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Conserved domains on  [gi|1895670020|gb|QNI37591|]
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PDZ domain-containing protein [Edaphobacter sp. 4G125]

Protein Classification

S41 family peptidase( domain architecture ID 11435057)

S41 family peptidase is a serine endopeptidase similar to Bartonella bacilliformis carboxy-terminal-processing protease that shows specific recognition of a C-terminal tripeptide, Xaa-Yaa-Zaa, and cleaves at a variable distance from the C-terminus

EC:  3.4.21.-
Gene Ontology:  GO:0006508|GO:0008236
MEROPS:  S41
PubMed:  26527717

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 44-405 1.73e-81

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


:

Pssm-ID: 440556 [Multi-domain]  Cd Length: 341  Bit Score: 253.64  E-value: 1.73e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  44 NVYSEVLRHIQTDYVVEPNIPQVTNGAMRGLLESL-DADSSYLTADDYKAFKADKEkGAKAQVGINVSKRWGYATVVSIV 122
Cdd:COG0793     1 QLFDEVWRLIRDNYVDEYDDRDLAEGALNGMLGELgDPHSYYLDPEEYEDFQESTS-GEFGGLGAELGEEDGKVVVVSVI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 123 PGSPADKVNLNDGDIIEAIDDHDTRDISLAMIRMMLEGAPGSQVSISVVRPRKAVPDKITMTRQMITQPATSETMYENSs 202
Cdd:COG0793    80 PGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAVKLLRGKAGTKVTLTIKRPGEGEPITVTLTRAEIKLPSVEAKLLEGK- 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 203 ILYLKPGILDREHVQQVESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEKQTFTAESSKA 282
Cdd:COG0793   159 IGYIRIPSFGENTAEEFKRALKELKKQGAKGLILDLRNNPGGLLDEAVELADLFLPKGPIVYTRGRNGKVETYKATPGGA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 283 InTTSPVVVLVNRGTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTPG 362
Cdd:COG0793   239 L-YDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGKGSVQTVFPLPDGGALKLTTARYYTPSGRSIQGKGVEPD 317

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 1895670020 363 VLVASNLDDngpIDDGDatvqtqpetkkpsvsvDDQLNKALDL 405
Cdd:COG0793   318 IEVPLTPED---LLKGR----------------DPQLEKALEL 341
 
Name Accession Description Interval E-value
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 44-405 1.73e-81

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


Pssm-ID: 440556 [Multi-domain]  Cd Length: 341  Bit Score: 253.64  E-value: 1.73e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  44 NVYSEVLRHIQTDYVVEPNIPQVTNGAMRGLLESL-DADSSYLTADDYKAFKADKEkGAKAQVGINVSKRWGYATVVSIV 122
Cdd:COG0793     1 QLFDEVWRLIRDNYVDEYDDRDLAEGALNGMLGELgDPHSYYLDPEEYEDFQESTS-GEFGGLGAELGEEDGKVVVVSVI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 123 PGSPADKVNLNDGDIIEAIDDHDTRDISLAMIRMMLEGAPGSQVSISVVRPRKAVPDKITMTRQMITQPATSETMYENSs 202
Cdd:COG0793    80 PGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAVKLLRGKAGTKVTLTIKRPGEGEPITVTLTRAEIKLPSVEAKLLEGK- 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 203 ILYLKPGILDREHVQQVESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEKQTFTAESSKA 282
Cdd:COG0793   159 IGYIRIPSFGENTAEEFKRALKELKKQGAKGLILDLRNNPGGLLDEAVELADLFLPKGPIVYTRGRNGKVETYKATPGGA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 283 InTTSPVVVLVNRGTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTPG 362
Cdd:COG0793   239 L-YDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGKGSVQTVFPLPDGGALKLTTARYYTPSGRSIQGKGVEPD 317

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 1895670020 363 VLVASNLDDngpIDDGDatvqtqpetkkpsvsvDDQLNKALDL 405
Cdd:COG0793   318 IEVPLTPED---LLKGR----------------DPQLEKALEL 341
PLN00049 PLN00049
carboxyl-terminal processing protease; Provisional
 67-361 3.78e-54

carboxyl-terminal processing protease; Provisional


Pssm-ID: 177681 [Multi-domain]  Cd Length: 389  Bit Score: 184.17  E-value: 3.78e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  67 TNGAMRGLLESLDAD-SSYLTADDYKAFKADKeKGAKAQVGINVskrwGYAT----------VVSIVPGSPADKVNLNDG 135
Cdd:PLN00049   49 TYAAIRKMLATLDDPfTRFLEPEKFKSLRSGT-KGAVTGVGLEV----GYPTgsdgppaglvVVAPAPGGPAARAGIRPG 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 136 DIIEAIDDHDTRDISLAMIRMMLEGAPGSQVSISVVRPRKavPDKITMTRQMIT-QPATSETMYENSS------ILYLKP 208
Cdd:PLN00049  124 DVILAIDGTSTEGLSLYEAADRLQGPEGSSVELTLRRGPE--TRLVTLTREKVSlNPVKSRLCEVPGPgagspkIGYIKL 201

