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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  136 VGYVIPNSPAFEAGFREGDKILTLNGRKINYWDDIIRTafVDDLT--KDLSFEVQRDGEKIFISI-----PRTKISefSS 208
Cdd:TIGR02037 261 VAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRA--IGTLKpgKKVTLGILRKGKEKTITVtlgasPEEQAS--SS 336

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  209 EDALGILPAHVE---------------VMVMAVEPGRPAQKIGIQSKDVIVSVNDEKIYSPAQLTSIIK-SNAGKEITLK 272
Cdd:TIGR02037 337 NPFLGLTVANLSpeirkelrlkgdvkgVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLArAKKGGRVALL 416

                  ....*
gi 825294554  273 IKRGD 277
Cdd:TIGR02037 417 ILRGG 421

RIP metalloprotease RseP; Members of this nearly universal bacterial protein family are regulated intramembrane proteolysis (RIP) proteases. Older and synonymous gene symbols include yaeL in E. coli, mmpA in Caulobacter crescentus, etc. This family includes a region that hits the PDZ domain, found in a number of proteins targeted to the membrane by binding to a peptide ligand. The N-terminal region of this family contains a perfectly conserved motif HEXGH as found in a number of metalloproteinases, where the Glu is the active site and the His residues coordinate the metal cation. Membership in this family is determined by a match to the full length of the seed alignment; the model also detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain. [Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554   12 ITIGILVLVHEFGHFIAAKLSKMKVEVFSIGFGTRLIGKKIGETDYRISAFPLGGYVKIAGMvDESLDTGFVSSKPEpyE 91
Cdd:TIGR00054  10 LALAVLIFVHELGHFLAARLCGIKVERFSIGFGPKILKFKKNGTEYAISLIPLGGYVKMKGL-DKEMEVKPPETDGD--L 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554   92 FRSKPFYQKFFVITAGVIMNMILAVFLFWAIFMVEGKTFRNVNEVGYVIPNSPAFEAGFREGDKILTLNGRKINYWDDIi 171
Cdd:TIGR00054  87 FNNKSVFQKAIIIFAGPLANFIFAIFVYIFISLIGVPGYEVGPVIELLDKNSIALEAGIEPGDEILSVNGNKIPGFKDV- 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  172 rTAFVDDLTKDLSFEVQRDGEKIfisiprtkisEFSSEDALGILPAHVEVMVMAVEPGRPAQKIGIQSKDVIVSVNDEKI 251
Cdd:TIGR00054 166 -RQQIADIAGEPMVEILAERENW----------TFEVMKELIPRGPKIEPVLSDVTPNSPAEKAGLKEGDYIQSINGEKL 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  252 YSPAQLTSIIKSNAGKEITLKIKRGDKIFDQKITPDADGRIGVQIAsfynGPVKK--ESYNPLEALWIGVRETYRVSALT 329
Cdd:TIGR00054 235 RSWTDFVSAVKENPGKSMDIKVERNGETLSISLTPEAKGKIGIGIS----PSLAPleVSYGILNAFAKGASATVDIVKLI 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  330 VNGIKQLITGKIPFqKGVAGPIRIAKFATRSADAGFTAFLGFMAILSISLAFLNIFPFPGLDGGHLAILVVEAIIRRELS 409
Cdd:TIGR00054 311 LTNLGKLITGSFKL-KNLSGPVGIVKGAGSSANSGIVYLLQFGAFLSINLGIMNLLPIPALDGGQLLFLFIEAIRGKPLP 389

                         410       420
                  ....*....|....*....|....*..
gi 825294554  410 YRVKVAIQQAGIIILIILMIFVLYNDI 436
Cdd:TIGR00054 390 EKVQAFVYRIGVAFLLFLMGLGLFNDL 416

Peptidase family M50;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554    9 YFAITIGILVLVHEFGHFIAAKLSKMKVEVFSIGFgtrligkkigetdYRISAFPLGGYVKIAGmvdesldtgfvsskpe 88
Cdd:pfam02163   1 AFILALGILVVVHELGHFLVARRFGVKVERFSIGF-------------YRIALIPLGGYVKMAD---------------- 51

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554   89 pyEFRSKPFYQKFFVITAGVIMNMILAVFLFWAIFMVEGKTFRNVNEVGYVIPNSPAFEAGFREGDKILTLNGRKINYWD 168
Cdd:pfam02163  52 --EFKSKSPWQRLAIALAGPLANFILAIILFAVLLFLSGVPPPAPPVIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQ 129

