NCBI Conserved Domain Search

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...

131-283

9.71e-11

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: 63.39 E-value: 9.71e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 131 VGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVD-RVGEtgKIQVQAERAGEIKTFSLPIQNFLNDQSQSPLD 209
Cdd:TIGR02037 261 VAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTlKPGK--KVTLGILRKGKEKTITVTLGASPEEQASSSNP 338

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 210 ILGFTPY--------RPQIPA-----IVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVVQASPEK-LLKVDVL 275
Cdd:TIGR02037 339 FLGLTVAnlspeirkELRLKGdvkgvVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKKGgRVALLIL 418


                  ....*...
gi 1253006069 276 RNNQVQQL 283
Cdd:TIGR02037 419 RGGATIFV 426

DegQ

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...

130-199

1.06e-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: 52.84 E-value: 1.06e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1253006069 130 RVGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVD-RVGETGKIQVQaeRAGEIKTFSLPIQNF 199
Cdd:COG0265   204 LVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRLLASlKPGDTVTLTVL--RGGKELTVTVTLGER 272

PDZ_2

PDZ domain;

131-196

1.16e-07

PDZ domain;

Pssm-ID: 433015 [Multi-domain] Cd Length: 74 Bit Score: 48.81 E-value: 1.16e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1253006069 131 VGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVD-RVGETgkIQVQAERAGEIKTFSLPI 196
Cdd:pfam13180  10 VVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALYGhKPGDT--VTLQVYRDGKLLTVEVKL 74

DegQ

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...

222-285

2.59e-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: 51.69 E-value: 2.59e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 222 AIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVVQA-SPEKLLKVDVLRNNQVQQLEV 285
Cdd:COG0265   203 VLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRLLASlKPGDTVTLTVLRGGKELTVTV 267

PDZ2_Scribble-like

cd06703

PDZ domain 2 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...

212-254

2.75e-07

PDZ domain 2 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. 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 Scribble-like family PDZ2 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: 467187 [Multi-domain] Cd Length: 92 Bit Score: 48.41 E-value: 2.75e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1253006069 212 GFTPYRPQIPAI-VSKLSEDGAAIRQG-MQVGDQIIAIDGVKMND 254
Cdd:cd06703    23 GSTPFRDGDEGIfISRITEGGAADRDGkLQVGDRVLSINGVDVTE 67

PDZ

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...

211-278

8.40e-07

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: 46.60 E-value: 8.40e-07

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1253006069  211 LGFT---PYRPQIPAIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDW--YDVVQVVQASPEKlLKVDVLRNN 278
Cdd:smart00228  14 LGFSlvgGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLthLEAVDLLKKAGGK-VTLTVLRGG 85

PDZ_2

PDZ domain;

222-285

1.80e-06

PDZ domain;

Pssm-ID: 433015 [Multi-domain] Cd Length: 74 Bit Score: 45.34 E-value: 1.80e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 222 AIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVV-QASPEKLLKVDVLRNNQVQQLEV 285
Cdd:pfam13180   8 VVVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALyGHKPGDTVTLQVYRDGKLLTVEV 72

degP_htrA_DO

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...

222-285

3.80e-05

Pssm-ID: 273938 [Multi-domain] Cd Length: 428 Bit Score: 45.68 E-value: 3.80e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 222 AIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVVQAS-PEKLLKVDVLRNNQVQQLEV 285
Cdd:TIGR02037 259 ALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLkPGKKVTLGILRKGKEKTITV 323

PDZ

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...

131-162

2.49e-04

Pssm-ID: 214570 [Multi-domain] Cd Length: 85 Bit Score: 39.67 E-value: 2.49e-04

                           10        20        30
                   ....*....|....*....|....*....|..
gi 1253006069  131 VGKVLADTPAAAAQMQVGDKITAIDGTPVTTW 162
Cdd:smart00228  30 VSSVVPGSPAAKAGLRVGDVILEVNGTSVEGL 61

Name

Accession

Description

Interval

E-value

RseP

COG0750

Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...

1-451

6.21e-142

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

Pssm-ID: 440513 [Multi-domain] Cd Length: 349 Bit Score: 409.86 E-value: 6.21e-142

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069   1 MSALFIVVAAILLLGPLIAIHEFGHYFVARKLGVKVLVYSIGFGPTILKWtsKKSGIQYQLSALPLGGYVKMLDEREE-N 79
Cdd:COG0750     1 MSFLLTILAFILVLGVLVFVHELGHFLVARLFGVKVEEFSIGFGPKLFSK--KRGETEYGIRAIPLGGYVKMAGMDPEsE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069  80 VAEADLPYAFNRQHPWKRIAIVAAGPLINLIFAILLFWLLFLPS--QEQLNTRVGKVLADTPAAAAQMQVGDKITAIDGT 157
Cdd:COG0750    79 VAPEDDPRAFNSKPVWQRLIIVLAGPLANFLLAIVLFAVLFMTVgvPVLTPPVVGEVVPGSPAAKAGLQPGDRIVAINGQ 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 158 PVTTWEklnfalvdrvgetgkiqvqaerageiktfslpiqnflndqsqspldilgftpyrpqipaivsklsedgaairqg 237
Cdd:COG0750   159 PVTSWD-------------------------------------------------------------------------- 164

