C-terminal processing peptidase-like; serine protease family S41; Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP). CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at variable distance from the C-terminus. The CPP active site consists of a serine/lysine catalytic dyad. Conservation of these residues is seen in the CPP-like proteins of this group. CPP proteins contain a PDZ domain that promotes protein-protein interactions and is important for substrate recognition however, most of CPP-like proteins only have an internal fragment or lack the PDZ domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 216 ETTLTAERLYPNPVLRAEVIEEGEHKIGYMVYNGFDAAYDDDLLDSLRKFRDAGITDLVLDLRYNGGGHVISAKMLATCI 295
Cdd:cd07561    40 EDFLESLLSEKDGKDRFSYIVDGGKKVGYLVYNSFTSGYDDELNQAFAEFKAQGVTELVLDLRYNGGGLVSSANLLASLL 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 296 AGEKCDGKVFQYYRYNDSRMADpaktqkqtgntydrekalfYENFSYGDYYGADLKQyaLGLQNIYVLTTGSTASSSEAV 375
Cdd:cd07561   120 APAVALGQVFATLEYNDKRSAN-------------------NEDLLFSSKTLAGGNS--LNLSKVYVLTSGSTASASELV 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 376 INGLRGIdISVTLIGEKTNGKNVGMEIdKFDDGDYSYELAPITFEGYNAKKETVNPAGLAVDYAVADWNNRLVDFG-PEE 454
Cdd:cd07561   179 INSLKPY-MDVVLIGETTYGKNVGSLT-FEDDRKHKWALQPVVFKVVNADGQGDYSNGLTPDIEVNEDSSNLLPLGdPNE 256

C-terminal processing peptidase-like; serine protease family S41; Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP). CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at variable distance from the C-terminus. The CPP active site consists of a serine/lysine catalytic dyad. Conservation of these residues is seen in the CPP-like proteins of this group. CPP proteins contain a PDZ domain that promotes protein-protein interactions and is important for substrate recognition however, most of CPP-like proteins only have an internal fragment or lack the PDZ domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 216 ETTLTAERLYPNPVLRAEVIEEGEHKIGYMVYNGFDAAYDDDLLDSLRKFRDAGITDLVLDLRYNGGGHVISAKMLATCI 295
Cdd:cd07561    40 EDFLESLLSEKDGKDRFSYIVDGGKKVGYLVYNSFTSGYDDELNQAFAEFKAQGVTELVLDLRYNGGGLVSSANLLASLL 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 296 AGEKCDGKVFQYYRYNDSRMADpaktqkqtgntydrekalfYENFSYGDYYGADLKQyaLGLQNIYVLTTGSTASSSEAV 375
Cdd:cd07561   120 APAVALGQVFATLEYNDKRSAN-------------------NEDLLFSSKTLAGGNS--LNLSKVYVLTSGSTASASELV 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 376 INGLRGIdISVTLIGEKTNGKNVGMEIdKFDDGDYSYELAPITFEGYNAKKETVNPAGLAVDYAVADWNNRLVDFG-PEE 454
Cdd:cd07561   179 INSLKPY-MDVVLIGETTYGKNVGSLT-FEDDRKHKWALQPVVFKVVNADGQGDYSNGLTPDIEVNEDSSNLLPLGdPNE 256

Peptidase family S41;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 241 KIGYMVYNGFDAAYDDDLLDSLRKFRDAGITDLVLDLRYNGGGHVISAKMLATCIAGEKCDGKVFQYYRYNDSRMADPak 320
Cdd:pfam03572   1 KIGYIRIPSFSEKTAKELAEALKELKKQGVKGLILDLRGNPGGLLSAAVEIASLFLPDGTIVSTRGRDGSKEVYFAAG-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 321 tqKQTGNTYDRekalfyenfsygdyygadlkqyalglqNIYVLTTGSTASSSEAVINGLRGIDIsVTLIGEKTNGKNVGM 400
Cdd:pfam03572  79 --KADEVLWKG---------------------------PLVVLVNEGSASASEIFAGALQDNGR-ATLVGERTFGKGTVQ 128

                  ....*...
gi 2550899171 401 EIDKFDDG 408
Cdd:pfam03572 129 TVYPLPDG 136

carboxyl-terminal processing protease; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 120 TRGVNHGVRKETEYGFGFARLGvvrfsntgkAGFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIAdSESEYTpVYKRLTS 199
Cdd:PLN00049   80 TKGAVTGVGLEVGYPTGSDGPP---------AGLVVVAPAPGGPAARAGIRPGDVILAIDGTSTE-GLSLYE-AADRLQG 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 200 PSGaASVLFKVRETGEE--TTLTAERLYPNPVLRA--EV--IEEGEHKIGYMVYNGFDAAYDDDLLDSLRKFRDAGITDL 273
Cdd:PLN00049  149 PEG-SSVELTLRRGPETrlVTLTREKVSLNPVKSRlcEVpgPGAGSPKIGYIKLTTFNQNASSAVKEAIETLRANGVDAF 227

