Nas2 N_terminal domain; Nas2 is a proteosome assembly chaperone. Nas2 bivalently binds the proteasome Rpt5 subunit. The Nas2 N-terminal helical domain masks the Rpt1-interacting surface of Rpt5.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025    11 LERLINAKKQLEAQINRNGQILAANdNVGMSGPLVDAEGFPRNDIDVYQVRLARQTIICLQNDHKELMNQIQTLLNQYHS 90
Cdd:pfam18265   1 LKELMAKKDEIEAELEELSDVLDSH-GVGMDGPLVDEEGFPRSDIDVYQVRLARHRIICLRNDYKALMKQIEEALHELHS 79

Nas2 N_terminal domain; Nas2 is a proteosome assembly chaperone. Nas2 bivalently binds the proteasome Rpt5 subunit. The Nas2 N-terminal helical domain masks the Rpt1-interacting surface of Rpt5.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025    11 LERLINAKKQLEAQINRNGQILAANdNVGMSGPLVDAEGFPRNDIDVYQVRLARQTIICLQNDHKELMNQIQTLLNQYHS 90
Cdd:pfam18265   1 LKELMAKKDEIEAELEELSDVLDSH-GVGMDGPLVDEEGFPRSDIDVYQVRLARHRIICLRNDYKALMKQIEEALHELHS 79

Peptidase family M50;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025   124 PARAIVVVNLVSPDSPAERAGLCAGDAILrfgSINsGNFKGDLAQIGELVRNMQSQNVQLKVKRGEQQLDLILVPKTWSG 203
Cdd:pfam02163  90 PPPAPPVIGGVAPGSPAAKAGLKPGDVIL---SIN-GKKITSWQDLVEALAKSPGKPITLTVERGGQTLTVTITPKSSEE 165

                  ....*
gi 21358025   204 RGLLG 208
Cdd:pfam02163 166 SKFIG 170

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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025    116 GANITDLAPARAIVVVNLVSPDSPAERAGLCAGDAILrfgSINsgnfkgdlaqiGELVRNMQSQNVQLKVKRGEQQLDLI 195
Cdd:smart00228  15 GFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVIL---EVN-----------GTSVEGLTHLEAVDLLKKAGGKVTLT 80

                   ....
gi 21358025    196 LVPK 199
Cdd:smart00228  81 VLRG 84

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 21358025    91 EIATTDPELvnrASALDLDSdrsPGGANITDlaparaivvvnlVSPDSPAERAGLCAGDAILRFG--SINSgnfKGDL-A 167
Cdd:TIGR02037 239 TIQEVTSDL---AKSLGLEK---QRGALVAQ------------VLPGSPAEKAGLKAGDVITSVNgkPISS---FADLrR 297

                          90       100       110
                  ....*....|....*....|....*....|.
gi 21358025   168 QIGELvrnMQSQNVQLKVKRG--EQQLDLIL 196
Cdd:TIGR02037 298 AIGTL---KPGKKVTLGILRKgkEKTITVTL 325

Nas2 N_terminal domain; Nas2 is a proteosome assembly chaperone. Nas2 bivalently binds the proteasome Rpt5 subunit. The Nas2 N-terminal helical domain masks the Rpt1-interacting surface of Rpt5.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025    11 LERLINAKKQLEAQINRNGQILAANdNVGMSGPLVDAEGFPRNDIDVYQVRLARQTIICLQNDHKELMNQIQTLLNQYHS 90
Cdd:pfam18265   1 LKELMAKKDEIEAELEELSDVLDSH-GVGMDGPLVDEEGFPRSDIDVYQVRLARHRIICLRNDYKALMKQIEEALHELHS 79

Peptidase family M50;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025   124 PARAIVVVNLVSPDSPAERAGLCAGDAILrfgSINsGNFKGDLAQIGELVRNMQSQNVQLKVKRGEQQLDLILVPKTWSG 203
Cdd:pfam02163  90 PPPAPPVIGGVAPGSPAAKAGLKPGDVIL---SIN-GKKITSWQDLVEALAKSPGKPITLTVERGGQTLTVTITPKSSEE 165