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 238 mqvgdqiiaidgvkmndwyDVVQVVQASPEKLLKVDVLRNNQVQQLEVMPqgkRDNMGNVSGVLGVQSDPGKIvipedfk 317
Cdd:COG0750   165 -------------------DLVDIIRASPGKPLTLTVERDGEELTLTVTP---RLVEEDGVGRIGVSPSGEVV------- 215

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 318 qTIQYSPSEALFMAVDKTGQLSSMILNSIVKMVRGLIGLDNLSGPITIAKVAGQSAEMGWQTFISFMALMSVSLGILNLL 397
Cdd:COG0750   216 -TVRYGPLEALGAGVKETWDMIVLTLKGLGKLITGKVSAKNLSGPIGIAGIAGEAASSGLASFLSFLALLSINLGVLNLL 294

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1253006069 398 PIPMLDGGHLVYYFIELIRGKPVSEQIQLVGLKIGMVLLGSMMLLALFNDIMRL 451
Cdd:COG0750   295 PIPALDGGHLLFLLIEAIRGRPVSEKVQEPIQRIGFALLLGLMVFATYNDIVRL 348

PRK10779

sigma E protease regulator RseP;

1-451

2.87e-123

sigma E protease regulator RseP;

Pssm-ID: 182723 [Multi-domain] Cd Length: 449 Bit Score: 365.93 E-value: 2.87e-123

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069   1 MSALFIVVAAILLLGPLIAIHEFGHYFVARKLGVKVLVYSIGFGPTILKWTSKKsGIQYQLSALPLGGYVKMLDEREENV 80
Cdd:PRK10779    1 LSILWNLAAFIVALGVLITVHEFGHFWVARRCGVRVERFSIGFGKALWRRTDRQ-GTEYVIALIPLGGYVKMLDERVEPV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069  81 AEADLPYAFNRQHPWKRIAIVAAGPLINLIFAILLFWLLFLPSQEQLNTRVGKVLADTPAAAAQMQVGDKITAIDGTPVT 160
Cdd:PRK10779   80 APELRHHAFNNKTVGQRAAIIAAGPIANFIFAIFAYWLVFIIGVPGVRPVVGEIAPNSIAAQAQIAPGTELKAVDGIETP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 161 TWEKLNFALVDRVGEtGKIQVQAERAGEI----KTFSLPIQNFLNDQsQSPLDILGFTPYRPQIPAIVSKLSEDGAAIRQ 236
Cdd:PRK10779  160 DWDAVRLALVSKIGD-ESTTITVAPFGSDqrrdKTLDLRHWAFEPDK-QDPVSSLGIRPRGPQIEPVLAEVQPNSAASKA 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 237 GMQVGDQIIAIDGVKMNDWYDVVQVVQASPEKLLKVDVLRNNQVQQLEVMPQGKRDNmGNVSGVLGVQsdPGKIVIPEDF 316
Cdd:PRK10779  238 GLQAGDRIVKVDGQPLTQWQTFVTLVRDNPGKPLALEIERQGSPLSLTLTPDSKPGN-GKAEGFAGVV--PKVIPLPDEY 314

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 317 KQTIQYSPSEALFMAVDKTGQLSSMILNSIVKMVRGLIGLDNLSGPITIAKVAGQSAEMGWQTFISFMALMSVSLGILNL 396
Cdd:PRK10779  315 KTVRQYGPFSAIYEATDKTWQLMKLTVSMLGKLITGDVKLNNLSGPISIAQGAGMSAEYGLVYYLMFLALISVNLGIINL 394

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 397 LPIPMLDGGHLVYYFIELIRGKPVSEQIQLVGLKIGMVLLGSMMLLALFNDIMRL 451
Cdd:PRK10779  395 FPLPVLDGGHLLFLAIEKLKGGPVSERVQDFSYRIGSILLVLLMGLALFNDFSRL 449

TIGR00054

RIP metalloprotease RseP; Members of this nearly universal bacterial protein family are ...