                         170
                  ....*....|
gi 2550899171 274 VLDLRYNGGG 283
Cdd:PLN00049  228 VLDLRDNSGG 237

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This NHERF-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 127 VRKETEyGFGFaRLGVVRfsntGKAGFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIADSESEYtpvykrltspsgaasV 206
Cdd:cd06768     5 LVKGPE-GYGF-NLHAEK----GRPGHFIREVDPGSPAERAGLKDGDRLVEVNGENVEGESHEQ---------------V 63

                          90
                  ....*....|....
gi 2550899171 207 LFKVRETGEETTLT 220
Cdd:cd06768    64 VEKIKASGNQVTLL 77

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2550899171 152 GFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIADSESeytpVYKRLTSPSGAASVLFKVRETGEETTLTAE 222
Cdd:COG0265   202 GVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARD----LQRLLASLKPGDTVTLTVLRGGKELTVTVT 268

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2550899171 152 GFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIaDSESEYtpVYKRLTSPSGAASVLfKVRETGEETTLTAE 222
Cdd:TIGR02037 258 GALVAQVLPGSPAEKAGLKAGDVITSVNGKPI-SSFADL--RRAIGTLKPGKKVTL-GILRKGKEKTITVT 324

C-terminal processing peptidase-like; serine protease family S41; Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP). CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at variable distance from the C-terminus. The CPP active site consists of a serine/lysine catalytic dyad. Conservation of these residues is seen in the CPP-like proteins of this group. CPP proteins contain a PDZ domain that promotes protein-protein interactions and is important for substrate recognition however, most of CPP-like proteins only have an internal fragment or lack the PDZ domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 216 ETTLTAERLYPNPVLRAEVIEEGEHKIGYMVYNGFDAAYDDDLLDSLRKFRDAGITDLVLDLRYNGGGHVISAKMLATCI 295
Cdd:cd07561    40 EDFLESLLSEKDGKDRFSYIVDGGKKVGYLVYNSFTSGYDDELNQAFAEFKAQGVTELVLDLRYNGGGLVSSANLLASLL 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 296 AGEKCDGKVFQYYRYNDSRMADpaktqkqtgntydrekalfYENFSYGDYYGADLKQyaLGLQNIYVLTTGSTASSSEAV 375
Cdd:cd07561   120 APAVALGQVFATLEYNDKRSAN-------------------NEDLLFSSKTLAGGNS--LNLSKVYVLTSGSTASASELV 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 376 INGLRGIdISVTLIGEKTNGKNVGMEIdKFDDGDYSYELAPITFEGYNAKKETVNPAGLAVDYAVADWNNRLVDFG-PEE 454
Cdd:cd07561   179 INSLKPY-MDVVLIGETTYGKNVGSLT-FEDDRKHKWALQPVVFKVVNADGQGDYSNGLTPDIEVNEDSSNLLPLGdPNE 256

C-terminal processing peptidase family S41; Peptidase family S41 (C-terminal processing peptidase or CTPase family) contains very different subfamilies; it includes photosystem II D1 C-terminal processing protease (CTPase), interphotoreceptor retinoid-binding protein IRBP and tricorn protease (TRI). CTPase and TRI both contain the PDZ domain while IRBP, although being very similar to the tail-specific protease domain, lacks the PDZ insertion domain and hydrolytic activity. These serine proteases have distinctly different active sites: in CTPase, the active site consists of a serine/lysine catalytic dyad while in tricorn core protease, it is a tetrad (serine, histidine, serine, glutamate). CPases with different substrate specificities in different species include processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein; and others such as tricorn protease (TRI) act as a carboxypeptidase, involved in the degradation of proteasomal products. CTPase homolog IRBP, secreted by photoreceptors into the interphotoreceptor matrix, having arisen in the early evolution of the vertebrate eye, promotes the release of all-trans retinol from photoreceptors and facilitates its delivery to the retinal pigment epithelium.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 242 IGYMVYNGFDAAYDDDLLDSLRKFRDAGITDLVLDLRYNGGGHVISAKMLATCIAGEkcdGKVFQYYRYNDSRMADPAKT 321
Cdd:cd06567    61 IGYIRIPSFSAESTAEELREALAELKKGVKGLILDLRNNPGGLLSAAVELASLFLPK---GKIVVTTRRRGGNETEYVAP 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 322 QKQTGNTYDrekalfyenfsygdyygadlkqyalglqnIYVLTTGSTASSSEAVINGLRGIDIsVTLIGEKTNGKNVGME 401
Cdd:cd06567   138 GGGSLYDGP-----------------------------LVVLVNEGSASASEIFAGALQDLGR-ATLVGERTFGKGSVQT 187

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2550899171 402 IdkFDDGDYSYELAPiTFEGYNAKKETVNPAGLAVDYAVA 441
Cdd:cd06567   188 V--FPLLDGSALKLT-TAKYYTPSGRSIEGKGVEPDIEVP 224