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 209 GILDREHVQQVESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEKQTFTAESSKAINTTSP 288
Cdd:PLN00049  202 TTFNQNASSAVKEAIETLRANGVDAFVLDLRDNSGGLFPAGIEIAKLWLDKGVIVYIADSRGVRDIYDADGSSAIATSEP 281

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1895670020 289 VVVLVNRGTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTP 361
Cdd:PLN00049  282 LAVLVNKGTASASEILAGALKDNKRAVVLGEPTFGKGLIQSVFELSDGSGLAVTVARYQTPAGTDIDKVGITP 354
prc TIGR00225
C-terminal peptidase (prc); A C-terminal peptidase with different substrates in different ...
 69-365 1.37e-51

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]


Pssm-ID: 272970 [Multi-domain]  Cd Length: 334  Bit Score: 176.01  E-value: 1.37e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  69 GAMRGLLESL-DADSSYLTADDYKAFKADKEkGAKAQVGINVSKRWGYATVVSIVPGSPADKVNLNDGDIIEAIDDHDTR 147
Cdd:TIGR00225  17 GAIKGMLASLnDPYTRYLSPETAKSFSETTS-GSLEGIGIQVGMDDGKIVIVSPFEGSPAEKAGIKPGDKIIKINGKSVA 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 148 DISLAMIRMMLEGAPGSQVSISVVRPRKAVPDKITMTRQMITQPATSETMYENS--SILYLKPGILDREHVQQVESKLKG 225
Cdd:TIGR00225  96 GMSLDDAVALIRGKKGTKVSLEILRAGKSKPLSFTLKRDRIELETVKASVKKVGghSVGYIRISSFSEHTAEDVAKALDK 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 226 MQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEKQTFTAESSKAinTTSPVVVLVNRGTAGPAEVVA 305
Cdd:TIGR00225 176 LEKKNAKGYILDLRGNPGGLLQSAVDISRLFITKGPIVQTKDRNGSKRHYKANGRQK--YNLPLVVLVNRGSASASEILA 253

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 306 AALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTPGVLV 365
Cdd:TIGR00225 254 GALQDNGRATIVGEKTFGKGTVQQVRPLNDGSGIKVTIAKYYTPNGGSIHKKGIEPDIVI 313
Peptidase_S41_CPP cd07560
C-terminal processing peptidase; serine protease family S41; The C-terminal processing ...
 217-365 4.41e-40

C-terminal processing peptidase; serine protease family S41; The C-terminal processing peptidase (CPP, EC 3.4.21.102) also known as tail-specific protease (tsp), the photosystem II D1 C-terminal processing protease (D1P), and other related S41 protease family members are present in this CD. CPP is synthesized as a precursor form with a carboxyl-terminal extension. It specifically recognizes a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. The C-terminal carboxylate group is essential, and proteins where this group is amidated are not substrates. This family of proteases contains the PDZ domain that promotes protein-protein interactions and is important for substrate recognition. The active site consists of a serine/lysine catalytic dyad. The bacterial CCP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. In E. coli, it is involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3 (PBP3). In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II, allowing the light-driven assembly of the tetranuclear manganese cluster, which is responsible for photosynthetic water oxidation.


Pssm-ID: 143476 [Multi-domain]  Cd Length: 211  Bit Score: 141.78  E-value: 4.41e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 217 QQVESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEKQTFTAESSKAINTtsPVVVLVNRG 296
Cdd:cd07560    64 EELKKALKELKKQGMKGLILDLRNNPGGLLDEAVEIADLFLPGGPIVSTKGRNGKREAYASDDGGLYDG--PLVVLVNGG 141

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1895670020 297 TAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTPGVLV 365
Cdd:cd07560   142 SASASEIVAGALQDNGRAVLVGERTFGKGSVQTVFPLSDGSALKLTTAKYYTPSGRSIQKKGIEPDIEV 210
Peptidase_S41 pfam03572
Peptidase family S41;
217-365 4.88e-33

