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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294    69 MLIYSSKTLELRETSVTPSNLWGGQGLLGVSIRFCSFDGANENVWHVLEVESNSPAALAGLRPHSDYIIGAD-TVMNESE 147
Cdd:pfam04495   1 LTVYNAKGQKIRDVYIVPSNTWGGQGLLGLSLRWCSFAKALENVWHVLDVHENSPAAKAGLQPYSDYIIGTPkGLLKGED 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 29826294   148 DLFSLIETHEAKPLKLYVYNTDTDNCREVIITPNSAWGGEGSLGCGIGYGYLHRIPT 204
Cdd:pfam04495  81 DLYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRNWGGEGALGCGLGYGLLHRIPV 137

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294   241 PPSLSPPGTTGIEQSLTGLSISSTPPAVSSVLST-GVPTVPLLPPQVNQSLTSVPPMNPATTLPGLMPLPAGLPNLPNLN 319
Cdd:PHA03247 2717 SATPLPPGPAAARQASPALPAAPAPPAVPAGPATpGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRE 2796

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294   320 LNLPA----PHIMPGVGLPELVNPGLPPLPSMPPRNLPGIAPLPLPSEFLPSfPLVPEssSAASSGELLSSLPPTSNAPS 395
Cdd:PHA03247 2797 SLPSPwdpaDPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPP-SLPLG--GSVAPGGDVRRRPPSRSPAA 2873

                  ..
gi 29826294   396 DP 397
Cdd:PHA03247 2874 KP 2875

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294    69 MLIYSSKTLELRETSVTPSNLWGGQGLLGVSIRFCSFDGANENVWHVLEVESNSPAALAGLRPHSDYIIGAD-TVMNESE 147
Cdd:pfam04495   1 LTVYNAKGQKIRDVYIVPSNTWGGQGLLGLSLRWCSFAKALENVWHVLDVHENSPAAKAGLQPYSDYIIGTPkGLLKGED 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 29826294   148 DLFSLIETHEAKPLKLYVYNTDTDNCREVIITPNSAWGGEGSLGCGIGYGYLHRIPT 204
Cdd:pfam04495  81 DLYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRNWGGEGALGCGLGYGLLHRIPV 137

Peripheral Golgi membrane protein [Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294  95 LLGVSIRFCSFDGANENVWHVLEVE-SNSPAALAGLRPHSDYIIGA-DTVMNES--EDLFSLIETHEAKPLKLYVYNTDT 170
Cdd:COG5233 170 LRGKDIQWSRLKDVVCSDSHILNVSiQDKPPAYALLSPDEDYIDGSsDGQPLEIgeLDLEDVNESPVNLPLSLYYYNPID 249

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294 171 DNCREVIITPNSAWGGEGSLGCGIGYGYLHRIPT---RPFEEGKKISLPGQMAGTPItplkdgfTEVQLSSVNPPSLSPP 247
Cdd:COG5233 250 DQERAKTERDGVHKGIVGILGCQVGHGFLHRLPLagvGQKPQLQKLGTTKRTEDPES-------HQVEQRGVEENFLPIP 322

                       170       180
                ....*....|....*....|.
gi 29826294 248 GTTGIEQSLTGLSISSTPPAV 268
Cdd:COG5233 323 KPDTHRSEFAAKNFLSSLPLS 343

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294  19 VLRVQENSPGHRAGLEPfFDFIVSINGSRLNkDNDTLKDLLKANVEKPVKMLIY-SSKTLELretSVTP-SNLWGGQGLL 96
Cdd:COG0750 132 VGEVVPGSPAAKAGLQP-GDRIVAINGQPVT-SWDDLVDIIRASPGKPLTLTVErDGEELTL---TVTPrLVEEDGVGRI 206

                ...
gi 29826294  97 GVS 99
Cdd:COG0750 207 GVS 209

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 29826294    14 TEGYHVLRVQENSPGHRAGLEPFfDFIVSINGSRLNKDND------TLK-------DLLKANVEKPVKMLIYSSKTLELR 80
Cdd:TIGR02037 256 QRGALVAQVLPGSPAEKAGLKAG-DVITSVNGKPISSFADlrraigTLKpgkkvtlGILRKGKEKTITVTLGASPEEQAS 334

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 29826294    81 ETSVTPsnlwggqGLLGVSIRFCSFDGANENVWH----VLEVESNSPAALAGLRPhSDYIIGAD 140
Cdd:TIGR02037 335 SSNPFL-------GLTVANLSPEIRKELRLKGDVkgvvVTKVVSGSPAARAGLQP-GDVILSVN 390

