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Conserved domains on  [gi|587333522|gb|EWW15422|]
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RIP metalloprotease RseP [Staphylococcus aureus H38239]

Protein Classification

M50 family metallopeptidase( domain architecture ID 11433527)

M50 family metallopeptidase cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms; belongs to the site-2 protease (S2P) class of zinc metalloproteases

EC:  3.4.24.-
Gene Ontology:  GO:0016020|GO:0008233|GO:0004222|GO:0046872|GO:0006508
MEROPS:  M50
PubMed:  16731018|24099006|27889944|7674922

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 1-427 1.46e-125

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


:

Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 367.10  E-value: 1.46e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   1 MSYLVTIIAFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMGPKIFSFRKNETLYTIRLLPVGGYVRMAGDgleeppv 80
Cdd:COG0750    1 MSFLLTILAFILVLGVLVFVHELGHFLVARLFGVKVEEFSIGFGPKLFSKKRGETEYGIRAIPLGGYVKMAGM------- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  81 epgmnvkiklneeneithiilddhhkfqqieaievkkcdfkddlfiegitaydnerhhfkiarksffvENGSLVQIAPRD 160
Cdd:COG0750   74 --------------------------------------------------------------------DPESEVAPEDDP 85

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 161 RQFAHKKPWPKFLTLFAGPLFNFILALVLFIGLAYYQGTPTS---TVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDD 237
Cdd:COG0750   86 RAFNSKPVWQRLIIVLAGPLANFLLAIVLFAVLFMTVGVPVLtppVVGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDD 165

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 238 VDKALDKVKDNKTTVKFERDGKTKSVELTPKKTERkltkvssETKYVLGFQPASE-----HTLFKPIVYGFESFLKGSTL 312
Cdd:COG0750  166 LVDIIRASPGKPLTLTVERDGEELTLTVTPRLVEE-------DGVGRIGVSPSGEvvtvrYGPLEALGAGVKETWDMIVL 238

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 313 IFtavvGMLASIFTGGFSFDMLNGPVGIYHNVDSVVKAGIISLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFR 392
Cdd:COG0750  239 TL----KGLGKLITGKVSAKNLSGPIGIAGIAGEAASSGLASFLSFLALLSINLGVLNLLPIPALDGGHLLFLLIEAIRG 314

                        410       420       430
                 ....*....|....*....|....*....|....*
gi 587333522 393 KPVNKKAETTIIAIGAIFMVVIMILVTWNDIRRYF 427
Cdd:COG0750  315 RPVSEKVQEPIQRIGFALLLGLMVFATYNDIVRLF 349
 
Name Accession Description Interval E-value
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 1-427 1.46e-125

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 367.10  E-value: 1.46e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   1 MSYLVTIIAFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMGPKIFSFRKNETLYTIRLLPVGGYVRMAGDgleeppv 80
Cdd:COG0750    1 MSFLLTILAFILVLGVLVFVHELGHFLVARLFGVKVEEFSIGFGPKLFSKKRGETEYGIRAIPLGGYVKMAGM------- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  81 epgmnvkiklneeneithiilddhhkfqqieaievkkcdfkddlfiegitaydnerhhfkiarksffvENGSLVQIAPRD 160
Cdd:COG0750   74 --------------------------------------------------------------------DPESEVAPEDDP 85

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 161 RQFAHKKPWPKFLTLFAGPLFNFILALVLFIGLAYYQGTPTS---TVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDD 237
Cdd:COG0750   86 RAFNSKPVWQRLIIVLAGPLANFLLAIVLFAVLFMTVGVPVLtppVVGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDD 165

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 238 VDKALDKVKDNKTTVKFERDGKTKSVELTPKKTERkltkvssETKYVLGFQPASE-----HTLFKPIVYGFESFLKGSTL 312
Cdd:COG0750  166 LVDIIRASPGKPLTLTVERDGEELTLTVTPRLVEE-------DGVGRIGVSPSGEvvtvrYGPLEALGAGVKETWDMIVL 238

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 313 IFtavvGMLASIFTGGFSFDMLNGPVGIYHNVDSVVKAGIISLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFR 392
Cdd:COG0750  239 TL----KGLGKLITGKVSAKNLSGPIGIAGIAGEAASSGLASFLSFLALLSINLGVLNLLPIPALDGGHLLFLLIEAIRG 314

                        410       420       430
                 ....*....|....*....|....*....|....*
gi 587333522 393 KPVNKKAETTIIAIGAIFMVVIMILVTWNDIRRYF 427
Cdd:COG0750  315 RPVSEKVQEPIQRIGFALLLGLMVFATYNDIVRLF 349
TIGR00054 TIGR00054
RIP metalloprotease RseP; Members of this nearly universal bacterial protein family are ...
 7-425 5.01e-80

