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 24667089    69 LTVYSSKTQTVRELTLTPSNNWGGQGLLGVSIRFCSFEGANESVWHILEVHPNSPAELAGLRAYSDYVIGAD-AIRHEND 147
Cdd:pfam04495   1 LTVYNAKGQKIRDVYIVPSNTWGGQGLLGLSLRWCSFAKALENVWHVLDVHENSPAAKAGLQPYSDYIIGTPkGLLKGED 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 24667089   148 DLFTLIETHEQQPLKMYVYNLDDDACREVTIKPNTAWGGEGALGCGIGFGYLHRIPVQ 205
Cdd:pfam04495  81 DLYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRNWGGEGALGCGLGYGLLHRIPVV 138

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 24667089    69 LTVYSSKTQTVRELTLTPSNNWGGQGLLGVSIRFCSFEGANESVWHILEVHPNSPAELAGLRAYSDYVIGAD-AIRHEND 147
Cdd:pfam04495   1 LTVYNAKGQKIRDVYIVPSNTWGGQGLLGLSLRWCSFAKALENVWHVLDVHENSPAAKAGLQPYSDYIIGTPkGLLKGED 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 24667089   148 DLFTLIETHEQQPLKMYVYNLDDDACREVTIKPNTAWGGEGALGCGIGFGYLHRIPVQ 205
Cdd:pfam04495  81 DLYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRNWGGEGALGCGLGYGLLHRIPVV 138

Peripheral Golgi membrane protein [Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24667089  19 VLKVQDNSPGQKAGLeAFFDFIVAIAGtrldqDNDMLKELLRqnvDKPVRLTVYSSKTQTVRELTLTpSNNWGGQG---- 94
Cdd:COG5233  67 VLRVNPESPAEKAGM-VVGDYILGINE-----DPLRFLEMNR---RRSVPLLVYNSDLEYVRAVSLQ-VGVDSLKGcqig 136

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24667089  95 ---------------------------------LLGVSIRFCSFEGANESVWHILEVH-PNSPAELAGLRAYSDYVIGA- 139
Cdd:COG5233 137 mgelykipfsqrrckvefnsdeirndvrrlrrkLRGKDIQWSRLKDVVCSDSHILNVSiQDKPPAYALLSPDEDYIDGSs 216

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24667089 140 DAIRHEND--DLFTLIETHEQQPLKMYVYNLDDDACREVTIKPNTAWGGEGALGCGIGFGYLHRIP 203
Cdd:COG5233 217 DGQPLEIGelDLEDVNESPVNLPLSLYYYNPIDDQERAKTERDGVHKGIVGILGCQVGHGFLHRLP 282

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 24667089   9 VPGGGTEGYHVLKVQDNSPGQKAGLEAfFDFIVAIAGTRLDQDNDMLKELLRQNVDKPVRLTVY-SSKTQTVrELTL 84
Cdd:cd06781  24 LPSNVNKGVYVAQVQSNSPAEKAGLKK-GDVITKLDGKKVESSSDLRQILYSHKVGDTVKVTIYrDGKEKTL-NIKL 98

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 24667089    69 LTVYSSKTQTVRELTLTPSNNWGGQGLLGVSIRFCSFEGANESVWHILEVHPNSPAELAGLRAYSDYVIGAD-AIRHEND 147
Cdd:pfam04495   1 LTVYNAKGQKIRDVYIVPSNTWGGQGLLGLSLRWCSFAKALENVWHVLDVHENSPAAKAGLQPYSDYIIGTPkGLLKGED 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 24667089   148 DLFTLIETHEQQPLKMYVYNLDDDACREVTIKPNTAWGGEGALGCGIGFGYLHRIPVQ 205
Cdd:pfam04495  81 DLYTLVEDHEDRPLRLYVYNSETDTVREVTITPNRNWGGEGALGCGLGYGLLHRIPVV 138

Peripheral Golgi membrane protein [Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24667089  19 VLKVQDNSPGQKAGLeAFFDFIVAIAGtrldqDNDMLKELLRqnvDKPVRLTVYSSKTQTVRELTLTpSNNWGGQG---- 94
Cdd:COG5233  67 VLRVNPESPAEKAGM-VVGDYILGINE-----DPLRFLEMNR---RRSVPLLVYNSDLEYVRAVSLQ-VGVDSLKGcqig 136

