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Conserved domains on  [gi|110815869|ref|NP_084403|]
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serine protease HTRA3 isoform a precursor [Mus musculus]

Protein Classification

Do family serine endopeptidase( domain architecture ID 13622476)

Do/DeqQ family serine endopeptidase belonging to the peptidase S1C family, contains a PDZ-domain, similar to Lactococcus lactis Do-like HtrA (High-temperature requirement A), which is a surface protease responsible for the housekeeping of exported proteins and plays a role in stress resistance during active exponential growth

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 179-449 3.01e-88

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: 270.10  E-value: 3.01e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 179 SSGSGFIMSEAGLIVTNAHVVSSSstasgrQQLKVQLQNGDAYEATIQDIDKKSDIATIVIHPKKkLPVLLLGHSADLRP 258
Cdd:COG0265    1 GLGSGVIISPDGYILTNNHVVEGA------DEITVTLADGREYPAKVVGRDPLTDLAVLKIDAKD-LPAAPLGDSDKLRV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 259 GEFVVAIGSPFALQNTVTTGIVSTAQRDGkELGLRDSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKV-----AAG 333
Cdd:COG0265   74 GDWVLAIGNPFGLGQTVTAGIVSALGRSI-GSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIIsrsggSQG 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 334 ISFAIPSDRITRFLSEF-QNKHVkdwkKR-FIGIRMRTITPSLVEELKAANPdfpavsSGIYVQEVVPNSPSQRGGIQDG 411
Cdd:COG0265  153 IGFAIPINLAKRVVEQLiETGRV----RRgWLGVTIQPVTPELAEALGLPEP------EGVLVARVEPGSPAAKAGLRPG 222

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 110815869 412 DIIVKVNGRPLADSSELQEAVLNE---SSLLLEVRRGNDDL 449
Cdd:COG0265  223 DVILAVDGKPVTSARDLQRLLASLkpgDTVTLTVLRGGKEL 263
IGFBP pfam00219
Insulin-like growth factor binding protein;
31-82 2.50e-18

Insulin-like growth factor binding protein;


:

Pssm-ID: 459717  Cd Length: 53  Bit Score: 78.52  E-value: 2.50e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 110815869   31 CPARCDVSRCPS--PRCPGGYVPDLCNCCLVCAASEGEPCGRpLDSPCGDSLEC 82
Cdd:pfam00219   1 CPPPCDPERCPPppPGCPAGVVLDGCGCCKVCARQEGEPCGV-YTPPCGKGLRC 53
Kazal_2 pfam07648
Kazal-type serine protease inhibitor domain; Usually indicative of serine protease inhibitors. ...
 95-132 5.38e-06

Kazal-type serine protease inhibitor domain; Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides.


:

Pssm-ID: 400135  Cd Length: 50  Bit Score: 43.25  E-value: 5.38e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 110815869   95 VCGTDGHTYADVCALQAASRRALQVSGTPVrQLQKGAC 132
Cdd:pfam07648  14 VCGSDGVTYPSPCALCAAGCKLGKEVKEEK-VKYDGSC 50
 
Name Accession Description Interval E-value
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 179-449 3.01e-88

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: 270.10  E-value: 3.01e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 179 SSGSGFIMSEAGLIVTNAHVVSSSstasgrQQLKVQLQNGDAYEATIQDIDKKSDIATIVIHPKKkLPVLLLGHSADLRP 258
Cdd:COG0265    1 GLGSGVIISPDGYILTNNHVVEGA------DEITVTLADGREYPAKVVGRDPLTDLAVLKIDAKD-LPAAPLGDSDKLRV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 259 GEFVVAIGSPFALQNTVTTGIVSTAQRDGkELGLRDSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKV-----AAG 333
Cdd:COG0265   74 GDWVLAIGNPFGLGQTVTAGIVSALGRSI-GSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIIsrsggSQG 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 334 ISFAIPSDRITRFLSEF-QNKHVkdwkKR-FIGIRMRTITPSLVEELKAANPdfpavsSGIYVQEVVPNSPSQRGGIQDG 411
Cdd:COG0265  153 IGFAIPINLAKRVVEQLiETGRV----RRgWLGVTIQPVTPELAEALGLPEP------EGVLVARVEPGSPAAKAGLRPG 222

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 110815869 412 DIIVKVNGRPLADSSELQEAVLNE---SSLLLEVRRGNDDL 449
Cdd:COG0265  223 DVILAVDGKPVTSARDLQRLLASLkpgDTVTLTVLRGGKEL 263
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 149-432 6.58e-84

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: 264.47  E-value: 6.58e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  149 IADVVEKIAPAVVHIEL---------------FLRHPlFGRNVPL-----------SSGSGFIMSEAGLIVTNAHVVSss 202
Cdd:TIGR02037   3 FAPLVEKVAPAVVNISVegtvkrrnrppalppFFRQF-FGDDMPDfprqqreqkvrGLGSGVIISADGYVLTNNHVVD-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  203 stasGRQQLKVQLQNGDAYEATIQDIDKKSDIATIVIHPKKKLPVLLLGHSADLRPGEFVVAIGSPFALQNTVTTGIVST 282
Cdd:TIGR02037  80 ----GADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSA 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  283 AQRDGkeLGLRDSDmDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVA-----AGISFAIPSDRITRFLSEF-QNKHVk 356
Cdd:TIGR02037 156 LGRSG--LGIGDYE-NFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSpsggnVGIGFAIPSNMAKNVVDQLiEGGKV- 231

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 110815869  357 dwKKRFIGIRMRTITPSLVEELKAANPdfpavsSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV 432
Cdd:TIGR02037 232 --KRGWLGVTIQEVTSDLAKSLGLEKQ------RGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAI 299
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 360-457 3.36e-51

circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of HtrA family serine proteases including human HtrA1, HtrA2 (mitochondrial), HtrA3, and HtrA4, and related domains. These proteases are key enzymes associated with pregnancy. Their diverse biological functions include cell growth proliferation, migration and apoptosis. They are also implicated in disorders including Alzheimer's, Parkinson's, arthritis and cancer. HtrA1 (also known as high-temperature requirement A serine peptidase 1, L56, and serine protease 11) substrates include extracellular matrix proteins, proteoglycans, and insulin-like growth factor (IGF)-binding proteins. HtrA1 also inhibits signaling by members of the transforming growth factor beta (TGF-beta) family. 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 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 HtrA-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: 467624 [Multi-domain]  Cd Length: 98  Bit Score: 168.45  E-value: 3.36e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 360 KRFIGIRMRTITPSLVEELKAANPDFPAVSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAVLNESSLL 439
Cdd:cd06785    1 KRYIGIRMLTLTPSLLEELKQRNPDFPDVSSGVYVHKVIPGSPAQRAGLKDGDVIISINGKPVKSSSDVYEAVKSGSSLL 80

                         90
                 ....*....|....*...
gi 110815869 440 LEVRRGNDDLLFSIIPEV 457
Cdd:cd06785   81 VVVRRGNEDLLLTVTPEE 98
PRK10139 PRK10139
serine endoprotease DegQ;
149-432 5.90e-51

serine endoprotease DegQ;


Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 178.99  E-value: 5.90e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 149 IADVVEKIAPAVVHIEL------FLRHP-----LFGRNVPLSS-------GSGFIMSEA-GLIVTNAHVVSSSstasgrQ 209
Cdd:PRK10139  42 LAPMLEKVLPAVVSVRVegtasqGQKIPeefkkFFGDDLPDQPaqpfeglGSGVIIDAAkGYVLTNNHVINQA------Q 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 210 QLKVQLQNGDAYEATIQDIDKKSDIATIVIHPKKKLPVLLLGHSADLRPGEFVVAIGSPFALQNTVTTGIVSTAQRDGKE 289
Cdd:PRK10139 116 KISIQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIADSDKLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLN 195

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 290 L-GLRdsdmDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVA-----AGISFAIPSDrITRFLSEfQNKHVKDWKKRFI 363
Cdd:PRK10139 196 LeGLE----NFIQTDASINRGNSGGALLNLNGELIGINTAILApgggsVGIGFAIPSN-MARTLAQ-QLIDFGEIKRGLL 269

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 110815869 364 GIRMRTITPSLVeelKAANPDfpaVSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV 432
Cdd:PRK10139 270 GIKGTEMSADIA---KAFNLD---VQRGAFVSEVLPNSGSAKAGVKAGDIITSLNGKPLNSFAELRSRI 332
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 181-325 1.58e-28

Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 109.82  E-value: 1.58e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  181 GSGFIMSEAGLIVTNAHVVSSSsTASGRQQLKVQLQNGDAYEATIQDIDKKSDIATI-VIHPKKKLPVLLLGHSADLRPG 259
Cdd:pfam13365   1 GTGFVVSSDGLVLTNAHVVDDA-EEAAVELVSVVLADGREYPATVVARDPDLDLALLrVSGDGRGLPPLPLGDSEPLVGG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 110815869  260 EFVVAIGSPFALQ-NTVTTGIVSTAQRDGKElglrDSDMDYIQTDAIINYGNSGGPLVNLDGEVIGI 325
Cdd:pfam13365  80 ERVYAVGYPLGGEkLSLSEGIVSGVDEGRDG----GDDGRVIQTDAALSPGSSGGPVFDADGRVVGI 142
IGFBP pfam00219
Insulin-like growth factor binding protein;
31-82 2.50e-18

Insulin-like growth factor binding protein;


Pssm-ID: 459717  Cd Length: 53  Bit Score: 78.52  E-value: 2.50e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 110815869   31 CPARCDVSRCPS--PRCPGGYVPDLCNCCLVCAASEGEPCGRpLDSPCGDSLEC 82
Cdd:pfam00219   1 CPPPCDPERCPPppPGCPAGVVLDGCGCCKVCARQEGEPCGV-YTPPCGKGLRC 53
IB smart00121
Insulin growth factor-binding protein homologues; High affinity binding partners of ...
 29-85 6.53e-14

Insulin growth factor-binding protein homologues; High affinity binding partners of insulin-like growth factors.