RIP metalloprotease RseP; Members of this nearly universal bacterial protein family are regulated intramembrane proteolysis (RIP) proteases. Older and synonymous gene symbols include yaeL in E. coli, mmpA in Caulobacter crescentus, etc. This family includes a region that hits the PDZ domain, found in a number of proteins targeted to the membrane by binding to a peptide ligand. The N-terminal region of this family contains a perfectly conserved motif HEXGH as found in a number of metalloproteinases, where the Glu is the active site and the His residues coordinate the metal cation. Membership in this family is determined by a match to the full length of the seed alignment; the model also detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 272878 [Multi-domain]  Cd Length: 419  Bit Score: 253.20  E-value: 5.01e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522    7 IIAFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMGPKIFSFRKNETLYTIRLLPVGGYVRMAGdgleeppVEPGMNV 86
Cdd:TIGR00054   5 ILASILALAVLIFVHELGHFLAARLCGIKVERFSIGFGPKILKFKKNGTEYAISLIPLGGYVKMKG-------LDKEMEV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   87 KIklneeNEITHIILDDHHKFQQIEAIEVKKcdFKDDLFIE---------GITAYD----NERHHFKIARKSFFVENGSL 153
Cdd:TIGR00054  78 KP-----PETDGDLFNNKSVFQKAIIIFAGP--LANFIFAIfvyifisliGVPGYEvgpvIELLDKNSIALEAGIEPGDE 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  154 VQIAPRDRQFAHKKPWpKFLTLFAGPLFNFILA----LVLFIGLAYYQGTPTS--TVEQVADKYPAQQAGLQKGDKIVQI 227
Cdd:TIGR00054 151 ILSVNGNKIPGFKDVR-QQIADIAGEPMVEILAerenWTFEVMKELIPRGPKIepVLSDVTPNSPAEKAGLKEGDYIQSI 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  228 GKYKISEFDDVDKALDKVKDNKTTVKFERDGKTKSVELTPKkterkltkvsSETKYVLGFQPASEHT-----LFKPIVYG 302
Cdd:TIGR00054 230 NGEKLRSWTDFVSAVKENPGKSMDIKVERNGETLSISLTPE----------AKGKIGIGISPSLAPLevsygILNAFAKG 299

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  303 FESFLKGSTLIFTavvgMLASIFTGGFSFDMLNGPVGIYHNVDSVVKAGIISLIGYTALLSVNLGIMNLIPIPALDGGRI 382
Cdd:TIGR00054 300 ASATVDIVKLILT----NLGKLITGSFKLKNLSGPVGIVKGAGSSANSGIVYLLQFGAFLSINLGIMNLLPIPALDGGQL 375

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|...
gi 587333522  383 LFVIYEAIFRKPVNKKAETTIIAIGAIFMVVIMILVTWNDIRR 425
Cdd:TIGR00054 376 LFLFIEAIRGKPLPEKVQAFVYRIGVAFLLFLMGLGLFNDLLR 418
Peptidase_M50 pfam02163
Peptidase family M50;
9-414 1.05e-77

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 242.78  E-value: 1.05e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522    9 AFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMgpkifsfrknetlYTIRLLPVGGYVRMAGDgleeppvepgmnvki 88
Cdd:pfam02163   1 AFILALGILVVVHELGHFLVARRFGVKVERFSIGF-------------YRIALIPLGGYVKMADE--------------- 52

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   89 klneeneithiilddhhkfqqieaievkkcdfkddlfiegitaydnerhhfkiarksffvengslvqiaprdrqFAHKKP 168
Cdd:pfam02163  53 --------------------------------------------------------------------------FKSKSP 58

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  169 WPKFLTLFAGPLFNFILALVLFIGLAYYQGTPTS---TVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKV 245
Cdd:pfam02163  59 WQRLAIALAGPLANFILAIILFAVLLFLSGVPPPappVIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQDLVEALAKS 138

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  246 KDNKTTVKFERDGKTKSVELTPKKTERKltkvssetkYVLGF-QPASEHTLFKPIVYGFESFLKGSTLIFTAVVGMLasi 324
Cdd:pfam02163 139 PGKPITLTVERGGQTLTVTITPKSSEES---------KFIGIgPVYVKYGLLEALGFALEKTVNLVTLTLKALGKLI--- 206

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  325 ftGGFSFDMLNGPVGIYhnvDSVVKAGIISLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFRKPVNKKAETTII 404
Cdd:pfam02163 207 --TGVSLKNLGGPIGIA---GQAAEAGLIAFLYFLALINLNLGIFNLLPVPPLDGGHILRALLEAIRGKPLSERAEEIAL 281

                         410
                  ....*....|
gi 587333522  405 AIGAIFMVVI 414
Cdd:pfam02163 282 RVGLALLLLL 291
S2P-M50_PDZ_RseP-like cd06163
RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave ...
 7-425 2.84e-52

RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.


Pssm-ID: 100084 [Multi-domain]  Cd Length: 182  Bit Score: 173.37  E-value: 2.84e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   7 IIAFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMGPKIFSFRKNETLYTIRLLPVGGYVRMAGDGLEEPPVEPgmnv 86
Cdd:cd06163    1 ILAFILVLGILIFVHELGHFLVAKLFGVKVEEFSIGFGPKLFSFKKGETEYSISAIPLGGYVKMLGEDPEEEADPE---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  87 kiklneeneithiilddhhkfqqieaievkkcdfkddlfiegitaydnerhhfkiarksffvengslvqiaPRDRQFAHK 166
Cdd:cd06163   77 -----------------------------------------------------------------------DDPRSFNSK 85