2-451

1.45e-104

Pssm-ID: 272878 [Multi-domain] Cd Length: 419 Bit Score: 317.15 E-value: 1.45e-104

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069   2 SALFIVvAAILLLGPLIAIHEFGHYFVARKLGVKVLVYSIGFGPTILKWtsKKSGIQYQLSALPLGGYVKM--LDEREEN 79
Cdd:TIGR00054   1 SFLWIL-ASILALAVLIFVHELGHFLAARLCGIKVERFSIGFGPKILKF--KKNGTEYAISLIPLGGYVKMkgLDKEMEV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069  80 VAEADLPYAFNRQHPWKRIAIVAAGPLINLIFAILLFWLLFLP--SQEQLNTRVGKVLADTPAAAAQMQVGDKITAIDGT 157
Cdd:TIGR00054  78 KPPETDGDLFNNKSVFQKAIIIFAGPLANFIFAIFVYIFISLIgvPGYEVGPVIELLDKNSIALEAGIEPGDEILSVNGN 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 158 PVTTWEKLNFALVDRVGETgkiqvqaerageiktfSLPIQNFLNDQSQSPLdiLGFTPYRPQIPAIVSKLSEDGAAIRQG 237
Cdd:TIGR00054 158 KIPGFKDVRQQIADIAGEP----------------MVEILAERENWTFEVM--KELIPRGPKIEPVLSDVTPNSPAEKAG 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 238 MQVGDQIIAIDGVKMNDWYDVVQVVQASPEKLLKVDVLRNNQVQQLEVMPQGKrdnmgnvsgvlgvqsdpGKIVI---PE 314
Cdd:TIGR00054 220 LKEGDYIQSINGEKLRSWTDFVSAVKENPGKSMDIKVERNGETLSISLTPEAK-----------------GKIGIgisPS 282

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 315 DFKQTIQYSPSEALFMAVDKTGQLSSMILNSIVKMVRGLIGLDNLSGPITIAKVAGQSAEMGWQTFISFMALMSVSLGIL 394
Cdd:TIGR00054 283 LAPLEVSYGILNAFAKGASATVDIVKLILTNLGKLITGSFKLKNLSGPVGIVKGAGSSANSGIVYLLQFGAFLSINLGIM 362

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1253006069 395 NLLPIPMLDGGHLVYYFIELIRGKPVSEQIQLVGLKIGMVLLGSMMLLALFNDIMRL 451
Cdd:TIGR00054 363 NLLPIPALDGGQLLFLFIEAIRGKPLPEKVQAFVYRIGVAFLLFLMGLGLFNDLLRL 419

Peptidase_M50

pfam02163

Peptidase family M50;

9-436

2.49e-67

Peptidase family M50;

Pssm-ID: 426630 [Multi-domain] Cd Length: 291 Bit Score: 216.97 E-value: 2.49e-67

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069   9 AAILLLGPLIAIHEFGHYFVARKLGVKVLVYSIGFgptilkwtskksgiqYQLSALPLGGYVKMLDEreenvaeadlpya 88
Cdd:pfam02163   1 AFILALGILVVVHELGHFLVARRFGVKVERFSIGF---------------YRIALIPLGGYVKMADE------------- 52

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069  89 FNRQHPWKRIAIVAAGPLINLIFAILLFWLLFL--PSQEQLNTRVGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEkln 166
Cdd:pfam02163  53 FKSKSPWQRLAIALAGPLANFILAIILFAVLLFlsGVPPPAPPVIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQ--- 129

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 167 falvdrvgetgkiqvqaerageiktfslpiqnflndqsqspldilgftpyrpqipaivsklsedgaairqgmqvgdqiia 246
Cdd:pfam02163     --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 247 idgvkmndwyDVVQVVQASPEKLLKVDVLRNNQVQQLEVMPQGKRDnmgnvSGVLGVqsdpgkivipedFKQTIQYSPSE 326
Cdd:pfam02163 130 ----------DLVEALAKSPGKPITLTVERGGQTLTVTITPKSSEE-----SKFIGI------------GPVYVKYGLLE 182

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 327 ALFMAVDKTGQLSSMILNSIVKMVRGlIGLDNLSGPITIAkvaGQSAEMGWQTFISFMALMSVSLGILNLLPIPMLDGGH 406
Cdd:pfam02163 183 ALGFALEKTVNLVTLTLKALGKLITG-VSLKNLGGPIGIA---GQAAEAGLIAFLYFLALINLNLGIFNLLPVPPLDGGH 258

                         410       420       430
                  ....*....|....*....|....*....|
gi 1253006069 407 LVYYFIELIRGKPVSEQIQLVGLKIGMVLL 436
Cdd:pfam02163 259 ILRALLEAIRGKPLSERAEEIALRVGLALL 288

S2P-M50_PDZ_RseP-like

cd06163

RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave ...