Pssm-ID: 197525  Cd Length: 75  Bit Score: 66.72  E-value: 6.53e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 110815869    29 APCPaRCDVSRCPS--PRCPGGYVPDLCNCCLVCAASEGEPCGRPLDsPCGDSLECVRG 85
Cdd:smart00121   1 ARCP-PCDPARCPPcpPGCAELVRLDGCGCCPVCARQEGEPCGVYTP-RCAPGLRCQPP 57
MarP_fam_protase NF033740
MarP family serine protease; The founding member of this family of membrane-spanning serine ...
 150-325 2.23e-11

MarP family serine protease; The founding member of this family of membrane-spanning serine proteases, which is restricted to Actinobacteria, is the acid resistance periplasmic serine protease MarP of Mycobacterium tuberculosis. Recent work shows that MarP is required to cleave and activate the peptidoglycan hydrolase RipA, and loss of RipA activity creates a defect in progeny separation during cell division. Therefore, the requirement for MarP in order to survive acidic conditions may be a consequence of peptidoglycan hydrolysis requirements, explaining why MarP family members are distributed more broadly in the Actinobacteria than the subset of species capable of surviving intracellularly as pathogens.


Pssm-ID: 468161 [Multi-domain]  Cd Length: 390  Bit Score: 65.21  E-value: 2.23e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 150 ADVVEKIAPAVVHIELflRHPLFGRNvplSSGSGFIMSEaGLIVTNAHVVsssstaSGRQQLKVQLQNGDAYEATIQDID 229
Cdd:NF033740 187 SPAVRRARPSVVKVRG--TAPSCGRA---LEGSGFVVAP-DRVMTNAHVV------AGTDEVTVETVGGGTLDARVVYYD 254

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 230 KKSDIAtiVIH-PKKKLPVLLLGhSADLRPGEFVVAIG----SPFalqnTVT-TGIVSTAQRDGKEL-GLRDSDMDYIQT 302
Cdd:NF033740 255 PDRDIA--VLAvPGLGLPPLPFA-DEPAETGDDAIVLGypegGPF----TATpARVRERIALSGPDIyGSGTVTREVYTL 327

                        170       180
                 ....*....|....*....|...
gi 110815869 303 DAIINYGNSGGPLVNLDGEVIGI 325
Cdd:NF033740 328 RGTVRPGNSGGPLLDPDGRVLGV 350
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 389-446 1.65e-10

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: 57.39  E-value: 1.65e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 110815869   389 SSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAVL---NESSLLLEVRRGN 446
Cdd:smart00228  25 GGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLlkkAGGKVTLTVLRGG 85
Kazal_2 pfam07648
Kazal-type serine protease inhibitor domain; Usually indicative of serine protease inhibitors. ...
 95-132 5.38e-06

Kazal-type serine protease inhibitor domain; Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides.


Pssm-ID: 400135  Cd Length: 50  Bit Score: 43.25  E-value: 5.38e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 110815869   95 VCGTDGHTYADVCALQAASRRALQVSGTPVrQLQKGAC 132
Cdd:pfam07648  14 VCGSDGVTYPSPCALCAAGCKLGKEVKEEK-VKYDGSC 50
KAZAL smart00280
Kazal type serine protease inhibitors; Kazal type serine protease inhibitors and ...
 95-132 5.91e-06

Kazal type serine protease inhibitors; Kazal type serine protease inhibitors and follistatin-like domains.


Pssm-ID: 197624  Cd Length: 46  Bit Score: 43.05  E-value: 5.91e-06
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 110815869    95 VCGTDGHTYADVCALQAASRRalqvSGTPVRQLQKGAC 132
Cdd:smart00280  13 VCGSDGVTYSNECHLCKAACE----SGKSIEVKHDGPC 46
KAZAL_FS cd00104
Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit ...
 95-132 3.30e-04

Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD.


Pssm-ID: 238052 [Multi-domain]  Cd Length: 41  Bit Score: 38.02  E-value: 3.30e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 110815869  95 VCGTDGHTYADVCALQAASRRalqvSGTPVRQLQKGAC 132
Cdd:cd00104    8 VCGSDGKTYSNECHLGCAACR----SGRSITVAHNGPC 41
 
Name Accession Description Interval E-value
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 179-449 3.01e-88

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: 270.10  E-value: 3.01e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 179 SSGSGFIMSEAGLIVTNAHVVSSSstasgrQQLKVQLQNGDAYEATIQDIDKKSDIATIVIHPKKkLPVLLLGHSADLRP 258
Cdd:COG0265    1 GLGSGVIISPDGYILTNNHVVEGA------DEITVTLADGREYPAKVVGRDPLTDLAVLKIDAKD-LPAAPLGDSDKLRV 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 259 GEFVVAIGSPFALQNTVTTGIVSTAQRDGkELGLRDSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKV-----AAG 333
Cdd:COG0265   74 GDWVLAIGNPFGLGQTVTAGIVSALGRSI-GSSGGGTYDDFIQTDAAINPGNSGGPLVNLNGEVIGINTAIIsrsggSQG 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 334 ISFAIPSDRITRFLSEF-QNKHVkdwkKR-FIGIRMRTITPSLVEELKAANPdfpavsSGIYVQEVVPNSPSQRGGIQDG 411
Cdd:COG0265  153 IGFAIPINLAKRVVEQLiETGRV----RRgWLGVTIQPVTPELAEALGLPEP------EGVLVARVEPGSPAAKAGLRPG 222

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 110815869 412 DIIVKVNGRPLADSSELQEAVLNE---SSLLLEVRRGNDDL 449
Cdd:COG0265  223 DVILAVDGKPVTSARDLQRLLASLkpgDTVTLTVLRGGKEL 263
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 149-432 6.58e-84

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: 264.47  E-value: 6.58e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  149 IADVVEKIAPAVVHIEL---------------FLRHPlFGRNVPL-----------SSGSGFIMSEAGLIVTNAHVVSss 202
Cdd:TIGR02037   3 FAPLVEKVAPAVVNISVegtvkrrnrppalppFFRQF-FGDDMPDfprqqreqkvrGLGSGVIISADGYVLTNNHVVD-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  203 stasGRQQLKVQLQNGDAYEATIQDIDKKSDIATIVIHPKKKLPVLLLGHSADLRPGEFVVAIGSPFALQNTVTTGIVST 282
Cdd:TIGR02037  80 ----GADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVIKLGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSA 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  283 AQRDGkeLGLRDSDmDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVA-----AGISFAIPSDRITRFLSEF-QNKHVk 356
Cdd:TIGR02037 156 LGRSG--LGIGDYE-NFIQTDAAINPGNSGGPLVNLRGEVIGINTAILSpsggnVGIGFAIPSNMAKNVVDQLiEGGKV- 231

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 110815869  357 dwKKRFIGIRMRTITPSLVEELKAANPdfpavsSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV 432
Cdd:TIGR02037 232 --KRGWLGVTIQEVTSDLAKSLGLEKQ------RGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAI 299
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 360-457 3.36e-51

circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of HtrA family serine proteases including human HtrA1, HtrA2 (mitochondrial), HtrA3, and HtrA4, and related domains. These proteases are key enzymes associated with pregnancy. Their diverse biological functions include cell growth proliferation, migration and apoptosis. They are also implicated in disorders including Alzheimer's, Parkinson's, arthritis and cancer. HtrA1 (also known as high-temperature requirement A serine peptidase 1, L56, and serine protease 11) substrates include extracellular matrix proteins, proteoglycans, and insulin-like growth factor (IGF)-binding proteins. HtrA1 also inhibits signaling by members of the transforming growth factor beta (TGF-beta) family. 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 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 HtrA-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: 467624 [Multi-domain]  Cd Length: 98  Bit Score: 168.45  E-value: 3.36e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 360 KRFIGIRMRTITPSLVEELKAANPDFPAVSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAVLNESSLL 439
Cdd:cd06785    1 KRYIGIRMLTLTPSLLEELKQRNPDFPDVSSGVYVHKVIPGSPAQRAGLKDGDVIISINGKPVKSSSDVYEAVKSGSSLL 80

                         90
                 ....*....|....*...
gi 110815869 440 LEVRRGNDDLLFSIIPEV 457
Cdd:cd06785   81 VVVRRGNEDLLLTVTPEE 98
PRK10139 PRK10139
serine endoprotease DegQ;
149-432 5.90e-51

serine endoprotease DegQ;