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 121.94  E-value: 4.88e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 217 QQVESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEK-QTFTAESSKAINTTSPVVVLVNR 295
Cdd:pfam03572  16 KELAEALKELKKQGVKGLILDLRGNPGGLLSAAVEIASLFLPDGTIVSTRGRDGSKeVYFAAGKADEVLWKGPLVVLVNE 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 296 GTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTPGVLV 365
Cdd:pfam03572  96 GSASASEIFAGALQDNGRATLVGERTFGKGTVQTVYPLPDGSALKLTIAKYYTPDGRSIEGKGIEPDIEV 165
TSPc smart00245
tail specific protease; tail specific protease
 181-365 9.72e-33

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 121.98  E-value: 9.72e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  181 ITMTRQMItqpatsETMYENSSILYLKPGILDREHVQQ--------VESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRM 252
Cdd:smart00245   6 IALIRDKI------KIETLEGNVGYLRFGFIGYIRIPEfsehtsnlVEKAWKKLEKTNVEGLILDLRNNPGGLLSAAIDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  253 ANFLLKSGTITILAGQKV-EKQTFTAESSKAINTtsPVVVLVNRGTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTF 331
Cdd:smart00245  80 SSLFLDKGVIVYTVYRRTgELWTYPANLGRKYSK--PLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKGLVQQTV 157

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1895670020  332 ELPDGAALILSVAKYESPSGKKLENEGVTPGVLV 365
Cdd:smart00245 158 PLGDGSGLKLTVAKYYTPSGKSIEKKGVEPDIQV 191
 
Name Accession Description Interval E-value
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 44-405 1.73e-81

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


Pssm-ID: 440556 [Multi-domain]  Cd Length: 341  Bit Score: 253.64  E-value: 1.73e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  44 NVYSEVLRHIQTDYVVEPNIPQVTNGAMRGLLESL-DADSSYLTADDYKAFKADKEkGAKAQVGINVSKRWGYATVVSIV 122
Cdd:COG0793     1 QLFDEVWRLIRDNYVDEYDDRDLAEGALNGMLGELgDPHSYYLDPEEYEDFQESTS-GEFGGLGAELGEEDGKVVVVSVI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 123 PGSPADKVNLNDGDIIEAIDDHDTRDISLAMIRMMLEGAPGSQVSISVVRPRKAVPDKITMTRQMITQPATSETMYENSs 202
Cdd:COG0793    80 PGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAVKLLRGKAGTKVTLTIKRPGEGEPITVTLTRAEIKLPSVEAKLLEGK- 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 203 ILYLKPGILDREHVQQVESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEKQTFTAESSKA 282
Cdd:COG0793   159 IGYIRIPSFGENTAEEFKRALKELKKQGAKGLILDLRNNPGGLLDEAVELADLFLPKGPIVYTRGRNGKVETYKATPGGA 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 283 InTTSPVVVLVNRGTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTPG 362
Cdd:COG0793   239 L-YDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGKGSVQTVFPLPDGGALKLTTARYYTPSGRSIQGKGVEPD 317

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 1895670020 363 VLVASNLDDngpIDDGDatvqtqpetkkpsvsvDDQLNKALDL 405
Cdd:COG0793   318 IEVPLTPED---LLKGR----------------DPQLEKALEL 341
PLN00049 PLN00049
carboxyl-terminal processing protease; Provisional
 67-361 3.78e-54

carboxyl-terminal processing protease; Provisional


Pssm-ID: 177681 [Multi-domain]  Cd Length: 389  Bit Score: 184.17  E-value: 3.78e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  67 TNGAMRGLLESLDAD-SSYLTADDYKAFKADKeKGAKAQVGINVskrwGYAT----------VVSIVPGSPADKVNLNDG 135
Cdd:PLN00049   49 TYAAIRKMLATLDDPfTRFLEPEKFKSLRSGT-KGAVTGVGLEV----GYPTgsdgppaglvVVAPAPGGPAARAGIRPG 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 136 DIIEAIDDHDTRDISLAMIRMMLEGAPGSQVSISVVRPRKavPDKITMTRQMIT-QPATSETMYENSS------ILYLKP 208
Cdd:PLN00049  124 DVILAIDGTSTEGLSLYEAADRLQGPEGSSVELTLRRGPE--TRLVTLTREKVSlNPVKSRLCEVPGPgagspkIGYIKL 201

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 209 GILDREHVQQVESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEKQTFTAESSKAINTTSP 288
Cdd:PLN00049  202 TTFNQNASSAVKEAIETLRANGVDAFVLDLRDNSGGLFPAGIEIAKLWLDKGVIVYIADSRGVRDIYDADGSSAIATSEP 281