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 167 KPWPKFLTLFAGPLFNFILALVLFIGlayyqgtptstveqvadkypaqqaglqkgdkivqigkykisefddvdkaldkvk 246
Cdd:cd06163   86 PVWQRILIVFAGPLANFLLAIVLFAV------------------------------------------------------ 111

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 247 dnkttvkferdgktksveltpkkterkltkvssetkyvlgfqpasehtlfkpivygfesflkgstliftavvgmlasift 326
Cdd:cd06163      --------------------------------------------------------------------------------

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 327 ggfsfdmlngpvgiyhnvdsvvkagiisLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFRKPVNKKAETTIIAI 406
Cdd:cd06163  112 ----------------------------LLSFLALLSINLGILNLLPIPALDGGHLLFLLIEAIRGRPLSEKVEEIIQTI 163

                        410
                 ....*....|....*....
gi 587333522 407 GAIFMVVIMILVTWNDIRR 425
Cdd:cd06163  164 GFALLLGLMLFVTFNDIVR 182
PRK10779 PRK10779
sigma E protease regulator RseP;
1-425 2.84e-34

sigma E protease regulator RseP;


Pssm-ID: 182723 [Multi-domain]  Cd Length: 449  Bit Score: 132.88  E-value: 2.84e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   1 MSYLVTIIAFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMGPKIFS-FRKNETLYTIRLLPVGGYVRMAGDGLEEPP 79
Cdd:PRK10779   1 LSILWNLAAFIVALGVLITVHEFGHFWVARRCGVRVERFSIGFGKALWRrTDRQGTEYVIALIPLGGYVKMLDERVEPVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  80 VE---PGMNVKIKLNEE---------NEITHI--------------------ILDDHHKFQ-QIEA-IEVKKCDfkddlf 125
Cdd:PRK10779  81 PElrhHAFNNKTVGQRAaiiaagpiaNFIFAIfaywlvfiigvpgvrpvvgeIAPNSIAAQaQIAPgTELKAVD------ 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 126 ieGITAYDNERHHFKIARK-----------SFFVENGSLVQIAPRDRQFAHKKPWPkfltlfagplfnfilalVLFIGLA 194
Cdd:PRK10779 155 --GIETPDWDAVRLALVSKigdesttitvaPFGSDQRRDKTLDLRHWAFEPDKQDP-----------------VSSLGIR 215

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 195 YYQGTPTSTVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNKTTVKFERDGKTKSVELTPKkTERKL 274
Cdd:PRK10779 216 PRGPQIEPVLAEVQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRDNPGKPLALEIERQGSPLSLTLTPD-SKPGN 294

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 275 TKVSSETKYVLGFQPASEHtlFKPI-VYG-FESFLKGST---LIFTAVVGMLASIFTGGFSFDMLNGPVGIYHNVDSVVK 349
Cdd:PRK10779 295 GKAEGFAGVVPKVIPLPDE--YKTVrQYGpFSAIYEATDktwQLMKLTVSMLGKLITGDVKLNNLSGPISIAQGAGMSAE 372

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 587333522 350 AGIISLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFRKPVNKKAETTIIAIGAIFMVVIMILVTWNDIRR 425
Cdd:PRK10779 373 YGLVYYLMFLALISVNLGIINLFPLPVLDGGHLLFLAIEKLKGGPVSERVQDFSYRIGSILLVLLMGLALFNDFSR 448
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 204-255 6.14e-03

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: 35.82  E-value: 6.14e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 587333522   204 VEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDvDKALDKVKDNKTTVKFE 255
Cdd:smart00228  30 VSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTH-LEAVDLLKKAGGKVTLT 80
 
Name Accession Description Interval E-value
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 1-427 1.46e-125

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 367.10  E-value: 1.46e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   1 MSYLVTIIAFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMGPKIFSFRKNETLYTIRLLPVGGYVRMAGDgleeppv 80
Cdd:COG0750    1 MSFLLTILAFILVLGVLVFVHELGHFLVARLFGVKVEEFSIGFGPKLFSKKRGETEYGIRAIPLGGYVKMAGM------- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  81 epgmnvkiklneeneithiilddhhkfqqieaievkkcdfkddlfiegitaydnerhhfkiarksffvENGSLVQIAPRD 160
Cdd:COG0750   74 --------------------------------------------------------------------DPESEVAPEDDP 85

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 161 RQFAHKKPWPKFLTLFAGPLFNFILALVLFIGLAYYQGTPTS---TVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDD 237
Cdd:COG0750   86 RAFNSKPVWQRLIIVLAGPLANFLLAIVLFAVLFMTVGVPVLtppVVGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDD 165

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 238 VDKALDKVKDNKTTVKFERDGKTKSVELTPKKTERkltkvssETKYVLGFQPASE-----HTLFKPIVYGFESFLKGSTL 312
Cdd:COG0750  166 LVDIIRASPGKPLTLTVERDGEELTLTVTPRLVEE-------DGVGRIGVSPSGEvvtvrYGPLEALGAGVKETWDMIVL 238

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 313 IFtavvGMLASIFTGGFSFDMLNGPVGIYHNVDSVVKAGIISLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFR 392
Cdd:COG0750  239 TL----KGLGKLITGKVSAKNLSGPIGIAGIAGEAASSGLASFLSFLALLSINLGVLNLLPIPALDGGHLLFLLIEAIRG 314