Pssm-ID: 182262 [Multi-domain]  Cd Length: 455  Bit Score: 178.99  E-value: 5.90e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 149 IADVVEKIAPAVVHIEL------FLRHP-----LFGRNVPLSS-------GSGFIMSEA-GLIVTNAHVVSSSstasgrQ 209
Cdd:PRK10139  42 LAPMLEKVLPAVVSVRVegtasqGQKIPeefkkFFGDDLPDQPaqpfeglGSGVIIDAAkGYVLTNNHVINQA------Q 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 210 QLKVQLQNGDAYEATIQDIDKKSDIATIVIHPKKKLPVLLLGHSADLRPGEFVVAIGSPFALQNTVTTGIVSTAQRDGKE 289
Cdd:PRK10139 116 KISIQLNDGREFDAKLIGSDDQSDIALLQIQNPSKLTQIAIADSDKLRVGDFAVAVGNPFGLGQTATSGIISALGRSGLN 195

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 290 L-GLRdsdmDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVA-----AGISFAIPSDrITRFLSEfQNKHVKDWKKRFI 363
Cdd:PRK10139 196 LeGLE----NFIQTDASINRGNSGGALLNLNGELIGINTAILApgggsVGIGFAIPSN-MARTLAQ-QLIDFGEIKRGLL 269

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 110815869 364 GIRMRTITPSLVeelKAANPDfpaVSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV 432
Cdd:PRK10139 270 GIKGTEMSADIA---KAFNLD---VQRGAFVSEVLPNSGSAKAGVKAGDIITSLNGKPLNSFAELRSRI 332
PRK10898 PRK10898
serine endoprotease DegS;
153-459 1.54e-49

serine endoprotease DegS;


Pssm-ID: 182820 [Multi-domain]  Cd Length: 353  Bit Score: 172.49  E-value: 1.54e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 153 VEKIAPAVVHIelflrhplFGRNVPLSS---------GSGFIMSEAGLIVTNAHVVSSSstasgrQQLKVQLQNGDAYEA 223
Cdd:PRK10898  51 VRRAAPAVVNV--------YNRSLNSTShnqleirtlGSGVIMDQRGYILTNKHVINDA------DQIIVALQDGRVFEA 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 224 TIQDIDKKSDIATIVIHPKKkLPVLLLGHSADLRPGEFVVAIGSPFALQNTVTTGIVSTAQRdgkeLGLRDSD-MDYIQT 302
Cdd:PRK10898 117 LLVGSDSLTDLAVLKINATN-LPVIPINPKRVPHIGDVVLAIGNPYNLGQTITQGIISATGR----IGLSPTGrQNFLQT 191

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 303 DAIINYGNSGGPLVNLDGEVIGINTL--------KVAAGISFAIPSDRITRFLsefqNKHVKDWK--KRFIGIRMRTITP 372
Cdd:PRK10898 192 DASINHGNSGGALVNSLGELMGINTLsfdksndgETPEGIGFAIPTQLATKIM----DKLIRDGRviRGYIGIGGREIAP 267

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 373 slveeLKAANPDFPAVsSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAVlnessllLEVRRGnddllfS 452
Cdd:PRK10898 268 -----LHAQGGGIDQL-QGIVVNEVSPDGPAAKAGIQVNDLIISVNNKPAISALETMDQV-------AEIRPG------S 328


                 ....*..
gi 110815869 453 IIPEVVM 459
Cdd:PRK10898 329 VIPVVVM 335
PRK10942 PRK10942
serine endoprotease DegP;
181-432 3.31e-48

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 171.87  E-value: 3.31e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 181 GSGFIMSEA-GLIVTNAHVVSSSSTasgrqqLKVQLQNGDAYEATIQDIDKKSDIATIVIHPKKKLPVLLLGHSADLRPG 259
Cdd:PRK10942 113 GSGVIIDADkGYVVTNNHVVDNATK------IKVQLSDGRKFDAKVVGKDPRSDIALIQLQNPKNLTAIKMADSDALRVG 186

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 260 EFVVAIGSPFALQNTVTTGIVSTAQRDGkeLGLRDSDmDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVAA-----GI 334
Cdd:PRK10942 187 DYTVAIGNPYGLGETVTSGIVSALGRSG--LNVENYE-NFIQTDAAINRGNSGGALVNLNGELIGINTAILAPdggniGI 263

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 335 SFAIPSDRITRFLSefQNKHVKDWKKRFIGIrMRTitpSLVEEL-KAANPDfpaVSSGIYVQEVVPNSPSQRGGIQDGDI 413
Cdd:PRK10942 264 GFAIPSNMVKNLTS--QMVEYGQVKRGELGI-MGT---ELNSELaKAMKVD---AQRGAFVSQVLPNSSAAKAGIKAGDV 334

                        250
                 ....*....|....*....
gi 110815869 414 IVKVNGRPLADSSELQEAV 432
Cdd:PRK10942 335 ITSLNGKPISSFAALRAQV 353
Trypsin_2 pfam13365
Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.
 181-325 1.58e-28

Trypsin-like peptidase domain; This family includes trypsin-like peptidase domains.


Pssm-ID: 433149 [Multi-domain]  Cd Length: 142  Bit Score: 109.82  E-value: 1.58e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  181 GSGFIMSEAGLIVTNAHVVSSSsTASGRQQLKVQLQNGDAYEATIQDIDKKSDIATI-VIHPKKKLPVLLLGHSADLRPG 259
Cdd:pfam13365   1 GTGFVVSSDGLVLTNAHVVDDA-EEAAVELVSVVLADGREYPATVVARDPDLDLALLrVSGDGRGLPPLPLGDSEPLVGG 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 110815869  260 EFVVAIGSPFALQ-NTVTTGIVSTAQRDGKElglrDSDMDYIQTDAIINYGNSGGPLVNLDGEVIGI 325
Cdd:pfam13365  80 ERVYAVGYPLGGEkLSLSEGIVSGVDEGRDG----GDDGRVIQTDAALSPGSSGGPVFDADGRVVGI 142
IGFBP pfam00219
Insulin-like growth factor binding protein;
31-82 2.50e-18

Insulin-like growth factor binding protein;


Pssm-ID: 459717  Cd Length: 53  Bit Score: 78.52  E-value: 2.50e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 110815869   31 CPARCDVSRCPS--PRCPGGYVPDLCNCCLVCAASEGEPCGRpLDSPCGDSLEC 82
Cdd:pfam00219   1 CPPPCDPERCPPppPGCPAGVVLDGCGCCKVCARQEGEPCGV-YTPPCGKGLRC 53
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 362-456 3.49e-16

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: 73.89  E-value: 3.49e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 362 FIGIRMRTITPSLVEELKAaNPDFPAV---SSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV----LN 434
Cdd:cd10838    3 YLGIQMTTLTPELAQQNNR-NPNSPVRipeVDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTADDVQRIVeqagVG 81

                         90       100
                 ....*....|....*....|..
gi 110815869 435 EsSLLLEVRRGNDDLLFSIIPE 456
Cdd:cd10838   82 E-ELELTVLRGDRRQTLAVKPG 102
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 360-453 5.70e-16

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: 73.10  E-value: 5.70e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 360 KRFIGIRMRTITPSLVEELkaanpdFPAVSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAVLNE---S 436
Cdd:cd06779    1 RPYLGIEMENISPLLAKEL------GLPVNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFNDLRAALDTKkpgD 74

                         90
                 ....*....|....*..
gi 110815869 437 SLLLEVRRGNDDLLFSI 453
Cdd:cd06779   75 SLNLTILRDGKTLTVTV 91
cpPDZ_AtDEGP14-like cd23085
circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) ...
 362-456 1.85e-15

circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Arabidopsis thaliana putative protease DEGP14 and related domains. DEGP14 is a putative protease belonging to the HtrA family of housekeeping proteases. 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 AtDEGP14-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: 467632 [Multi-domain]  Cd Length: 101  Bit Score: 71.72  E-value: 1.85e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 362 FIGIRMRTITPSLVEELKAANPDFPAVSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAVLNE--SSLL 439
Cdd:cd23085    3 WLGMKMLELNEHIIAQLKERDPMFPDVKAGVLVPQVIPGSPAERAGLRPGDVIVEFDGKPVDSTKQIIDALGDKvgKPFK 82

                         90
                 ....*....|....*...
gi 110815869 440 LEVRRGNDDLL-FSIIPE 456
Cdd:cd23085   83 VVVKRANKVQVtLTVTPE 100
IB smart00121
Insulin growth factor-binding protein homologues; High affinity binding partners of ...
 29-85 6.53e-14

Insulin growth factor-binding protein homologues; High affinity binding partners of insulin-like growth factors.