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294    69 MLIYSSKTLELRETSVTPSNLWGGQGLLGVSIRFCSFDGANENVWHVLEVESNSPAALAGLRPHSDYIIGAD-TVMNESE 147
Cdd:pfam04495   1 LTVYNAKGQKIRDVYIVPSNTWGGQGLLGLSLRWCSFAKALENVWHVLDVHENSPAAKAGLQPYSDYIIGTPkGLLKGED 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 29826294   148 DLFSLIETHEAKPLKLYVYNTDTDNCREVIITPNSAWGGEGSLGCGIGYGYLHRIPT 204
Cdd:pfam04495  81 DLYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRNWGGEGALGCGLGYGLLHRIPV 137

Peripheral Golgi membrane protein [Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294  95 LLGVSIRFCSFDGANENVWHVLEVE-SNSPAALAGLRPHSDYIIGA-DTVMNES--EDLFSLIETHEAKPLKLYVYNTDT 170
Cdd:COG5233 170 LRGKDIQWSRLKDVVCSDSHILNVSiQDKPPAYALLSPDEDYIDGSsDGQPLEIgeLDLEDVNESPVNLPLSLYYYNPID 249

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294 171 DNCREVIITPNSAWGGEGSLGCGIGYGYLHRIPT---RPFEEGKKISLPGQMAGTPItplkdgfTEVQLSSVNPPSLSPP 247
Cdd:COG5233 250 DQERAKTERDGVHKGIVGILGCQVGHGFLHRLPLagvGQKPQLQKLGTTKRTEDPES-------HQVEQRGVEENFLPIP 322

                       170       180
                ....*....|....*....|.
gi 29826294 248 GTTGIEQSLTGLSISSTPPAV 268
Cdd:COG5233 323 KPDTHRSEFAAKNFLSSLPLS 343

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 29826294    18 HVLRVQENSPGHRAGLEPfFDFIVSINGSRLNKDNDtLKDLLKANVEKPVKMLI 71
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRV-GDVILAVNGKPVRSLED-VARLLQGSAGESVTLTV 52

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 29826294  19 VLRVQENSPGHRAGLEPfFDFIVSINGSRLNKDNdtLKDLLK-ANVEKPVKMLIYSSKtlELRETSVTP 86
Cdd:COG3975 498 VTSVLWGSPAYKAGLSA-GDELLAIDGLRVTADN--LDDALAaYKPGDPIELLVFRRD--ELRTVTVTL 561

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 29826294   5 QSVEIPGGGTEGYHVLRVQENSPGHRAGLEPfFDFIVSINGSRLNKDNDTLKDLLKANVEKPVKMLIY---SSKTLEL 79
Cdd:cd06781  20 QSLKLPSNVNKGVYVAQVQSNSPAEKAGLKK-GDVITKLDGKKVESSSDLRQILYSHKVGDTVKVTIYrdgKEKTLNI 96

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
                ....*....|....*....|....*....|....*....|
gi 29826294  14 TEGYHVLRVQENSPGHRAGLEPfFDFIVSINGSRLNKDND 53
Cdd:cd10838  32 VDGVLIMQVLPNSPAARAGLRR-GDVIQAVDGQPVTTADD 70

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
                ....*....|....*....|....*...
gi 29826294  19 VLRVQENSPGHRAGLEPfFDFIVSINGS 46
Cdd:cd06713  39 VCRVHEDSPAYLAGLTA-GDVILSVNGV 65

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 29826294  22 VQENSPGHRAGLEPfFDFIVSINGSRLNKDNDtLKDLLKANVEKPVKMLIysSKTLELRETSVTPSN---LWGGQGLLGV 98
Cdd:cd23081   6 VVANSPAAEAGLKP-GDRILKIDGQKVRTWED-IVRIVRENPGKPLTLKI--ERDGKILTVTVTPELvevEGKGVGRIGV 81

                .
gi 29826294  99 S 99
Cdd:cd23081  82 Q 82

Peptidase family M50;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29826294   115 VLEVESNSPAALAGLRPhSDYIIGAD-TVMNESEDLFSLIETHEAKPLKLYVYNTDTDncREVIITPNSAwggEGSLGCG 193
Cdd:pfam02163  97 IGGVAPGSPAAKAGLKP-GDVILSINgKKITSWQDLVEALAKSPGKPITLTVERGGQT--LTVTITPKSS---EESKFIG 170

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 29826294   194 IGYGYLHRIPTRPFEEGKKISlpGQMAGTPITPLKDGFTEVQLSSVNPP 242
Cdd:pfam02163 171 IGPVYVKYGLLEALGFALEKT--VNLVTLTLKALGKLITGVSLKNLGGP 217

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29826294  19 VLRVQENSPGHRAGLEPfFDFIVSINGSRLNKDNDTLKDLLKANVEKPVKMLIYSSKtlELRETSVTPSNL 89
Cdd:COG0265 205 VARVEPGSPAAKAGLRP-GDVILAVDGKPVTSARDLQRLLASLKPGDTVTLTVLRGG--KELTVTVTLGER 272