7-121

1.44e-49

Pssm-ID: 100084 [Multi-domain] Cd Length: 182 Bit Score: 166.82 E-value: 1.44e-49

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069   7 VVAAILLLGPLIAIHEFGHYFVARKLGVKVLVYSIGFGPTILKWtsKKSGIQYQLSALPLGGYVKMLDEREENVA-EADL 85
Cdd:cd06163     1 ILAFILVLGILIFVHELGHFLVAKLFGVKVEEFSIGFGPKLFSF--KKGETEYSISAIPLGGYVKMLGEDPEEEAdPEDD 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1253006069  86 PYAFNRQHPWKRIAIVAAGPLINLIFAILLFWLLFL 121
Cdd:cd06163    79 PRSFNSKPVWQRILIVFAGPLANFLLAIVLFAVLLS 114

S2P-M50_PDZ_RseP-like

cd06163

RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave ...

380-450

2.40e-29

Pssm-ID: 100084 [Multi-domain] Cd Length: 182 Bit Score: 112.89 E-value: 2.40e-29

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1253006069 380 FISFMALMSVSLGILNLLPIPMLDGGHLVYYFIELIRGKPVSEQIQLVGLKIGMVLLGSMMLLALFNDIMR 450
Cdd:cd06163   112 LLSFLALLSINLGILNLLPIPALDGGHLLFLLIEAIRGRPLSEKVEEIIQTIGFALLLGLMLFVTFNDIVR 182

S2P-M50

cd05709

Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane ...

8-121

2.10e-25

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: 102.32 E-value: 2.10e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069   8 VAAILLLGPLIAIHEFGHYFVARKLGVKVLVYSIGFGptilkWTSKKSGIQYQLSALPLGGYVKMLDEREENVaeadlpy 87
Cdd:cd05709     1 LAFILALLISVTVHELGHALVARRLGVKVARFSGGFT-----LNPLKHGDPYGIILIPLGGYAKPVGENPRAF------- 68

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1253006069  88 afnRQHPWKRIAIVAAGPLINLIFAILLFWLLFL 121
Cdd:cd05709    69 ---KKPRWQRLLVALAGPLANLLLALLLLLLLLL 99

cpPDZ_EcRseP-like

cd23081

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...

222-304

9.54e-16

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: 71.84 E-value: 9.54e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 222 AIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVVQASPEKLLKVDVLRNNQVQQLEVMPQgKRDNMGNVSGVL 301
Cdd:cd23081     1 PVVGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRIVRENPGKPLTLKIERDGKILTVTVTPE-LVEVEGKGVGRI 79


                  ...
gi 1253006069 302 GVQ 304
Cdd:cd23081    80 GVQ 82

S2P-M50

cd05709

Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane ...

370-446

2.75e-15

Pssm-ID: 100078 [Multi-domain] Cd Length: 180 Bit Score: 73.81 E-value: 2.75e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1253006069 370 GQSAEMGWQTFISFMALMSVSLGILNLLPIPMLDGGHLVYYFIELIRGKpvseqIQLVGLKIGMVLLGSMMLLALFN 446
Cdd:cd05709   109 GQAASSGLANLLAFLALINLNLAVFNLLPIPPLDGGRILRALLEAIRGR-----VEERLEAYGFAILLGLLLLLLLN 180

cpPDZ2_EcRseP-like

cd23083

circularly permuted PDZ domain 2 (PDZ-C) of Escherichia coli Regulator of sigma-E protease ...

223-303

1.74e-14

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: 68.69 E-value: 1.74e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 223 IVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVVQASPEKLLKVDVLRNNQVQQLEVMPQGKRDNMGNVSGVLG 302
Cdd:cd23083     2 VLANVQPNSAAEKAGLQAGDRIVKVDGQPLTQWQTFVMAVRDNPGKPLALEIERQGSPLSLTLIPDSKELNQGKAIGFAG 81


                  .
gi 1253006069 303 V 303
Cdd:cd23083    82 I 82

cpPDZ1_EcRseP-like

cd23082

circularly permuted PDZ domain 1 (PDZ-N) of Escherichia coli Regulator of sigma-E protease ...

131-215

6.24e-14

Pssm-ID: 467639 [Multi-domain] Cd Length: 89 Bit Score: 67.01 E-value: 6.24e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 131 VGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVDRVGEtGKIQVQAERAG----EIKTFSLPIQNFLNDQsQS 206
Cdd:cd23082     3 IGEIAPNSIAAQAGIEPGDEIKAVDGIEVPDWDSVRLQLVDKLGA-GSVQITVQPFGsgaeREVTLDLRDWTFDPDK-ED 80


                  ....*....
gi 1253006069 207 PLDILGFTP 215
Cdd:cd23082    81 PVSSLGIRP 89

degP_htrA_DO

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...