Pssm-ID: 197525  Cd Length: 75  Bit Score: 66.72  E-value: 6.53e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 110815869    29 APCPaRCDVSRCPS--PRCPGGYVPDLCNCCLVCAASEGEPCGRPLDsPCGDSLECVRG 85
Cdd:smart00121   1 ARCP-PCDPARCPPcpPGCAELVRLDGCGCCPVCARQEGEPCGVYTP-RCAPGLRCQPP 57
Trypsin pfam00089
Trypsin;
183-347 2.37e-12

Trypsin;


Pssm-ID: 459667 [Multi-domain]  Cd Length: 219  Bit Score: 66.31  E-value: 2.37e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  183 GFIMSEaGLIVTNAHVVSSSSTASGRQ-QLKVQLQNGDAYEATIQDI---------DKKSDIATIVIHPKKKL-----PV 247
Cdd:pfam00089  29 GSLISE-NWVLTAAHCVSGASDVKVVLgAHNIVLREGGEQKFDVEKIivhpnynpdTLDNDIALLKLESPVTLgdtvrPI 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  248 LLLGHSADLRPGE--FVVAIGSPFALQ-----NTVTTGIVSTAQRDGKELGLRDSDMdyIQTDAI---INYGNSGGPLVN 317
Cdd:pfam00089 108 CLPDASSDLPVGTtcTVSGWGNTKTLGpsdtlQEVTVPVVSRETCRSAYGGTVTDTM--ICAGAGgkdACQGDSGGPLVC 185

                         170       180       190
                  ....*....|....*....|....*....|....
gi 110815869  318 LDGEVIGINTLKVAAG----ISFAIPSDRITRFL 347
Cdd:pfam00089 186 SDGELIGIVSWGYGCAsgnyPGVYTPVSSYLDWI 219
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 362-432 3.04e-12

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: 62.50  E-value: 3.04e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 110815869 362 FIGIRMRTITPSLVEELKAANPdfpavsSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV 432
Cdd:cd10839    3 WLGVQIQELTPDLAESFGLKEP------KGALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSSADLRNRV 67
PDZ_2 pfam13180
PDZ domain;
385-453 5.68e-12

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 61.13  E-value: 5.68e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 110815869  385 FPAVSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAVLNE---SSLLLEVRRGNDDLLFSI 453
Cdd:pfam13180   1 FVDLEGGVVVVSVKSSGPAAKAGLKAGDVILSIDGRKINDLTDLESALYGHkpgDTVTLQVYRDGKLLTVEV 72
MarP_fam_protase NF033740
MarP family serine protease; The founding member of this family of membrane-spanning serine ...
 150-325 2.23e-11

MarP family serine protease; The founding member of this family of membrane-spanning serine proteases, which is restricted to Actinobacteria, is the acid resistance periplasmic serine protease MarP of Mycobacterium tuberculosis. Recent work shows that MarP is required to cleave and activate the peptidoglycan hydrolase RipA, and loss of RipA activity creates a defect in progeny separation during cell division. Therefore, the requirement for MarP in order to survive acidic conditions may be a consequence of peptidoglycan hydrolysis requirements, explaining why MarP family members are distributed more broadly in the Actinobacteria than the subset of species capable of surviving intracellularly as pathogens.


Pssm-ID: 468161 [Multi-domain]  Cd Length: 390  Bit Score: 65.21  E-value: 2.23e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 150 ADVVEKIAPAVVHIELflRHPLFGRNvplSSGSGFIMSEaGLIVTNAHVVsssstaSGRQQLKVQLQNGDAYEATIQDID 229
Cdd:NF033740 187 SPAVRRARPSVVKVRG--TAPSCGRA---LEGSGFVVAP-DRVMTNAHVV------AGTDEVTVETVGGGTLDARVVYYD 254

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 230 KKSDIAtiVIH-PKKKLPVLLLGhSADLRPGEFVVAIG----SPFalqnTVT-TGIVSTAQRDGKEL-GLRDSDMDYIQT 302
Cdd:NF033740 255 PDRDIA--VLAvPGLGLPPLPFA-DEPAETGDDAIVLGypegGPF----TATpARVRERIALSGPDIyGSGTVTREVYTL 327

                        170       180
                 ....*....|....*....|...
gi 110815869 303 DAIINYGNSGGPLVNLDGEVIGI 325
Cdd:NF033740 328 RGTVRPGNSGGPLLDPDGRVLGV 350
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 362-432 3.51e-11

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: 59.57  E-value: 3.51e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110815869 362 FIGIRMR---TITPSLVEELKaanpdFPA-VSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV 432
Cdd:cd06781    3 SLGISMVdlsDVPEYEQQSLK-----LPSnVNKGVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSSDLRQIL 72
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 394-458 3.83e-11

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 64.34  E-value: 3.83e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 110815869 394 VQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV--LNESSLLLEVRRGNDDLLFSIIPEVV 458
Cdd:COG0750  132 VGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDDLVDIIraSPGKPLTLTVERDGEELTLTVTPRLV 198
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 389-446 1.65e-10

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: 57.39  E-value: 1.65e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 110815869   389 SSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAVL---NESSLLLEVRRGN 446
Cdd:smart00228  25 GGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLlkkAGGKVTLTVLRGG 85
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 394-458 2.96e-10

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: 56.43  E-value: 2.96e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 110815869 394 VQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV--LNESSLLLEVRRGNDDLLFSIIPEVV 458
Cdd:cd23081    3 VGEVVANSPAAEAGLKPGDRILKIDGQKVRTWEDIVRIVreNPGKPLTLKIERDGKILTVTVTPELV 69
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 390-447 1.37e-09

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: 54.56  E-value: 1.37e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 110815869 390 SGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV-LNESSLLLEVRRGND 447
Cdd:cd23084   18 KGVVVTEVDPGSPAAQSGLKKGDVIIGVNRQPVKSIAELRKVLkSKPSAVLLQIKRGDS 76
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 393-444 1.57e-09

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 53.30  E-value: 1.57e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 110815869  393 YVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV--LNESSLLLEVRR 444
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDVARLLqgSAGESVTLTVRR 54
Peptidase_M50 pfam02163
Peptidase family M50;
336-456 4.09e-09

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 57.50  E-value: 4.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869  336 FAIPSDRITRFLSEFQNKHVkdWKKRFI---GIRMRTITPSLVEELKAANPDFPAVSSGIyVQEVVPNSPSQRGGIQDGD 412
Cdd:pfam02163  39 ALIPLGGYVKMADEFKSKSP--WQRLAIalaGPLANFILAIILFAVLLFLSGVPPPAPPV-IGGVAPGSPAAKAGLKPGD 115

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 110815869  413 IIVKVNGRPLADSSELQEAVLN--ESSLLLEVRRGNDDLLFSIIPE 456
Cdd:pfam02163 116 VILSINGKKITSWQDLVEALAKspGKPITLTVERGGQTLTVTITPK 161
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 391-453 7.84e-09

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: 57.19  E-value: 7.84e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSeLQEAV-----LNESSLLLEVRRGNDDLLFSI 453
Cdd:COG0793   72 KVVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGLT-LDDAVkllrgKAGTKVTLTIKRPGEGEPITV 138
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 391-429 1.81e-08

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 51.51  E-value: 1.81e-08
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 110815869  391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQ 429
Cdd:pfam00595  26 GIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEE 64
SdrC COG3480
Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];
378-432 1.84e-08

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


Pssm-ID: 442703 [Multi-domain]  Cd Length: 344  Bit Score: 55.97  E-value: 1.84e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 110815869 378 LKAANPDfpaVSSGIYVQEVVPNSPSQrGGIQDGDIIVKVNGRPLADSSELQEAV 432
Cdd:COG3480  129 LRAAGYP---VTEGVYVASVLEGSPAD-GVLQPGDVITAVDGKPVTTAEDLRDAL 179
PRK10779 PRK10779
sigma E protease regulator RseP;
386-457 6.52e-08

sigma E protease regulator RseP;


Pssm-ID: 182723 [Multi-domain]  Cd Length: 449  Bit Score: 54.69  E-value: 6.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 386 PAVSSGI---------YVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAVLN--ESSLLLEVRRGNDDLLFSII 454
Cdd:PRK10779 208 PVSSLGIrprgpqiepVLAEVQPNSAASKAGLQAGDRIVKVDGQPLTQWQTFVTLVRDnpGKPLALEIERQGSPLSLTLT 287


                 ...
gi 110815869 455 PEV 457
Cdd:PRK10779 288 PDS 290
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 389-432 2.41e-07

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467153 [Multi-domain]  Cd Length: 81  Bit Score: 48.31  E-value: 2.41e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 110815869 389 SSGIYVQEVVPNSPSQR-GGIQDGDIIVKVNGRPLADSSeLQEAV 432
Cdd:cd00136   23 GGGIFVSRVEPGGPAARdGRLRVGDRILEVNGVSLEGLT-HEEAV 66
cpPDZ2_EcRseP-like cd23083
circularly permuted PDZ domain 2 (PDZ-C) of Escherichia coli Regulator of sigma-E protease ...
 396-456 2.80e-07

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: 48.28  E-value: 2.80e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 110815869 396 EVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAVLN--ESSLLLEVRRGNDDLLFSIIPE 456
Cdd:cd23083    5 NVQPNSAAEKAGLQAGDRIVKVDGQPLTQWQTFVMAVRDnpGKPLALEIERQGSPLSLTLIPD 67
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 389-448 5.12e-07

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: 47.48  E-value: 5.12e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 110815869 389 SSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSeLQEAVlnesSLL---------LEVRRGNDD 448
Cdd:cd06782   13 DGYLVVVSPIPGGPAEKAGIKPGDVIVAVDGESVRGMS-LDEVV----KLLrgpkgtkvkLTIRRGGEG 76
eMpr COG3591
V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, ...
 179-350 9.05e-07