                        410       420       430
                 ....*....|....*....|....*....|....*
gi 587333522 393 KPVNKKAETTIIAIGAIFMVVIMILVTWNDIRRYF 427
Cdd:COG0750  315 RPVSEKVQEPIQRIGFALLLGLMVFATYNDIVRLF 349
TIGR00054 TIGR00054
RIP metalloprotease RseP; Members of this nearly universal bacterial protein family are ...
 7-425 5.01e-80

RIP metalloprotease RseP; Members of this nearly universal bacterial protein family are regulated intramembrane proteolysis (RIP) proteases. Older and synonymous gene symbols include yaeL in E. coli, mmpA in Caulobacter crescentus, etc. This family includes a region that hits the PDZ domain, found in a number of proteins targeted to the membrane by binding to a peptide ligand. The N-terminal region of this family contains a perfectly conserved motif HEXGH as found in a number of metalloproteinases, where the Glu is the active site and the His residues coordinate the metal cation. Membership in this family is determined by a match to the full length of the seed alignment; the model also detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 272878 [Multi-domain]  Cd Length: 419  Bit Score: 253.20  E-value: 5.01e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522    7 IIAFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMGPKIFSFRKNETLYTIRLLPVGGYVRMAGdgleeppVEPGMNV 86
Cdd:TIGR00054   5 ILASILALAVLIFVHELGHFLAARLCGIKVERFSIGFGPKILKFKKNGTEYAISLIPLGGYVKMKG-------LDKEMEV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   87 KIklneeNEITHIILDDHHKFQQIEAIEVKKcdFKDDLFIE---------GITAYD----NERHHFKIARKSFFVENGSL 153
Cdd:TIGR00054  78 KP-----PETDGDLFNNKSVFQKAIIIFAGP--LANFIFAIfvyifisliGVPGYEvgpvIELLDKNSIALEAGIEPGDE 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  154 VQIAPRDRQFAHKKPWpKFLTLFAGPLFNFILA----LVLFIGLAYYQGTPTS--TVEQVADKYPAQQAGLQKGDKIVQI 227
Cdd:TIGR00054 151 ILSVNGNKIPGFKDVR-QQIADIAGEPMVEILAerenWTFEVMKELIPRGPKIepVLSDVTPNSPAEKAGLKEGDYIQSI 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  228 GKYKISEFDDVDKALDKVKDNKTTVKFERDGKTKSVELTPKkterkltkvsSETKYVLGFQPASEHT-----LFKPIVYG 302
Cdd:TIGR00054 230 NGEKLRSWTDFVSAVKENPGKSMDIKVERNGETLSISLTPE----------AKGKIGIGISPSLAPLevsygILNAFAKG 299

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  303 FESFLKGSTLIFTavvgMLASIFTGGFSFDMLNGPVGIYHNVDSVVKAGIISLIGYTALLSVNLGIMNLIPIPALDGGRI 382
Cdd:TIGR00054 300 ASATVDIVKLILT----NLGKLITGSFKLKNLSGPVGIVKGAGSSANSGIVYLLQFGAFLSINLGIMNLLPIPALDGGQL 375

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|...
gi 587333522  383 LFVIYEAIFRKPVNKKAETTIIAIGAIFMVVIMILVTWNDIRR 425
Cdd:TIGR00054 376 LFLFIEAIRGKPLPEKVQAFVYRIGVAFLLFLMGLGLFNDLLR 418
Peptidase_M50 pfam02163
Peptidase family M50;
9-414 1.05e-77

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 242.78  E-value: 1.05e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522    9 AFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMgpkifsfrknetlYTIRLLPVGGYVRMAGDgleeppvepgmnvki 88
Cdd:pfam02163   1 AFILALGILVVVHELGHFLVARRFGVKVERFSIGF-------------YRIALIPLGGYVKMADE--------------- 52

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   89 klneeneithiilddhhkfqqieaievkkcdfkddlfiegitaydnerhhfkiarksffvengslvqiaprdrqFAHKKP 168
Cdd:pfam02163  53 --------------------------------------------------------------------------FKSKSP 58

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  169 WPKFLTLFAGPLFNFILALVLFIGLAYYQGTPTS---TVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKV 245
Cdd:pfam02163  59 WQRLAIALAGPLANFILAIILFAVLLFLSGVPPPappVIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQDLVEALAKS 138

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  246 KDNKTTVKFERDGKTKSVELTPKKTERKltkvssetkYVLGF-QPASEHTLFKPIVYGFESFLKGSTLIFTAVVGMLasi 324
Cdd:pfam02163 139 PGKPITLTVERGGQTLTVTITPKSSEES---------KFIGIgPVYVKYGLLEALGFALEKTVNLVTLTLKALGKLI--- 206

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  325 ftGGFSFDMLNGPVGIYhnvDSVVKAGIISLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFRKPVNKKAETTII 404
Cdd:pfam02163 207 --TGVSLKNLGGPIGIA---GQAAEAGLIAFLYFLALINLNLGIFNLLPVPPLDGGHILRALLEAIRGKPLSERAEEIAL 281

                         410
                  ....*....|
gi 587333522  405 AIGAIFMVVI 414
Cdd:pfam02163 282 RVGLALLLLL 291
S2P-M50_PDZ_RseP-like cd06163
RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave ...
 7-425 2.84e-52

RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.