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1895670020 289 VVVLVNRGTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTP 361
Cdd:PLN00049  282 LAVLVNKGTASASEILAGALKDNKRAVVLGEPTFGKGLIQSVFELSDGSGLAVTVARYQTPAGTDIDKVGITP 354
prc TIGR00225
C-terminal peptidase (prc); A C-terminal peptidase with different substrates in different ...
 69-365 1.37e-51

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]


Pssm-ID: 272970 [Multi-domain]  Cd Length: 334  Bit Score: 176.01  E-value: 1.37e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  69 GAMRGLLESL-DADSSYLTADDYKAFKADKEkGAKAQVGINVSKRWGYATVVSIVPGSPADKVNLNDGDIIEAIDDHDTR 147
Cdd:TIGR00225  17 GAIKGMLASLnDPYTRYLSPETAKSFSETTS-GSLEGIGIQVGMDDGKIVIVSPFEGSPAEKAGIKPGDKIIKINGKSVA 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 148 DISLAMIRMMLEGAPGSQVSISVVRPRKAVPDKITMTRQMITQPATSETMYENS--SILYLKPGILDREHVQQVESKLKG 225
Cdd:TIGR00225  96 GMSLDDAVALIRGKKGTKVSLEILRAGKSKPLSFTLKRDRIELETVKASVKKVGghSVGYIRISSFSEHTAEDVAKALDK 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 226 MQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEKQTFTAESSKAinTTSPVVVLVNRGTAGPAEVVA 305
Cdd:TIGR00225 176 LEKKNAKGYILDLRGNPGGLLQSAVDISRLFITKGPIVQTKDRNGSKRHYKANGRQK--YNLPLVVLVNRGSASASEILA 253

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 306 AALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTPGVLV 365
Cdd:TIGR00225 254 GALQDNGRATIVGEKTFGKGTVQQVRPLNDGSGIKVTIAKYYTPNGGSIHKKGIEPDIVI 313
Peptidase_S41_CPP cd07560
C-terminal processing peptidase; serine protease family S41; The C-terminal processing ...
 217-365 4.41e-40

C-terminal processing peptidase; serine protease family S41; The C-terminal processing peptidase (CPP, EC 3.4.21.102) also known as tail-specific protease (tsp), the photosystem II D1 C-terminal processing protease (D1P), and other related S41 protease family members are present in this CD. CPP is synthesized as a precursor form with a carboxyl-terminal extension. It specifically recognizes a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. The C-terminal carboxylate group is essential, and proteins where this group is amidated are not substrates. This family of proteases contains the PDZ domain that promotes protein-protein interactions and is important for substrate recognition. The active site consists of a serine/lysine catalytic dyad. The bacterial CCP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. In E. coli, it is involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3 (PBP3). In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II, allowing the light-driven assembly of the tetranuclear manganese cluster, which is responsible for photosynthetic water oxidation.


Pssm-ID: 143476 [Multi-domain]  Cd Length: 211  Bit Score: 141.78  E-value: 4.41e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 217 QQVESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEKQTFTAESSKAINTtsPVVVLVNRG 296
Cdd:cd07560    64 EELKKALKELKKQGMKGLILDLRNNPGGLLDEAVEIADLFLPGGPIVSTKGRNGKREAYASDDGGLYDG--PLVVLVNGG 141

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1895670020 297 TAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTPGVLV 365
Cdd:cd07560   142 SASASEIVAGALQDNGRAVLVGERTFGKGSVQTVFPLSDGSALKLTTAKYYTPSGRSIQKKGIEPDIEV 210
Peptidase_S41 cd06567
C-terminal processing peptidase family S41; Peptidase family S41 (C-terminal processing ...
 201-366 8.35e-36

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.


Pssm-ID: 143475 [Multi-domain]  Cd Length: 224  Bit Score: 130.88  E-value: 8.35e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 201 SSILYLK-PGILDREHVQQVESKLKGMQKaGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEKQTFTAES 279
Cdd:cd06567    59 LTIGYIRiPSFSAESTAEELREALAELKK-GVKGLILDLRNNPGGLLSAAVELASLFLPKGKIVVTTRRRGGNETEYVAP 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 280 SKAINTTSPVVVLVNRGTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGV 359
Cdd:cd06567   138 GGGSLYDGPLVVLVNEGSASASEIFAGALQDLGRATLVGERTFGKGSVQTVFPLLDGSALKLTTAKYYTPSGRSIEGKGV 217