131-283

9.71e-11

Pssm-ID: 273938 [Multi-domain] Cd Length: 428 Bit Score: 63.39 E-value: 9.71e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 131 VGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVD-RVGEtgKIQVQAERAGEIKTFSLPIQNFLNDQSQSPLD 209
Cdd:TIGR02037 261 VAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTlKPGK--KVTLGILRKGKEKTITVTLGASPEEQASSSNP 338

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 210 ILGFTPY--------RPQIPA-----IVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVVQASPEK-LLKVDVL 275
Cdd:TIGR02037 339 FLGLTVAnlspeirkELRLKGdvkgvVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKKGgRVALLIL 418


                  ....*...
gi 1253006069 276 RNNQVQQL 283
Cdd:TIGR02037 419 RGGATIFV 426

cpPDZ_EcRseP-like

cd23081

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...

131-197

1.02e-10

Pssm-ID: 467638 [Multi-domain] Cd Length: 83 Bit Score: 57.59 E-value: 1.02e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1253006069 131 VGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVDRVGEtgKIQVQAERAGEIKTFSLPIQ 197
Cdd:cd23081     3 VGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRIVRENPGK--PLTLKIERDGKILTVTVTPE 67

COG3975

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

123-197

5.84e-08

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

Pssm-ID: 443174 [Multi-domain] Cd Length: 591 Bit Score: 54.83 E-value: 5.84e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 123 SQEQLNTRVGKVLADTPAAAAQMQVGDKITAIDGTPVTTwEKLNfALVDRVGETGKIQVQAERAGEIKTFSLPIQ 197
Cdd:COG3975   490 SADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVTA-DNLD-DALAAYKPGDPIELLVFRRDELRTVTVTLA 562

DegQ

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...

130-199

1.06e-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: 52.84 E-value: 1.06e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1253006069 130 RVGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVD-RVGETGKIQVQaeRAGEIKTFSLPIQNF 199
Cdd:COG0265   204 LVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRLLASlKPGDTVTLTVL--RGGKELTVTVTLGER 272

PDZ_2

PDZ domain;

131-196

1.16e-07

PDZ domain;

Pssm-ID: 433015 [Multi-domain] Cd Length: 74 Bit Score: 48.81 E-value: 1.16e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1253006069 131 VGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVD-RVGETgkIQVQAERAGEIKTFSLPI 196
Cdd:pfam13180  10 VVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALYGhKPGDT--VTLQVYRDGKLLTVEVKL 74

DegQ

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...

222-285

2.59e-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: 51.69 E-value: 2.59e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 222 AIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVVQA-SPEKLLKVDVLRNNQVQQLEV 285
Cdd:COG0265   203 VLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRLLASlKPGDTVTLTVLRGGKELTVTV 267

PDZ2_Scribble-like

cd06703

PDZ domain 2 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...

212-254

2.75e-07

Pssm-ID: 467187 [Multi-domain] Cd Length: 92 Bit Score: 48.41 E-value: 2.75e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1253006069 212 GFTPYRPQIPAI-VSKLSEDGAAIRQG-MQVGDQIIAIDGVKMND 254
Cdd:cd06703    23 GSTPFRDGDEGIfISRITEGGAADRDGkLQVGDRVLSINGVDVTE 67

CtpA

COG0793

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...

130-194

6.13e-07

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: 51.02 E-value: 6.13e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1253006069 130 RVGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFA--LVDRVGETGKIQVQAERAGEIKTFSL 194
Cdd:COG0793    74 VVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAVklLRGKAGTKVTLTIKRPGEGEPITVTL 140

prc

TIGR00225

C-terminal peptidase (prc); A C-terminal peptidase with different substrates in different ...

134-196

6.82e-07

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: 50.82 E-value: 6.82e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 134 VLADTPAAAAQMQVGDKITAIDGTPVTTWEkLNFAlVDRV-GETG-KIQVQAERAGEIKTFSLPI 196
Cdd:TIGR00225  69 PFEGSPAEKAGIKPGDKIIKINGKSVAGMS-LDDA-VALIrGKKGtKVSLEILRAGKSKPLSFTL 131

PDZ

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...

211-278

8.40e-07

Pssm-ID: 214570 [Multi-domain] Cd Length: 85 Bit Score: 46.60 E-value: 8.40e-07

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1253006069  211 LGFT---PYRPQIPAIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDW--YDVVQVVQASPEKlLKVDVLRNN 278
Cdd:smart00228  14 LGFSlvgGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLthLEAVDLLKKAGGK-VTLTVLRGG 85

S2P-M50_PDZ_Arch

cd06159

Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS ...

8-121

8.86e-07

Uncharacterized Archaeal 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 appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.