Pssm-ID: 100084 [Multi-domain]  Cd Length: 182  Bit Score: 173.37  E-value: 2.84e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   7 IIAFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMGPKIFSFRKNETLYTIRLLPVGGYVRMAGDGLEEPPVEPgmnv 86
Cdd:cd06163    1 ILAFILVLGILIFVHELGHFLVAKLFGVKVEEFSIGFGPKLFSFKKGETEYSISAIPLGGYVKMLGEDPEEEADPE---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  87 kiklneeneithiilddhhkfqqieaievkkcdfkddlfiegitaydnerhhfkiarksffvengslvqiaPRDRQFAHK 166
Cdd:cd06163   77 -----------------------------------------------------------------------DDPRSFNSK 85

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 167 KPWPKFLTLFAGPLFNFILALVLFIGlayyqgtptstveqvadkypaqqaglqkgdkivqigkykisefddvdkaldkvk 246
Cdd:cd06163   86 PVWQRILIVFAGPLANFLLAIVLFAV------------------------------------------------------ 111

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 247 dnkttvkferdgktksveltpkkterkltkvssetkyvlgfqpasehtlfkpivygfesflkgstliftavvgmlasift 326
Cdd:cd06163      --------------------------------------------------------------------------------

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 327 ggfsfdmlngpvgiyhnvdsvvkagiisLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFRKPVNKKAETTIIAI 406
Cdd:cd06163  112 ----------------------------LLSFLALLSINLGILNLLPIPALDGGHLLFLLIEAIRGRPLSEKVEEIIQTI 163

                        410
                 ....*....|....*....
gi 587333522 407 GAIFMVVIMILVTWNDIRR 425
Cdd:cd06163  164 GFALLLGLMLFVTFNDIVR 182
PRK10779 PRK10779
sigma E protease regulator RseP;
1-425 2.84e-34

sigma E protease regulator RseP;


Pssm-ID: 182723 [Multi-domain]  Cd Length: 449  Bit Score: 132.88  E-value: 2.84e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   1 MSYLVTIIAFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMGPKIFS-FRKNETLYTIRLLPVGGYVRMAGDGLEEPP 79
Cdd:PRK10779   1 LSILWNLAAFIVALGVLITVHEFGHFWVARRCGVRVERFSIGFGKALWRrTDRQGTEYVIALIPLGGYVKMLDERVEPVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  80 VE---PGMNVKIKLNEE---------NEITHI--------------------ILDDHHKFQ-QIEA-IEVKKCDfkddlf 125
Cdd:PRK10779  81 PElrhHAFNNKTVGQRAaiiaagpiaNFIFAIfaywlvfiigvpgvrpvvgeIAPNSIAAQaQIAPgTELKAVD------ 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 126 ieGITAYDNERHHFKIARK-----------SFFVENGSLVQIAPRDRQFAHKKPWPkfltlfagplfnfilalVLFIGLA 194
Cdd:PRK10779 155 --GIETPDWDAVRLALVSKigdesttitvaPFGSDQRRDKTLDLRHWAFEPDKQDP-----------------VSSLGIR 215

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 195 YYQGTPTSTVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNKTTVKFERDGKTKSVELTPKkTERKL 274
Cdd:PRK10779 216 PRGPQIEPVLAEVQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRDNPGKPLALEIERQGSPLSLTLTPD-SKPGN 294

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 275 TKVSSETKYVLGFQPASEHtlFKPI-VYG-FESFLKGST---LIFTAVVGMLASIFTGGFSFDMLNGPVGIYHNVDSVVK 349
Cdd:PRK10779 295 GKAEGFAGVVPKVIPLPDE--YKTVrQYGpFSAIYEATDktwQLMKLTVSMLGKLITGDVKLNNLSGPISIAQGAGMSAE 372

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 587333522 350 AGIISLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFRKPVNKKAETTIIAIGAIFMVVIMILVTWNDIRR 425
Cdd:PRK10779 373 YGLVYYLMFLALISVNLGIINLFPLPVLDGGHLLFLAIEKLKGGPVSERVQDFSYRIGSILLVLLMGLALFNDFSR 448
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 203-289 1.46e-21

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.


Pssm-ID: 467638 [Multi-domain]  Cd Length: 83  Bit Score: 88.02  E-value: 1.46e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 203 TVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNKTTVKFERDGKTKSVELTPKKTERKLTKVssetk 282
Cdd:cd23081    2 VVGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRIVRENPGKPLTLKIERDGKILTVTVTPELVEVEGKGV----- 76


                 ....*..
gi 587333522 283 YVLGFQP 289
Cdd:cd23081   77 GRIGVQP 83
S2P-M50 cd05709
Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane ...
 8-421 1.95e-21

Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-binding proteins (SREBPs) from membranes of the ER. These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD superfamily. Prokaryotic S2P/M50 homologs have been shown to regulate stress responses, sporulation, cell division, and cell differentiation. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses, and in Bacillus subtilis, the S2P homolog SpoIVFB is involved in the pro-sigmaK pathway of spore formation. Some of the subfamilies within this hierarchy contain one or two PDZ domain insertions, with putative regulatory roles, such as the inhibition of substrate cleavage as seen by the RseP PDZ domain.