                  ....*..
gi 1895670020 360 TPGVLVA 366
Cdd:cd06567   218 EPDIEVP 224
Peptidase_S41 pfam03572
Peptidase family S41;
217-365 4.88e-33

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 121.94  E-value: 4.88e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 217 QQVESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITILAGQKVEK-QTFTAESSKAINTTSPVVVLVNR 295
Cdd:pfam03572  16 KELAEALKELKKQGVKGLILDLRGNPGGLLSAAVEIASLFLPDGTIVSTRGRDGSKeVYFAAGKADEVLWKGPLVVLVNE 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 296 GTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENEGVTPGVLV 365
Cdd:pfam03572  96 GSASASEIFAGALQDNGRATLVGERTFGKGTVQTVYPLPDGSALKLTIAKYYTPDGRSIEGKGIEPDIEV 165
TSPc smart00245
tail specific protease; tail specific protease
 181-365 9.72e-33

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 121.98  E-value: 9.72e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  181 ITMTRQMItqpatsETMYENSSILYLKPGILDREHVQQ--------VESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRM 252
Cdd:smart00245   6 IALIRDKI------KIETLEGNVGYLRFGFIGYIRIPEfsehtsnlVEKAWKKLEKTNVEGLILDLRNNPGGLLSAAIDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  253 ANFLLKSGTITILAGQKV-EKQTFTAESSKAINTtsPVVVLVNRGTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTF 331
Cdd:smart00245  80 SSLFLDKGVIVYTVYRRTgELWTYPANLGRKYSK--PLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKGLVQQTV 157

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1895670020  332 ELPDGAALILSVAKYESPSGKKLENEGVTPGVLV 365
Cdd:smart00245 158 PLGDGSGLKLTVAKYYTPSGKSIEKKGVEPDIQV 191
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 105-188 3.82e-16

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.


Pssm-ID: 467623 [Multi-domain]  Cd Length: 88  Bit Score: 72.90  E-value: 3.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 105 VGINVSKRW-GYATVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISLAMIRMMLEGAPGSQVSISVVRPRKAVPDKITM 183
Cdd:cd06782     4 IGIEIGKDDdGYLVVVSPIPGGPAEKAGIKPGDVIVAVDGESVRGMSLDEVVKLLRGPKGTKVKLTIRRGGEGEPRDVTL 83


                  ....*
gi 1895670020 184 TRQMI 188
Cdd:cd06782    84 TREKI 88
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 227-367 1.04e-15

Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium (RPE). IRBP is secreted by photoreceptors into the interphotoreceptor matrix (IPM) where it is rapidly turned over by a combination of RPE and photoreceptor endocytosis. It is the most abundant soluble protein component of the IPM, consisting of homologous modules, each repeat structure arising through the duplication (as in teleost IRBP) or quadruplication (in tetrapods) of an ancient gene, arisen in the early evolution of the vertebrate eye. IRBP has been shown to promote the release of all-trans retinol from photoreceptors and facilitates its delivery to the RPE. Conversely, IRBP can promote the release of 11-cis-retinal from the RPE, prevent its isomerization in the subretinal space, and transfer it to photoreceptors. In vivo evidence implicates IRBP as a retinoid transporter in the visual cycle, suggesting a critical role for IRBP in cone function essential for human vision. IRBP is a dominant autoimmune antigen in the eye; IRBP proteolysis analysis has proven a useful biomarker for autoimmune uveitis (AU) disorders, a major cause of blindness. This family also includes a chlamydia-secreted protein, designated chlamydia protease-like activity factor (CPAF), known to degrade host proteins, enabling Chlamydia to evade host defenses and replicate.


Pssm-ID: 143479 [Multi-domain]  Cd Length: 250  Bit Score: 76.18  E-value: 1.04e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 227 QKAGNKKILLDLRDVAAGDIPEAIRMANFLLKSGTITIL-------AGQKVEKQTFTAESSKAINTTSPVVVLVNRGTAG 299
Cdd:cd07563    91 KLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLytiykrpGNTTTELWTLPVVPGGRYGYTKPVYVLTSPVTFS 170

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1895670020 300 PAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESP-SGKKLENEGVTPGVLVAS 367
Cdd:cd07563   171 AAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPNGLYLTVPTSRSVDPiTGTNWEGVGVPPDIEVPA 239
Peptidase_S41_TRI cd07562
Tricorn protease; serine protease family S41; The tricorn protease (TRI), a member of the S41 ...
 203-407 1.44e-11