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  169 Diirtafvddltkdlsfevqrdgekifisiprtkisefssedalgilpahvevmvmavepgrpaqkigiqskdvivsvnd 248
Cdd:pfam02163 130 D------------------------------------------------------------------------------- 130

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  249 ekiyspaqLTSIIKSNAGKEITLKIKRGDKIFDQKITPDADG---RIGVQIasfyngpvKKESYNPLEALWIGVRETYRV 325
Cdd:pfam02163 131 --------LVEALAKSPGKPITLTVERGGQTLTVTITPKSSEeskFIGIGP--------VYVKYGLLEALGFALEKTVNL 194

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  326 SALTVNGIKQLITGKIPfqKGVAGPIRIAkfaTRSADAGFTAFLGFMAILSISLAFLNIFPFPGLDGGHLAILVVEAIIR 405
Cdd:pfam02163 195 VTLTLKALGKLITGVSL--KNLGGPIGIA---GQAAEAGLIAFLYFLALINLNLGIFNLLPVPPLDGGHILRALLEAIRG 269

                         410
                  ....*....|....*
gi 825294554  406 RELSYRVKVAIQQAG 420
Cdd:pfam02163 270 KPLSERAEEIALRVG 284

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  136 VGYVIPNSPAFEAGFREGDKILTLNGRKINYWDDIIRTafVDDLT--KDLSFEVQRDGEKIFISI-----PRTKISefSS 208
Cdd:TIGR02037 261 VAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRA--IGTLKpgKKVTLGILRKGKEKTITVtlgasPEEQAS--SS 336

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  209 EDALGILPAHVE---------------VMVMAVEPGRPAQKIGIQSKDVIVSVNDEKIYSPAQLTSIIK-SNAGKEITLK 272
Cdd:TIGR02037 337 NPFLGLTVANLSpeirkelrlkgdvkgVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLArAKKGGRVALL 416

                  ....*
gi 825294554  273 IKRGD 277
Cdd:TIGR02037 417 ILRGG 421

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 825294554 215 LPAHVEVMVMAVEPGRPAQKIGIQSKDVIVSVNDEKIYSPAQLTSIIKS-NAGKEITLKIKRGDKIFDQKITPDA 288
Cdd:COG0265  197 LPEPEGVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRLLASlKPGDTVTLTVLRGGKELTVTVTLGE 271

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 825294554  223 VMAVEPGRPAQKIGIQSKDVIVSVNDEKIYSPAQLTSIIKSNAGKEITLKIKR 275
Cdd:pfam17820   2 VTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLQGSAGESVTLTVRR 54

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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554   122 IFMVEGKTFRNVNEVGYVIPNSPAFEAGFREGDKILTLNGRKINYWDDIIRTAFVDDLTKDLSFEVQRDG 191
Cdd:smart00228  16 FSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRGG 85

RIP metalloprotease RseP; Members of this nearly universal bacterial protein family are regulated intramembrane proteolysis (RIP) proteases. Older and synonymous gene symbols include yaeL in E. coli, mmpA in Caulobacter crescentus, etc. This family includes a region that hits the PDZ domain, found in a number of proteins targeted to the membrane by binding to a peptide ligand. The N-terminal region of this family contains a perfectly conserved motif HEXGH as found in a number of metalloproteinases, where the Glu is the active site and the His residues coordinate the metal cation. Membership in this family is determined by a match to the full length of the seed alignment; the model also detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain. [Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554   12 ITIGILVLVHEFGHFIAAKLSKMKVEVFSIGFGTRLIGKKIGETDYRISAFPLGGYVKIAGMvDESLDTGFVSSKPEpyE 91
Cdd:TIGR00054  10 LALAVLIFVHELGHFLAARLCGIKVERFSIGFGPKILKFKKNGTEYAISLIPLGGYVKMKGL-DKEMEVKPPETDGD--L 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554   92 FRSKPFYQKFFVITAGVIMNMILAVFLFWAIFMVEGKTFRNVNEVGYVIPNSPAFEAGFREGDKILTLNGRKINYWDDIi 171
Cdd:TIGR00054  87 FNNKSVFQKAIIIFAGPLANFIFAIFVYIFISLIGVPGYEVGPVIELLDKNSIALEAGIEPGDEILSVNGNKIPGFKDV- 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  172 rTAFVDDLTKDLSFEVQRDGEKIfisiprtkisEFSSEDALGILPAHVEVMVMAVEPGRPAQKIGIQSKDVIVSVNDEKI 251
Cdd:TIGR00054 166 -RQQIADIAGEPMVEILAERENW----------TFEVMKELIPRGPKIEPVLSDVTPNSPAEKAGLKEGDYIQSINGEKL 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  252 YSPAQLTSIIKSNAGKEITLKIKRGDKIFDQKITPDADGRIGVQIAsfynGPVKK--ESYNPLEALWIGVRETYRVSALT 329
Cdd:TIGR00054 235 RSWTDFVSAVKENPGKSMDIKVERNGETLSISLTPEAKGKIGIGIS----PSLAPleVSYGILNAFAKGASATVDIVKLI 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  330 VNGIKQLITGKIPFqKGVAGPIRIAKFATRSADAGFTAFLGFMAILSISLAFLNIFPFPGLDGGHLAILVVEAIIRRELS 409
Cdd:TIGR00054 311 LTNLGKLITGSFKL-KNLSGPVGIVKGAGSSANSGIVYLLQFGAFLSINLGIMNLLPIPALDGGQLLFLFIEAIRGKPLP 389