Pssm-ID: 100080 [Multi-domain] Cd Length: 263 Bit Score: 49.99 E-value: 8.86e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069   8 VAAILLLGPLIAIHEFGHYFVARKLGVKVlvysigfgptilkwtskKSGIqYQLSALPLGGYVKmLDEREENVAEadlpy 87
Cdd:cd06159   111 PYGIIALVVGVVVHELSHGILARVEGIKV-----------------KSGG-LLLLIIPPGAFVE-PDEEELNKAD----- 166

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1253006069  88 afnrqhPWKRIAIVAAGPLINLIFAILLFWLLFL 121
Cdd:cd06159   167 ------RRIRLRIFAAGVTANFVVALIAFALFFL 194

SpoIVFB

COG1994

Zn-dependent protease (includes sporulation protein SpoIVFB) [Posttranslational modification, ...

5-121

1.22e-06

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

Pssm-ID: 441597 Cd Length: 175 Bit Score: 48.28 E-value: 1.22e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069   5 FIVVAAILLLGplIAIHEFGHYFVARKLGVKVLvysigfgptilkwtskksgiqyQLSALPL-GGYVKMldereenvaea 83
Cdd:COG1994    11 ILIFALALFLS--VLLHELAHALVARRLGDPTA----------------------KITLNPLkGGWAKI----------- 55

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1253006069  84 dlpyAFNRQHPWKRIAIVAAGPLINLIFAILLFWLLFL 121
Cdd:COG1994    56 ----NRNFRNPRDEALVALAGPLANLLLALLFALLLRL 89

SdrC

COG3480

Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];

130-215

1.49e-06

Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];

Pssm-ID: 442703 [Multi-domain] Cd Length: 344 Bit Score: 49.81 E-value: 1.49e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 130 RVGKVLADTPAAAaQMQVGDKITAIDGTPVTTWEKLnFALVDRVGETGKIQVQAERAGEIKTFSLPIQNFLNDQSQSpld 209
Cdd:COG3480   141 YVASVLEGSPADG-VLQPGDVITAVDGKPVTTAEDL-RDALAAKKPGDTVTLTVTRDGKEKTVTVTLVKLPDDDGRA--- 215


                  ....*.
gi 1253006069 210 ILGFTP 215
Cdd:COG3480   216 GIGISL 221

PDZ_2

PDZ domain;

222-285

1.80e-06

PDZ domain;

Pssm-ID: 433015 [Multi-domain] Cd Length: 74 Bit Score: 45.34 E-value: 1.80e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 222 AIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVV-QASPEKLLKVDVLRNNQVQQLEV 285
Cdd:pfam13180   8 VVVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALyGHKPGDTVTLQVYRDGKLLTVEV 72

PDZ

pfam00595

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

218-269

3.17e-06

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

Pssm-ID: 395476 [Multi-domain] Cd Length: 81 Bit Score: 44.96 E-value: 3.17e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1253006069 218 PQIPAIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWY--DVVQVVQASPEKL 269
Cdd:pfam00595  23 GDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTheEAVLALKGSGGKV 76

cpPDZ_Deg_HtrA-like

cd06779

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...

222-285

3.20e-06

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: 45.36 E-value: 3.20e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1253006069 222 AIVSKLSEDGAAIRQGMQVGDQIIAIDG---VKMNDWYDVVQvvQASPEKLLKVDVLRNNQVQQLEV 285
Cdd:cd06779    27 VLVAEVIPGSPAAKAGLKEGDVILSVNGkpvTSFNDLRAALD--TKKPGDSLNLTILRDGKTLTVTV 91

cpPDZ1_DegP-like

cd10839

circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...

131-194

4.08e-06

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: 44.78 E-value: 4.08e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 131 VGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVD-RVGETGKIQVQaeRAGEIKTFSL 194
Cdd:cd10839    29 VAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRVATtKPGTKVELKIL--RDGKEKTLTV 91

cpPDZ_CPP-like

cd06782

circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...

223-285

4.53e-06

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: 44.78 E-value: 4.53e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 223 IVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDW--YDVVQVVQASPEKLLKVDVLRNNQVQQLEV 285
Cdd:cd06782    17 VVVSPIPGGPAEKAGIKPGDVIVAVDGESVRGMslDEVVKLLRGPKGTKVKLTIRRGGEGEPRDV 81

cpPDZ1_DegP-like

cd10839

circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...

222-285

5.26e-06

Pssm-ID: 467630 [Multi-domain] Cd Length: 91 Bit Score: 44.78 E-value: 5.26e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 222 AIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDV-VQVVQASPEKLLKVDVLRNNQVQQLEV 285
Cdd:cd10839    27 ALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLrNRVATTKPGTKVELKILRDGKEKTLTV 91

PDZ1_Scribble-like

cd06704

PDZ domain 1 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...