C-terminal peptidase (prc); A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database. [Protein fate, Degradation of proteins, peptides, and glycopeptides, Protein fate, Protein modification and repair]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 155 VMAVYPGSPADRAGFRRGTIFSEIDGAEIADSESEytPVYKRLTSPSGAaSVLFKVRETGEETTLTAER---LYPNPVLR 231
Cdd:TIGR00225  66 IVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLD--DAVALIRGKKGT-KVSLEILRAGKSKPLSFTLkrdRIELETVK 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 232 AEVIEEGEHKIGYMVYNGFDAAYDDDLLDSLRKFRDAGITDLVLDLRYNGGGHVISAKMLATCIAGEkcDGKVFQYYRYN 311
Cdd:TIGR00225 143 ASVKKVGGHSVGYIRISSFSEHTAEDVAKALDKLEKKNAKGYILDLRGNPGGLLQSAVDISRLFITK--GPIVQTKDRNG 220

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 312 DSRMADPAKTQKqtgntYDREkalfyenfsygdyygadlkqyalglqnIYVLTTGSTASSSEAVINGLRgiDIS-VTLIG 390
Cdd:TIGR00225 221 SKRHYKANGRQK-----YNLP---------------------------LVVLVNRGSASASEILAGALQ--DNGrATIVG 266

                         250
                  ....*....|....*...
gi 2550899171 391 EKTNGKNVGMEIDKFDDG 408
Cdd:TIGR00225 267 EKTFGKGTVQQVRPLNDG 284

tail specific protease; tail specific protease

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171  228 PVLRAEVIEEGEHKIGYMVYNGFDAAYDDDLLDSLRKFRDAGITDLVLDLRYNGGGHVISAKMLATCIAgeKCDGKVFQY 307
Cdd:smart00245  16 ETLEGNVGYLRFGFIGYIRIPEFSEHTSNLVEKAWKKLEKTNVEGLILDLRNNPGGLLSAAIDVSSLFL--DKGVIVYTV 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171  308 YRYNDSRMADPAKTQKQtgntydrekalfyenfsygdyYGADlkqyalglqnIYVLTTGSTASSSEAVINGLRGIDIsVT 387
Cdd:smart00245  94 YRRTGELWTYPANLGRK---------------------YSKP----------LVVLVNKGTASASEIFAGALKDLGR-AT 141

                          170       180
                   ....*....|....*....|...
gi 2550899171  388 LIGEKTNGKNVGMEIDKFDDGDY 410
Cdd:smart00245 142 IVGERTFGKGLVQQTVPLGDGSG 164

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This NHERF-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2550899171 127 VRKETEyGFGFaRLGVVRfsntGKAGFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIADSESEYtpvykrltspsgaasV 206
Cdd:cd06768     5 LVKGPE-GYGF-NLHAEK----GRPGHFIREVDPGSPAERAGLKDGDRLVEVNGENVEGESHEQ---------------V 63

                          90
                  ....*....|....
gi 2550899171 207 LFKVRETGEETTLT 220
Cdd:cd06768    64 VEKIKASGNQVTLL 77

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2550899171 152 GFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIADSESeytpVYKRLTSPSGAASVLFKVRETGEETTLT 220
Cdd:cd06779    26 GVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFND----LRAALDTKKPGDSLNLTILRDGKTLTVT 90

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2550899171 152 GFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIADSESeytpVYKRLTSPSGAASVLFKVRETGEETTLTAE 222
Cdd:COG0265   202 GVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARD----LQRLLASLKPGDTVTLTVLRGGKELTVTVT 268

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.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 2550899171 150 KAGFYVMAVYPGSPADRAGFRRGTIFSEIDG 180
Cdd:cd23085    30 KAGVLVPQVIPGSPAERAGLRPGDVIVEFDG 60

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.

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gi 2550899171 152 GFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIADSE 187
Cdd:cd10838    34 GVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTAD 69

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 2550899171 150 KAGFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIADSESEYTPVYK 195
Cdd:cd06781    29 NKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILYS 74

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.

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gi 2550899171  127 VRKETEyGFGFARLGVVRFSNtgkaGFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIADSESEYtpVYKRLTSPSGAASV 206
Cdd:smart00228   7 LEKGGG-GLGFSLVGGKDEGG----GVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLE--AVDLLKKAGGKVTL 79

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gi 2550899171  207 L 207
Cdd:smart00228  80 T 80

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.

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gi 2550899171 152 GFYVMAVYPGSPADRAGFRRGTIFSEIDGAEIADSESEY 190
Cdd:cd06785    32 GVYVHKVIPGSPAQRAGLKDGDVIISINGKPVKSSSDVY 70

PDZ domain 4 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 4 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 PDZ4 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.

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gi 2550899171 128 RKETEyGFGFarlgVVRFSNTGKAGFYVMAVYPGSPADRAG 168
Cdd:cd06734     8 RRENE-GFGF----VIISSVNKKSGSKIGRIIPGSPADRCG 43