Tricorn protease; serine protease family S41; The tricorn protease (TRI), a member of the S41 peptidase family and named for its tricorn-like shape, exists only in some archaea and eubacteria. It has been shown to act as a carboxypeptidase, involved in the degradation of proteasomal products to preferentially yield di- and tripeptides, with subsequent and final degradations to free amino acid residues by tricorn interacting factors, F1, F2 and F3. Tricorn is a hexameric D3-symmetric protease of 720kD, and can self-associate further into a giant icosahedral capsid structure containing twenty copies of the complex. Each tricorn peptidase monomer consists of five structural domains: a six-bladed beta-propeller and a seven-bladed beta-propeller that limit access to the active site, the two domains (C1 and C2) that carry the active site residues, and a PDZ-like domain (proposed to be important for substrate recognition) between the C1 and C2 domains. The active site tetrad residues are distributed between the C1 and C2 domains, with serine and histidine on C1 and serine and glutamate on C2.


Pssm-ID: 143478 [Multi-domain]  Cd Length: 266  Bit Score: 64.53  E-value: 1.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 203 ILYLK-PGILDREHVQQVESKLKGMQKAGnkkILLDLRDVAAGDIPEAIrmanfllksgtITILAGQK----VEKQTFTA 277
Cdd:cd07562    89 IGYVHiPDMGDDGFAEFLRDLLAEVDKDG---LIIDVRFNGGGNVADLL-----------LDFLSRRRygydIPRGGGKP 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 278 ESSKAINTTSPVVVLVNRGTAGPAEVVAAALMDNHRADLVGEKTFGEGSQQKTFELPDGAALILSVAKYESPSGKKLENE 357
Cdd:cd07562   155 VTYPSGRWRGPVVVLVNEGSASDAEIFAYGFRALGLGPVVGTRTAGGVIISGRYRLPDGGSLTVPEFGVYLPDGGPLENR 234

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1895670020 358 GVTPGVLVASNLDDngpIDDGDatvqtqpetkkpsvsvDDQLNKALDLLK 407
Cdd:cd07562   235 GVAPDIEVENTPED---VAAGR----------------DPQLEAAIEELL 265
PRK11186 PRK11186
carboxy terminal-processing peptidase;
115-328 1.22e-10

carboxy terminal-processing peptidase;


Pssm-ID: 236873 [Multi-domain]  Cd Length: 667  Bit Score: 63.38  E-value: 1.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 115 YATVVSIVPGSPADKVN-LNDGDIIEAI--DDHDTRDIslamIRMMLE-------GAPGSQVSISVVRPRK-AVPDKITM 183
Cdd:PRK11186  256 YTVINSLVAGGPAAKSKkLSVGDKIVGVgqDGKPIVDV----IGWRLDdvvalikGPKGSKVRLEILPAGKgTKTRIVTL 331

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020 184 TRQMI---TQPATSETMYENSSilylKPGILDREH-----VQQVESKLKGMQKAGNKKILLDLRDVAAGDIPEAIRMANF 255
Cdd:PRK11186  332 TRDKIrleDRAVKMSVKTVGGE----KVGVLDIPGfyvglTDDVKKQLQKLEKQNVSGIIIDLRGNGGGALTEAVSLSGL 407

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1895670020 256 LLKSGTITIL--AGQKVEKQtftAESSKAINTTSPVVVLVNRGTAGPAEVVAAALMDNHRADLVGEKTFGEGS-QQ 328
Cdd:PRK11186  408 FIPSGPVVQVrdNNGRVRVD---SDTDGVVYYKGPLVVLVDRYSASASEIFAAAMQDYGRALIVGEPTFGKGTvQQ 480
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 85-172 2.57e-08

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


Pssm-ID: 440035 [Multi-domain]  Cd Length: 274  Bit Score: 54.77  E-value: 2.57e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  85 LTADDYKAFKADKEKGAkaqvginvskrwgyaTVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISlAMIRMMLEGAPGS 164
Cdd:COG0265   187 VTPELAEALGLPEPEGV---------------LVARVEPGSPAAKAGLRPGDVILAVDGKPVTSAR-DLQRLLASLKPGD 250


                  ....*...
gi 1895670020 165 QVSISVVR 172
Cdd:COG0265   251 TVTLTVLR 258
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 118-173 1.43e-06

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.


Pssm-ID: 214570 [Multi-domain]  Cd Length: 85  Bit Score: 45.83  E-value: 1.43e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1895670020  118 VVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISLAMIRMMLEGApGSQVSISVVRP 173
Cdd:smart00228  30 VSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKA-GGKVTLTVLRG 84
PDZ_ZASP52-like cd23068
PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), ...
 117-172 2.04e-06

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.