                         410       420
                  ....*....|....*....|....*..
gi 825294554  410 YRVKVAIQQAGIIILIILMIFVLYNDI 436
Cdd:TIGR00054 390 EKVQAFVYRIGVAFLLFLMGLGLFNDL 416

Peptidase family M50;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554    9 YFAITIGILVLVHEFGHFIAAKLSKMKVEVFSIGFgtrligkkigetdYRISAFPLGGYVKIAGmvdesldtgfvsskpe 88
Cdd:pfam02163   1 AFILALGILVVVHELGHFLVARRFGVKVERFSIGF-------------YRIALIPLGGYVKMAD---------------- 51

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554   89 pyEFRSKPFYQKFFVITAGVIMNMILAVFLFWAIFMVEGKTFRNVNEVGYVIPNSPAFEAGFREGDKILTLNGRKINYWD 168
Cdd:pfam02163  52 --EFKSKSPWQRLAIALAGPLANFILAIILFAVLLFLSGVPPPAPPVIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQ 129

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  169 Diirtafvddltkdlsfevqrdgekifisiprtkisefssedalgilpahvevmvmavepgrpaqkigiqskdvivsvnd 248
Cdd:pfam02163 130 D------------------------------------------------------------------------------- 130

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  249 ekiyspaqLTSIIKSNAGKEITLKIKRGDKIFDQKITPDADG---RIGVQIasfyngpvKKESYNPLEALWIGVRETYRV 325
Cdd:pfam02163 131 --------LVEALAKSPGKPITLTVERGGQTLTVTITPKSSEeskFIGIGP--------VYVKYGLLEALGFALEKTVNL 194

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  326 SALTVNGIKQLITGKIPfqKGVAGPIRIAkfaTRSADAGFTAFLGFMAILSISLAFLNIFPFPGLDGGHLAILVVEAIIR 405
Cdd:pfam02163 195 VTLTLKALGKLITGVSL--KNLGGPIGIA---GQAAEAGLIAFLYFLALINLNLGIFNLLPVPPLDGGHILRALLEAIRG 269

                         410
                  ....*....|....*
gi 825294554  406 RELSYRVKVAIQQAG 420
Cdd:pfam02163 270 KPLSERAEEIALRVG 284

Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-binding proteins (SREBPs) from membranes of the ER. These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD superfamily. Prokaryotic S2P/M50 homologs have been shown to regulate stress responses, sporulation, cell division, and cell differentiation. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses, and in Bacillus subtilis, the S2P homolog SpoIVFB is involved in the pro-sigmaK pathway of spore formation. Some of the subfamilies within this hierarchy contain one or two PDZ domain insertions, with putative regulatory roles, such as the inhibition of substrate cleavage as seen by the RseP PDZ domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554   8 FYFAITIGILVLVHEFGHFIAAKLSKMKVEVFSIGFgtrLIGKKIGETDYRISAFPLGGYVKIAGMVDESLdtgfvsskp 87
Cdd:cd05709    1 LAFILALLISVTVHELGHALVARRLGVKVARFSGGF---TLNPLKHGDPYGIILIPLGGYAKPVGENPRAF--------- 68