212-276

6.29e-06

PDZ domain 1 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. 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 Scribble-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467188 [Multi-domain] Cd Length: 87 Bit Score: 44.19 E-value: 6.29e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1253006069 212 GFTPYRPQIPAI-VSKLSEDGAAIRQGMQVGDQIIAIDGVKMND--WYDVVQVVQASPEKLLKVdVLR 276
Cdd:cd06704    21 GSTPYKGDDEGIfISRVTEGGPAAKAGVRVGDKLLEVNGVDLVDadHHEAVEALKNSGNTVTMV-VLR 87

cpPDZ_DegS

cd06777

circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...

222-285

8.81e-06

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: 43.92 E-value: 8.81e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 222 AIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVV-QVVQASPEKLLKVDVLRNNQVQQLEV 285
Cdd:cd06777    27 ALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVLELMdLVAEIRPGTVIPVVVLRDGKQLTLEV 91

S2P-M50_SpoIVFB

cd06161

SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates ...

2-119

9.62e-06

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: 46.38 E-value: 9.62e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069   2 SALFIVVAAILLLGPLIAIHEFGHYFVARKLGVKVlvysigFGPTIlkwtskksgiqyqlsaLPLGGYVKMLDEREEnva 81
Cdd:cd06161    25 VAWLLGLLEALLLFLSVLLHELGHALVARRYGIRV------RSITL----------------LPFGGVAELEEEPET--- 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1253006069  82 eadlpyafnrqhPWKRIAIVAAGPLINLIFAILLFWLL 119
Cdd:cd06161    80 ------------PKEEFVIALAGPLVSLLLAGLFYLLY 105

cpPDZ_RseP_YlbL-like

cd10824

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), ...

131-211

9.84e-06

Pssm-ID: 467636 [Multi-domain] Cd Length: 82 Bit Score: 43.72 E-value: 9.84e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 131 VGKVLADTPAAAAQmQVGDKITAIDGTPVTTWEKLNFALVDR-VGETGKIQVqaERAGEIKTFSLPIQNFLNDQSQSPLD 209
Cdd:cd10824     3 VLSVKPNSPAAKAL-HAGDLITEIDGQPTKSWQTFIDYIHDKkVGESVKITY--KHGNKNEEASLKLTAIPKEKGTPGIG 79


                  ..
gi 1253006069 210 IL 211
Cdd:cd10824    80 IR 81

SpoIVFB

COG1994

Zn-dependent protease (includes sporulation protein SpoIVFB) [Posttranslational modification, ...

365-436

1.18e-05

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

Pssm-ID: 441597 Cd Length: 175 Bit Score: 45.58 E-value: 1.18e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1253006069 365 IAKVAGQSAEMGWQTFISFMALMSVSLGILNLLPIPMLDGGHLVYYFIELIRGkPVSEQIQLVGLKIGMVLL 436
Cdd:COG1994    86 LLRLLPALGLGPLALLLGYLALINLVLAVFNLLPIPPLDGGRILRALLPRRTA-RRATRLEPYGFLILLLLI 156

cpPDZ_CPP-like

cd06782

circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...

130-194

1.34e-05

Pssm-ID: 467623 [Multi-domain] Cd Length: 88 Bit Score: 43.24 E-value: 1.34e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1253006069 130 RVGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEklNFALVDRV-GETG---KIQVQAERAGEIKTFSL 194
Cdd:cd06782    17 VVVSPIPGGPAEKAGIKPGDVIVAVDGESVRGMS--LDEVVKLLrGPKGtkvKLTIRRGGEGEPRDVTL 83

PDZ_6

pfam17820

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

223-276

1.55e-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: 42.13 E-value: 1.55e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1253006069 223 IVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVVQASPEKLLKVDVLR 276
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLQGSAGESVTLTVRR 54

cpPDZ_Deg_HtrA-like

cd06779

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...

131-194

1.86e-05

Pssm-ID: 467621 [Multi-domain] Cd Length: 91 Bit Score: 43.05 E-value: 1.86e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 131 VGKVLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVD-RVGETGKIQVQaeRAGEIKTFSL 194
Cdd:cd06779    29 VAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTkKPGDSLNLTIL--RDGKTLTVTV 91

degP_htrA_DO

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...

222-285

3.80e-05

Pssm-ID: 273938 [Multi-domain] Cd Length: 428 Bit Score: 45.68 E-value: 3.80e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1253006069 222 AIVSKLSEDGAAIRQGMQVGDQIIAIDGVKMNDWYDVVQVVQAS-PEKLLKVDVLRNNQVQQLEV 285
Cdd:TIGR02037 259 ALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGTLkPGKKVTLGILRKGKEKTITV 323

PDZ_ARHGEF11-12-like

cd23069

PDZ domain of ARHGEF11, ARHGEF12, and related domains; PDZ (PSD-95 (Postsynaptic density ...

