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Conserved domains on  [gi|7657261|ref|NP_055062|]
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rap guanine nucleotide exchange factor 2 isoform 5 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RasGEF cd00155
Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of ...
 713-938 7.71e-84

Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors.


:

Pssm-ID: 238087 [Multi-domain]  Cd Length: 237  Bit Score: 274.51  E-value: 7.71e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   713 LLQLSTVEVATQLSMRNFELFRNIEPTEYIDDLFKLRSKT--SCANLKRFEEVINQETFWVASEILRETNQLKRMKIIKH 790
Cdd:cd00155    1 FLSLDPKELAEQLTLLDFELFRKIEPFELLGSLWSKKDKNihLSPNLERFIERFNNLSNWVASEILLCTNPKKRARLLSK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   791 FIKIALHCRECKNFNSMFAIISGLNLAPVARLRTTWEKLPNKYEKLFQDLQDLFDPSRNMAKYRNVLNSQNLQPPIIPLF 870
Cdd:cd00155   81 FIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEVLSSKLKKLFEELEELVDPSRNFKNYRKLLKSVGPNPPCVPFL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7657261   871 PVIKKDLTFLHEGNDSKVD-GLVNFEKLRMIAKEIRHVGRMASV--NMDPALMFRTRKKKWRSLGSLSQGS 938
Cdd:cd00155  161 GVYLKDLTFLHEGNPDFLEgNLVNFEKRRKIAEILREIRQLQSNsyELNRDEDILAFLWKLLELILNEDEL 231
PDZ_RapGEF2_RapGEF6-like cd06755
PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange ...
 384-466 7.72e-52

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: 176.69  E-value: 7.72e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   384 RLMTLTKPSREAPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITV 463
Cdd:cd06755    1 RTVTLTRPSRESPLHFSLLGGSEKGFGIFVSKVEKGSKAAEAGLKRGDQILEVNGQNFENITLKKALEILRNNTHLSITV 80


                 ...
gi 7657261   464 KTN 466
Cdd:cd06755   81 KTN 83
RA_PDZ-GEF1 cd01785
Ras-associating (RA) domain found in PDZ domain-containing guanine nucleotide exchange factor ...
 608-690 1.30e-45

Ras-associating (RA) domain found in PDZ domain-containing guanine nucleotide exchange factor 1 (PDZ-GEF1) and similar proteins; PDZ-GEF1, also termed Rap guanine nucleotide exchange factor 2, or cyclic nucleotide ras GEF (CNrasGEF), or neural RAP guanine nucleotide exchange protein (nRap GEP), or Ras/Rap1-associating GEF-1 (RA-GEF-1), is a Rap-specific guanine nucleotide exchange factor (GEF) that has a PSD-95/DlgA/ZO-1 (PDZ) domain, a RA domain and a region related to a cyclic nucleotide binding domain (RCBD). The RA domain of PDZ-GEF interacts with Rap1 and also contributes to the membrane localization of PDZ-GEF. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and involve in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes.


:

Pssm-ID: 340483  Cd Length: 85  Bit Score: 159.01  E-value: 1.30e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   608 QVLRVFKADQQSRYIMISKDTTAKEVVIQAIREFAVTAT--PDQYSLCEVSVTPEGVIKQRRLPDQLSKLADRIQLSGRY 685
Cdd:cd01785    1 QVLKVYRADQSSKYILIHKETTAREVVMLALREFGITDDenSDNYSLCEVTVTPEGLIKQRRLPDQLSNLANRISLNGRY 80


                 ....*
gi 7657261   686 YLKNN 690
Cdd:cd01785   81 YLKNN 85
RasGEFN smart00229
Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif; A subset of guanine ...
 267-380 3.46e-29

Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif; A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).


:

Pssm-ID: 214571  Cd Length: 127  Bit Score: 113.58  E-value: 3.46e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      267 KGHIVIKGTSERLTMHLVEEHSVVDPTFIEDFLLTYRTFLSSPMEVGKKLLEWFNDPS------------LRDKVTRVVL 334
Cdd:smart00229    1 DGGLIKGGTLEALIEHLTEAFDKADPSFVETFLLTYRSFITTQELLQLLLYRYNAIPPeswveekvnprrVKNRVLNILR 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 7657261      335 LWVNNHFNDFEGDPAMTRFLEEFENNLEREKM-GGHLRLLNIACAAK 380
Cdd:smart00229   81 TWVENYWEDFEDDPKLISFLLEFLELVDDEKYpGLVTSLLNLLRRLS 127
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 136-251 4.57e-14

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


:

Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 70.12  E-value: 4.57e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      136 FANMTMSVRRELCAVMvFAVVERAGTIVLNDGEELDSWSVILNGSVEVTY--PDGKAEILCM---GNSFGVSPTMDkeYM 210
Cdd:smart00100    2 FKNLDAEELRELADAL-EPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKvlEDGEEQIVGTlgpGDFFGELALLT--NS 78

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 7657261      211 KGVMRTKVDDCQFVCIAQQDYCRILNQVEKNMQKVEEEGEI 251
Cdd:smart00100   79 RRAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLE 119
 
Name Accession Description Interval E-value
RasGEF cd00155
Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of ...
 713-938 7.71e-84

Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors.


Pssm-ID: 238087 [Multi-domain]  Cd Length: 237  Bit Score: 274.51  E-value: 7.71e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   713 LLQLSTVEVATQLSMRNFELFRNIEPTEYIDDLFKLRSKT--SCANLKRFEEVINQETFWVASEILRETNQLKRMKIIKH 790
Cdd:cd00155    1 FLSLDPKELAEQLTLLDFELFRKIEPFELLGSLWSKKDKNihLSPNLERFIERFNNLSNWVASEILLCTNPKKRARLLSK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   791 FIKIALHCRECKNFNSMFAIISGLNLAPVARLRTTWEKLPNKYEKLFQDLQDLFDPSRNMAKYRNVLNSQNLQPPIIPLF 870
Cdd:cd00155   81 FIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEVLSSKLKKLFEELEELVDPSRNFKNYRKLLKSVGPNPPCVPFL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7657261   871 PVIKKDLTFLHEGNDSKVD-GLVNFEKLRMIAKEIRHVGRMASV--NMDPALMFRTRKKKWRSLGSLSQGS 938
Cdd:cd00155  161 GVYLKDLTFLHEGNPDFLEgNLVNFEKRRKIAEILREIRQLQSNsyELNRDEDILAFLWKLLELILNEDEL 231
RasGEF smart00147
Guanine nucleotide exchange factor for Ras-like small GTPases;
713-936 7.66e-83

Guanine nucleotide exchange factor for Ras-like small GTPases;


Pssm-ID: 214539  Cd Length: 242  Bit Score: 271.81  E-value: 7.66e-83
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      713 LLQLSTVEVATQLSMRNFELFRNIEPTEYIDDLFKLRSKTSCA--NLKRFEEVINQETFWVASEILRETNQLKRMKIIKH 790
Cdd:smart00147    1 LLLLDPKELAEQLTLLDFELFRKIDPSELLGSVWGKRSKKSPSplNLEAFIRRFNEVSNWVATEILKQTTPKDRAELLSK 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      791 FIKIALHCRECKNFNSMFAIISGLNLAPVARLRTTWEKLPNKYEKLFQDLQDLFDPSRNMAKYRNVLNSQNlQPPIIPLF 870
Cdd:smart00147   81 FIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEKLPSKYKKLFEELEELLSPERNYKNYREALSSCN-LPPCIPFL 159

                           170       180       190       200       210       220
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 7657261      871 PVIKKDLTFLHEGNDSKV-DGLVNFEKLRMIAKEIRHVGRMASVNMDPALMFRTRKKKWRSLGSLSQ 936
Cdd:smart00147  160 GVLLKDLTFIDEGNPDFLeNGLVNFEKRRQIAEILREIRQLQSQPYNLRPNRSDIQSLLQQLLDHLD 226
RasGEF pfam00617
RasGEF domain; Guanine nucleotide exchange factor for Ras-like small GTPases.
 720-898 1.12e-72

RasGEF domain; Guanine nucleotide exchange factor for Ras-like small GTPases.