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 825294554  88 epyefrSKPFYQKFFVITAGVIMNMILAVFLFWAIFMVEGKTFRNVNEVGYVIPNSPAFEAGF 150
Cdd:cd05709   69 ------KKPRWQRLLVALAGPLANLLLALLLLLLLLLLGGLPPAPVGQAASSGLANLLAFLAL 125

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]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  136 VGYVIPNSPAFEAGFREGDKILTLNGRKINYWDDIIRTafVDDLT--KDLSFEVQRDGEKIFISI-----PRTKISefSS 208
Cdd:TIGR02037 261 VAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRA--IGTLKpgKKVTLGILRKGKEKTITVtlgasPEEQAS--SS 336

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554  209 EDALGILPAHVE---------------VMVMAVEPGRPAQKIGIQSKDVIVSVNDEKIYSPAQLTSIIK-SNAGKEITLK 272
Cdd:TIGR02037 337 NPFLGLTVANLSpeirkelrlkgdvkgVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLArAKKGGRVALL 416

                  ....*
gi 825294554  273 IKRGD 277
Cdd:TIGR02037 417 ILRGG 421

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554 136 VGYVIPNSPAFEAGFREGDKILTLNGRKINYWDDIIRTaFVDDLTKDLSFEVQRDGEKIFISI-PRTKISEFSSEDALGI 214
Cdd:cd23081    3 VGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRI-VRENPGKPLTLKIERDGKILTVTVtPELVEVEGKGVGRIGV 81

                 ..
gi 825294554 215 LP 216
Cdd:cd23081   82 QP 83

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 825294554 214 ILPAHVEVMVMAVEPGRPAQKIGIQSKDVIVSVNDEKIYSPAQLTSIIKSNA-GKEITLKIKRGDK 278
Cdd:cd10838   28 RIPEVDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRIVEQAGvGEELELTVLRGDR 93

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 825294554 211 ALGILPAHVEVMVMAVEPGRPAQKIGIQSKDVIVSVNDEKIYSPAQLTSIIKSN-AGKEITLKIKRGDKIFD 281
Cdd:cd06779   17 KELGLPVNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTKkPGDSLNLTILRDGKTLT 88

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

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                  ....*....|....*....|....*....|....*....|....*....|...
gi 825294554  223 VMAVEPGRPAQKIGIQSKDVIVSVNDEKIYSPAQLTSIIKSNAGKEITLKIKR 275
Cdd:pfam17820   2 VTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLQGSAGESVTLTVRR 54

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 825294554 221 VMVMAVEPGRPAQKIGIQSKDVIVSVNDEKIYSPAQLTSII-KSNAGKEITLKIKRGDKIFDQKIT 285
Cdd:cd06781   32 VYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILySHKVGDTVKVTIYRDGKEKTLNIK 97

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 825294554 135 EVGYVIPNSPAFEAGFREGDKILTLNGRKINYWDDIIRTAfvDDLTKDLSFEVQRDGEKIFISIP 199
Cdd:cd23084   21 VVTEVDPGSPAAQSGLKKGDVIIGVNRQPVKSIAELRKVL--KSKPSAVLLQIKRGDSSRYLALP 83

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]

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 825294554  221 VMVMAVEPGRPAQKIGIQSKDVIVSVNDEKIYSPAQLTSII-KSNAGKEITLKIKRGDKIFDQKIT 285
Cdd:TIGR02037 259 ALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIgTLKPGKKVTLGILRKGKEKTITVT 324

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 825294554 220 EVMVMAVEPGRPAQKIGIQSKDVIVSVNDEKIY--SPAQLTSIIKSNAGKEITLKIKRGD--KIFDQKIT 285
Cdd:cd06782   15 YLVVVSPIPGGPAEKAGIKPGDVIVAVDGESVRgmSLDEVVKLLRGPKGTKVKLTIRRGGegEPRDVTLT 84

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.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 825294554 139 VIPNSPAFEAGFREGDKILTLNG---RKINYWDDIIRTAFVDDltkDLSFEVQRDGEKIFISI 198
Cdd:cd06779   32 VIPGSPAAKAGLKEGDVILSVNGkpvTSFNDLRAALDTKKPGD---SLNLTILRDGKTLTVTV 91