221-265

9.47e-05

PDZ domain of ARHGEF11, ARHGEF12, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ARHGEF11, ARHGEF12, and related domains. This subfamily includes the GEFs (guanine exchange factors) ARHGEF11 (Rho guanine nucleotide exchange factor 11, known as PDZ-RhoGEF) and ARHGEF12 (Rho guanine nucleotide exchange factor 12, also known as leukemia-associated RhoGEF). GEFs activate Rho GTPases by promoting GTP binding. ARHGEF11/12 are regulators of G protein signaling (RGS) domain-containing GEFs; the RGS domain mediates their binding to and activation of Galpha (and Gq also in the case of ARHGEF12), in response to G-protein coupled receptor activation. ARHGEF11 and 12 are involved in serum-signaling, and regulate Yes-Associated Protein (YAP1)-dependent transcription. The ARHGEF12 PDZ domain binds plexin-B1 and the receptor tyrosine kinase insulin-like growth factor receptor (IGF-R1) beta-subunit. ARHGEF12 also interacts with glutamate receptor delta-1(GluD1), a postsynaptic organizer of inhibitory synapses in cortical pyramidal neurons. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ARHGEF11-12-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: 467282 [Multi-domain] Cd Length: 76 Bit Score: 40.45 E-value: 9.47e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1253006069 221 PAIVSKLSEDGAAIRQGMQVGDQIIAIDG--VKMNDWYDVVQVVQAS 265
Cdd:cd23069    22 PVFVQSVKEGGAAYRAGVQEGDRIIKVNGtlVTHSNHLEVVKLIKSG 68

PDZ_rhophilin-like

cd06712

PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...

211-274

1.59e-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: 39.88 E-value: 1.59e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1253006069 211 LGFTpYRPQIPAIVSKLSEDGAAIRQGMQVGDQIIAIDGVkmnD--WY---DVVQVVQASPEKLLKVDV 274
Cdd:cd06712    13 FGFT-LRGDSPVQVASVDPGSCAAEAGLKEGDYIVSVGGV---DckWSkhsEVVKLLKSAGEEGLELQV 77

SdrC

COG3480

Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];

222-304

1.59e-04

Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];

Pssm-ID: 442703 [Multi-domain] Cd Length: 344 Bit Score: 43.65 E-value: 1.59e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1253006069 222 AIVSKLSEDGAAIRQgMQVGDQIIAIDGVKMNDWYDVVQVVQA-SPEKLLKVDVLRNNQVQQLEVMPQGKRDNMGnvSGV 300
Cdd:COG3480   140 VYVASVLEGSPADGV-LQPGDVITAVDGKPVTTAEDLRDALAAkKPGDTVTLTVTRDGKEKTVTVTLVKLPDDDG--RAG 216


                  ....
gi 1253006069 301 LGVQ 304
Cdd:COG3480   217 IGIS 220

cpPDZ2_EcRseP-like

cd23083

circularly permuted PDZ domain 2 (PDZ-C) of Escherichia coli Regulator of sigma-E protease ...

134-194

1.89e-04

Pssm-ID: 467640 [Multi-domain] Cd Length: 85 Bit Score: 40.19 E-value: 1.89e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1253006069 134 VLADTPAAAAQMQVGDKITAIDGTPVTTWEKLNFALVDRVGETgkIQVQAERAGEIKTFSL 194
Cdd:cd23083     6 VQPNSAAEKAGLQAGDRIVKVDGQPLTQWQTFVMAVRDNPGKP--LALEIERQGSPLSLTL 64

PDZ_SYNJ2BP-like

cd06709

PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 ...

209-272

2.14e-04

PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNJ2BP, and related domains. SYNJ2BP (also known as mitochondrial outer membrane protein 25, OMP25) regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction. Binding partners of the SYNJ2BP PDZ domain include activin type II receptors (ActR-II), and SYNJ2. SYNJ2BP interacts with the PDZ binding motif of the Notch Delta-like ligand 1 (DLL1) and DLL4, promoting Delta-Notch signaling, and inhibiting sprouting angiogenesis. 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 SYNJ2BP-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: 467193 [Multi-domain] Cd Length: 86 Bit Score: 39.97 E-value: 2.14e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1253006069 209 DILGFT--PYRPQIPAI-VSKLSEDGAAIRQG-MQVGDQIIAIDGVKMNDWY--DVVQVVQASPEK-LLKV 272
Cdd:cd06709    15 NIVGGTdqPYIPNDSGIyVAKIKEDGAAAIDGrLQEGDKILEINGQSLENLThqDAVELFRNAGEDvKLKV 85

PDZ