Pssm-ID: 100078 [Multi-domain]  Cd Length: 180  Bit Score: 90.76  E-value: 1.95e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   8 IAFIIVFGVLVTVHEYGHMFFAKRAGIMCPEFAIGMgpkIFSFRKNETLYTIRLLPVGGYVRMAGDgleeppvepgmnvk 87
Cdd:cd05709    1 LAFILALLISVTVHELGHALVARRLGVKVARFSGGF---TLNPLKHGDPYGIILIPLGGYAKPVGE-------------- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  88 iklneeneithiilddhhkfqqieaievkkcdfkddlfiegitaydnerhhfkiarksffvengslvqiaprDRQFAHKK 167
Cdd:cd05709   64 ------------------------------------------------------------------------NPRAFKKP 71

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 168 PWPKFLTLFAGPLFNFILALVLFIGLAYYQGTPTSTVEQVAdkypaqqaglqkgdkivqigkykisefddvdkaldkvkd 247
Cdd:cd05709   72 RWQRLLVALAGPLANLLLALLLLLLLLLLGGLPPAPVGQAA--------------------------------------- 112

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 248 nkttvkferdgktksveltpkkterkltkvssetkyvlgfqpasehtlfkpivygfesflkgstliftavvgmlasiftg 327
Cdd:cd05709      --------------------------------------------------------------------------------

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 328 gfsfdmlngpvgiyhnvdsvvKAGIISLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFRKPVNKkaettIIAIG 407
Cdd:cd05709  113 ---------------------SSGLANLLAFLALINLNLAVFNLLPIPPLDGGRILRALLEAIRGRVEER-----LEAYG 166

                        410
                 ....*....|....
gi 587333522 408 AIFMVVIMILVTWN 421
Cdd:cd05709  167 FAILLGLLLLLLLN 180
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 204-266 3.42e-10

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.


Pssm-ID: 467622 [Multi-domain]  Cd Length: 98  Bit Score: 56.49  E-value: 3.42e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 587333522 204 VEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNKT-TVKFERDGKTKSVELT 266
Cdd:cd06781   34 VAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQILYSHKVGDTvKVTIYRDGKEKTLNIK 97
SpoIVFB COG1994
Zn-dependent protease (includes sporulation protein SpoIVFB) [Posttranslational modification, ...
 313-417 4.15e-09

Zn-dependent protease (includes sporulation protein SpoIVFB) [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441597  Cd Length: 175  Bit Score: 55.60  E-value: 4.15e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 313 IFTAVVGMLASIFTGGFSFdmlngpvGIYHNVDSVVKAGIISLIGYTALLSVNLGIMNLIPIPALDGGRILfviyEAIFR 392
Cdd:COG1994   66 ALVALAGPLANLLLALLFA-------LLLRLLPALGLGPLALLLGYLALINLVLAVFNLLPIPPLDGGRIL----RALLP 134

                         90       100
                 ....*....|....*....|....*
gi 587333522 393 KPVNKKAeTTIIAIGAIFMVVIMIL 417
Cdd:COG1994  135 RRTARRA-TRLEPYGFLILLLLIFL 158
PDZ_2 pfam13180
PDZ domain;
203-266 3.92e-08

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 49.96  E-value: 3.92e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 587333522  203 TVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNKT-TVKFERDGKTKSVELT 266
Cdd:pfam13180   9 VVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALYGHKPGDTvTLQVYRDGKLLTVEVK 73
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 204-267 1.72e-07

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: 52.46  E-value: 1.72e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 587333522 204 VEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVK-DNKTTVKFERDGKTKSVELTP 267
Cdd:COG0265  205 VARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRLLASLKpGDTVTLTVLRGGKELTVTVTL 269
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
191-282 3.84e-07

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


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 52.13  E-value: 3.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 191 IGLAYYQGTPTSTVEQVADKYPAQQAGLQKGDKIVQIGKYKISEfDDVDKALDKVKDNKT-TVKFERDGKTKSVELTPKK 269
Cdd:COG3975  485 LGLRVSADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVTA-DNLDDALAAYKPGDPiELLVFRRDELRTVTVTLAA 563

                         90
                 ....*....|....*.
gi 587333522 270 TER---KLTKVSSETK 282
Cdd:COG3975  564 APAdtyKLERVEGATP 579
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 204-265 7.33e-07

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: 46.90  E-value: 7.33e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 587333522 204 VEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNKT-TVKFERDGKTKSVEL 265
Cdd:cd06779   29 VAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTKKPGDSlNLTILRDGKTLTVTV 91
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 204-268 7.96e-07

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.


Pssm-ID: 467629 [Multi-domain]  Cd Length: 104  Bit Score: 47.31  E-value: 7.96e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 587333522 204 VEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNKT-TVKFERDGKTKSVELTPK 268
Cdd:cd10838   37 IMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRIVEQAGVGEElELTVLRGDRRQTLAVKPG 102
cpPDZ2_EcRseP-like cd23083
circularly permuted PDZ domain 2 (PDZ-C) of Escherichia coli Regulator of sigma-E protease ...
 202-271 1.82e-06

circularly permuted PDZ domain 2 (PDZ-C) of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL) and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with it associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.