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24667089  95 ---------------------------------LLGVSIRFCSFEGANESVWHILEVH-PNSPAELAGLRAYSDYVIGA- 139
Cdd:COG5233 137 mgelykipfsqrrckvefnsdeirndvrrlrrkLRGKDIQWSRLKDVVCSDSHILNVSiQDKPPAYALLSPDEDYIDGSs 216

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24667089 140 DAIRHEND--DLFTLIETHEQQPLKMYVYNLDDDACREVTIKPNTAWGGEGALGCGIGFGYLHRIP 203
Cdd:COG5233 217 DGQPLEIGelDLEDVNESPVNLPLSLYYYNPIDDQERAKTERDGVHKGIVGILGCQVGHGFLHRLP 282

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 24667089   9 VPGGGTEGYHVLKVQDNSPGQKAGLEAfFDFIVAIAGTRLDQDNDMLKELLRQNVDKPVRLTVY-SSKTQTVrELTL 84
Cdd:cd06781  24 LPSNVNKGVYVAQVQSNSPAEKAGLKK-GDVITKLDGKKVESSSDLRQILYSHKVGDTVKVTIYrDGKEKTL-NIKL 98

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24667089  19 VLKVQDNSPGQKAGLEAFfDFIVAIAGTRLDQDNDMLKELLRQNVDKPVRLTVY-SSKTQTVrELTLT 85
Cdd:COG0265 205 VARVEPGSPAAKAGLRPG-DVILAVDGKPVTSARDLQRLLASLKPGDTVTLTVLrGGKELTV-TVTLG 270

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24667089  16 GYHVLKVQDNSPGQKAGLEAFfDFIVAIAGTRLDQDNDM-LKELLRQNVDKPVRLTVYSSKTQTVRELTLT 85
Cdd:COG0793  72 KVVVVSVIPGSPAEKAGIKPG-DIILAIDGKSVAGLTLDdAVKLLRGKAGTKVTLTIKRPGEGEPITVTLT 141

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24667089  19 VLKVQDNSPGQKAGLEAfFDFIVAIAGTRLDQDNdmLKELL-RQNVDKPVRLTVYSskTQTVRELTLTP 86
Cdd:COG3975 498 VTSVLWGSPAYKAGLSA-GDELLAIDGLRVTADN--LDDALaAYKPGDPIELLVFR--RDELRTVTVTL 561

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24667089  18 HVLKVQDNSPGQKAGLEAFfDFIVAIAGTRL-DQDNDMLKELLRQNVDKPVRLTVYSSKTQTVRELTLT 85
Cdd:cd06782  17 VVVSPIPGGPAEKAGIKPG-DVIVAVDGESVrGMSLDEVVKLLRGPKGTKVKLTIRRGGEGEPRDVTLT 84

sigma E protease regulator RseP;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24667089   19 VLKVQDNSPGQKAGLEAfFDFIVAIAGTRLDQDNDMLKeLLRQNVDKPVRLTVysSKTQTVRELTLTPSNNWGG---QGL 95
Cdd:PRK10779 225 LAEVQPNSAASKAGLQA-GDRIVKVDGQPLTQWQTFVT-LVRDNPGKPLALEI--ERQGSPLSLTLTPDSKPGNgkaEGF 300

                 ....*..
gi 24667089   96 LGVSIRF 102
Cdd:PRK10779 301 AGVVPKV 307

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 24667089   1 MGSSHSIHVPGGGTEGYHVLKVQDNSPGQKAGLEAfFDFIVAIAGTRLDQDNDMLKELLRQNVDKPVRLTVYS-SKTQTV 79
Cdd:cd06779  11 ISPLLAKELGLPVNRGVLVAEVIPGSPAAKAGLKE-GDVILSVNGKPVTSFNDLRAALDTKKPGDSLNLTILRdGKTLTV 89

                .
gi 24667089  80 R 80
Cdd:cd06779  90 T 90