Pssm-ID: 467281 [Multi-domain]  Cd Length: 82  Bit Score: 45.21  E-value: 2.04e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1895670020 117 TVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISLAMIRMMLEGApGSQVSISVVR 172
Cdd:cd23068    28 SIQKVNPGSPADKAGLRRGDVILRINGTDTSNLTHKQAQDLIKRA-GNDLQLTVQR 82
PDZ_2 pfam13180
PDZ domain;
114-175 4.38e-06

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 44.18  E-value: 4.38e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1895670020 114 GYATVVSIVPGSPADKVNLNDGDIIEAIDD---HDTRDislaMIRMMLEGAPGSQVSISVVRPRK 175
Cdd:pfam13180   6 GGVVVVSVKSSGPAAKAGLKAGDVILSIDGrkiNDLTD----LESALYGHKPGDTVTLQVYRDGK 66
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 117-172 7.23e-06

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 42.90  E-value: 7.23e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1895670020 117 TVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDIslAMIRMMLEGAPGSQVSISVVR 172
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSL--EDVARLLQGSAGESVTLTVRR 54
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 85-175 2.43e-05

circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine endoprotease DegP and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Escherichia coli DegP (also known as heat shock protein DegP and Protease Do) and related domains. DegP belongs to the HtrA family of housekeeping proteases. It acts as a protease, degrading transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions, and as a molecular chaperone at low temperatures. DegP has two PDZ domains in addition to the protease domain; its PDZ1 domain is responsible for identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for combining with other DegP monomers to form a stable oligomer structure. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegP family PDZ domain 1 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.


Pssm-ID: 467630 [Multi-domain]  Cd Length: 91  Bit Score: 42.47  E-value: 2.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  85 LTADDYKAFKADKEKGAkaqvginvskrwgyaTVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDisLAMIRMMLEG-APG 163
Cdd:cd10839    11 LTPDLAESFGLKEPKGA---------------LVAQVLPDSPAAKAGLKAGDVILSLNGKPITS--SADLRNRVATtKPG 73

                          90
                  ....*....|..
gi 1895670020 164 SQVSISVVRPRK 175
Cdd:cd10839    74 TKVELKILRDGK 85
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
92-172 5.12e-05

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


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 45.58  E-value: 5.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  92 AFKADKEKGAKAQVGINVSKRWGYATVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISLAmiRMMLEGAPGSQVSISVV 171
Cdd:COG3975   472 KLVYEDAPSLKPSLGLRVSADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVTADNLD--DALAAYKPGDPIELLVF 549


                  .
gi 1895670020 172 R 172
Cdd:COG3975   550 R 550
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 97-163 8.83e-05

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 40.73  E-value: 8.83e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1895670020  97 KEKGAKAQVGINVS----KRWGYATVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISLAMIRMMLEGAPG 163
Cdd:pfam00595   4 LEKDGRGGLGFSLKggsdQGDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSGG 74
PDZ_PDLIM-like cd06753
PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 117-152 1.28e-04

PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). 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 PDLIM-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.


Pssm-ID: 467235 [Multi-domain]  Cd Length: 79  Bit Score: 40.21  E-value: 1.28e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1895670020 117 TVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISLA 152
Cdd:cd06753    25 TISRVTPGGKAAQANLRPGDVILAINGESTEGMTHL 60
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 85-184 1.32e-04

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]


Pssm-ID: 273938 [Multi-domain]  Cd Length: 428  Bit Score: 43.75  E-value: 1.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895670020  85 LTADDYKAFKADKEKGAkaqvginvskrwgyaTVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISlAMIRMMLEGAPGS 164
Cdd:TIGR02037 243 VTSDLAKSLGLEKQRGA---------------LVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFA-DLRRAIGTLKPGK 306

                          90       100
                  ....*....|....*....|
gi 1895670020 165 QVSISVVrpRKAVPDKITMT 184
Cdd:TIGR02037 307 KVTLGIL--RKGKEKTITVT 324
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 105-172 4.59e-04

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 42.00  E-value: 4.59e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1895670020 105 VGINVSKrwgYATVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISLamIRMMLEGAPGSQVSISVVR 172
Cdd:COG0750   122 VGVPVLT---PPVVGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDD--LVDIIRASPGKPLTLTVER 184
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 118-178 5.43e-04

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.


