 1.00e-07

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: 49.30  E-value: 1.00e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002259351  353 IAYQLNVRTGSLILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRG 430
Cdd:smart00228  18 LVGGKDEGGGVVVSSVVPGSPAAKAGLRV-----------GDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRG 84
MarP_fam_protase NF033740
MarP family serine protease; The founding member of this family of membrane-spanning serine ...
 152-330 2.39e-07

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: 52.50  E-value: 2.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 152 GSGVVWDDsGHIVTNYHVVGNalskkpkpgevVARVNILAADGIQknFEGKLVGADRSKDLAVLKVdaPTDLLKPINVGQ 231
Cdd:NF033740  213 GSGFVVAP-DRVMTNAHVVAG-----------TDEVTVETVGGGT--LDARVVYYDPDRDIAVLAV--PGLGLPPLPFAD 276

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 232 SSALRvGQQCLAIGNPFG--FDHA----LTVGVISGLN--------RDIFSQAGVtigggiqtdaaINPGNSGGPLLDSK 297
Cdd:NF033740  277 EPAET-GDDAIVLGYPEGgpFTATparvRERIALSGPDiygsgtvtREVYTLRGT-----------VRPGNSGGPLLDPD 344

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1002259351 298 GHMIGIntaIFTQTGTSAGVGFAIPSSTVLKIA 330
Cdd:NF033740  345 GRVLGV---VFAAAVDDSDTGYALTADEVRPDL 374
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 371-438 2.67e-07

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: 48.25  E-value: 2.67e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002259351 371 GSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSdlsrvLDDYG------VGDKVSLTIQRG--AETLEVTL 438
Cdd:cd06782    24 GGPAEKAGIKP-----------GDVIVAVDGESVRGMS-----LDEVVkllrgpKGTKVKLTIRRGgeGEPRDVTL 83
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 371-438 5.59e-07

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: 51.41  E-value: 5.59e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002259351 371 GSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKS--DLSRVLDDyGVGDKVSLTIQRG--AETLEVTL 438
Cdd:COG0793    81 GSPAEKAGIKP-----------GDIILAIDGKSVAGLTldDAVKLLRG-KAGTKVTLTIKRPgeGEPITVTL 140
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 360-439 6.78e-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: 46.85  E-value: 6.78e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 360 RTGSLILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDygVGDKVSLTIQRGAETLEVTLP 439
Cdd:cd23084    17 GKGVVVTEVDPGSPAAQSGLKK-----------GDVIIGVNRQPVKSIAELRKVLKS--KPSAVLLQIKRGDSSRYLALP 83
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 371-429 1.33e-06

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 45.21  E-value: 1.33e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1002259351 371 GSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDyGVGDKVSLTIQR 429
Cdd:pfam17820   8 GSPAERAGLRV-----------GDVILAVNGKPVRSLEDVARLLQG-SAGESVTLTVRR 54
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 371-442 1.43e-06

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: 46.03  E-value: 1.43e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002259351 371 GSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGvGDKVSLTIQRGAETLEVTLPLEE 442
Cdd:cd23081     9 NSPAAEAGLKP-----------GDRILKIDGQKVRTWEDIVRIVRENP-GKPLTLKIERDGKILTVTVTPEL 68
PLN00049 PLN00049
carboxyl-terminal processing protease; Provisional
 368-445 2.04e-06

carboxyl-terminal processing protease; Provisional


Pssm-ID: 177681 [Multi-domain]  Cd Length: 389  Bit Score: 49.73  E-value: 2.04e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 368 VPGGSAAaKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKS--DLSRVLDDyGVGDKVSLTIQRGAETLEVTLPLEEASI 445
Cdd:PLN00049  110 APGGPAA-RAGIRP-----------GDVILAIDGTSTEGLSlyEAADRLQG-PEGSSVELTLRRGPETRLVTLTREKVSL 176
cpPDZ_AtDEGP14-like cd23085
circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) ...
 358-441 3.79e-06

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: 45.14  E-value: 3.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 358 NVRTGSLILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYgVGDKVSLTIQRG---AETL 434
Cdd:cd23085    28 DVKAGVLVPQVIPGSPAERAGLRP-----------GDVIVEFDGKPVDSTKQIIDALGDK-VGKPFKVVVKRAnkvQVTL 95


                  ....*..
gi 1002259351 435 EVTlPLE 441
Cdd:cd23085    96 TVT-PEE 101
cpPDZ_BsYlbL-like cd23080
circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ ...
 386-440 5.00e-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: 44.41  E-value: 5.00e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1002259351 386 FAGNIVLGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPL 440
Cdd:cd23080    13 AKGILEAGDKITAIDGQNFQSSEKLIDYISSKKAGDKVKVKYERDEKEKEAELKL 67
Peptidase_M50 pfam02163
Peptidase family M50;
364-438 1.53e-05

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 46.72  E-value: 1.53e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002259351 364 LILQVPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGvGDKVSLTIQRGAETLEVTL 438
Cdd:pfam02163  96 VIGGVAPGSPAAKAGLKP-----------GDVILSINGKKITSWQDLVEALAKSP-GKPITLTVERGGQTLTVTI 158
cpPDZ1_ScNma111-like cd06786
circularly permuted first PDZ domain (PDZ1) of Saccharomyces cerevisiae pro-apoptotic serine ...
 339-438 5.18e-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: 41.79  E-value: 5.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 339 VRRAGLNVEFAPDpiayqlnVR------TGSLILQ--VPGGSAAAKaglvptsrgfagnIVLGDVIVAVDGKPIKGKSDL 410
Cdd:cd06786     1 CRRLGLTPETEAA-------VRkafpseTGMLVAEtvLPEGPADGK-------------LEEGDVLISVNGELITQFIRL 60