Pssm-ID: 459872  Cd Length: 179  Bit Score: 240.19  E-value: 1.12e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     720 EVATQLSMRNFELFRNIEPTEYIDDLF-KLRSKTSCANLKRFEEVINQETFWVASEILRETNQLKRMKIIKHFIKIALHC 798
Cdd:pfam00617    1 ELARQLTLIEFELFRKIKPRELLGSAWsKKDKKENSPNIEAMIARFNKLSNWVASEILSEEDLKKRAKVIKKFIKIAEHC 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     799 RECKNFNSMFAIISGLNLAPVARLRTTWEKLPNKYEKLFQDLQDLFDPSRNMAKYRNVLnsQNLQPPIIPLFPVIKKDLT 878
Cdd:pfam00617   81 RELNNFNSLMAILSGLNSSPISRLKKTWELVSKKYKKTLEELEKLMSPSRNFKNYREAL--SSASPPCIPFLGLYLTDLT 158

                          170       180
                   ....*....|....*....|.
gi 7657261     879 FLHEGNDSKV-DGLVNFEKLR 898
Cdd:pfam00617  159 FIEEGNPDFLeGGLINFEKRR 179
PDZ_RapGEF2_RapGEF6-like cd06755
PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange ...
 384-466 7.72e-52

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: 176.69  E-value: 7.72e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   384 RLMTLTKPSREAPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITV 463
Cdd:cd06755    1 RTVTLTRPSRESPLHFSLLGGSEKGFGIFVSKVEKGSKAAEAGLKRGDQILEVNGQNFENITLKKALEILRNNTHLSITV 80


                 ...
gi 7657261   464 KTN 466
Cdd:cd06755   81 KTN 83
RA_PDZ-GEF1 cd01785
Ras-associating (RA) domain found in PDZ domain-containing guanine nucleotide exchange factor ...
 608-690 1.30e-45

Ras-associating (RA) domain found in PDZ domain-containing guanine nucleotide exchange factor 1 (PDZ-GEF1) and similar proteins; PDZ-GEF1, also termed Rap guanine nucleotide exchange factor 2, or cyclic nucleotide ras GEF (CNrasGEF), or neural RAP guanine nucleotide exchange protein (nRap GEP), or Ras/Rap1-associating GEF-1 (RA-GEF-1), is a Rap-specific guanine nucleotide exchange factor (GEF) that has a PSD-95/DlgA/ZO-1 (PDZ) domain, a RA domain and a region related to a cyclic nucleotide binding domain (RCBD). The RA domain of PDZ-GEF interacts with Rap1 and also contributes to the membrane localization of PDZ-GEF. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and involve in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes.


Pssm-ID: 340483  Cd Length: 85  Bit Score: 159.01  E-value: 1.30e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   608 QVLRVFKADQQSRYIMISKDTTAKEVVIQAIREFAVTAT--PDQYSLCEVSVTPEGVIKQRRLPDQLSKLADRIQLSGRY 685
Cdd:cd01785    1 QVLKVYRADQSSKYILIHKETTAREVVMLALREFGITDDenSDNYSLCEVTVTPEGLIKQRRLPDQLSNLANRISLNGRY 80


                 ....*
gi 7657261   686 YLKNN 690
Cdd:cd01785   81 YLKNN 85
RasGEFN smart00229
Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif; A subset of guanine ...
 267-380 3.46e-29

Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif; A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).


Pssm-ID: 214571  Cd Length: 127  Bit Score: 113.58  E-value: 3.46e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      267 KGHIVIKGTSERLTMHLVEEHSVVDPTFIEDFLLTYRTFLSSPMEVGKKLLEWFNDPS------------LRDKVTRVVL 334
Cdd:smart00229    1 DGGLIKGGTLEALIEHLTEAFDKADPSFVETFLLTYRSFITTQELLQLLLYRYNAIPPeswveekvnprrVKNRVLNILR 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 7657261      335 LWVNNHFNDFEGDPAMTRFLEEFENNLEREKM-GGHLRLLNIACAAK 380
Cdd:smart00229   81 TWVENYWEDFEDDPKLISFLLEFLELVDDEKYpGLVTSLLNLLRRLS 127
REM cd06224
Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also ...
 275-380 8.58e-22

Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.


Pssm-ID: 100121  Cd Length: 122  Bit Score: 92.09  E-value: 8.58e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   275 TSERLTMHLVEEHSVVDPTFIEDFLLTYRTFLsSPMEVGKKLLEWFNDP----------------SLRDKVTRVVLLWVN 338
Cdd:cd06224    1 TLEALIEHLTSTFDMPDPSFVSTFLLTYRSFT-TPTELLEKLIERYEIAppenleyndwdkkkskPIRLRVLNVLRTWVE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 7657261   339 NHFNDFEGDPAMTRFLEEFENNLEREKMGGHLRLLNIACAAK 380
Cdd:cd06224   80 NYPYDFFDDEELLELLEEFLNRLVQEGALLQELKKLLRKLLK 121
RasGEF_N pfam00618
RasGEF N-terminal motif; A subset of guanine nucleotide exchange factor for Ras-like small ...
 270-357 2.14e-17

RasGEF N-terminal motif; A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this motif/domain N-terminal to the RasGef (Cdc25-like) domain.


Pssm-ID: 459873  Cd Length: 104  Bit Score: 78.89  E-value: 2.14e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     270 IVIKGTSERLTMHLVEEHSVVDPTFIEDFLLTYRTFLsSPMEVGKKLLEWFNDPSLRD-----------------KVTRV 332
Cdd:pfam00618    1 QVKAGTLEKLVEYLTSTRIMLDDSFLSTFLLTYRSFT-TPAELLELLIERYNIPPPLDlssdsywiskktlpiriRVLSV 79

                           90       100
                   ....*....|....*....|....*
gi 7657261     333 VLLWVNNHFNDFEGDPAMTRFLEEF 357
Cdd:pfam00618   80 LRHWVENYFSDFNDDPVLLSRLEKF 104
RA smart00314
Ras association (RalGDS/AF-6) domain; RasGTP effectors (in cases of AF6, canoe and RalGDS); ...
 608-690 4.59e-16

Ras association (RalGDS/AF-6) domain; RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.)


Pssm-ID: 214612  Cd Length: 90  Bit Score: 74.64  E-value: 4.59e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      608 QVLRVFKAD---QQSRYIMISKDTTAKEVVIQAIREFAVTATPDQYSLCEV-SVTPEGVIKQRRLPDQLSKLADRIQLSG 683
Cdd:smart00314    3 FVLRVYVDDlpgGTYKTLRVSSRTTARDVIQQLLEKFHLTDDPEEYVLVEVlPDGKERVLPDDENPLQLQKLWPRRGPNL 82


                    ....*..
gi 7657261      684 RYYLKNN 690
Cdd:smart00314   83 RFVLRKR 89
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 382-464 3.79e-15

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: 72.03  E-value: 3.79e-15
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      382 KRRLMTLTKpsREAPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNN-THLS 460
Cdd:smart00228    1 EPRLVELEK--GGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAgGKVT 78


                    ....
gi 7657261      461 ITVK 464
Cdd:smart00228   79 LTVL 82
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 136-251 4.57e-14

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 70.12  E-value: 4.57e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      136 FANMTMSVRRELCAVMvFAVVERAGTIVLNDGEELDSWSVILNGSVEVTY--PDGKAEILCM---GNSFGVSPTMDkeYM 210
Cdd:smart00100    2 FKNLDAEELRELADAL-EPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKvlEDGEEQIVGTlgpGDFFGELALLT--NS 78

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 7657261      211 KGVMRTKVDDCQFVCIAQQDYCRILNQVEKNMQKVEEEGEI 251
Cdd:smart00100   79 RRAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLE 119
RA pfam00788
Ras association (RalGDS/AF-6) domain; RasGTP effectors (in cases of AF6, canoe and RalGDS); ...
 606-691 1.58e-12

Ras association (RalGDS/AF-6) domain; RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Recent evidence (not yet in MEDLINE) shows that some RA domains do NOT bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase.


Pssm-ID: 425871  Cd Length: 93  Bit Score: 64.66  E-value: 1.58e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     606 PDQVLRVF----KADQQSRYIMISKDTTAKEVVIQAIREFAVTATPDQYSLCEVSvtpEGVIKQRRLPDQLSKLADRIQL 681
Cdd:pfam00788    1 DDGVLKVYtedgKPGTTYKTILVSSSTTAEEVIEALLEKFGLEDDPRDYVLVEVL---ERGGGERRLPDDECPLQIQLQW 77

                           90
                   ....*....|....*
gi 7657261     682 -----SGRYYLKNNM 691
Cdd:pfam00788   78 prdasDSRFLLRKRD 92
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 135-245 6.36e-11

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 60.80  E-value: 6.36e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   135 AFANMTMSVRRELCAVMVFAVVErAGTIVLNDGEELDSWSVILNGSVEVTY--PDGKAEILCM---GNSFGVSPTMDKEY 209
Cdd:cd00038    1 LFSGLDDEELEELADALEERRFP-AGEVIIRQGDPADSLYIVLSGSVEVYKldEDGREQIVGFlgpGDLFGELALLGNGP 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 7657261   210 MKGVMRTKvDDCQFVCIAQQDYCRILNQVEKNMQKV 245
Cdd:cd00038   80 RSATVRAL-TDSELLVLPRSDFRRLLQEYPELARRL 114
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 385-464 3.41e-10

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 57.68  E-value: 3.41e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     385 LMTLTKPSREaPLPFILLGGSEKGF-GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN-NTHLSIT 462
Cdd:pfam00595    1 QVTLEKDGRG-GLGFSLKGGSDQGDpGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGsGGKVTLT 79


                   ..
gi 7657261     463 VK 464
Cdd:pfam00595   80 IL 81
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 410-464 2.64e-06

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: 50.92  E-value: 2.64e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENI-QLSKAM-----------EILRNNTHLSITVK 464
Cdd:COG0265  202 GVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSArDLQRLLaslkpgdtvtlTVLRGGKELTVTVT 268
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 410-463 6.40e-06

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: 50.30  E-value: 6.40e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 7657261     410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENI-QLSKAMEILRNNTHLSITV 463
Cdd:TIGR02037  363 GVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVaELRKVLARAKKGGRVALLI 417
PRK10942 PRK10942
serine endoprotease DegP;
410-459 7.35e-04

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 43.99  E-value: 7.35e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261    410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENI-QLSK---------AMEILRNNTHL 459
Cdd:PRK10942  409 GVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIaELRKildskpsvlALNIQRGDSSI 468
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 158-237 8.26e-04

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 39.90  E-value: 8.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     158 RAGTIVLNDGEELDSWSVILNGSVEV--TYPDGKAEILCM---GNSFGVSPTMDKEYMKGVMRTkVDDCQFVCIAQQDYC 232
Cdd:pfam00027    5 KAGEVIFREGDPADSLYIVLSGKVKVyrTLEDGREQILAVlgpGDFFGELALLGGEPRSATVVA-LTDSELLVIPREDFL 83


                   ....*
gi 7657261     233 RILNQ 237
Cdd:pfam00027   84 ELLER 88
 
Name Accession Description Interval E-value
RasGEF cd00155
Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of ...
 713-938 7.71e-84

Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors.


Pssm-ID: 238087 [Multi-domain]  Cd Length: 237  Bit Score: 274.51  E-value: 7.71e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   713 LLQLSTVEVATQLSMRNFELFRNIEPTEYIDDLFKLRSKT--SCANLKRFEEVINQETFWVASEILRETNQLKRMKIIKH 790
Cdd:cd00155    1 FLSLDPKELAEQLTLLDFELFRKIEPFELLGSLWSKKDKNihLSPNLERFIERFNNLSNWVASEILLCTNPKKRARLLSK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   791 FIKIALHCRECKNFNSMFAIISGLNLAPVARLRTTWEKLPNKYEKLFQDLQDLFDPSRNMAKYRNVLNSQNLQPPIIPLF 870
Cdd:cd00155   81 FIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEVLSSKLKKLFEELEELVDPSRNFKNYRKLLKSVGPNPPCVPFL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7657261   871 PVIKKDLTFLHEGNDSKVD-GLVNFEKLRMIAKEIRHVGRMASV--NMDPALMFRTRKKKWRSLGSLSQGS 938
Cdd:cd00155  161 GVYLKDLTFLHEGNPDFLEgNLVNFEKRRKIAEILREIRQLQSNsyELNRDEDILAFLWKLLELILNEDEL 231
RasGEF smart00147
Guanine nucleotide exchange factor for Ras-like small GTPases;
713-936 7.66e-83

Guanine nucleotide exchange factor for Ras-like small GTPases;


Pssm-ID: 214539  Cd Length: 242  Bit Score: 271.81  E-value: 7.66e-83
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      713 LLQLSTVEVATQLSMRNFELFRNIEPTEYIDDLFKLRSKTSCA--NLKRFEEVINQETFWVASEILRETNQLKRMKIIKH 790
Cdd:smart00147    1 LLLLDPKELAEQLTLLDFELFRKIDPSELLGSVWGKRSKKSPSplNLEAFIRRFNEVSNWVATEILKQTTPKDRAELLSK 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      791 FIKIALHCRECKNFNSMFAIISGLNLAPVARLRTTWEKLPNKYEKLFQDLQDLFDPSRNMAKYRNVLNSQNlQPPIIPLF 870
Cdd:smart00147   81 FIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEKLPSKYKKLFEELEELLSPERNYKNYREALSSCN-LPPCIPFL 159

                           170       180       190       200       210       220
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 7657261      871 PVIKKDLTFLHEGNDSKV-DGLVNFEKLRMIAKEIRHVGRMASVNMDPALMFRTRKKKWRSLGSLSQ 936
Cdd:smart00147  160 GVLLKDLTFIDEGNPDFLeNGLVNFEKRRQIAEILREIRQLQSQPYNLRPNRSDIQSLLQQLLDHLD 226
RasGEF pfam00617
RasGEF domain; Guanine nucleotide exchange factor for Ras-like small GTPases.
 720-898 1.12e-72

RasGEF domain; Guanine nucleotide exchange factor for Ras-like small GTPases.


Pssm-ID: 459872  Cd Length: 179  Bit Score: 240.19  E-value: 1.12e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     720 EVATQLSMRNFELFRNIEPTEYIDDLF-KLRSKTSCANLKRFEEVINQETFWVASEILRETNQLKRMKIIKHFIKIALHC 798
Cdd:pfam00617    1 ELARQLTLIEFELFRKIKPRELLGSAWsKKDKKENSPNIEAMIARFNKLSNWVASEILSEEDLKKRAKVIKKFIKIAEHC 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     799 RECKNFNSMFAIISGLNLAPVARLRTTWEKLPNKYEKLFQDLQDLFDPSRNMAKYRNVLnsQNLQPPIIPLFPVIKKDLT 878
Cdd:pfam00617   81 RELNNFNSLMAILSGLNSSPISRLKKTWELVSKKYKKTLEELEKLMSPSRNFKNYREAL--SSASPPCIPFLGLYLTDLT 158

                          170       180
                   ....*....|....*....|.
gi 7657261     879 FLHEGNDSKV-DGLVNFEKLR 898
Cdd:pfam00617  159 FIEEGNPDFLeGGLINFEKRR 179
PDZ_RapGEF2_RapGEF6-like cd06755
PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange ...
 384-466 7.72e-52

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: 176.69  E-value: 7.72e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   384 RLMTLTKPSREAPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITV 463
Cdd:cd06755    1 RTVTLTRPSRESPLHFSLLGGSEKGFGIFVSKVEKGSKAAEAGLKRGDQILEVNGQNFENITLKKALEILRNNTHLSITV 80


                 ...
gi 7657261   464 KTN 466
Cdd:cd06755   81 KTN 83
RA_PDZ-GEF1 cd01785
Ras-associating (RA) domain found in PDZ domain-containing guanine nucleotide exchange factor ...
 608-690 1.30e-45

Ras-associating (RA) domain found in PDZ domain-containing guanine nucleotide exchange factor 1 (PDZ-GEF1) and similar proteins; PDZ-GEF1, also termed Rap guanine nucleotide exchange factor 2, or cyclic nucleotide ras GEF (CNrasGEF), or neural RAP guanine nucleotide exchange protein (nRap GEP), or Ras/Rap1-associating GEF-1 (RA-GEF-1), is a Rap-specific guanine nucleotide exchange factor (GEF) that has a PSD-95/DlgA/ZO-1 (PDZ) domain, a RA domain and a region related to a cyclic nucleotide binding domain (RCBD). The RA domain of PDZ-GEF interacts with Rap1 and also contributes to the membrane localization of PDZ-GEF. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and involve in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes.


Pssm-ID: 340483  Cd Length: 85  Bit Score: 159.01  E-value: 1.30e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   608 QVLRVFKADQQSRYIMISKDTTAKEVVIQAIREFAVTAT--PDQYSLCEVSVTPEGVIKQRRLPDQLSKLADRIQLSGRY 685
Cdd:cd01785    1 QVLKVYRADQSSKYILIHKETTAREVVMLALREFGITDDenSDNYSLCEVTVTPEGLIKQRRLPDQLSNLANRISLNGRY 80


                 ....*
gi 7657261   686 YLKNN 690
Cdd:cd01785   81 YLKNN 85
RasGEFN smart00229
Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif; A subset of guanine ...
 267-380 3.46e-29

Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif; A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).


Pssm-ID: 214571  Cd Length: 127  Bit Score: 113.58  E-value: 3.46e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      267 KGHIVIKGTSERLTMHLVEEHSVVDPTFIEDFLLTYRTFLSSPMEVGKKLLEWFNDPS------------LRDKVTRVVL 334
Cdd:smart00229    1 DGGLIKGGTLEALIEHLTEAFDKADPSFVETFLLTYRSFITTQELLQLLLYRYNAIPPeswveekvnprrVKNRVLNILR 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 7657261      335 LWVNNHFNDFEGDPAMTRFLEEFENNLEREKM-GGHLRLLNIACAAK 380
Cdd:smart00229   81 TWVENYWEDFEDDPKLISFLLEFLELVDDEKYpGLVTSLLNLLRRLS 127
REM cd06224
Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also ...
 275-380 8.58e-22

Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.


Pssm-ID: 100121  Cd Length: 122  Bit Score: 92.09  E-value: 8.58e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   275 TSERLTMHLVEEHSVVDPTFIEDFLLTYRTFLsSPMEVGKKLLEWFNDP----------------SLRDKVTRVVLLWVN 338
Cdd:cd06224    1 TLEALIEHLTSTFDMPDPSFVSTFLLTYRSFT-TPTELLEKLIERYEIAppenleyndwdkkkskPIRLRVLNVLRTWVE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 7657261   339 NHFNDFEGDPAMTRFLEEFENNLEREKMGGHLRLLNIACAAK 380
Cdd:cd06224   80 NYPYDFFDDEELLELLEEFLNRLVQEGALLQELKKLLRKLLK 121
PDZ2_PDZD7-like cd10834
PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related ...
 383-464 2.08e-21

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: 89.75  E-value: 2.08e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   383 RRLMTLTKPSREAPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSIT 462
Cdd:cd10834    1 RRIVHLYTTSDDYCLGFNIRGGSEYGLGIYVSKVDPGGLAEQNGIKVGDQILAVNGVSFEDITHSKAVEVLKSQTHLMLT 80


                 ..
gi 7657261   463 VK 464
Cdd:cd10834   81 IK 82
PDZ2_FL-whirlin cd06741
PDZ domain 2 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 ...
 403-464 7.87e-21

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: 88.09  E-value: 7.87e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 7657261   403 GGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITVK 464
Cdd:cd06741   20 GGAEYGLGIYVTGVDPGSVAENAGLKVGDQILEVNGRSFLDITHDEAVKILKSSKHLIMTVK 81
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
 387-464 2.59e-18

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: 80.66  E-value: 2.59e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   387 TLTKPSREaPLPFILLGGSEKGFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRNNT-HLSITVK 464
Cdd:cd00136    3 TLEKDPGG-GLGFSIRGGKDGGGGIFVSRVEPGGPAARDGrLRVGDRILEVNGVSLEGLTHEEAVELLKSAGgEVTLTVR 81
PDZ_PDZD11-like cd06752
PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic ...
 384-464 5.75e-18

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: 80.05  E-value: 5.75e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   384 RLMTLTKPSREaPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITV 463
Cdd:cd06752    1 RTVVLKRPPGE-QLGFNIRGGKASGLGIFISKVIPDSDAHRLGLKEGDQILSVNGVDFEDIEHSEAVKVLKTAREIQMRV 79


                 .
gi 7657261   464 K 464
Cdd:cd06752   80 R 80
PDZ1_PDZD7-like cd10833
PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related ...
 392-464 1.22e-17

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: 79.01  E-value: 1.22e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 7657261   392 SREAPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITVK 464
Cdd:cd10833    9 SPDGSLGFSVRGGSEHGLGIFVSKVEEGSAAERAGLCVGDKITEVNGVSLENITMSSAVKVLTGSNRLRMVVR 81
RasGEF_N pfam00618
RasGEF N-terminal motif; A subset of guanine nucleotide exchange factor for Ras-like small ...
 270-357 2.14e-17

RasGEF N-terminal motif; A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this motif/domain N-terminal to the RasGef (Cdc25-like) domain.


Pssm-ID: 459873  Cd Length: 104  Bit Score: 78.89  E-value: 2.14e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     270 IVIKGTSERLTMHLVEEHSVVDPTFIEDFLLTYRTFLsSPMEVGKKLLEWFNDPSLRD-----------------KVTRV 332
Cdd:pfam00618    1 QVKAGTLEKLVEYLTSTRIMLDDSFLSTFLLTYRSFT-TPAELLELLIERYNIPPPLDlssdsywiskktlpiriRVLSV 79

                           90       100
                   ....*....|....*....|....*
gi 7657261     333 VLLWVNNHFNDFEGDPAMTRFLEEF 357
Cdd:pfam00618   80 LRHWVENYFSDFNDDPVLLSRLEKF 104
RA smart00314
Ras association (RalGDS/AF-6) domain; RasGTP effectors (in cases of AF6, canoe and RalGDS); ...
 608-690 4.59e-16

Ras association (RalGDS/AF-6) domain; RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.)


Pssm-ID: 214612  Cd Length: 90  Bit Score: 74.64  E-value: 4.59e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      608 QVLRVFKAD---QQSRYIMISKDTTAKEVVIQAIREFAVTATPDQYSLCEV-SVTPEGVIKQRRLPDQLSKLADRIQLSG 683
Cdd:smart00314    3 FVLRVYVDDlpgGTYKTLRVSSRTTARDVIQQLLEKFHLTDDPEEYVLVEVlPDGKERVLPDDENPLQLQKLWPRRGPNL 82


                    ....*..
gi 7657261      684 RYYLKNN 690
Cdd:smart00314   83 RFVLRKR 89
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
 382-464 3.79e-15

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: 72.03  E-value: 3.79e-15
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      382 KRRLMTLTKpsREAPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNN-THLS 460
Cdd:smart00228    1 EPRLVELEK--GGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAgGKVT 78


                    ....
gi 7657261      461 ITVK 464
Cdd:smart00228   79 LTVL 82
PDZ1_FL-whirlin cd06740
PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 ...
 383-464 4.66e-15

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: 71.63  E-value: 4.66e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   383 RRLMTLTKPSREAPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSIT 462
Cdd:cd06740    1 VRQVTLKRSKSHEGLGFSIRGGAEHGVGIYVSLVEPGSLAEKEGLRVGDQILRVNDVSFEKVTHAEAVKILRVSKKLVLS 80


                 ..
gi 7657261   463 VK 464
Cdd:cd06740   81 VR 82
RA cd17043
Ras-associating (RA) domain, structurally similar to a beta-grasp ubiquitin-like fold; RA ...
 609-689 3.75e-14

Ras-associating (RA) domain, structurally similar to a beta-grasp ubiquitin-like fold; RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in various functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub); Ub is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. RA-containing proteins include RalGDS, AF6, RIN, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.


Pssm-ID: 340563  Cd Length: 87  Bit Score: 69.27  E-value: 3.75e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   609 VLRVFKAD----QQSRYIMISKDTTAKEVVIQAIREFAVTATPDQYSLCEVSvtpEGVIKQRRLPD-----QLSKLADRI 679
Cdd:cd17043    1 VLKVYDDDlapgSAYKSILVSSTTTAREVVQLLLEKYGLEEDPEDYSLYEVS---EKQETERVLHDdecplLIQLEWGPQ 77

                         90
                 ....*....|
gi 7657261   680 QLSGRYYLKN 689
Cdd:cd17043   78 GTEFRFVLKR 87
PDZ2_harmonin cd06738
PDZ domain 2 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic ...
 400-464 4.19e-14

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: 68.89  E-value: 4.19e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 7657261   400 ILLGGSEKGfGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITVK 464
Cdd:cd06738   19 ISSGPTQKP-GIFISNVKPGSLAEEVGLEVGDQIVEVNGTSFTNVDHKEAVMALKSSRHLTITVR 82
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 136-251 4.57e-14

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 70.12  E-value: 4.57e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261      136 FANMTMSVRRELCAVMvFAVVERAGTIVLNDGEELDSWSVILNGSVEVTY--PDGKAEILCM---GNSFGVSPTMDkeYM 210
Cdd:smart00100    2 FKNLDAEELRELADAL-EPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKvlEDGEEQIVGTlgpGDFFGELALLT--NS 78

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 7657261      211 KGVMRTKVDDCQFVCIAQQDYCRILNQVEKNMQKVEEEGEI 251
Cdd:smart00100   79 RRAASAAAVALELATLLRIDFRDFLQLLPELPQLLLELLLE 119
RA pfam00788
Ras association (RalGDS/AF-6) domain; RasGTP effectors (in cases of AF6, canoe and RalGDS); ...
 606-691 1.58e-12

Ras association (RalGDS/AF-6) domain; RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Recent evidence (not yet in MEDLINE) shows that some RA domains do NOT bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase.


Pssm-ID: 425871  Cd Length: 93  Bit Score: 64.66  E-value: 1.58e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     606 PDQVLRVF----KADQQSRYIMISKDTTAKEVVIQAIREFAVTATPDQYSLCEVSvtpEGVIKQRRLPDQLSKLADRIQL 681
Cdd:pfam00788    1 DDGVLKVYtedgKPGTTYKTILVSSSTTAEEVIEALLEKFGLEDDPRDYVLVEVL---ERGGGERRLPDDECPLQIQLQW 77

                           90
                   ....*....|....*
gi 7657261     682 -----SGRYYLKNNM 691
Cdd:pfam00788   78 prdasDSRFLLRKRD 92
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 135-245 6.36e-11

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 60.80  E-value: 6.36e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   135 AFANMTMSVRRELCAVMVFAVVErAGTIVLNDGEELDSWSVILNGSVEVTY--PDGKAEILCM---GNSFGVSPTMDKEY 209
Cdd:cd00038    1 LFSGLDDEELEELADALEERRFP-AGEVIIRQGDPADSLYIVLSGSVEVYKldEDGREQIVGFlgpGDLFGELALLGNGP 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 7657261   210 MKGVMRTKvDDCQFVCIAQQDYCRILNQVEKNMQKV 245
Cdd:cd00038   80 RSATVRAL-TDSELLVLPRSDFRRLLQEYPELARRL 114
PDZ3_DLG5-like cd06767
PDZ domain 3 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density ...
 384-464 2.02e-10

PDZ domain 3 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. 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 Dlg5-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: 467248 [Multi-domain]  Cd Length: 82  Bit Score: 58.49  E-value: 2.02e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   384 RLMTLTKPSReaPLPFILLGGseKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRnNTHLSITV 463
Cdd:cd06767    4 RHVSIEKGSE--PLGISIVSG--ENGGIFVSSVTEGSLAHQAGLEYGDQLLEVNGINLRNATEQQAALILR-QCGDTITM 78


                 .
gi 7657261   464 K 464
Cdd:cd06767   79 L 79
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
 385-464 3.41e-10

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 57.68  E-value: 3.41e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     385 LMTLTKPSREaPLPFILLGGSEKGF-GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN-NTHLSIT 462
Cdd:pfam00595    1 QVTLEKDGRG-GLGFSLKGGSDQGDpGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGsGGKVTLT 79


                   ..
gi 7657261     463 VK 464
Cdd:pfam00595   80 IL 81
PDZ1_harmonin cd06737
PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic ...
 382-465 5.13e-10

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: 57.27  E-value: 5.13e-10
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gi 7657261   382 KRRLMTLTKPSREaPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSI 461
Cdd:cd06737    1 KLRLVRLDRRGPE-SLGFSVRGGLEHGCGLFVSHVSPGSQADNKGLRVGDEIVRINGYSISQCTHEEVINLIKTKKTVSL 79


                 ....
gi 7657261   462 TVKT 465
Cdd:cd06737   80 KVRH 83
PDZ5_DrPTPN13-like cd23060
PDZ domain 5 of Danio rerio tyrosine-protein phosphatase non-receptor type 13 (Ptpn13) and ...
 386-454 4.21e-09

PDZ domain 5 of Danio rerio tyrosine-protein 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 Danio rerio Ptpn13, and related domains. Protein-tyrosine phosphatases (PTPs) dephosphorylate phosphotyrosyl residues in proteins that are phosphorylated by protein tyrosine kinases (PTKs). Danio rerio Ptpn13 is a classical non-receptor-like PTP. 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 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: 467273 [Multi-domain]  Cd Length: 80  Bit Score: 54.66  E-value: 4.21e-09
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gi 7657261   386 MTLTKPSREApLPFILLGGsEKGFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILR 454
Cdd:cd23060    2 IELEKPANGG-LGFSLVGG-EGGSGIFVKSISPGGVADRDGrLQVGDRLLQVNGESVIGLSHSKAVNILR 69
PDZ3_Dlg1-2-4-like cd06795
PDZ domain 3 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg) ...
 384-455 7.34e-09

PDZ domain 3 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila Dlg1, human Dlg1, 2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197; SAP-97), Dlg2 (also known as channel-associated protein of synapse-110; postsynaptic density protein 93, PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95; synapse-associated protein 90, SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling, regulating surface expression of NMDA receptors in dorsal horn neurons of the spinal cord; it interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. The Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development; postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two 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 Dlg-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: 467257 [Multi-domain]  Cd Length: 91  Bit Score: 54.28  E-value: 7.34e-09
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gi 7657261   384 RLMTLTKPSreAPLPFILLGGsEKGFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06795    3 RKIVLHKGS--TGLGFNIVGG-EDGEGIFISFILAGGPADLSGeLRRGDQILSVNGVDLRNATHEQAAAALKN 72
PDZ1_PTPN13_FRMPD2-like cd06694
PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13),FERM and PDZ ...
 385-457 1.55e-08

PDZ domain 1 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 1 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. 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. 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 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: 467180 [Multi-domain]  Cd Length: 92  Bit Score: 53.55  E-value: 1.55e-08
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gi 7657261   385 LMTLTKPSREApLPFILLGGSEKG---FGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRNNT 457
Cdd:cd06694    4 IVTLKKDPQKG-LGFTIVGGENSGsldLGIFVKSIIPGGPADKDGrIKPGDRIIAINGQSLEGKTHHAAVEIIQNAP 79
PDZ_SYNPO2-like cd10820
PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related ...
 395-464 1.74e-08

PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNPO2, SYNPO2L, and related domains. SYNPO2 (also known as genethonin-2, myopodin) is a cytoskeleton adaptor protein. It participates in chaperone-assisted selective autophagy (CASA), a mechanism for the disposal of misfolded and damaged proteins and provides a link between the CASA chaperone complex and a membrane-tethering and fusion machinery that generates autophagosome membranes. The SYNPO2 PPxY motif binds CASA cochaperone BCL2-associated athanogene 3 (BAG3) and the SYNPO2 PDZ domain binds vacuolar protein sorting 18 homolog (VPS18). There are three isoforms of SYNPO2, which possess an amino-terminal PDZ domain (SYNPO2a, b, c); the short isoform SYNPO2d, lacks the PDZ domain. 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 SYNPO2-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: 467264 [Multi-domain]  Cd Length: 78  Bit Score: 52.70  E-value: 1.74e-08
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gi 7657261   395 APLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTH-LSITVK 464
Cdd:cd10820    8 APWGFRLQGGSEQKKPLQVAKIRKKSKAALAGLCEGDELLSINGKPCADLSHSEAMDLIDSSGDtLQLLIK 78
PDZ_Lin-7-like cd06796
PDZ domain of protein Lin-7 and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), ...
 384-455 2.86e-08

PDZ domain of protein Lin-7 and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Lin-7 (also known as LIN-7 or LIN7), and related domains. Lin-7 targets and organize protein complexes to epithelial and synaptic plasma membranes. There are three mammalian Lin-7 homologs: Lin-7A (protein lin-7 homolog A, also known as mammalian lin-seven protein 1 (MALS-1), vertebrate lin-7 homolog 1 (Veli-1), tax interaction protein 33); Lin-7B (also known as MALS-2, Veli-2); and Lin-7C (also known as MALS-3, Veli-3). Lin-7 is involved in localization of the Let-23 growth factor receptor to the basolateral membrane of epithelial cells, in tight junction localization of insulin receptor substrate p53 (IRSp53), in retaining gamma-aminobutyric (GABA) transporter (BGT-1) at the basolateral surface of epithelial cells, and in regulating recruitment of neurotransmitter receptors to the postsynaptic density (PSD). The Lin7 PDZ domain binds Let-23, BGT and beta-catenin, and NMDA (N-methyl-D-aspartate) receptor NR2B. Lin-7 also binds to the PDZ binding motif located in the C-terminal tail of Rhotekin, an effector protein for small GTPase Rho. 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 Lin-7-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: 467258 [Multi-domain]  Cd Length: 86  Bit Score: 52.44  E-value: 2.86e-08
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gi 7657261   384 RLMTLTKPsrEAPLPFILLGGSEKGFGIFVDSVDSGSKA-TEAGLKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06796    3 RVVELPKT--EEGLGFNVMGGKEQNSPIYISRIIPGGVAdRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKA 73
PDZ3_ZO1-like_domain cd06729
PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ ...
 401-444 2.98e-08

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: 52.18  E-value: 2.98e-08
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gi 7657261   401 LLGGSEkgFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENI 444
Cdd:cd06729   17 LAGGND--VGIFVAGVQEGSPAEKQGLQEGDQILKVNGVDFRNL 58
PDZ1_GgSTXBP4-like cd06692
PDZ1 domain of Gallus gallus uncharacterized syntaxin-binding protein 4 (STXBP4) isoform X1, ...
 405-455 3.41e-08

PDZ1 domain of Gallus gallus uncharacterized syntaxin-binding protein 4 (STXBP4) isoform X1, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Gallus gallus uncharacterized syntaxin-binding protein 4 (STXBP4) isoform X1, and related domains. Gallus gallus STXBP4 isoform X1 contains 2 PDZ domains (PDZ1 and PDZ2). 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 STXBP4-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: 467179 [Multi-domain]  Cd Length: 88  Bit Score: 52.22  E-value: 3.41e-08
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gi 7657261   405 SEKGFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06692   22 TGEEFGIFIKRILPGGLAATDGrLKEGDLILEVNGESLQGVTNERAVSILRS 73
PDZ_SYNJ2BP-like cd06709
PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 ...
 397-455 3.89e-08

PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNJ2BP, and related domains. SYNJ2BP (also known as mitochondrial outer membrane protein 25, OMP25) regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction. Binding partners of the SYNJ2BP PDZ domain include activin type II receptors (ActR-II), and SYNJ2. SYNJ2BP interacts with the PDZ binding motif of the Notch Delta-like ligand 1 (DLL1) and DLL4, promoting Delta-Notch signaling, and inhibiting sprouting angiogenesis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNJ2BP-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467193 [Multi-domain]  Cd Length: 86  Bit Score: 51.91  E-value: 3.89e-08
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gi 7657261   397 LPFILLGGSEKGF-----GIFVDSV-DSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06709   12 LGFNIVGGTDQPYipndsGIYVAKIkEDGAAAIDGRLQEGDKILEINGQSLENLTHQDAVELFRN 76
PDZ_PDLIM-like cd06753
PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 387-464 5.65e-08

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: 51.38  E-value: 5.65e-08
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gi 7657261   387 TLTKPsreAPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNT-HLSITVK 464
Cdd:cd06753    3 TLSGP---APWGFRLQGGKDFNQPLTISRVTPGGKAAQANLRPGDVILAINGESTEGMTHLEAQNKIKAATgSLSLTLE 78
PDZ2-PTPN13_FRMPD2-like cd06792
PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and ...
 410-463 9.50e-08

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: 51.06  E-value: 9.50e-08
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gi 7657261   410 GIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITV 463
Cdd:cd06792   30 GIYVKSLVPGGAAEQDGrIQKGDRLLEVNGVSLEGVTHKQAVECLKNAGQVVTLV 84
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
 412-464 1.57e-07

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 49.45  E-value: 1.57e-07
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gi 7657261     412 FVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQlsKAMEILRNNTHLSITVK 464
Cdd:pfam17820    1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLE--DVARLLQGSAGESVTLT 51
PDZ_NHERF-like cd06768
PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related ...
 405-463 1.74e-07

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: 50.13  E-value: 1.74e-07
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gi 7657261   405 SEKGF-GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNT-HLSITV 463
Cdd:cd06768   18 AEKGRpGHFIREVDPGSPAERAGLKDGDRLVEVNGENVEGESHEQVVEKIKASGnQVTLLV 78
PDZ1_syntenin-like cd06721
PDZ domain 1 of syntenin-1, syntenin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 410-463 2.11e-07

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: 49.92  E-value: 2.11e-07
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gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITV 463
Cdd:cd06721   23 GVFVQLVQANSPAALAGLRFGDQILQINGENVAGWSSDKAHKVLKKASPERITL 76
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
 410-464 2.29e-07

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: 49.93  E-value: 2.29e-07
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gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQ------NFENIQLSK----AMEILRNNTHLSITVK 464
Cdd:cd23084   19 GVVVTEVDPGSPAAQSGLKKGDVIIGVNRQpvksiaELRKVLKSKpsavLLQIKRGDSSRYLALP 83
PDZ_ZASP52-like cd23068
PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), ...
 388-464 2.30e-07

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: 49.83  E-value: 2.30e-07
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gi 7657261   388 LTKPSREAPLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKA-MEILRNNTHLSITVK 464
Cdd:cd23068    4 LRRDDSNTPWGFRLQGGADFGQPLSIQKVNPGSPADKAGLRRGDVILRINGTDTSNLTHKQAqDLIKRAGNDLQLTVQ 81
PDZ13_MUPP1-like cd06676
PDZ domain 13 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 ...
 397-463 2.68e-07

PDZ domain 13 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 13 of MUPP1. 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. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ13 domain is therefore absent from PATJ. 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). 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 PDZ13 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: 467164 [Multi-domain]  Cd Length: 83  Bit Score: 49.65  E-value: 2.68e-07
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gi 7657261   397 LPFILLGG---SEKGFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN-NTHLSITV 463
Cdd:cd06676   11 LGFSIVGGfgsPHGDLPIYVKTVFEKGAAAEDGrLKRGDQILAVNGESLEGVTHEEAVNILKKtKGTVTLTV 82
PDZ1_L-delphilin-like cd06743
PDZ domain 1 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 ...
 408-440 3.49e-07

PDZ domain 1 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of delphilin (also known as glutamate receptor, ionotropic, delta 2-interacting protein 1, L-delphilin). Delphilin, a postsynaptic protein which is selectively expressed at cerebellar Purkinje cells, links the glutamate receptor delta 2 subunit (GluRdelta2) with the actin cytoskeleton and various signaling molecules. Two alternatively spliced isoforms of delphilin have been characterized: L-delphilin has two PDZ domains, PDZ1 and PDZ2, and S-delphilin has a single PDZ domain (PDZ2). These two isoforms are differently palmitoylated and may be involved in controlling GluRdelta2 signaling in Purkinje cells. 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 delphilin-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: 467225 [Multi-domain]  Cd Length: 76  Bit Score: 49.20  E-value: 3.49e-07
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gi 7657261   408 GFGI------FVDSVDSGSKATEAGLKRGDQILEVNGQN 440
Cdd:cd06743   12 GFSIggsgpcYILSVEEGSSAHAAGLQPGDQILELDGQD 50
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
 410-463 4.18e-07

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: 49.40  E-value: 4.18e-07
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gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFEN-------IQLSKA-----MEILRNNTHLSITV 463
Cdd:cd10839   26 GALVAQVLPDSPAAKAGLKAGDVILSLNGKPITSsadlrnrVATTKPgtkveLKILRDGKEKTLTV 91
PDZ4_PDZD2-PDZ2_hPro-IL-16-like cd06760
PDZ domain 4 of PDZ domain containing 2 (PDZD2), PDZ domain 2 of human pro-interleukin-16 ...
 410-453 6.95e-07

PDZ domain 4 of PDZ domain containing 2 (PDZD2), PDZ domain 2 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 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. PDZD2 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. This family also includes the second PDZ domain (PDZ2) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers 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 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: 467241 [Multi-domain]  Cd Length: 90  Bit Score: 48.81  E-value: 6.95e-07
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gi 7657261   410 GIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEIL 453
Cdd:cd06760   32 GIFIHHLSPGSVAHMDGrLRRGDQILEINGTSLRNVTLNEAYAIL 76
PDZ1_Scribble-like cd06704
PDZ domain 1 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...
 410-455 1.15e-06

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


Pssm-ID: 467188 [Multi-domain]  Cd Length: 87  Bit Score: 48.04  E-value: 1.15e-06
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gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06704   31 GIFISRVTEGGPAAKAGVRVGDKLLEVNGVDLVDADHHEAVEALKN 76
PDZ_densin_erbin-like cd06749
PDZ domain of densin, erbin, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95) ...
 410-458 1.41e-06

PDZ domain of densin, erbin, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of densin, erbin, and related domains. Densin (also known as leucine-rich repeat-containing protein 7, LRRC7, densin-180, protein LAP1) and erbin (also known as densin-180-like protein, Erbb2-interacting protein, protein LAP2) belong to the LAP (leucine-rich repeat and PDZ domain) family of scaffolding proteins that play roles in the maintenance of cell shape and apical-basal polarity. Densin and erbin are components of the excitatory postsynaptic compartment and are regulators of dendritic morphology and postsynaptic structure. The densin PDZ domain binds CaV1.3 alpha1 subunit, delta-catenin, and MAGUIN-1. Binding partners of the erbin PDZ domain include ErbB receptor tyrosine kinase ErbB2, HTLV-1 Tax1, Cav1.3 Ca2+channels, and constituents of the cadherin:catenin cell adhesion complex, in particular delta-catenin, p0071 and ARVCF. The erbin PDZ domain binds Smad3, a transductor of the TGFbeta pathway, possibly by a novel interface of binding. Erbin and two other LAP proteins (scribble and lano) redundantly regulate epithelial polarity and apical adhesion 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 densin and erbin-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: 467231 [Multi-domain]  Cd Length: 87  Bit Score: 47.71  E-value: 1.41e-06
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gi 7657261   410 GIFVDSVDSGSKATEAgLKRGDQILEVNGQNFENIQLSKAMEILRNNTH 458
Cdd:cd06749   32 GIFVTKVQPDGPASKL-LQPGDKILEVNGYDFVNIEHGQAVSLLKSFQN 79
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
 410-464 2.64e-06

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: 50.92  E-value: 2.64e-06
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gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENI-QLSKAM-----------EILRNNTHLSITVK 464
Cdd:COG0265  202 GVLVARVEPGSPAAKAGLRPGDVILAVDGKPVTSArDLQRLLaslkpgdtvtlTVLRGGKELTVTVT 268
PDZ_SHANK1_3-like cd06746
PDZ domain of SH3 and multiple ankyrin repeat domains protein 1 (SHANK1), SHANK2, SHANK3, and ...
 412-465 2.75e-06

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: 47.20  E-value: 2.75e-06
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gi 7657261   412 FVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN-NTHLSITVKT 465
Cdd:cd06746   45 YLESVDPGGVADKAGLKKGDFLLEINGEDVVKASHEQVVNLIRQsGNTLVLKVVT 99
PDZ_TAX1BP3-like cd10822
PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic ...
 410-457 3.44e-06

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: 46.95  E-value: 3.44e-06
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                 ....*....|....*....|....*....|....*....|....*...
gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNT 457
Cdd:cd10822   38 GIYVTRVSEGGPAEKAGLQVGDKILQVNGWDMTMVTHKQAVKRLTKKK 85
PDZ2_PDZD2-like cd06758
PDZ domain 2 of PDZ domain containing 2 (PDZD2), and related domains; PDZ (PSD-95 ...
 404-455 3.92e-06

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: 46.58  E-value: 3.92e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 7657261   404 GSEKG-FGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06758   23 GSKRGdIGIFVAGVEEGGSADRDGrLKKGDELLMINGQSLIGLSHQEAVAILRS 76
PDZ_Par6-like cd06718
PDZ domain of partitioning defective 6 (Par6), Drosophila Rho GTPase-activating protein 100F ...
 404-465 3.93e-06

PDZ domain of partitioning defective 6 (Par6), Drosophila Rho GTPase-activating protein 100F (RhoGAP100F), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Par6 (also known as PAR6 or Par-6), RhoGAP100F, and related domains. Par6 is part of a conserved machinery that directs metazoan cell polarity, a process necessary for the function of diverse cell types. Par6 forms a cell polarity-regulatory complex with atypical protein kinase C (aPKC) and Par3. Par6 can also directly associate with PALS1 (proteins associated with Lin7, also known as Stardust) providing a link between the Par3/aPKC/Par6 complex and the PALS1-PATJ (protein-associated TJ) complex. Binding partners of the Par6-PDZ domain include Par3, PALS1/Stardust; leucine-rich repeat-containing protein netrin-G ligand-2 (NGL-2), human crumbs (CRB3) involve in the morphogenesis of the tight junctions in mammalian epithelial cells, and PAR-6 co-operates with the Par6 semi-CRIB domain to bind CDC42. CDC42 regulates the Par6 PDZ domain through an allosteric CRIB-PDZ transition. Drosophila RhoGAP100F, also known as synapse defective protein 1 homolog (syd-1 homolog), is a GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound form. The RhoGAP100F-PDZ domain binds the neurexin C terminus to control synapse formation at the Drosophila neuromuscular junction. 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 Par6-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: 467202 [Multi-domain]  Cd Length: 84  Bit Score: 46.41  E-value: 3.93e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 7657261   404 GSEKGFGIFVDSVDSGSKATEAGLKR-GDQILEVNGQNFENIQLSKAMEILRNNTHLSITVKT 465
Cdd:cd06718   22 GVERVPGIFISRLVLGSLADSTGLLAvGDEILEVNGVEVTGKSLDDVTDMMVAPTRLIITVKP 84
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
 410-463 4.81e-06

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Deg/HtrA-type serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. Typically, these proteases have an N-terminal serine protease domain and at least one C-terminal PDZ domain that recognizes substrates, and in some cases activates the protease function. An exception is yeast Nma11p which has two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. HtrA-type proteases include the human HtrA1-4 and MBTPS2, tricorn protease, DegS, DegP and C-terminal processing peptidase, cyanobacterial serine proteases Hhoa, HhoB, and HtrA, and yeast Nma11p. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-termini of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This Deg/HtrA family PDZ domain is a circularly permuted PDZ domain which places beta-strand A at the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467621 [Multi-domain]  Cd Length: 91  Bit Score: 46.13  E-value: 4.81e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQ---NFENIQ--LSKA-------MEILRNNTHLSITV 463
Cdd:cd06779   26 GVLVAEVIPGSPAAKAGLKEGDVILSVNGKpvtSFNDLRaaLDTKkpgdslnLTILRDGKTLTVTV 91
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
 413-467 4.81e-06

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 50.47  E-value: 4.81e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 7657261   413 VDSVDSGSKATEAGLKRGDQILEVNGQNFENI-QLSKA----------MEILRNNTHLSITVKTNL 467
Cdd:COG0750  132 VGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWdDLVDIiraspgkpltLTVERDGEELTLTVTPRL 197
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 410-463 6.40e-06

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: 50.30  E-value: 6.40e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 7657261     410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENI-QLSKAMEILRNNTHLSITV 463
Cdd:TIGR02037  363 GVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVaELRKVLARAKKGGRVALLI 417
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 410-464 8.68e-06

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: 49.48  E-value: 8.68e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN--NTHLSITVK 464
Cdd:COG0793   72 KVVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAVKLLRGkaGTKVTLTIK 128
PDZ3_PDZD2-PDZ1_hPro-IL-16-like cd06759
PDZ domain 3 of PDZ domain containing 2 (PDZD2), PDZ domain 1 of human pro-interleukin-16 ...
 387-471 9.61e-06