V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442810 [Multi-domain]  Cd Length: 194  Bit Score: 49.29  E-value: 9.05e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 179 SSGSGFIMSEaGLIVTNAHVVSSSSTASGRQQLKVQL-QNGDAYEAT-----------IQDIDKKSDIATIVIHPKKKLP 246
Cdd:COG3591   12 GVCTGTLIGP-NLVLTAGHCVYDGAGGGWATNIVFVPgYNGGPYGTAtatrfrvppgwVASGDAGYDYALLRLDEPLGDT 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 247 V--LLLGHSADLRPGEFVVAIGSPFALQNTVttgivsTAQRDGKelgLRDSDMDYIQTDAIINYGNSGGPLVNLD---GE 321
Cdd:COG3591   91 TgwLGLAFNDAPLAGEPVTIIGYPGDRPKDL------SLDCSGR---VTGVQGNRLSYDCDTTGGSSGSPVLDDSdggGR 161

                        170       180       190
                 ....*....|....*....|....*....|
gi 110815869 322 VIGINTLKVAAGISFAIP-SDRITRFLSEF 350
Cdd:COG3591  162 VVGVHSAGGADRANTGVRlTSAIVAALRAW 191
PDZ3_ZO1-like_domain cd06729
PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ ...
 391-447 1.22e-06

PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. 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 ZO family PDZ3 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: 467211 [Multi-domain]  Cd Length: 82  Bit Score: 46.02  E-value: 1.22e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSElQEAVLnessLLLEVRRGND 447
Cdd:cd06729   24 GIFVAGVQEGSPAEKQGLQEGDQILKVNGVDFRNLTR-EEAVL----FLLDLPKGEE 75
PDZ2_ZO1-like_ds cd06728
PDZ domain 2 of Zonula Occludens-1 (ZO-1), ZO-2 and ZO-3, and related domains; form ...
 392-431 1.61e-06

PDZ domain 2 of Zonula Occludens-1 (ZO-1), ZO-2 and ZO-3, and related domains; form domain-swapping dimers; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. 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 ZO 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: 467210 [Multi-domain]  Cd Length: 79  Bit Score: 45.68  E-value: 1.61e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 110815869 392 IYVQEVVPNSPSQR-GGIQDGDIIVKVNGRPLADSSeLQEA 431
Cdd:cd06728   22 IFVKEITPDSLAAKdGNLQEGDIILKINGTPVENLS-LSEA 61
PDZ_NHERF-like cd06768
PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related ...
 391-419 3.16e-06

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. 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 NHERF-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: 467249 [Multi-domain]  Cd Length: 80  Bit Score: 44.74  E-value: 3.16e-06
                         10        20
                 ....*....|....*....|....*....
gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNG 419
Cdd:cd06768   24 GHFIREVDPGSPAERAGLKDGDRLVEVNG 52
Kazal_2 pfam07648
Kazal-type serine protease inhibitor domain; Usually indicative of serine protease inhibitors. ...
 95-132 5.38e-06

Kazal-type serine protease inhibitor domain; Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides.


Pssm-ID: 400135  Cd Length: 50  Bit Score: 43.25  E-value: 5.38e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 110815869   95 VCGTDGHTYADVCALQAASRRALQVSGTPVrQLQKGAC 132
Cdd:pfam07648  14 VCGSDGVTYPSPCALCAAGCKLGKEVKEEK-VKYDGSC 50
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 391-445 5.51e-06

Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 47.28  E-value: 5.51e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEA---VLNESSLLLEVRRG 445
Cdd:COG3031  152 GYRVNPGRPGSLFSKLGLQPGDVITSINGQDLTDPAQALELlqqLRDASEVTLTVERN 209
KAZAL smart00280
Kazal type serine protease inhibitors; Kazal type serine protease inhibitors and ...
 95-132 5.91e-06

Kazal type serine protease inhibitors; Kazal type serine protease inhibitors and follistatin-like domains.


Pssm-ID: 197624  Cd Length: 46  Bit Score: 43.05  E-value: 5.91e-06
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 110815869    95 VCGTDGHTYADVCALQAASRRalqvSGTPVRQLQKGAC 132
Cdd:smart00280  13 VCGSDGVTYSNECHLCKAACE----SGKSIEVKHDGPC 46
cpPDZ_AtDEGP1-like cd00990
circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 ...
 388-449 1.01e-05

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: 44.11  E-value: 1.01e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 110815869 388 VSSGIYVQEVVPNSPSQRGGIQD-----------GDIIVKVNGRPLADSSELQeAVLNESS----LLLEVRRGNDDL 449
Cdd:cd00990   21 VRSGVLVLDVPPGGPAAKAGLRGtkrdefgrivlGDVIVAVDGKPVKNESDLY-RALDEYKvgdvVTLKVLRGGTKV 96
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 381-428 1.38e-05

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: 43.54  E-value: 1.38e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 110815869 381 ANPDFPAVSS--------GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSEL 428
Cdd:cd06777    8 LSEIPPAMARgggidqlqGALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVLEL 63
cpPDZ_RseP_YlbL-like cd10824
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), ...
 392-456 2.11e-05

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), Bacillus subtilis YlbL protease, 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), Bacillus subtilis YlbL, and related domains, including archaeal and chloroplast PDZ domains. RseP participates in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. PDZ domains usually bind in 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 beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP-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: 467636 [Multi-domain]  Cd Length: 82  Bit Score: 42.56  E-value: 2.11e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 110815869 392 IYVQEVVPNSPSQRGGiQDGDIIVKVNGRPLADSSELQEAVLNES---SLLLEVRRGNDDLLFSIIPE 456
Cdd:cd10824    1 VVVLSVKPNSPAAKAL-HAGDLITEIDGQPTKSWQTFIDYIHDKKvgeSVKITYKHGNKNEEASLKLT 67
PDZ1_FL-whirlin cd06740
PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 ...
 391-443 4.31e-05

PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. 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 whirlin 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: 467222 [Multi-domain]  Cd Length: 82  Bit Score: 41.97  E-value: 4.31e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLAD--SSELQEAVLNESSLLLEVR 443
Cdd:cd06740   28 GIYVSLVEPGSLAEKEGLRVGDQILRVNDVSFEKvtHAEAVKILRVSKKLVLSVR 82
cpPDZ1_MamE-like cd23087
circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease ...
 391-447 5.62e-05

circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease MamE and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Magnetospirillum magneticum MamE (also known as magnetochrome MamE and magnetosome serine protease MamE), and related domains. MamE is a serine protease required to produce magnetite crystals in the magnetotactic bacterium M. magneticum. It is involved in localization of some proteins (at least MamA, MamC, MamF, MamI and MamJ) to the magnetosome, and likely cleaves at least itself, MamO and MamP. MamE-PDZ1 may bind MamB. Its autoproteolysis is stimulated by exogenous substrates or peptides that bind to its PDZ domains. Peptide binding to either the first or the second PDZ domain of MamE can activate proteolysis; activation through PDZ2 is much weaker. 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 MamE-like 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: 467634 [Multi-domain]  Cd Length: 91  Bit Score: 41.78  E-value: 5.62e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPL---ADSSELQEAVLNESSLLLEVRRGND 447
Cdd:cd23087   26 GVFVSGVTPNTPAAAAGLRPGDVILKVDGRPVhqpEEVSAIMAEMPNGRSVRLGVLRDGD 85
PDZ2_harmonin cd06738
PDZ domain 2 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic ...
 386-443 8.00e-05

PDZ domain 2 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. 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 harmonin 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: 467220 [Multi-domain]  Cd Length: 82  Bit Score: 41.15  E-value: 8.00e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 386 PAVSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPL--ADSSELQEAVLNESSLLLEVR 443
Cdd:cd06738   23 PTQKPGIFISNVKPGSLAEEVGLEVGDQIVEVNGTSFtnVDHKEAVMALKSSRHLTITVR 82
PDZ_TAX1BP3-like cd10822
PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic ...
 380-419 8.26e-05

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: 41.17  E-value: 8.26e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 110815869 380 AANPdFPAVSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNG 419
Cdd:cd10822   28 SKNP-FSYTDKGIYVTRVSEGGPAEKAGLQVGDKILQVNG 66
PDZ_PDZD11-like cd06752
PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic ...
 390-419 8.47e-05

PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZD11, and related domains. PDZD11 (also known as ATPase-interacting PDZ protein, plasma membrane calcium ATPase-interacting single-PDZ protein, PMCA-interacting single-PDZ protein, PISP) is involved in the dynamic assembly of apical junctions (AJs). It is recruited by PLEKHA7 to AJs to promote the efficient junctional recruitment and stabilization of nectins, and the efficient early phases of assembly of AJs in epithelial cells. The PDZD11 PDZ domain binds nectin-1 and nectin-3. PDZD11 also binds to a PDZ binding motif located in the C-terminal tail of the human sodium-dependent multivitamin transporter, to the cytoplasmic tail of the Menkes copper ATPase ATP7A, and to the cytoplasmic tail of all plasma membrane Ca2+-ATPase b-splice variants. 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 PDZD11-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: 467234 [Multi-domain]  Cd Length: 83  Bit Score: 41.15  E-value: 8.47e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 110815869 390 SGIYVQEVVPNSPSQRGGIQDGDIIVKVNG 419
Cdd:cd06752   25 LGIFISKVIPDSDAHRLGLKEGDQILSVNG 54
PDZ_ZASP52-like cd23068
PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), ...
 392-444 9.13e-05

PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Zasp52-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467281 [Multi-domain]  Cd Length: 82  Bit Score: 40.97  E-value: 9.13e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 110815869 392 IYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLAD--SSELQEAVLNESS-LLLEVRR 444
Cdd:cd23068   27 LSIQKVNPGSPADKAGLRRGDVILRINGTDTSNltHKQAQDLIKRAGNdLQLTVQR 82
PDZ_ARHGEF11-12-like cd23069
PDZ domain of ARHGEF11, ARHGEF12, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 392-419 9.28e-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: 40.84  E-value: 9.28e-05
                         10        20
                 ....*....|....*....|....*...
gi 110815869 392 IYVQEVVPNSPSQRGGIQDGDIIVKVNG 419
Cdd:cd23069   23 VFVQSVKEGGAAYRAGVQEGDRIIKVNG 50
PDZ2_FL-whirlin cd06741
PDZ domain 2 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 ...
 391-444 1.10e-04

PDZ domain 2 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. 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 whirlin 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: 467223 [Multi-domain]  Cd Length: 84  Bit Score: 40.71  E-value: 1.10e-04
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gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSElQEAV--LNESSLL-LEVRR 444
Cdd:cd06741   27 GIYVTGVDPGSVAENAGLKVGDQILEVNGRSFLDITH-DEAVkiLKSSKHLiMTVKD 82
cpPDZ1_ScNma111-like cd06786
circularly permuted first PDZ domain (PDZ1) of Saccharomyces cerevisiae pro-apoptotic serine ...
 371-453 1.24e-04

circularly permuted first PDZ domain (PDZ1) of Saccharomyces cerevisiae pro-apoptotic serine protease Nma111p and related domains; First PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the HtrA-type protease Saccharomyces cerevisiae Nma111p (also known as Ynm3p), and related domains. Nma111p is a nuclear serine protease which mediates apoptosis through proteolysis of the apoptotic inhibitor Bir1p. Nma111p is composed of 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. 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 ScNma111-like PDZ1 domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation places both beta-strands A and B on the C-terminus.


Pssm-ID: 467625 [Multi-domain]  Cd Length: 89  Bit Score: 40.64  E-value: 1.24e-04
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gi 110815869 371 TPSLVEELKAANPDfpavSSGIYVQE-VVPNSPSQrGGIQDGDIIVKVNGRPLADSSELqEAVLNES---SLLLEVRRGN 446
Cdd:cd06786    7 TPETEAAVRKAFPS----ETGMLVAEtVLPEGPAD-GKLEEGDVLISVNGELITQFIRL-EEILDENvgkTVELVVQRGG 80


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gi 110815869 447 DDLLFSI 453
Cdd:cd06786   81 EEITVTI 87
PDZ1-PDZRN4-like cd06715
PDZ domain 1 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related ...
 389-432 1.73e-04

PDZ domain 1 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. 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 PDZRN4-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: 467199 [Multi-domain]  Cd Length: 92  Bit Score: 40.45  E-value: 1.73e-04
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gi 110815869 389 SSGIYVQEVVPNSPS-QRGGIQDGDIIVKVNGRPLADSSElQEAV 432
Cdd:cd06715   33 SEGIYVSKIVENGPAaDEGGLQVHDRIIEVNGKDLSKATH-EEAV 76
PDZ2-PDZRN4-like cd06716
PDZ domain 2 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related ...
 390-444 1.74e-04

PDZ domain 2 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. 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 PDZRN4-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: 467200 [Multi-domain]  Cd Length: 88  Bit Score: 40.33  E-value: 1.74e-04
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gi 110815869 390 SGIYVQEVVPNSPSQRGG-IQDGDIIVKVNGRPLADSSELqEAVL--NESSLLLEVRR 444
Cdd:cd06716   31 TGIYVSEVDPNSIAAKDGrIREGDQILQINGVDVQNREEA-IALLseEEKSITLLVAR 87
PDZ3_Scribble-like cd06702
PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...
 391-444 2.37e-04

PDZ domain 3 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 PDZ3 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: 467186 [Multi-domain]  Cd Length: 89  Bit Score: 39.93  E-value: 2.37e-04
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gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSElQEAVL----NESSLLLEVRR 444
Cdd:cd06702   33 GIFISKVIPDGAAAKSGLRIGDRILSVNGKDLRHATH-QEAVSallsPGQEIKLLVRH 89
PDZ1_harmonin cd06737
PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic ...
 391-444 2.48e-04

PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. 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 harmonin 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: 467219 [Multi-domain]  Cd Length: 85  Bit Score: 39.55  E-value: 2.48e-04
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gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSS--ELQEAVLNESSLLLEVRR 444
Cdd:cd06737   28 GLFVSHVSPGSQADNKGLRVGDEIVRINGYSISQCTheEVINLIKTKKTVSLKVRH 83
KAZAL_FS cd00104
Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit ...
 95-132 3.30e-04

Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD.


Pssm-ID: 238052 [Multi-domain]  Cd Length: 41  Bit Score: 38.02  E-value: 3.30e-04
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gi 110815869  95 VCGTDGHTYADVCALQAASRRalqvSGTPVRQLQKGAC 132
Cdd:cd00104    8 VCGSDGKTYSNECHLGCAACR----SGRSITVAHNGPC 41
PDZ_SHANK1_3-like cd06746
PDZ domain of SH3 and multiple ankyrin repeat domains protein 1 (SHANK1), SHANK2, SHANK3, and ...
 364-432 3.63e-04

PDZ domain of SH3 and multiple ankyrin repeat domains protein 1 (SHANK1), SHANK2, SHANK3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SHANK1, SHANK2, SHANK3, and related domains. SHANK family proteins, SHANK1 (also known as somatostatin receptor-interacting protein, SSTR-interacting protein, SSTRIP), SHANK2 (also known as cortactin-binding protein 1, proline-rich synapse-associated protein 1), and SHANK3 (proline-rich synapse-associated protein 2) are synaptic scaffolding proteins which are highly enriched in the post-synaptic densities of excitatory synapses. They have been implicated in synaptic transmission, synapse formation, synaptic plasticity, and cytoskeletal remodeling, and are regulators of Cav1 calcium current and CREB target expression. Many protein ligands have been identified for the Shank PDZ domain, such as GKAP (also known as SAPAP), betaPIX (a guanine nucleotide exchange factor used by Rho GTPase family members Rac1 and Cdc42), alpha-latrotoxin, neuroligin, group I metabotropic glutamate receptors (mGluRs), and L-type calcium channels. 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 SHANK-like family domain is a canonical PDZ domain containing 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.


Pssm-ID: 467228 [Multi-domain]  Cd Length: 101  Bit Score: 39.50  E-value: 3.63e-04
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gi 110815869 364 GIRMRTITPSLVEELKAANPDFPAVSsgiYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSeLQEAV 432
Cdd:cd06746   19 GFVLRGAKAVGPILEFTPTPAFPALQ---YLESVDPGGVADKAGLKKGDFLLEINGEDVVKAS-HEQVV 83
PDZ2-PTPN13_FRMPD2-like cd06792
PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and ...
 391-432 4.17e-04

PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of human PTPN13, and related domains. PTPN13, also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1), negatively regulates FAS-mediated apoptosis and NGFR-mediated pro-apoptotic signaling, and may also regulate phosphoinositide 3-kinase (PI3K) signaling. It contains 5 PDZ domains; interaction partners of its second PDZ domain (PDZ2) include the Fas receptor (TNFRSF6) and thyroid receptor-interacting protein 6 (TRIP6). The second PDZ (PDZ2) domain, but not PDZ1 or PDZ3, of FRMPD2 binds to GluN2A and GluN2B, two subunits of N-methyl-d-aspartic acid (NMDA) receptors. Other binding partners of the FRMPDZ2 PDZ2 domain include NOD2, and catenin family members, delta catenin (CTNND2), armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF) and p0071 (also known as plakophilin 4; PKP4). 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 PTPN13-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: 467254 [Multi-domain]  Cd Length: 87  Bit Score: 39.12  E-value: 4.17e-04
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gi 110815869 391 GIYVQEVVPNSPSQRGG-IQDGDIIVKVNGRPLADSSElQEAV 432
Cdd:cd06792   30 GIYVKSLVPGGAAEQDGrIQKGDRLLEVNGVSLEGVTH-KQAV 71
cpPDZ2_MamE-like cd23086
circularly permuted PDZ domain 2 of Magnetospirillum magneticum magnetosome formation protease ...
 391-447 6.18e-04

circularly permuted PDZ domain 2 of Magnetospirillum magneticum magnetosome formation protease MamE, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Magnetospirillum magneticum MamE (also known as magnetochrome MamE and magnetosome serine protease MamE), and related domains. MamE is a serine protease required to produce magnetite crystals in the magnetotactic bacterium M. magneticum. It is involved in localization of some proteins (at least MamA, MamC, MamF, MamI and MamJ) to the magnetosome, and likely cleaves at least itself, MamO and MamP. Its autoproteolysis is stimulated by exogenous substrates or peptides that bind to its PDZ domains. Peptide binding to either the first or the second PDZ domain of MamE can activate proteolysis; activation through PDZ2 is much weaker. 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 MamE-like 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: 467633 [Multi-domain]  Cd Length: 96  Bit Score: 38.77  E-value: 6.18e-04
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gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV----LNESSLLLEVRRGND 447
Cdd:cd23086   31 GAQVAEVLAGSRAAVAGLQANDLILEVNNRPVTSPARLDAAIkgatAGQQILLKVHRNGQE 91
PDZ1_MUPP1-like cd06689
PDZ domain 1 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) ...
 391-432 1.14e-03