                          90       100
                  ....*....|....*....|....*...
gi 1002259351 411 SRVLDDyGVGDKVSLTIQRGAETLEVTL 438
Cdd:cd06786    61 EEILDE-NVGKTVELVVQRGGEEITVTI 87
eMpr COG3591
V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, ...
 141-322 9.15e-05

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


Pssm-ID: 442810 [Multi-domain]  Cd Length: 194  Bit Score: 43.13  E-value: 9.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 141 VTGVVEIPEGNGSGvvwddSG------HIVTNYHVVGNALSKKPkPGEVVARVNILAA-DGIQKNFEGKLVGA-----DR 208
Cdd:COG3591     1 AVGRLETDGGGGVC-----TGtligpnLVLTAGHCVYDGAGGGW-ATNIVFVPGYNGGpYGTATATRFRVPPGwvasgDA 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 209 SKDLAVLKVDAP-TDLLKPINVGQSSALRVGQQCLAIGNPFGFDHALTVG----VISGLNRDIFSQAGVTigggiqtdaa 283
Cdd:COG3591    75 GYDYALLRLDEPlGDTTGWLGLAFNDAPLAGEPVTIIGYPGDRPKDLSLDcsgrVTGVQGNRLSYDCDTT---------- 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1002259351 284 inPGNSGGPLL---DSKGHMIGINTAiftqtGTSAGVGFAIP 322
Cdd:COG3591   145 --GGSSGSPVLddsDGGGRVVGVHSA-----GGADRANTGVR 179
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 368-441 1.14e-04

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


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 43.43  E-value: 1.14e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002259351 368 VPGGSAAAKAGLVPtsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPLE 441
Cdd:COG3031   158 GRPGSLFSKLGLQP-----------GDVITSINGQDLTDPAQALELLQQLRDASEVTLTVERNGQPVTLTYNLR 220
cpPDZ1_MamE-like cd23087
circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease ...
 352-438 2.33e-04

circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease MamE and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Magnetospirillum magneticum MamE (also known as magnetochrome MamE and magnetosome serine protease MamE), and related domains. MamE is a serine protease required to produce magnetite crystals in the magnetotactic bacterium M. magneticum. It is involved in localization of some proteins (at least MamA, MamC, MamF, MamI and MamJ) to the magnetosome, and likely cleaves at least itself, MamO and MamP. MamE-PDZ1 may bind MamB. Its autoproteolysis is stimulated by exogenous substrates or peptides that bind to its PDZ domains. Peptide binding to either the first or the second PDZ domain of MamE can activate proteolysis; activation through PDZ2 is much weaker. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This MamE-like PDZ domain 1 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467634 [Multi-domain]  Cd Length: 91  Bit Score: 39.86  E-value: 2.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 352 PIAYQLNVRTGslilqVPGGSAAAKAGLVPTSRGFAGNIVLGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGA 431
Cdd:cd23087    10 PMQQRLGQQTN-----LPAGRGVFVSGVTPNTPAAAAGLRPGDVILKVDGRPVHQPEEVSAIMAEMPNGRSVRLGVLRDG 84


                  ....*..
gi 1002259351 432 ETLEVTL 438
Cdd:cd23087    85 DVRNMSL 91
GRASP55_65 pfam04495
GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 ...
 365-417 9.80e-04

GRASP55/65 PDZ-like domain; GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. This region appears to be related to the PDZ domain.


Pssm-ID: 427981 [Multi-domain]  Cd Length: 138  Bit Score: 39.17  E-value: 9.80e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1002259351 365 ILQVPGGSAAAKAGLVPTSrgfagnivlgDVIVAVDGKPIKGKSDLSRVLDDY 417
Cdd:pfam04495  47 VLDVHENSPAAKAGLQPYS----------DYIIGTPKGLLKGEDDLYTLVEDH 89
alphaLP-like cd21112
alpha-lytic protease (alpha-LP), a bacterial serine protease of the chymotrypsin family, and ...
 211-327 1.59e-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: 39.60  E-value: 1.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002259351 211 DLAVLKVDAPTDLLKP---------INVGQSSALRVGQQ-CLAiGNPFGFdhalTVGVISGLNRDIFSQAGvTIGGGIQT 280
Cdd:cd21112    65 DYALVRVTNPGWTPPPevrtygggtVPITGSAEPVVGAPvCKS-GRTTGW----TCGTVTAVNVTVNYPGG-TVTGLTRT 138

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1002259351 281 DAAINPGNSGGPLLdSKGHMIGINTAIFTQTGTSAGVGFAIPSSTVL 327
Cdd:cd21112   139 NACAEPGDSGGPVF-SGTQALGITSGGSGNCGSGGGTSYFQPVNPVL 184
cpPDZ_RseP_YlbL-like cd10824
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), ...
 365-441 2.00e-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: 37.17  E-value: 2.00e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002259351 365 ILQVPGGSAAAKAGLVptsrgfagnivlGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAETLEVTLPLE 441
Cdd:cd10824     3 VLSVKPNSPAAKALHA------------GDLITEIDGQPTKSWQTFIDYIHDKKVGESVKITYKHGNKNEEASLKLT 67
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 362-438 6.38e-03

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


Pssm-ID: 467620 [Multi-domain]  Cd Length: 93  Bit Score: 35.83  E-value: 6.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002259351 362 GSLILQVPGGSAAAKAGlvptsrgfagnIVLGDVIVAVDGKPIKGKSDLSRVLDDYGVGDKVSLTIQRGAE--TLEVTL 438
Cdd:cd06777    26 GALVKGVSPDSPAAKAG-----------IQVGDIILQFDNKPVISVLELMDLVAEIRPGTVIPVVVLRDGKqlTLEVTI 93
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH