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Conserved domains on  [gi|960426816|ref|WP_058318675|]
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trypsin-like peptidase domain-containing protein [Thalassovita mediterranea]

Protein Classification

Do family serine endopeptidase( domain architecture ID 1000019)

Do/DeqQ family serine endopeptidase belonging to the peptidase S1C family, contains a PDZ-domain, similar to Lactococcus lactis Do-like HtrA (High-temperature requirement A), which is a surface protease responsible for the housekeeping of exported proteins and plays a role in stress resistance during active exponential growth

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
degP_htrA_DO super family cl37035
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 36-462 1.37e-148

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]


The actual alignment was detected with superfamily member TIGR02037:

Pssm-ID: 273938 [Multi-domain]  Cd Length: 428  Bit Score: 430.10  E-value: 1.37e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816   36 LGFAPLVKQAAPAVVNIYAKRVVQTRSSPFSNDPFFREFFRDFG-----ETRPEVQNSLGSGVILSADGYVVSNYHVVGG 110
Cdd:TIGR02037   1 PSFAPLVEKVAPAVVNISVEGTVKRRNRPPALPPFFRQFFGDDMpdfprQQREQKVRGLGSGVIISADGYVLTNNHVVDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  111 ATDIRVVLKDRREFAAKVMLADQASDLAILKLEDAPDMPFLTLRDSDGVEVGELALAIGNPFGIGQTVSSGIVSGLARSG 190
Cdd:TIGR02037  81 ADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSALGRSG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  191 aATGAGRAYFIQTDAAINPGNSGGALIDINGELIGVNTSILTRSGGSNGVGFAIPADLVEQFVAQARQgYDSFLRPWAGM 270
Cdd:TIGR02037 161 -LGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAKNVVDQLIE-GGKVKRGWLGV 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  271 SGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDGVA 350
Cdd:TIGR02037 239 TIQEVTSDLAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKGKE 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  351 EEVDVGLILPPETPArdtvtlTEAEVLPGLQMSQVNPAVIAEFSLPLDAMGVIV--EGTGPYAARVGLQRGDILLGINGE 428
Cdd:TIGR02037 319 KTITVTLGASPEEQA------SSSNPFLGLTVANLSPEIRKELRLKGDVKGVVVtkVVSGSPAARAGLQPGDVILSVNQQ 392

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 960426816  429 QVTTPSEAREILSQL--GSRVAITVQRGLQRVQIRF 462
Cdd:TIGR02037 393 PVSSVAELRKVLARAkkGGRVALLILRGGATIFVTL 428
 
Name Accession Description Interval E-value
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 36-462 1.37e-148

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: 430.10  E-value: 1.37e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816   36 LGFAPLVKQAAPAVVNIYAKRVVQTRSSPFSNDPFFREFFRDFG-----ETRPEVQNSLGSGVILSADGYVVSNYHVVGG 110
Cdd:TIGR02037   1 PSFAPLVEKVAPAVVNISVEGTVKRRNRPPALPPFFRQFFGDDMpdfprQQREQKVRGLGSGVIISADGYVLTNNHVVDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  111 ATDIRVVLKDRREFAAKVMLADQASDLAILKLEDAPDMPFLTLRDSDGVEVGELALAIGNPFGIGQTVSSGIVSGLARSG 190
Cdd:TIGR02037  81 ADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSALGRSG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  191 aATGAGRAYFIQTDAAINPGNSGGALIDINGELIGVNTSILTRSGGSNGVGFAIPADLVEQFVAQARQgYDSFLRPWAGM 270
Cdd:TIGR02037 161 -LGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAKNVVDQLIE-GGKVKRGWLGV 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  271 SGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDGVA 350
Cdd:TIGR02037 239 TIQEVTSDLAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKGKE 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  351 EEVDVGLILPPETPArdtvtlTEAEVLPGLQMSQVNPAVIAEFSLPLDAMGVIV--EGTGPYAARVGLQRGDILLGINGE 428
Cdd:TIGR02037 319 KTITVTLGASPEEQA------SSSNPFLGLTVANLSPEIRKELRLKGDVKGVVVtkVVSGSPAARAGLQPGDVILSVNQQ 392

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 960426816  429 QVTTPSEAREILSQL--GSRVAITVQRGLQRVQIRF 462
Cdd:TIGR02037 393 PVSSVAELRKVLARAkkGGRVALLILRGGATIFVTL 428
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 88-362 7.95e-112

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: 330.57  E-value: 7.95e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  88 SLGSGVILSADGYVVSNYHVVGGATDIRVVLKDRREFAAKVMLADQASDLAILKLeDAPDMPFLTLRDSDGVEVGELALA 167
Cdd:COG0265    1 GLGSGVIISPDGYILTNNHVVEGADEITVTLADGREYPAKVVGRDPLTDLAVLKI-DAKDLPAAPLGDSDKLRVGDWVLA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 168 IGNPFGIGQTVSSGIVSGLARS-GAATGAGRAYFIQTDAAINPGNSGGALIDINGELIGVNTSILTRSGGSNGVGFAIPA 246
Cdd:COG0265   80 IGNPFGLGQTVTAGIVSALGRSiGSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIISRSGGSQGIGFAIPI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 247 DLVEQFVAQARQgYDSFLRPWAGMSGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQE 326
Cdd:COG0265  160 NLAKRVVEQLIE-TGRVRRGWLGVTIQPVTPELAEALGLPEPEGVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARD 238

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 960426816 327 MIYRMSVAGMGSRVAVTYYRDGVAEEVDVGLILPPE 362
Cdd:COG0265  239 LQRLLASLKPGDTVTLTVLRGGKELTVTVTLGERPE 274
HhoA_HhoB_HtrA NF041521
HhoA/HhoB/HtrA family serine endopeptidase; Members of this family include the paralogous ...
 42-355 1.41e-83

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: 260.49  E-value: 1.41e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  42 VKQAAPAVVNIYAKRVVQTRSSPFSNDPFFREFF-RDFGETRPE--VQNSLGSGVILSADGYVVSNYHVVGGATDIRVVL 118
Cdd:NF041521   7 VEKVGPAVVRIDAERTVVTQVPPFFNDPFFRRFFgSDIPPPPPQerVERGTGSGFIISSDGIILTNAHVVDGADTVTVTL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 119 KDRREFAAKVMLADQASDLAILKLeDAPDMPFLTLRDSDGVEVGELALAIGNPFGIGQTVSSGIVSGLARSGAATGAG-- 196
Cdd:NF041521  87 KDGRTFEGKVLGTDPVTDVAVVKI-EAKNLPTVPLGNSDQLQPGEWAIAIGNPLGLDNTVTLGIISATGRSSSQVGVPdk 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 197 RAYFIQTDAAINPGNSGGALIDINGELIGVNTSILtrsGGSNGVGFAIPADLVEQFVAQ-ARQGydSFLRPWAGMS---- 271
Cdd:NF041521 166 RVDFIQTDAAINPGNSGGPLLNARGEVIGINTAIR---AGAQGLGFAIPINTAQRIADQlIAGG--KVEHPYLGIQmvtl 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 272 ----GQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRD 347
Cdd:NF041521 241 tpelKQEINSDPNSGFTVPEDEGVLIVRVVPNSPAARAGLRAGDVIQKINGQPVTTAEQVQQIVENSQVGQTLQLEVQRN 320


                 ....*...
gi 960426816 348 GVAEEVDV 355
Cdd:NF041521 321 GQTQTLTV 328
PRK10942 PRK10942
serine endoprotease DegP;
24-454 5.41e-83

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 263.55  E-value: 5.41e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  24 ETKVPTSqAEIALGFAPLVKQAAPAVVNIYAKRVVQTRS---------------------SPFSNDPFFREFFRDFGETR 82
Cdd:PRK10942  27 ETSSATT-AQQMPSLAPMLEKVMPSVVSINVEGSTTVNTprmprqfqqffgdnspfcqegSPFQSSPFCQGGQGGNGGGQ 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  83 PEVQNSLGSGVILSAD-GYVVSNYHVVGGATDIRVVLKDRREFAAKVMLADQASDLAILKLEDAPDMPFLTLRDSDGVEV 161
Cdd:PRK10942 106 QQKFMALGSGVIIDADkGYVVTNNHVVDNATKIKVQLSDGRKFDAKVVGKDPRSDIALIQLQNPKNLTAIKMADSDALRV 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 162 GELALAIGNPFGIGQTVSSGIVSGLARSGAATgAGRAYFIQTDAAINPGNSGGALIDINGELIGVNTSILTRSGGSNGVG 241
Cdd:PRK10942 186 GDYTVAIGNPYGLGETVTSGIVSALGRSGLNV-ENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIG 264

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 242 FAIPADLVEQFVAQARQgYDSFLRPWAGMSGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEV 321
Cdd:PRK10942 265 FAIPSNMVKNLTSQMVE-YGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPI 343

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 322 NSPQEMIYRMSVAGMGSRVAVTYYRDGVAEEVDVglilppetpardtvtlteaEVLPGLQmSQVNPAVI------AEFSL 395
Cdd:PRK10942 344 SSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNV-------------------ELQQSSQ-NQVDSSNIfngiegAELSN 403

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 960426816 396 PLDAMGVIVEGTGPY--AARVGLQRGDILLGINGEQVTTPSEAREILSQLGSRVAITVQRG 454
Cdd:PRK10942 404 KGGDKGVVVDNVKPGtpAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKPSVLALNIQRG 464
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 90-226 2.62e-32

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


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 119.83  E-value: 2.62e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816   90 GSGVILSADGYVVSNYHVVGGATDIRV-----VLKDRREFAAKVMLADQASDLAILKL-EDAPDMPFLTLRDSDGVEVGE 163
Cdd:pfam13365   1 GTGFVVSSDGLVLTNAHVVDDAEEAAVelvsvVLADGREYPATVVARDPDLDLALLRVsGDGRGLPPLPLGDSEPLVGGE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 960426816  164 LALAIGNPFGIG-QTVSSGIVSGLARSGAATGAGRayFIQTDAAINPGNSGGALIDINGELIGV 226
Cdd:pfam13365  81 RVYAVGYPLGGEkLSLSEGIVSGVDEGRDGGDDGR--VIQTDAALSPGSSGGPVFDADGRVVGI 142
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 265-355 1.47e-18

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: 80.22  E-value: 1.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 265 RPWAGMSGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTY 344
Cdd:cd10839    1 RGWLGVQIQELTPDLAESFGLKEPKGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATTKPGTKVELKI 80

                         90
                 ....*....|.
gi 960426816 345 YRDGVAEEVDV 355
Cdd:cd10839   81 LRDGKEKTLTV 91
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 411-454 1.17e-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: 1.17e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 960426816   411 AARVGLQRGDILLGINGEQVT--TPSEAREILSQLGSRVAITVQRG 454
Cdd:smart00228  39 AAKAGLRVGDVILEVNGTSVEglTHLEAVDLLKKAGGKVTLTVLRG 84
GspC_delta NF041515
type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are ...
 412-463 1.66e-04

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


Pssm-ID: 469401 [Multi-domain]  Cd Length: 310  Bit Score: 43.32  E-value: 1.66e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 960426816 412 ARVGLQRGDILLGINGEQVTTPSEAREILSQL--GSRVAITVQRGLQRVQIRFR 463
Cdd:NF041515 255 GKLGLQNGDVLQSINGFDMTSPDKALEAYARLrsADHLTVSVERRGKPVTLDYN 308
 
Name Accession Description Interval E-value
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 36-462 1.37e-148

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: 430.10  E-value: 1.37e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816   36 LGFAPLVKQAAPAVVNIYAKRVVQTRSSPFSNDPFFREFFRDFG-----ETRPEVQNSLGSGVILSADGYVVSNYHVVGG 110
Cdd:TIGR02037   1 PSFAPLVEKVAPAVVNISVEGTVKRRNRPPALPPFFRQFFGDDMpdfprQQREQKVRGLGSGVIISADGYVLTNNHVVDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  111 ATDIRVVLKDRREFAAKVMLADQASDLAILKLEDAPDMPFLTLRDSDGVEVGELALAIGNPFGIGQTVSSGIVSGLARSG 190
Cdd:TIGR02037  81 ADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSALGRSG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  191 aATGAGRAYFIQTDAAINPGNSGGALIDINGELIGVNTSILTRSGGSNGVGFAIPADLVEQFVAQARQgYDSFLRPWAGM 270
Cdd:TIGR02037 161 -LGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAKNVVDQLIE-GGKVKRGWLGV 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  271 SGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDGVA 350
Cdd:TIGR02037 239 TIQEVTSDLAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKGKE 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  351 EEVDVGLILPPETPArdtvtlTEAEVLPGLQMSQVNPAVIAEFSLPLDAMGVIV--EGTGPYAARVGLQRGDILLGINGE 428
Cdd:TIGR02037 319 KTITVTLGASPEEQA------SSSNPFLGLTVANLSPEIRKELRLKGDVKGVVVtkVVSGSPAARAGLQPGDVILSVNQQ 392

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 960426816  429 QVTTPSEAREILSQL--GSRVAITVQRGLQRVQIRF 462
Cdd:TIGR02037 393 PVSSVAELRKVLARAkkGGRVALLILRGGATIFVTL 428
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 88-362 7.95e-112

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: 330.57  E-value: 7.95e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  88 SLGSGVILSADGYVVSNYHVVGGATDIRVVLKDRREFAAKVMLADQASDLAILKLeDAPDMPFLTLRDSDGVEVGELALA 167
Cdd:COG0265    1 GLGSGVIISPDGYILTNNHVVEGADEITVTLADGREYPAKVVGRDPLTDLAVLKI-DAKDLPAAPLGDSDKLRVGDWVLA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 168 IGNPFGIGQTVSSGIVSGLARS-GAATGAGRAYFIQTDAAINPGNSGGALIDINGELIGVNTSILTRSGGSNGVGFAIPA 246
Cdd:COG0265   80 IGNPFGLGQTVTAGIVSALGRSiGSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIISRSGGSQGIGFAIPI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 247 DLVEQFVAQARQgYDSFLRPWAGMSGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQE 326
Cdd:COG0265  160 NLAKRVVEQLIE-TGRVRRGWLGVTIQPVTPELAEALGLPEPEGVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARD 238

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 960426816 327 MIYRMSVAGMGSRVAVTYYRDGVAEEVDVGLILPPE 362
Cdd:COG0265  239 LQRLLASLKPGDTVTLTVLRGGKELTVTVTLGERPE 274
HhoA_HhoB_HtrA NF041521
HhoA/HhoB/HtrA family serine endopeptidase; Members of this family include the paralogous ...
 42-355 1.41e-83

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: 260.49  E-value: 1.41e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  42 VKQAAPAVVNIYAKRVVQTRSSPFSNDPFFREFF-RDFGETRPE--VQNSLGSGVILSADGYVVSNYHVVGGATDIRVVL 118
Cdd:NF041521   7 VEKVGPAVVRIDAERTVVTQVPPFFNDPFFRRFFgSDIPPPPPQerVERGTGSGFIISSDGIILTNAHVVDGADTVTVTL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 119 KDRREFAAKVMLADQASDLAILKLeDAPDMPFLTLRDSDGVEVGELALAIGNPFGIGQTVSSGIVSGLARSGAATGAG-- 196
Cdd:NF041521  87 KDGRTFEGKVLGTDPVTDVAVVKI-EAKNLPTVPLGNSDQLQPGEWAIAIGNPLGLDNTVTLGIISATGRSSSQVGVPdk 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 197 RAYFIQTDAAINPGNSGGALIDINGELIGVNTSILtrsGGSNGVGFAIPADLVEQFVAQ-ARQGydSFLRPWAGMS---- 271
Cdd:NF041521 166 RVDFIQTDAAINPGNSGGPLLNARGEVIGINTAIR---AGAQGLGFAIPINTAQRIADQlIAGG--KVEHPYLGIQmvtl 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 272 ----GQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRD 347
Cdd:NF041521 241 tpelKQEINSDPNSGFTVPEDEGVLIVRVVPNSPAARAGLRAGDVIQKINGQPVTTAEQVQQIVENSQVGQTLQLEVQRN 320


                 ....*...
gi 960426816 348 GVAEEVDV 355
Cdd:NF041521 321 GQTQTLTV 328
PRK10942 PRK10942
serine endoprotease DegP;
24-454 5.41e-83

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 263.55  E-value: 5.41e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  24 ETKVPTSqAEIALGFAPLVKQAAPAVVNIYAKRVVQTRS---------------------SPFSNDPFFREFFRDFGETR 82
Cdd:PRK10942  27 ETSSATT-AQQMPSLAPMLEKVMPSVVSINVEGSTTVNTprmprqfqqffgdnspfcqegSPFQSSPFCQGGQGGNGGGQ 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  83 PEVQNSLGSGVILSAD-GYVVSNYHVVGGATDIRVVLKDRREFAAKVMLADQASDLAILKLEDAPDMPFLTLRDSDGVEV 161
Cdd:PRK10942 106 QQKFMALGSGVIIDADkGYVVTNNHVVDNATKIKVQLSDGRKFDAKVVGKDPRSDIALIQLQNPKNLTAIKMADSDALRV 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 162 GELALAIGNPFGIGQTVSSGIVSGLARSGAATgAGRAYFIQTDAAINPGNSGGALIDINGELIGVNTSILTRSGGSNGVG 241
Cdd:PRK10942 186 GDYTVAIGNPYGLGETVTSGIVSALGRSGLNV-ENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIG 264

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 242 FAIPADLVEQFVAQARQgYDSFLRPWAGMSGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEV 321
Cdd:PRK10942 265 FAIPSNMVKNLTSQMVE-YGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPI 343

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 322 NSPQEMIYRMSVAGMGSRVAVTYYRDGVAEEVDVglilppetpardtvtlteaEVLPGLQmSQVNPAVI------AEFSL 395
Cdd:PRK10942 344 SSFAALRAQVGTMPVGSKLTLGLLRDGKPVNVNV-------------------ELQQSSQ-NQVDSSNIfngiegAELSN 403

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 960426816 396 PLDAMGVIVEGTGPY--AARVGLQRGDILLGINGEQVTTPSEAREILSQLGSRVAITVQRG 454
Cdd:PRK10942 404 KGGDKGVVVDNVKPGtpAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKPSVLALNIQRG 464
PRK10139 PRK10139
serine endoprotease DegQ;
38-463 2.00e-80

serine endoprotease DegQ;


Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 256.41  E-value: 2.00e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  38 FAPLVKQAAPAVVNIYAK-RVVQTRSSPfsndpffREFFRDFGETRPEVQ----NSLGSGVIL-SADGYVVSNYHVVGGA 111
Cdd:PRK10139  42 LAPMLEKVLPAVVSVRVEgTASQGQKIP-------EEFKKFFGDDLPDQPaqpfEGLGSGVIIdAAKGYVLTNNHVINQA 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 112 TDIRVVLKDRREFAAKVMLADQASDLAILKLEDAPDMPFLTLRDSDGVEVGELALAIGNPFGIGQTVSSGIVSGLARSGA 191
Cdd:PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIADSDKLRVGDFAVAVGNPFGLGQTATSGIISALGRSGL 194

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 192 ATgAGRAYFIQTDAAINPGNSGGALIDINGELIGVNTSILTRSGGSNGVGFAIPADLVEQFVAQARQgYDSFLRPWAGMS 271
Cdd:PRK10139 195 NL-EGLENFIQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIPSNMARTLAQQLID-FGEIKRGLLGIK 272

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 272 GQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDGVAE 351
Cdd:PRK10139 273 GTEMSADIAKAFNLDVQRGAFVSEVLPNSGSAKAGVKAGDIITSLNGKPLNSFAELRSRIATTEPGTKVKLGLLRNGKPL 352

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 352 EVDVGLilppetparDTVTLTEAE---VLPGLQmsqvnPAVIAEFSLPLDAMGVIVEGT--GPYAARVGLQRGDILLGIN 426
Cdd:PRK10139 353 EVEVTL---------DTSTSSSASaemITPALQ-----GATLSDGQLKDGTKGIKIDEVvkGSPAAQAGLQKDDVIIGVN 418

                        410       420       430
                 ....*....|....*....|....*....|....*..
gi 960426816 427 GEQVTTPSEAREILSQLGSRVAITVQRGLQRVQIRFR 463
Cdd:PRK10139 419 RDRVNSIAEMRKVLAAKPAIIALQIVRGNESIYLLLR 455
PRK10898 PRK10898
serine endoprotease DegS;
30-348 3.27e-55

serine endoprotease DegS;


Pssm-ID: 182820 [Multi-domain]  Cd Length: 353  Bit Score: 187.52  E-value: 3.27e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  30 SQAEIALGFAPLVKQAAPAVVNIYAKrvvqtrsspfSNDPFFREFFrdfgETRPevqnsLGSGVILSADGYVVSNYHVVG 109
Cdd:PRK10898  39 STDETPASYNQAVRRAAPAVVNVYNR----------SLNSTSHNQL----EIRT-----LGSGVIMDQRGYILTNKHVIN 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 110 GATDIRVVLKDRREFAAKVMLADQASDLAILKLeDAPDMPFLTLRDSDGVEVGELALAIGNPFGIGQTVSSGIVSGLARS 189
Cdd:PRK10898 100 DADQIIVALQDGRVFEALLVGSDSLTDLAVLKI-NATNLPVIPINPKRVPHIGDVVLAIGNPYNLGQTITQGIISATGRI 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 190 GAATgAGRAYFIQTDAAINPGNSGGALIDINGELIGVNTsiLTRSGGSN-----GVGFAIPADLVEQFVAQ-ARQGydSF 263
Cdd:PRK10898 179 GLSP-TGRQNFLQTDASINHGNSGGALVNSLGELMGINT--LSFDKSNDgetpeGIGFAIPTQLATKIMDKlIRDG--RV 253

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 264 LRPWAGMSGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVT 343
Cdd:PRK10898 254 IRGYIGIGGREIAPLHAQGGGIDQLQGIVVNEVSPDGPAAKAGIQVNDLIISVNNKPAISALETMDQVAEIRPGSVIPVV 333


                 ....*
gi 960426816 344 YYRDG 348
Cdd:PRK10898 334 VMRDD 338
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 90-226 2.62e-32

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


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 119.83  E-value: 2.62e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816   90 GSGVILSADGYVVSNYHVVGGATDIRV-----VLKDRREFAAKVMLADQASDLAILKL-EDAPDMPFLTLRDSDGVEVGE 163
Cdd:pfam13365   1 GTGFVVSSDGLVLTNAHVVDDAEEAAVelvsvVLADGREYPATVVARDPDLDLALLRVsGDGRGLPPLPLGDSEPLVGGE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 960426816  164 LALAIGNPFGIG-QTVSSGIVSGLARSGAATGAGRayFIQTDAAINPGNSGGALIDINGELIGV 226
Cdd:pfam13365  81 RVYAVGYPLGGEkLSLSEGIVSGVDEGRDGGDDGR--VIQTDAALSPGSSGGPVFDADGRVVGI 142
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 265-355 1.47e-18

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: 80.22  E-value: 1.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 265 RPWAGMSGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTY 344
Cdd:cd10839    1 RGWLGVQIQELTPDLAESFGLKEPKGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATTKPGTKVELKI 80

                         90
                 ....*....|.
gi 960426816 345 YRDGVAEEVDV 355
Cdd:cd10839   81 LRDGKEKTLTV 91
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 265-355 8.51e-13

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: 63.85  E-value: 8.51e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 265 RPWAGMSGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTY 344
Cdd:cd06779    1 RPYLGIEMENISPLLAKELGLPVNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTKKPGDSLNLTI 80

                         90
                 ....*....|.
gi 960426816 345 YRDGVAEEVDV 355
Cdd:cd06779   81 LRDGKTLTVTV 91
Trypsin pfam00089
Trypsin;
92-245 1.09e-12

Trypsin;


Pssm-ID: 459667 [Multi-domain]  Cd Length: 219  Bit Score: 67.08  E-value: 1.09e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816   92 GVILSADgYVVSNYHVVGGATDIRVVLKD--RREFAAKVMLAD--------------QASDLAILKLEDAPD-----MPF 150
Cdd:pfam00089  29 GSLISEN-WVLTAAHCVSGASDVKVVLGAhnIVLREGGEQKFDvekiivhpnynpdtLDNDIALLKLESPVTlgdtvRPI 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  151 LTLRDSDGVEVGELALAIG----NPFGIGQTVSSGIVSGLAR---SGAATGAGRAYFIQTDA---AINPGNSGGALIDIN 220
Cdd:pfam00089 108 CLPDASSDLPVGTTCTVSGwgntKTLGPSDTLQEVTVPVVSRetcRSAYGGTVTDTMICAGAggkDACQGDSGGPLVCSD 187

                         170       180
                  ....*....|....*....|....*
gi 960426816  221 GELIGVNTSILTRSGGsNGVGFAIP 245
Cdd:pfam00089 188 GELIGIVSWGYGCASG-NYPGVYTP 211
PDZ_2 pfam13180
PDZ domain;
289-357 1.95e-10

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 56.51  E-value: 1.95e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 960426816  289 GGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDGVAEEVDVGL 357
Cdd:pfam13180   6 GGVVVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALYGHKPGDTVTLQVYRDGKLLTVEVKL 74
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 379-464 8.78e-10

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


Pssm-ID: 467629 [Multi-domain]  Cd Length: 104  Bit Score: 55.79  E-value: 8.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 379 GLQMSQVNPAVIAE--------FSLPLDAmGVIVEGTGPY--AARVGLQRGDILLGINGEQVTTPSEAREI--LSQLGSR 446
Cdd:cd10838    5 GIQMTTLTPELAQQnnrnpnspVRIPEVD-GVLIMQVLPNspAARAGLRRGDVIQAVDGQPVTTADDVQRIveQAGVGEE 83

                         90
                 ....*....|....*...
gi 960426816 447 VAITVQRGLQRVQIRFRT 464
Cdd:cd10838   84 LELTVLRGDRRQTLAVKP 101
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 273-355 4.10e-08

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


Pssm-ID: 467629 [Multi-domain]  Cd Length: 104  Bit Score: 51.17  E-value: 4.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 273 QSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDGVAEE 352
Cdd:cd10838   17 QQNNRNPNSPVRIPEVDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRIVEQAGVGEELELTVLRGDRRQT 96


                 ...
gi 960426816 353 VDV 355
Cdd:cd10838   97 LAV 99
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 388-454 6.47e-08

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: 49.93  E-value: 6.47e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 388 AVIAEFSLPLDAMGVI---VEGTGPyAARVGLQRGDILLGINGEQVTTPSEAREILSQLGSRVAITVQRG 454
Cdd:cd23084    6 ATVSNVTDEDGGKGVVvteVDPGSP-AAQSGLKKGDVIIGVNRQPVKSIAELRKVLKSKPSAVLLQIKRG 74
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 412-463 6.73e-08

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


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 53.06  E-value: 6.73e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 960426816 412 ARVGLQRGDILLGINGEQVTTPSEAREILSQL--GSRVAITVQRGLQRVQIRFR 463
Cdd:COG3031  165 SKLGLQPGDVITSINGQDLTDPAQALELLQQLrdASEVTLTVERNGQPVTLTYN 218
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 401-453 1.20e-07

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 48.29  E-value: 1.20e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 960426816  401 GVIVEGTGPYAARVGLQRGDILLGINGEQVTTPSEAREIL-SQLGSRVAITVQR 453
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLqGSAGESVTLTVRR 54
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 379-461 1.73e-07

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: 48.83  E-value: 1.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 379 GLQMSQVNPAVIAEFSLPlDAMGVI---VEGTGPyAARVGLQRGDILLGINGEQVTTPSEAREILSQ--LGSRVAITVQR 453
Cdd:cd06779    5 GIEMENISPLLAKELGLP-VNRGVLvaeVIPGSP-AAKAGLKEGDVILSVNGKPVTSFNDLRAALDTkkPGDSLNLTILR 82


                 ....*...
gi 960426816 454 GLQRVQIR 461
Cdd:cd06779   83 DGKTLTVT 90
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 265-357 2.15e-07

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: 48.79  E-value: 2.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 265 RPWAGMSGQSIDnDIAET------LGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSP---QEMIYRMSVag 335
Cdd:cd06781    1 RPSLGISMVDLS-DVPEYeqqslkLPSNVNKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSsdlRQILYSHKV-- 77

                         90       100
                 ....*....|....*....|..
gi 960426816 336 mGSRVAVTYYRDGVAEEVDVGL 357
Cdd:cd06781   78 -GDTVKVTIYRDGKEKTLNIKL 98
SdrC COG3480
Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];
273-366 5.37e-07

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


Pssm-ID: 442703 [Multi-domain]  Cd Length: 344  Bit Score: 51.35  E-value: 5.37e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 273 QSIDNDIA---ETLGLDRPGGVLISGLHPASPfAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDGV 349
Cdd:COG3480  119 SSQENAIAaalRAAGYPVTEGVYVASVLEGSP-ADGVLQPGDVITAVDGKPVTTAEDLRDALAAKKPGDTVTLTVTRDGK 197

                         90
                 ....*....|....*..
gi 960426816 350 AEEVDVGLILPPETPAR 366
Cdd:COG3480  198 EKTVTVTLVKLPDDDGR 214
cpPDZ1_MamE-like cd23087
circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease ...
 269-348 7.90e-07

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


Pssm-ID: 467634 [Multi-domain]  Cd Length: 91  Bit Score: 47.18  E-value: 7.90e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 269 GMSGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDG 348
Cdd:cd23087    5 GAALTPMQQRLGQQTNLPAGRGVFVSGVTPNTPAAAAGLRPGDVILKVDGRPVHQPEEVSAIMAEMPNGRSVRLGVLRDG 84
eMpr COG3591
V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, ...
 86-258 1.19e-06

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


Pssm-ID: 442810 [Multi-domain]  Cd Length: 194  Bit Score: 48.90  E-value: 1.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816  86 QNSLGSGVILSADgYVVSNYHVV------GGATDIRVV--LKDRREFAAKVMLA----------DQASDLAILKLEDA-- 145
Cdd:COG3591   10 GGGVCTGTLIGPN-LVLTAGHCVydgaggGWATNIVFVpgYNGGPYGTATATRFrvppgwvasgDAGYDYALLRLDEPlg 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 146 PDMPFLTLRDSDGVEVGELALAIGNPFGIGQTVSsgivsgLARSGAATGAGrAYFIQTDAAINPGNSGGALIDIN---GE 222
Cdd:COG3591   89 DTTGWLGLAFNDAPLAGEPVTIIGYPGDRPKDLS------LDCSGRVTGVQ-GNRLSYDCDTTGGSSGSPVLDDSdggGR 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 960426816 223 LIGVNTSiltRSGGSNGVGFAIPADLVEQFVAQARQ 258
Cdd:COG3591  162 VVGVHSA---GGADRANTGVRLTSAIVAALRAWASA 194
cpPDZ_AtDEGP14-like cd23085
circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) ...
 265-331 3.50e-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: 45.53  E-value: 3.50e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 960426816 265 RPWAGMSGQSIDNDIAETLGLDRPG------GVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRM 331
Cdd:cd23085    1 RPWLGMKMLELNEHIIAQLKERDPMfpdvkaGVLVPQVIPGSPAERAGLRPGDVIVEFDGKPVDSTKQIIDAL 73
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 265-357 4.96e-06

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: 44.69  E-value: 4.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 265 RPWAGMSGQSIDNDIAETLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTY 344
Cdd:cd06777    1 RGYLGITLSEIPPAMARGGGIDQLQGALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVLELMDLVAEIRPGTVIPVVV 80

                         90
                 ....*....|...
gi 960426816 345 YRDGVAEEVDVGL 357
Cdd:cd06777   81 LRDGKQLTLEVTI 93
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 411-454 1.17e-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: 1.17e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 960426816   411 AARVGLQRGDILLGINGEQVT--TPSEAREILSQLGSRVAITVQRG 454
Cdd:smart00228  39 AAKAGLRVGDVILEVNGTSVEglTHLEAVDLLKKAGGKVTLTVLRG 84
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 379-454 2.68e-05

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: 43.01  E-value: 2.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 379 GLQM---SQVNPAVIAEFSLPLDAM-GVIVEGT---GPyAARVGLQRGDILLGINGEQVTTPSEAREILSQ--LGSRVAI 449
Cdd:cd06781    5 GISMvdlSDVPEYEQQSLKLPSNVNkGVYVAQVqsnSP-AEKAGLKKGDVITKLDGKKVESSSDLRQILYShkVGDTVKV 83


                 ....*
gi 960426816 450 TVQRG 454
Cdd:cd06781   84 TIYRD 88
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 411-460 2.72e-05

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 46.23  E-value: 2.72e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 960426816 411 AARVGLQRGDILLGINGEQVTTPSEAREILSQL-GSRVAITVQRGLQRVQI 460
Cdd:COG0750  141 AAKAGLQPGDRIVAINGQPVTSWDDLVDIIRASpGKPLTLTVERDGEELTL 191
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 379-453 3.00e-05

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: 42.47  E-value: 3.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 379 GLQMSQVNPAvIAEfSLPLD-AMGVIV---EGTGPyAARVGLQRGDILLGINGEQVTTPSEAREILSQL--GSRVAITVQ 452
Cdd:cd10839    5 GVQIQELTPD-LAE-SFGLKePKGALVaqvLPDSP-AAKAGLKAGDVILSLNGKPITSSADLRNRVATTkpGTKVELKIL 81


                 .
gi 960426816 453 R 453
Cdd:cd10839   82 R 82
cpPDZ_BsYlbL-like cd23080
circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ ...
 290-373 3.81e-05

circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis YlbL and related domains. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. Deletion of both proteases leads to accumulation of the cell division inhibitor YneA. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This YlbL family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.


Pssm-ID: 467637 [Multi-domain]  Cd Length: 83  Bit Score: 42.10  E-value: 3.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 290 GVLISGLHPASPFAAAgLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDGVAEEVDVGLILPPETPARDTV 369
Cdd:cd23080    1 GVYVLSVVENMPAKGI-LEAGDKITAIDGQNFQSSEKLIDYISSKKAGDKVKVKYERDEKEKEAELKLKQFPDEKNRIGI 79


                 ....
gi 960426816 370 TLTE 373
Cdd:cd23080   80 GVTL 83
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 282-355 4.38e-05

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 45.46  E-value: 4.38e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 960426816 282 TLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGmGSRVAVTYYRDGVAEEVDV 355
Cdd:COG0750  121 TVGVPVLTPPVVGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDDLVDIIRASP-GKPLTLTVERDGEELTLTV 193
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 283-393 1.54e-04

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: 43.71  E-value: 1.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 283 LGLD---RPGGVLISGLHPASPFAAAGLQPGDVVQMVSGgevnspqemiyrMSVAGM-------------GSRVAVTYYR 346
Cdd:COG0793   62 LGAElgeEDGKVVVVSVIPGSPAEKAGIKPGDIILAIDG------------KSVAGLtlddavkllrgkaGTKVTLTIKR 129

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 960426816 347 DGVAEEVDVGLIlppetpaRDTVTL--TEAEVLPG----LQMSQVNPAVIAEF 393
Cdd:COG0793  130 PGEGEPITVTLT-------RAEIKLpsVEAKLLEGkigyIRIPSFGENTAEEF 175
GspC_delta NF041515
type II secretion system protein GspC, deltaproteobacterial-type; Members of this family are ...
 412-463 1.66e-04

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


Pssm-ID: 469401 [Multi-domain]  Cd Length: 310  Bit Score: 43.32  E-value: 1.66e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 960426816 412 ARVGLQRGDILLGINGEQVTTPSEAREILSQL--GSRVAITVQRGLQRVQIRFR 463
Cdd:NF041515 255 GKLGLQNGDVLQSINGFDMTSPDKALEAYARLrsADHLTVSVERRGKPVTLDYN 308
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 290-357 1.79e-04

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


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 42.66  E-value: 1.79e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 960426816 290 GVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDGVAEEVDVGL 357
Cdd:COG3031  152 GYRVNPGRPGSLFSKLGLQPGDVITSINGQDLTDPAQALELLQQLRDASEVTLTVERNGQPVTLTYNL 219
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 403-463 2.20e-04

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: 39.77  E-value: 2.20e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 960426816 403 IVEGTgpYAARVGLQRGDILLGINGEQVTTPSeAREILSQL----GSRVAITVQRGLQRVQIRFR 463
Cdd:cd06782   21 PIPGG--PAEKAGIKPGDVIVAVDGESVRGMS-LDEVVKLLrgpkGTKVKLTIRRGGEGEPRDVT 82
cpPDZ_AtDEGP14-like cd23085
circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) ...
 379-454 2.28e-04

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


Pssm-ID: 467632 [Multi-domain]  Cd Length: 101  Bit Score: 40.14  E-value: 2.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 379 GLQMSQVNPAVIAEF-----SLPLDAMGVIVEGTGPY--AARVGLQRGDILLGINGEQVTTPSEAREILS-QLGSRVAIT 450
Cdd:cd23085    5 GMKMLELNEHIIAQLkerdpMFPDVKAGVLVPQVIPGspAERAGLRPGDVIVEFDGKPVDSTKQIIDALGdKVGKPFKVV 84


                 ....
gi 960426816 451 VQRG 454
Cdd:cd23085   85 VKRA 88
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 379-456 3.31e-04

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: 39.79  E-value: 3.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 379 GLQMSQVNPAVIAEF-----SLPLDAMGV----IVEGTgPyAARVGLQRGDILLGINGEQVTTPSEAREILSQlGSRVAI 449
Cdd:cd06785    5 GIRMLTLTPSLLEELkqrnpDFPDVSSGVyvhkVIPGS-P-AQRAGLKDGDVIISINGKPVKSSSDVYEAVKS-GSSLLV 81


                 ....*..
gi 960426816 450 TVQRGLQ 456
Cdd:cd06785   82 VVRRGNE 88
PDZ_ZASP52-like cd23068
PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), ...
 391-453 3.94e-04

PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Zasp52-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467281 [Multi-domain]  Cd Length: 82  Bit Score: 39.05  E-value: 3.94e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 960426816 391 AEFSLPLdamgvIVEGTGP--YAARVGLQRGDILLGINGEQVT--TPSEAREILSQLGSRVAITVQR 453
Cdd:cd23068   21 ADFGQPL-----SIQKVNPgsPADKAGLRRGDVILRINGTDTSnlTHKQAQDLIKRAGNDLQLTVQR 82
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 403-454 6.00e-04