Pssm-ID: 467640 [Multi-domain]  Cd Length: 85  Bit Score: 45.58  E-value: 1.82e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 587333522 202 STVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKAldkVKDNKTT---VKFERDGKTKSVELTPKKTE 271
Cdd:cd23083    1 PVLANVQPNSAAEKAGLQAGDRIVKVDGQPLTQWQTFVMA---VRDNPGKplaLEIERQGSPLSLTLIPDSKE 70
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 204-290 2.03e-05

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: 46.45  E-value: 2.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522  204 VEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNKT-TVKFERDGKTKSVELTPKKTERklTKVSSEtK 282
Cdd:TIGR02037 261 VAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKvTLGILRKGKEKTITVTLGASPE--EQASSS-N 337


                  ....*...
gi 587333522  283 YVLGFQPA 290
Cdd:TIGR02037 338 PFLGLTVA 345
S2P-M50_SpoIVFB_CBS cd06164
SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates ...
 316-423 2.49e-05

SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.


Pssm-ID: 100085  Cd Length: 227  Bit Score: 45.22  E-value: 2.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 316 AVVGMLASIFTGGFSFdmlngpvGIYHNVDSVVKAGIISLIGYTALLSVNLGIMNLIPIPALDGGRILfviyEAIFRKPV 395
Cdd:cd06164  102 AIAGPLVSLVLALLFL-------LLSLALPGSGAGPLGVLLGYLALINLLLAVFNLLPAFPLDGGRVL----RALLWRRT 170

                         90       100       110
                 ....*....|....*....|....*....|...
gi 587333522 396 NKKAETTIIA--IG---AIFMVVIMILVTWNDI 423
Cdd:cd06164  171 GDYLKATRIAawVGrgfAVLLIILGLLSLFLNL 203
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 203-256 3.26e-05

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 41.36  E-value: 3.26e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 587333522  203 TVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNKTTVKFER 256
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLQGSAGESVTLTVRR 54
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 203-243 6.09e-05

circularly permuted second PDZ domain (PDZ2) 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 2 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 the identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for the 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 2 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: 467631 [Multi-domain]  Cd Length: 83  Bit Score: 41.46  E-value: 6.09e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 587333522 203 TVEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALD 243
Cdd:cd23084   21 VVTEVDPGSPAAQSGLKKGDVIIGVNRQPVKSIAELRKVLK 61
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 191-266 7.67e-05

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: 44.48  E-value: 7.67e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 587333522 191 IGLAYYQGTPTSTVEQVADKYPAQQAGLQKGDKIVQIGKYKISE--FDDVDKALDKVKDNKTTVKFERDGKTKSVELT 266
Cdd:COG0793   62 LGAELGEEDGKVVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGltLDDAVKLLRGKAGTKVTLTIKRPGEGEPITVT 139
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 204-260 2.77e-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: 42.98  E-value: 2.77e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 587333522  204 VEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNK-TTVKFERDGKT 260
Cdd:TIGR02037 366 VTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKKGGrVALLILRGGAT 423
S2P-M50_like_1 cd06158
Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) ...
 352-420 3.01e-04

Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.


Pssm-ID: 100079  Cd Length: 181  Bit Score: 41.38  E-value: 3.01e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 587333522 352 IISLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFRKPVNKkaettIIAIGaiFMVVIMILVTW 420
Cdd:cd06158  117 LFLMLAYGVLINLVLAVFNLLPIPPLDGSKILAALLPRRLAEAYAR-----LEPYG--FLILLALLFTG 178
S2P-M50_SpoIVFB cd06161
SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates ...
 316-428 6.74e-04

SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB.


Pssm-ID: 100082 [Multi-domain]  Cd Length: 208  Bit Score: 40.60  E-value: 6.74e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522 316 AVVGMLASIFTGGFSFdMLNGPVGIYHNVDSvvkagiisLIGYTALLSVNLGIMNLIPIPALDGGRILFVIYEAIFRKpv 395
Cdd:cd06161   87 ALAGPLVSLLLAGLFY-LLYLLLPGGGPLSS--------LLEFLAQVNLILGLFNLLPALPLDGGRVLRALLWRRTGY-- 155

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 587333522 396 nKKAETTIIAIG---AIFMVVIMILVTWNDIRRYFL 428
Cdd:cd06161  156 -RRATRIAARIGqlfAILLVVLGLFLLFLGLGNLWL 190
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 204-265 1.06e-03

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: 37.85  E-value: 1.06e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 587333522 204 VEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDVDKALDKVKDNKT-TVKFERDGKTKSVEL 265
Cdd:cd10839   29 VAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATTKPGTKvELKILRDGKEKTLTV 91
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 204-266 1.55e-03

circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Arabidopsis thaliana DEGP1 (also known as protease Do-like 1, chloroplastic, protein DEGRADATION OF PERIPLASMIC PROTEINS 1, DEGP PROTEASE 1 and DEG1), and related domains. DEGP1 is a serine protease that is required at high temperature and may be involved in the degradation of damaged proteins. This family also includes Arabidopsis protease DEGP8/Do-like 8 (chloroplastic), a probable serine protease. 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 AtDEGP-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: 467618 [Multi-domain]  Cd Length: 102  Bit Score: 37.94  E-value: 1.55e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 587333522 204 VEQVADKYPAQQAGLQK-----------GDKIVQIGKYKISEFDDVDKALDKVK-DNKTTVKFERDGKTKSVELT 266
Cdd:cd00990   27 VLDVPPGGPAAKAGLRGtkrdefgrivlGDVIVAVDGKPVKNESDLYRALDEYKvGDVVTLKVLRGGTKVDLKVT 101
PDZ_TAX1BP3-like cd10822
PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic ...
 204-253 4.06e-03

PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of TAX1BP3, and related domains. TAX1BP3 (also known as glutaminase-interacting protein 3, tax interaction protein 1, TIP-1, tax-interacting protein 1) may regulate a number of protein-protein interactions by competing for PDZ domain binding sites. TAX1BP3 binds beta-catenin and may act as an inhibitor of the Wnt signaling pathway. It competes with LIN7A (also known as Lin-7A or LIN-7A) for inward rectifier potassium channel 4 (KCNJ4) binding, and thereby promotes KCNJ4 internalization. It may play a role in the Rho signaling pathway, and in the activation of CDC42 by the viral protein HPV16 E6. Binding partners of the TAX1BP3 PDZ domain include beta-catenin, KCNJ4, glutaminase liver isoform (GLS2), rho guanine nucleotide exchange factor 16 (ARHGEF16), rhotekin, and CDK5 regulatory subunit-associated protein 3 (also known as LAPZ). 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 TAX1BP3-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: 467265 [Multi-domain]  Cd Length: 94  Bit Score: 36.55  E-value: 4.06e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 587333522 204 VEQVADKYPAQQAGLQKGDKIVQIGKYkisEFDDV--DKALDKVKDNKTTVK 253
Cdd:cd10822   41 VTRVSEGGPAEKAGLQVGDKILQVNGW---DMTMVthKQAVKRLTKKKPVLR 89
cpPDZ_BsYlbL-like cd23080
circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ ...
 204-268 5.53e-03

circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis YlbL and related domains. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. Deletion of both proteases leads to accumulation of the cell division inhibitor YneA. 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 YlbL 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: 467637 [Multi-domain]  Cd Length: 83  Bit Score: 35.93  E-value: 5.53e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 587333522 204 VEQVADKYPAqqAG-LQKGDKIVQI-GK-YKISEfDDVDKALDKVKDNKTTVKFERDGKTKSVELTPK 268
Cdd:cd23080    4 VLSVVENMPA--KGiLEAGDKITAIdGQnFQSSE-KLIDYISSKKAGDKVKVKYERDEKEKEAELKLK 68
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 204-255 6.14e-03

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: 35.82  E-value: 6.14e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 587333522   204 VEQVADKYPAQQAGLQKGDKIVQIGKYKISEFDDvDKALDKVKDNKTTVKFE 255
Cdd:smart00228  30 VSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTH-LEAVDLLKKAGGKVTLT 80
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 204-266 6.68e-03

circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Escherichia coli DegS and related domains. DegS (also known as Site-1 protease DegS, S1P protease DegS, and Site-1-type intramembrane protease) participates in the activation of the sigma(E) extracytoplasmic stress response. Initially, there is an accumulation of misfolded membrane proteins (OMPs) in the periplasm which bind by their YXF motif to the DegS PDZ domain, activating DegS-catalyzed cleavage of the RseA periplasmic domain and making RseA a substrate for cleavage by another membrane protease RseP. 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 DegS family 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: 467620 [Multi-domain]  Cd Length: 93  Bit Score: 35.83  E-value: 6.68e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 587333522 204 VEQVADKYPAQQAGLQKGDKIVQIGKYKISefdDVDKALDKVKDNK--TTVKFE--RDGKTKSVELT 266
Cdd:cd06777   29 VKGVSPDSPAAKAGIQVGDIILQFDNKPVI---SVLELMDLVAEIRpgTVIPVVvlRDGKQLTLEVT 92
S2P-M50_SpoIVFB cd06161
SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates ...
 2-88 8.26e-03

SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB.


Pssm-ID: 100082 [Multi-domain]  Cd Length: 208  Bit Score: 37.52  E-value: 8.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 587333522   2 SYLVTIIAFIIVFGVLVTVHEYGHMFFAKRAGImcpefaigmgpKIFSfrknetlytIRLLPVGGYVRMagdglEEPPVE 81
Cdd:cd06161   25 VAWLLGLLEALLLFLSVLLHELGHALVARRYGI-----------RVRS---------ITLLPFGGVAEL-----EEEPET 79


                 ....*..
gi 587333522  82 PGMNVKI 88
Cdd:cd06161   80 PKEEFVI 86
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 212-266 8.69e-03

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: 35.15  E-value: 8.69e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 587333522 212 PAQQAGLQKGDKIVQIGKYKISEFdDVDKALDKV---KDNKTTVKFERDGKTKSVELT 266
Cdd:cd06782   26 PAEKAGIKPGDVIVAVDGESVRGM-SLDEVVKLLrgpKGTKVKLTIRRGGEGEPRDVT 82
 
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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