                  ....*
gi 21358025   204 RGLLG 208
Cdd:pfam02163 166 SKFIG 170

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 21358025   130 VVNLVSPDSPAERAGLCAGDAILRFGSINSgnfkGDLAQIGELVRNMQSQNVQLKVKR 187
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPV----RSLEDVARLLQGSAGESVTLTVRR 54

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025 116 GANITdLAPARAIVVVNLVsPDSPAERAGLCAGDAILrfgSINSGNFKG-DLAQIGELVRNMQSQNVQLKVKRGE--QQL 192
Cdd:cd06782   5 GIEIG-KDDDGYLVVVSPI-PGGPAEKAGIKPGDVIV---AVDGESVRGmSLDEVVKLLRGPKGTKVKLTIRRGGegEPR 79

                ....*
gi 21358025 193 DLILV 197
Cdd:cd06782  80 DVTLT 84

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025 110 SDRSPGGANITDLAPARAIVVVNlVSPDSPAERAGLCAGDAILRFG--SINSgnfkgdlaqIGELVRNMQS----QNVQL 183
Cdd:COG0265 185 QPVTPELAEALGLPEPEGVLVAR-VEPGSPAAKAGLRPGDVILAVDgkPVTS---------ARDLQRLLASlkpgDTVTL 254

                        90
                ....*....|....*
gi 21358025 184 KVKRGEQQLDLILVP 198
Cdd:COG0265 255 TVLRGGKELTVTVTL 269

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025  77 LMNQIQTLLNQYHSEIATTDpelvnRASALDLDSDRSPG--GANITdlAPARAIVVVNLVsPDSPAERAGLCAGDAILrf 154
Cdd:COG0793  27 ALNGMLGELGDPHSYYLDPE-----EYEDFQESTSGEFGglGAELG--EEDGKVVVVSVI-PGSPAEKAGIKPGDIIL-- 96

                        90       100       110
                ....*....|....*....|....*....|....*
gi 21358025 155 gSINSGNFKG-DLAQIGELVRNMQSQNVQLKVKRG 188
Cdd:COG0793  97 -AIDGKSVAGlTLDDAVKLLRGKAGTKVTLTIKRP 130

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025 129 VVVNLVSPDSPAERAGLCAGDAILrfgSINSGNFKgDLAQIGELVRNmqSQNVQLKVKRGEQQLDLILVP 198
Cdd:cd06785  33 VYVHKVIPGSPAQRAGLKDGDVII---SINGKPVK-SSSDVYEAVKS--GSSLLVVVRRGNEDLLLTVTP 96

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        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025 116 GANITDLAPARAI---------VVVNLVSPDSPAERAGLCAGDAILRFGSINSGNFkgdlAQIGELVRNMQS-QNVQLKV 185
Cdd:cd06779   5 GIEMENISPLLAKelglpvnrgVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSF----NDLRAALDTKKPgDSLNLTI 80

                ....*....
gi 21358025 186 KRGEQQLDL 194
Cdd:cd06779  81 LRDGKTLTV 89

PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of tamalin, cytohesin-1-interacting protein, and related domains. Tamalin (trafficking regulator and scaffold protein tamalin, also known as general receptor for phosphoinositides 1-associated scaffold protein, GRASP) functions to link receptors, including group 1 metabotropic glutamate receptors (mGluRs), to neuronal proteins. The tamalin PDZ domain binds the C-terminal domains of group I mGluRs; it also binds potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2), neurotrophin-3 (NT3) TrkCT1-truncated receptor, SAP90/PSD-95-associated protein, and tamalin itself. CYTIP (cytohesin-1-interacting protein, also known as Pleckstrin homology Sec7 and coiled-coil domain-binding protein) sequesters cytohesin-1 in the cytoplasm, limiting its interaction with beta2 integrins; cytohesin-1 binds the CYTIP coiled coil domain. The CYTIP PDZ domain can bind the C-terminal peptide of protocadherin alpha-1 (PCDHA1), indicating a possible interaction between the two. 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 tamalin-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
                ....*....|....*....|....*....|....*....|....*....|..
gi 21358025 131 VNLVSPDSPAERAGLCAGDAILrfgSINSGNFKG-DLAQIGELVRnmQSQNV 181
Cdd:cd06713  39 VCRVHEDSPAYLAGLTAGDVIL---SVNGVSVEGaSHQEIVELIR--SSGNT 85