PDZ domain 1 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. 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 MUPP1-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: 467176 [Multi-domain]  Cd Length: 102  Bit Score: 38.38  E-value: 1.14e-03
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gi 110815869 391 GIYVQEVVPNSPSQRGG-IQDGDIIVKVNGRPLADSSELQEAV 432
Cdd:cd06689   44 GIFVQEIQPGSVAARDGrLKENDQILAINGQPLDQSISHQQAI 86
PDZ_RGS3-like cd06711
PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 ...
 390-441 1.20e-03

PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS3, and related domains. RGS3 down-regulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. It downregulates G-protein-mediated release of inositol phosphates and activation of MAP kinases. In Eph/ephrin signaling, RGS3 binds via its PDZ domain to the cytoplasmic C terminus of Eph receptor tyrosine kinase EphB. 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 RGS3-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: 467195 [Multi-domain]  Cd Length: 77  Bit Score: 37.75  E-value: 1.20e-03
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gi 110815869 390 SGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSS--ELQEAVLN---ESSLLLE 441
Cdd:cd06711   20 SPVRVQAVDPGGPAEQAGLQQGDTVLQINGQPVERSKcvELAHAIRNcpsEIILLVW 76
PDZ5_PTPN13-like cd06697
PDZ domain 5 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related ...
 388-432 1.23e-03

PDZ domain 5 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), Protein-tyrosine phosphatase 1E (PTP-E1), and Protein-tyrosine phosphatase (PTPL1)] and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. 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 PTPN13 family PDZ5 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: 467183 [Multi-domain]  Cd Length: 87  Bit Score: 37.71  E-value: 1.23e-03
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gi 110815869 388 VSSGIYVQEVVPNSP-SQRGGIQDGDIIVKVNGRPLADSSeLQEAV 432
Cdd:cd06697   26 KYQVIYVLEIVPGSAaAEEGSLQPLDIIHYINGVSTQGMT-LEDAV 70
PDZ3_MUPP1-like cd06791
PDZ domain 3 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) ...
 389-432 1.30e-03

PDZ domain 3 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. 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 MUPP1-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: 467253 [Multi-domain]  Cd Length: 89  Bit Score: 37.98  E-value: 1.30e-03
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gi 110815869 389 SSGIYVQEVVPNSPS-QRGGIQDGDIIVKVNGRPLADSSElQEAV 432
Cdd:cd06791   30 LSGIFVKSIIPGSAAdQDGRIQVNDQIIAVDGVNLQGFTN-QEAV 73
PDZ1_INAD-like cd23063
PDZ domain 1 of inactivation-no-after-potential D (INAD), and related domains; PDZ (PSD-95 ...
 387-434 1.34e-03

PDZ domain 1 of inactivation-no-after-potential D (INAD), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ4,5 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. 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 INAD-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: 467276 [Multi-domain]  Cd Length: 87  Bit Score: 37.88  E-value: 1.34e-03
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gi 110815869 387 AVSSGIYVQEVVPNSPSQR-GGIQDGDIIVKVNGRPLADSSElqEAVLN 434
Cdd:cd23063   27 TKTTGIFIKGIIPDSPAHKcGRLKVGDRILSVNGNDVRNSTE--QAAID 73
PDZ_tamalin_CYTIP-like cd06713
PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains; PDZ ...
 393-419 1.35e-03

PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of tamalin, cytohesin-1-interacting protein, and related domains. Tamalin (trafficking regulator and scaffold protein tamalin, also known as general receptor for phosphoinositides 1-associated scaffold protein, GRASP) functions to link receptors, including group 1 metabotropic glutamate receptors (mGluRs), to neuronal proteins. The tamalin PDZ domain binds the C-terminal domains of group I mGluRs; it also binds potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2), neurotrophin-3 (NT3) TrkCT1-truncated receptor, SAP90/PSD-95-associated protein, and tamalin itself. CYTIP (cytohesin-1-interacting protein, also known as Pleckstrin homology Sec7 and coiled-coil domain-binding protein) sequesters cytohesin-1 in the cytoplasm, limiting its interaction with beta2 integrins; cytohesin-1 binds the CYTIP coiled coil domain. The CYTIP PDZ domain can bind the C-terminal peptide of protocadherin alpha-1 (PCDHA1), indicating a possible interaction between the two. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This tamalin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467197 [Multi-domain]  Cd Length: 91  Bit Score: 37.99  E-value: 1.35e-03
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                 ....*....|....*....|....*..
gi 110815869 393 YVQEVVPNSPSQRGGIQDGDIIVKVNG 419
Cdd:cd06713   38 YVCRVHEDSPAYLAGLTAGDVILSVNG 64
cpPDZ_RseP_YlbL-like_arch cd10823
circularly permuted PDZ domains of uncharacterized archaeal proteins related to Escherichia ...
 392-432 1.44e-03

circularly permuted PDZ domains of uncharacterized archaeal proteins related to Escherichia coli Regulator of sigma-E protease (RseP) and Bacillus subtilis YlbL protease; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of uncharacterized archaeal proteins related to Escherichia coli ResP (also known as Site-2 protease RseP, and YaeL) and Bacillus subtilis YlbL protease. RseP participates in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP-YlbL archaeal family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.


Pssm-ID: 467635 [Multi-domain]  Cd Length: 79  Bit Score: 37.45  E-value: 1.44e-03
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                 ....*....|....*....|....*....|....*....|.
gi 110815869 392 IYVQEVVPNSPSQrGGIQDGDIIVKVNGRPLADSSELQEAV 432
Cdd:cd10823    1 VEVDRVVEGSPSS-KVLPEGMVIESIDGYSVKDLSSYSEAL 40
PDZ2_PDZD7-like cd10834
PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related ...
 391-419 1.83e-03

PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the second PDZ domain of the canonical isoform of PDZD7- isoform 1. 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 PDZD7-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: 467270 [Multi-domain]  Cd Length: 85  Bit Score: 37.37  E-value: 1.83e-03
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gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNG 419
Cdd:cd10834   28 GIYVSKVDPGGLAEQNGIKVGDQILAVNG 56
PDZ_AFDN-like cd06789
PDZ domain of afadin (AFDN), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95) ...
 391-433 1.88e-03

PDZ domain of afadin (AFDN), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of afadin (AFDN, also known as ALL1-fused gene from chromosome 6 protein (AF6) and MLLT4), and related domains. AFDN belongs to the adhesion system, probably together with the E-cadherin-catenin system, that plays a role in the organization of homotypic, interneuronal, and heterotypic cell-cell adherens junctions. The AFDN PDZ domain interaction partners include poliovirus receptor-related protein PRR2/nectin, the junctional adhesion molecule (JAM), the breakpoint-cluster-region protein (BCR), connexin36 (Cx36), and a subset of Eph-related receptor tyrosine kinases; it can also bind low molecular weight ligands, in competition with a natural peptide ligand. Other AFDN-binding proteins have been identified. 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 AFDN 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: 467251 [Multi-domain]  Cd Length: 89  Bit Score: 37.27  E-value: 1.88e-03
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gi 110815869 391 GIYVQEVVPNSPSQRGG-IQDGDIIVKVNGRPLADSSELQEAVL 433
Cdd:cd06789   31 GIYIKSVVKGGAADLDGrLQAGDQLLSVDGHSLVGLSQERAAEL 74
PDZ1_PDZD7-like cd10833
PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related ...
 391-444 2.46e-03

PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the first PDZ domain of the canonical isoform of PDZD7- isoform 1. 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 PDZD7-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: 467269 [Multi-domain]  Cd Length: 84  Bit Score: 37.03  E-value: 2.46e-03
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gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPL---ADSSELQeaVLNESSLL-LEVRR 444
Cdd:cd10833   27 GIFVSKVEEGSAAERAGLCVGDKITEVNGVSLeniTMSSAVK--VLTGSNRLrMVVRR 82
PDZ4_GRIP1-2-like cd06686
PDZ domain 4 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related ...
 399-442 2.67e-03

PDZ domain 4 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. 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 GRIP family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467174 [Multi-domain]  Cd Length: 99  Bit Score: 37.32  E-value: 2.67e-03
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gi 110815869 399 PNSPSQRGG-IQDGDIIVKVNGRPLADSSeLQEA--VLNESS--LLLEV 442
Cdd:cd06686   45 PDSPAERCGvLQVGDRVLSINGIPTEDRT-LEEAnqLLRDSAskVTLEI 92
cpPDZ_BsYlbL-like cd23080
circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ ...
 391-428 2.89e-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: 36.70  E-value: 2.89e-03
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                 ....*....|....*....|....*....|....*...
gi 110815869 391 GIYVQEVVPNSPSqRGGIQDGDIIVKVNGRPLADSSEL 428
Cdd:cd23080    1 GVYVLSVVENMPA-KGILEAGDKITAIDGQNFQSSEKL 37
PDZ_Radil-like cd06690
PDZ domain of Ras-associating and dilute domain-containing protein (Radil) and related domains; ...
 386-422 3.57e-03