Pssm-ID: 467621 [Multi-domain]  Cd Length: 91  Bit Score: 38.81  E-value: 5.43e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1895670020 118 VVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISlAMIRMMLEGAPGSQVSISVVRPRKAVP 178
Cdd:cd06779    29 VAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFN-DLRAALDTKKPGDSLNLTILRDGKTLT 88
PDZ_rhophilin-like cd06712
PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 118-171 5.72e-04

PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of rhophilin-1, rhophilin-2, and related domains. Rhophilin-1 (RHPN1, also known as GTP-Rho-binding protein 1) and rhophilin-2 (RHPN2, also known as GTP-Rho-binding protein 2) are Rho-GTP binding proteins involved in cytoskeletal dynamics. Rhophilin-2 inhibits RhoA's activity to induce F-actin stress fibers. 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 rhophilin-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.


Pssm-ID: 467196 [Multi-domain]  Cd Length: 78  Bit Score: 38.33  E-value: 5.72e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1895670020 118 VVSIVPGSPADKVNLNDGDIIEAIDDHDTRDISLAMIRMMLEGAPGSQVSISVV 171
Cdd:cd06712    25 VASVDPGSCAAEAGLKEGDYIVSVGGVDCKWSKHSEVVKLLKSAGEEGLELQVV 78
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 98-171 8.31e-04

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains 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.


Pssm-ID: 467153 [Multi-domain]  Cd Length: 81  Bit Score: 37.91  E-value: 8.31e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1895670020  98 EKGAKAQVGINVS---KRWGYATVVSIVPGSPADKV-NLNDGDIIEAIDDHDTRDISLAMIRMMLEGAPGsQVSISVV 171
Cdd:cd00136     5 EKDPGGGLGFSIRggkDGGGGIFVSRVEPGGPAARDgRLRVGDRILEVNGVSLEGLTHEEAVELLKSAGG-EVTLTVR 81
NifB COG1625
Fe-S oxidoreductase, related to NifB/MoaA family [Energy production and conversion];
115-149 1.53e-03

Fe-S oxidoreductase, related to NifB/MoaA family [Energy production and conversion];


Pssm-ID: 441232 [Multi-domain]  Cd Length: 441  Bit Score: 40.51  E-value: 1.53e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1895670020 115 YATVVSIVPGSPADKVNLNDGDIIEAIDDHDTRDI 149
Cdd:COG1625     5 GAKISKVEPGSIAEELGIEPGDRLLSINGQPIRDI 39
PDZ4_LNX1_2-like cd06680
PDZ domain 4 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ ...
 118-171 1.93e-03

PDZ domain 4 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2)and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. 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 LNX family PDZ4 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.


Pssm-ID: 467168 [Multi-domain]  Cd Length: 89  Bit Score: 37.33  E-value: 1.93e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1895670020 118 VVSIVPGSPADKVN-LNDGDIIEAIDDHDTRDISLAMIRMMLEGAPGSqVSISVV 171
Cdd:cd06680    32 VKSIVPGTPAYNDGrLKCGDIILAVNGVSTVGMSHAALVPLLKEQRGR-VTLTVV 85
Peptidase_M50 pfam02163
Peptidase family M50;
115-182 2.65e-03

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 39.40  E-value: 2.65e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1895670020 115 YATVVSIVPGSPADKVNLNDGDIIEAIDDHDTRdiSLAMIRMMLEGAPGSQVSISVVRPRKAVPDKIT 182
Cdd:pfam02163  94 PPVIGGVAPGSPAAKAGLKPGDVILSINGKKIT--SWQDLVEALAKSPGKPITLTVERGGQTLTVTIT 159
cpPDZ_RseP_YlbL-like_arch cd10823
circularly permuted PDZ domains of uncharacterized archaeal proteins related to Escherichia ...
 118-168 5.27e-03

circularly permuted PDZ domains of uncharacterized archaeal proteins related to Escherichia coli Regulator of sigma-E protease (RseP) and Bacillus subtilis YlbL protease; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of uncharacterized archaeal proteins related to Escherichia coli ResP (also known as Site-2 protease RseP, and YaeL) and Bacillus subtilis YlbL protease. RseP participates in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. 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-YlbL archaeal 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.


Pssm-ID: 467635 [Multi-domain]  Cd Length: 79  Bit Score: 35.52  E-value: 5.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1895670020 118 VVSIVPGSPADKVnLNDGDIIEAIDDHDTRDISlAMIRMMLEGAPGSQVSI 168
Cdd:cd10823     3 VDRVVEGSPSSKV-LPEGMVIESIDGYSVKDLS-SYSEALRKFKPGDNIYI 51
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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