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21358025 134 VSPDSPAERAGLCAGDAILRFGSINsgnfkgdlaqigelVRNMQSQNVQLKVKRGEQQLDLIL 196
Cdd:cd23068  32 VNPGSPADKAGLRRGDVILRINGTD--------------TSNLTHKQAQDLIKRAGNDLQLTV 80

circularly permuted PDZ domain 2 (PDZ-C) 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-sigmaE) 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 it 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025 134 VSPDSPAERAGLCAGDAILRfgsINsGNFKGDLAQIGELVRNMQSQNVQLKVKRGEQQLDLILVPKTWSG 203
Cdd:cd23083   6 VQPNSAAEKAGLQAGDRIVK---VD-GQPLTQWQTFVMAVRDNPGKPLALEIERQGSPLSLTLIPDSKEL 71

PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. 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 whirlin family PDZ1 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
                ....*....|....*....|....*...
gi 21358025 131 VNLVSPDSPAERAGLCAGDAILRFGSIN 158
Cdd:cd06740  31 VSLVEPGSLAEKEGLRVGDQILRVNDVS 58

PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS3, and related domains. RGS3 down-regulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. It downregulates G-protein-mediated release of inositol phosphates and activation of MAP kinases. In Eph/ephrin signaling, RGS3 binds via its PDZ domain to the cytoplasmic C terminus of Eph receptor tyrosine kinase EphB. 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 RGS3-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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21358025 116 GANITDLAPARaivvVNLVSPDSPAERAGLCAGDAILRFGSINSGNFKG-DLAQIgelVRNMQSQNVQL 183
Cdd:cd06711  13 GFTICDDSPVR----VQAVDPGGPAEQAGLQQGDTVLQINGQPVERSKCvELAHA---IRNCPSEIILL 74

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358025   116 GANITDLAPARAI-VVVNLVSPDSPAERAGLCAGDAILrfgSINsgnfkgdlaqiGELVRNMQSQNVQLKVKRGEQQLDL 194
Cdd:pfam00595  13 GFSLKGGSDQGDPgIFVSEVLPGGAAEAGGLKVGDRIL---SIN-----------GQDVENMTHEEAVLALKGSGGKVTL 78

                  ..
gi 21358025   195 IL 196
Cdd:pfam00595  79 TI 80

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21358025   129 VVVNLVSPDSPAERAGLCAGDAILRFG--SINSGNfkgDLAQIgeLVRNMQSQNVQLKVKRGEQQL 192
Cdd:TIGR02037 364 VVVTKVVSGSPAARAGLQPGDVILSVNqqPVSSVA---ELRKV--LARAKKGGRVALLILRGGATI 424

PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the first PDZ domain of the canonical isoform of PDZD7- isoform 1. 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 PDZD7-like family PDZ1 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
                ....*....|....*....|....*....|
gi 21358025 129 VVVNLVSPDSPAERAGLCAGDAILRFGSIN 158
Cdd:cd10833  28 IFVSKVEEGSAAERAGLCVGDKITEVNGVS 57

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 21358025 129 VVVNLVSPDSPAERAGLCAGDAILRFG--SINSGnfkGDLAQIgeLVRNMQSQNVQLKVKRG--EQQLDLIL 196
Cdd:cd06781  32 VYVAQVQSNSPAEKAGLKKGDVITKLDgkKVESS---SDLRQI--LYSHKVGDTVKVTIYRDgkEKTLNIKL 98