PDZ domain of Ras-associating and dilute domain-containing protein (Radil) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Radil (also known as protein KIAA1849) and related domains. Radil is required for cell adhesion and migration of neural crest precursors during development. Radil is a component of a Rasip1-Radil-ARHGAP29 complex at endothelial cell-cell junctions. Rap1, via its effectors Radil and Rasip1 and their binding partner ArhGAP29, controls the endothelial barrier by decreasing Rho-mediated radial tension on cell-cell junctions. ArhGAP29 binds the Radil PDZ domain. The Radil PDZ domain also binds kinesin family protein 14 (KIF14); KIF14 negatively regulates Rap1-mediated inside-out integrin activation by tethering Radil on microtubules. 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 Radil-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: 467177 [Multi-domain]  Cd Length: 88  Bit Score: 36.50  E-value: 3.57e-03
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gi 110815869 386 PAVSSGIYVQEVVPNSPSQRGG-IQDGDIIVKVNGRPL 422
Cdd:cd06690   26 PLRSPGIYIRTLVPDSPAARDGrLRLGDRILAVNGTSL 63
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
377-446 3.61e-03

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


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 39.80  E-value: 3.61e-03
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gi 110815869 377 ELKAANPDFPAVSSGIYVQE---------VVPNSPSQRGGIQDGDIIVKVNGRPLaDSSELQEAVLN---ESSLLLEVRR 444
Cdd:COG3975  472 KLVYEDAPSLKPSLGLRVSAdggglvvtsVLWGSPAYKAGLSAGDELLAIDGLRV-TADNLDDALAAykpGDPIELLVFR 550


                 ..
gi 110815869 445 GN 446
Cdd:COG3975  551 RD 552
PDZ2_PDZD2-like cd06758
PDZ domain 2 of PDZ domain containing 2 (PDZD2), and related domains; PDZ (PSD-95 ...
 391-432 4.21e-03

PDZ domain 2 of PDZ domain containing 2 (PDZD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains, and is expressed at exceptionally high levels in the pancreas and certain cancer tissues such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. 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 PDZD2-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: 467239 [Multi-domain]  Cd Length: 88  Bit Score: 36.18  E-value: 4.21e-03
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gi 110815869 391 GIYVQEVVPNSPSQRGG-IQDGDIIVKVNGRPLADSSeLQEAV 432
Cdd:cd06758   30 GIFVAGVEEGGSADRDGrLKKGDELLMINGQSLIGLS-HQEAV 71
cpPDZ1_EcRseP-like cd23082
circularly permuted PDZ domain 1 (PDZ-N) of Escherichia coli Regulator of sigma-E protease ...
 393-449 4.23e-03

circularly permuted PDZ domain 1 (PDZ-N) 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: 467639 [Multi-domain]  Cd Length: 89  Bit Score: 36.20  E-value: 4.23e-03
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                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 110815869 393 YVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSSELQEAV---LNESSLLLEVRRGNDDL 449
Cdd:cd23082    2 VIGEIAPNSIAAQAGIEPGDEIKAVDGIEVPDWDSVRLQLvdkLGAGSVQITVQPFGSGA 61
PDZ5_INAD-like cd23066
PDZ domain 5 of inactivation no after potential D (INAD), and related domains; PDZ (PSD-95 ...
 386-422 5.02e-03

PDZ domain 5 of inactivation no after potential D (INAD), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ45 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. 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 INAD-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: 467279 [Multi-domain]  Cd Length: 80  Bit Score: 35.94  E-value: 5.02e-03
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gi 110815869 386 PAVSSGIYVQEVVPNSPSQ-RGGIQDGDIIVKVNGRPL 422
Cdd:cd23066   18 PNEGIGCTIADLLPGGYAEiDGKLQKGDIITKFNGDAL 55
PDZ3_PTPN13_FRMPD2-like cd06695
PDZ domain 3 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), FERM and PDZ ...
 382-432 5.32e-03

PDZ domain 3 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], FRMPD2 (also known as PDZ domain-containing protein 4; PDZ domain-containing protein 5C), and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. 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). FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ3 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: 467181 [Multi-domain]  Cd Length: 90  Bit Score: 36.08  E-value: 5.32e-03
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                 ....*....|....*....|....*....|....*....|....*....|..
gi 110815869 382 NPDFPAVSSGIYVQEVVPNSPSQRGG-IQDGDIIVKVNGRPLADSSeLQEAV 432
Cdd:cd06695   23 NSPEDPFSGLVRIKKLFPGQPAAESGlIQEGDVILAVNGEPLKGLS-YQEVL 73
PDZ1_Par3-like cd06691
PDZ domain 1 of partitioning defective 3 (Par3), and related domains; PDZ (PSD-95 ...
 391-426 6.43e-03

PDZ domain 1 of partitioning defective 3 (Par3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP) and related domains; Drosophila bazooka PDZ1 belongs to a different PDZ family. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par3 and the Par complex include: Par-3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. 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 Par3 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: 467178 [Multi-domain]  Cd Length: 98  Bit Score: 36.05  E-value: 6.43e-03
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                 ....*....|....*....|....*....|....*..
gi 110815869 391 GIYVQEVVPNSPSQRGG-IQDGDIIVKVNGRPLADSS 426
Cdd:cd06691   34 GLLIRGIEEGSRAERDGrFQENDCIVEINGVDLIDKS 70
PDZ1_syntenin-like cd06721
PDZ domain 1 of syntenin-1, syntenin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 387-423 6.72e-03

PDZ domain 1 of syntenin-1, syntenin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of syntenin-1, syntenin-2, and related domains. Syntenins are implicated in various cellular processes such as trafficking, signaling, and cancer metastasis. They bind to signaling and adhesion molecules, such as syndecans, neurexins, ephrin B, and phospholipid PIP2. Through its tandem PDZ domains (PDZ1 and PDZ2), syntenin links syndecans to other cell surface receptors and kinases, such as E-cadherin and ephrin-B, establishing signaling crosstalk. During syndecan binding, syntenin PDZ2 serves as a high-affinity domain, and PDZ1, also necessary for binding, acts as a complementary, low-affinity domain; this is also the case for syntenin binding to proto-oncogene c-Src. The syntenin PDZ domain-PIP2 interaction controls Arf6-mediated syndecan recycling through endosomal compartments; both PDZ1 and PDZ2 interact with PIP2. Different binding partners and downstream regulators of syntenin1 PDZ domains, such as to proto-oncogene c-Src, mitogen-activated protein kinase (MAPK), and focal adhesion kinase (FAK), have been identified that promote the progression and invasion of a variety of cancers, such as melanoma, glioblastoma multiforme and breast cancer. 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 syntenin-like family domain is a canonical PDZ domain containing 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.


Pssm-ID: 467204 [Multi-domain]  Cd Length: 79  Bit Score: 35.67  E-value: 6.72e-03
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                 ....*....|....*....|....*....|....*..
gi 110815869 387 AVSSGIYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLA 423
Cdd:cd06721   19 SIDKGVFVQLVQANSPAALAGLRFGDQILQINGENVA 55
PDZ_PDLIM-like cd06753
PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 392-444 6.94e-03

PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDLIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467235 [Multi-domain]  Cd Length: 79  Bit Score: 35.58  E-value: 6.94e-03
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                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 110815869 392 IYVQEVVPNSPSQRGGIQDGDIIVKVNGRPLADSS--ELQEAVLNES-SLLLEVRR 444
Cdd:cd06753   24 LTISRVTPGGKAAQANLRPGDVILAINGESTEGMThlEAQNKIKAATgSLSLTLER 79
PDZ_RapGEF2_RapGEF6-like cd06755
PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange ...
 391-419 7.13e-03

PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange factor 6, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Rap guanine nucleotide exchange factor 2 (RapGEF2, also named RA-GEF-1, PDZ-GEF1, CNrasGEF and nRapGEP) and Rap guanine nucleotide exchange factor 6 (RapGEF6, also named RA-GEF-2 and PDZ-GEF2). RapGEF2 and RapGEF6 constitute a subfamily of guanine nucleotide exchange factors (GEFs) for RAP small GTPases that is characterized by the possession of the PDZ and Ras/Rap-associating domains. They activate Rap small GTPases, by catalyzing the release of GDP from the inactive GDP-bound forms, thereby accelerating GTP loading to yield the active GTP-bound forms. The PDZ domain of RapGEF6 (also known as PDZ-GEF2) binds junctional adhesion molecule A (JAM-A). 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 RapGEF2 and RapGEF6 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: 467237 [Multi-domain]  Cd Length: 83  Bit Score: 35.70  E-value: 7.13e-03
                         10        20
                 ....*....|....*....|....*....
gi 110815869 391 GIYVQEVVPNSPSQRGGIQDGDIIVKVNG 419
Cdd:cd06755   27 GIFVSKVEKGSKAAEAGLKRGDQILEVNG 55
PDZ1_ZO1-like cd06727
PDZ domain 1 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ ...
 382-422 8.29e-03

PDZ domain 1 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins, and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. 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 ZO 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: 467209 [Multi-domain]  Cd Length: 87  Bit Score: 35.33  E-value: 8.29e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 110815869 382 NPDFPAVSSGIYVQEVVPNSPSQrGGIQDGDIIVKVNGRPL 422
Cdd:cd06727   23 NPHFQSGDTSIVISDVLKGGPAE-GKLQENDRVVSVNGVSM 62
 
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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