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: 41.78  E-value: 6.00e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 960426816 403 IVEGtGPyAARVGLQRGDILLGINGEQVT--TPSEAREILS-QLGSRVAITVQRG 454
Cdd:COG0793   78 VIPG-SP-AEKAGIKPGDIILAIDGKSVAglTLDDAVKLLRgKAGTKVTLTIKRP 130
typeII_sec_gspC TIGR01713
type II secretion system protein C; This model represents GspC, protein C of the main terminal ...
 413-460 6.35e-04

type II secretion system protein C; This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 273770 [Multi-domain]  Cd Length: 259  Bit Score: 41.35  E-value: 6.35e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 960426816  413 RVGLQRGDILLGINGEQVTTPSEAREILSQLGS--RVAITVQRGLQRVQI 460
Cdd:TIGR01713 206 KSGLQDGDIAVALNGLDLRDPEQAFQALQMLREetNLTLTVERDGQREDI 255
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 282-355 7.39e-04

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: 38.62  E-value: 7.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 282 TLGLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGgevnspqemiyrMSVAGM-------------GSRVAVTYYRDG 348
Cdd:cd06782    7 EIGKDDDGYLVVVSPIPGGPAEKAGIKPGDVIVAVDG------------ESVRGMsldevvkllrgpkGTKVKLTIRRGG 74


                 ....*..
gi 960426816 349 VAEEVDV 355
Cdd:cd06782   75 EGEPRDV 81
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 284-348 1.04e-03

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


Pssm-ID: 214570 [Multi-domain]  Cd Length: 85  Bit Score: 38.13  E-value: 1.04e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 960426816   284 GLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRDG 348
Cdd:smart00228  21 GKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 290-327 1.08e-03

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: 37.99  E-value: 1.08e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 960426816 290 GVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEM 327
Cdd:cd23084   19 GVVVTEVDPGSPAAQSGLKKGDVIIGVNRQPVKSIAEL 56
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 398-452 1.24e-03

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 37.65  E-value: 1.24e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 960426816  398 DAMGVIVEGT--GPYAARVGLQRGDILLGINGEQVT--TPSEAREILSQLGSRVAITVQ 452
Cdd:pfam00595  23 GDPGIFVSEVlpGGAAEAGGLKVGDRILSINGQDVEnmTHEEAVLALKGSGGKVTLTIL 81
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 408-452 1.46e-03

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


Pssm-ID: 467153 [Multi-domain]  Cd Length: 81  Bit Score: 37.52  E-value: 1.46e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 960426816 408 GPYAARVG-LQRGDILLGINGEQVT--TPSEAREILSQLGSRVAITVQ 452
Cdd:cd00136   34 GGPAARDGrLRVGDRILEVNGVSLEglTHEEAVELLKSAGGEVTLTVR 81
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 279-357 2.07e-03

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: 37.56  E-value: 2.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 279 IAETLGLdrPGGVLISGLHPASPFAAAGLQP-----------GDVVQMVSGGEVNSPQEMIYRMSVAGMGSRVAVTYYRD 347
Cdd:cd00990   15 VARQLGV--RSGVLVLDVPPGGPAAKAGLRGtkrdefgrivlGDVIVAVDGKPVKNESDLYRALDEYKVGDVVTLKVLRG 92

                         90
                 ....*....|
gi 960426816 348 GVAEEVDVGL 357
Cdd:cd00990   93 GTKVDLKVTL 102
PDZ2_MAGI-1_3-like cd06732
PDZ domain 2 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, ...
 415-454 4.14e-03

PDZ domain 2 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467214 [Multi-domain]  Cd Length: 82  Bit Score: 35.99  E-value: 4.14e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 960426816 415 GLQRGDILLGINGEQVT--TPSEAREILSQL--GSRVAITVQRG 454
Cdd:cd06732   39 GLQEGDLIVEINGQNVQnlSHAQVVDVLKECpkGSEVTLLVQRG 82
Peptidase_M50 pfam02163
Peptidase family M50;
388-461 6.74e-03

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 38.24  E-value: 6.74e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 960426816  388 AVIAEFSLPLDAMGVIVEGTGPY-AARVGLQRGDILLGINGEQVTTPSEAREILSQL-GSRVAITVQRGLQRVQIR 461
Cdd:pfam02163  82 VLLFLSGVPPPAPPVIGGVAPGSpAAKAGLKPGDVILSINGKKITSWQDLVEALAKSpGKPITLTVERGGQTLTVT 157
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
245-375 8.86e-03

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


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 38.65  E-value: 8.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 960426816 245 PADLVEQFVAQARQGYDSFLRPWAGMSGQsidndiaetlglDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVnSP 324
Cdd:COG3975  462 LAELLAPFGLKLVYEDAPSLKPSLGLRVS------------ADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRV-TA 528

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 960426816 325 QEMIYRMSVAGMGSRVAVTYYRDGVAEEVDVglilPPETPARDTVTLTEAE 375
Cdd:COG3975  529 DNLDDALAAYKPGDPIELLVFRRDELRTVTV----TLAAAPADTYKLERVE 575
Peptidase_M50 pfam02163
Peptidase family M50;
284-355 8.94e-03

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 37.86  E-value: 8.94e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 960426816  284 GLDRPGGVLISGLHPASPFAAAGLQPGDVVQMVSGGEVNSPQEMIYRMSVAGmGSRVAVTYYRDGVAEEVDV 355
Cdd:pfam02163  88 GVPPPAPPVIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQDLVEALAKSP-GKPITLTVERGGQTLTVTI 158
 
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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