PDZ domain 3 of PDZ domain containing 2 (PDZD2), PDZ domain 1 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 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. PDZD2 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. This family also includes the first PDZ domain (PDZ1) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. 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 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: 467240 [Multi-domain]  Cd Length: 87  Bit Score: 45.34  E-value: 9.61e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   387 TLTKPSREAPLPFILLGG--SEKG-FGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRNnthlsit 462
Cdd:cd06759    4 VLMKGAGGKGLGFSIVGGrdSPRGpMGIYVKTIFPGGAAAEDGrLKEGDEILEVNGESLQGLTHQEAIQKFKQ------- 76


                 ....*....
gi 7657261   463 VKTNLFVFK 471
Cdd:cd06759   77 IKKGLVVLT 85
PDZ3_MUPP1-like cd06791
PDZ domain 3 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) ...
 399-455 1.06e-05

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: 45.30  E-value: 1.06e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 7657261   399 FILLGGSEKGFGIFVDSVDSGSKATEAGLKR-GDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06791   21 YVGEKASGELSGIFVKSIIPGSAADQDGRIQvNDQIIAVDGVNLQGFTNQEAVEVLRN 78
PDZ3_Par3-like cd23059
PDZ domain 3 of partitioning defective 3 (Par3), and related domains; PDZ (PSD-95 ...
 403-455 1.39e-05

PDZ domain 3 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 3 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP, Drosophila Bazooka) and related domains. 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 Par-3 and the Par complex include Par3 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 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: 467272 [Multi-domain]  Cd Length: 103  Bit Score: 45.35  E-value: 1.39e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 7657261   403 GGSEKGFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd23059   31 NGGKADLGIFIKSIIHGGAASKDGrLRVNDQLIAVNGESLLGLTNSEAMETLRR 84
PDZ_CARD11_CARD14-like cd06736
PDZ domain of caspase recruitment domain-containing protein 11 (CARD11), CARD14, and related ...
 401-438 1.63e-05

PDZ domain of caspase recruitment domain-containing protein 11 (CARD11), CARD14, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CARD11, CARD14, and related domains. CARD11 (also known as CARD-containing MAGUK protein 1, CARMA1, Bimp3) and CARD14 (also known as CARD-containing MAGUK protein 2, CARMA2, Bimp2) belong to the CARD-containing membrane-associated guanylate kinase (MAGUK) protein family. They play several crucial biological functions, including regulation of immune response and inflammation. The CARD11-Bcl10-MALT1 (CBM) complex bridges T cell receptor signaling to the canonical IkappaB kinase (IKK)/NF-kappaB pathway. CARD14 can form an analogous biochemical complex to activate NF-kappaB during specialized immunity. The CBM complex of CARD14/CARMA2 may bind with TRAF6 and get involved in IL-17 pathways in keratinocytes. The preponderance of protein interactions occurs through the N-terminal half of CARD11 that includes the CARD, LATCH, and coiled-coil domains; the C-terminal PDZ-SH3-MAGUK region binds the adhesion and degranulation-promoting adapter protein (ADAP) and aryl hydrocarbon receptor interacting protein (AIP). 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 CARD11 and CARD14-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: 467218 [Multi-domain]  Cd Length: 75  Bit Score: 44.18  E-value: 1.63e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 7657261   401 LLGGSEKGfgIFVDSVDSGSKATEAGLKRGDQILEVNG 438
Cdd:cd06736   15 IIGGNRTG--IFIHSVQPGSAAEKAGLREGTQLLLLEG 50
PDZ2_DLG5-like cd06765
PDZ domain 2 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density ...
 410-457 1.67e-05

PDZ domain 2 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. 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 Dlg5-like family PSZ2 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: 467246 [Multi-domain]  Cd Length: 77  Bit Score: 44.26  E-value: 1.67e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 7657261   410 GIFVDSVDSGSK-ATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNT 457
Cdd:cd06765   17 GVFISRIVPGSPaAKEGSLTVGDRIIAINGIALDNKSLSECEALLRSCR 65
PDZ10_MUPP1-PDZ8_PATJ-like cd06673
PDZ domain 10 of multi-PDZ-domain protein 1 (MUPP1), domain 8 of PATJ (protein-associated ...
 401-455 2.15e-05

PDZ domain 10 of multi-PDZ-domain protein 1 (MUPP1), domain 8 of PATJ (protein-associated tight junction) and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 10 of MUPP1, PDZ domain 8 of 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 PDZ10 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: 467161 [Multi-domain]  Cd Length: 86  Bit Score: 44.20  E-value: 2.15e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 7657261   401 LLGGSEKGFG-IFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06673   19 IVGGSDTLLGaIIIHEVYEDGAAAKDGrLWAGDQILEVNGEDLRKATHDEAINVLRQ 75
cpPDZ_HhoA-like cd10838
circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, ...
 384-465 2.18e-05

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: 45.00  E-value: 2.18e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   384 RLMTLTkPS------REAPLPFILlggsEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFEN-------IQLSK-- 448
Cdd:cd10838    7 QMTTLT-PElaqqnnRNPNSPVRI----PEVDGVLIMQVLPNSPAARAGLRRGDVIQAVDGQPVTTaddvqriVEQAGvg 81

                         90       100
                 ....*....|....*....|
gi 7657261   449 ---AMEILRNNTHLSITVKT 465
Cdd:cd10838   82 eelELTVLRGDRRQTLAVKP 101
PDZ7_MUPP1-PD6_PATJ-like cd06671
PDZ domain 7 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 6 of PATJ (protein-associated ...
 410-455 2.18e-05

PDZ domain 7 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 6 of 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 7 of MUPP1 and PDZ domain 6 of 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 PDZ7 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: 467159 [Multi-domain]  Cd Length: 96  Bit Score: 44.62  E-value: 2.18e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 7657261   410 GIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06671   37 GIFIKHVLEDSPAGRNGtLKTGDRILEVNGVDLRNATHEEAVEAIRN 83
Peptidase_M50 pfam02163
Peptidase family M50;
397-530 2.42e-05

Peptidase family M50;


Pssm-ID: 426630 [Multi-domain]  Cd Length: 291  Bit Score: 47.87  E-value: 2.42e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     397 LPFILLGGSEKGFGI------FVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQ-LSKAMEiLRNNTHLSITVKTNLFV 469
Cdd:pfam02163   75 LAIILFAVLLFLSGVpppappVIGGVAPGSPAAKAGLKPGDVILSINGKKITSWQdLVEALA-KSPGKPITLTVERGGQT 153

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 7657261     470 FKELLTRLSEEKRNgaphlpKIGDIKKASRYSIPD-LAVDVEQVIGLEKVNKKSKANTVGGR 530
Cdd:pfam02163  154 LTVTITPKSSEESK------FIGIGPVYVKYGLLEaLGFALEKTVNLVTLTLKALGKLITGV 209
cpPDZ_EcRseP-like cd23081
circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and ...
 413-464 2.62e-05

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: 44.10  E-value: 2.62e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 7657261   413 VDSVDSGSKATEAGLKRGDQILEVNGQNFEN-------IQLSKA----MEILRNNTHLSITVK 464
Cdd:cd23081    3 VGEVVANSPAAEAGLKPGDRILKIDGQKVRTwedivriVRENPGkpltLKIERDGKILTVTVT 65
PDZ1_PDZ3_bazooka-like cd06665
PDZ domain 1 and PDZ domain 3 of Drosophila bazooka (DmPar3), and related domains; PDZ (PSD-95 ...
 395-454 4.20e-05

PDZ domain 1 and PDZ domain 3 of Drosophila bazooka (DmPar3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 and 3 of Drosophila bazooka (DmPar3), and related domains. The Par complex comprises atypical protein kinase C (aPKC) and two scaffolding proteins, Par3 (Bazooka (Baz) in Drosophila) and Par6; bazooka (DmPar3) has three central PDZ domains. Both PDZ1 and PDZ3 domains, but not PDZ2, in bazooka (DmPar3) engage in a canonical interaction with the PDZ domain-binding motif in Par6. 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 bazooka-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: 467154 [Multi-domain]  Cd Length: 87  Bit Score: 43.50  E-value: 4.20e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   395 APLPFILLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILR 454
Cdd:cd06665   13 SPLGLTALPDKEHGGGLLVQHVEPGSRAERGRLRRDDRILEINGIKLIGLTESQVQEQLR 72
PDZ4_DLG5-like cd06766
PDZ domain 4 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density ...
 384-454 4.79e-05

PDZ domain 4 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. 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 Dlg5-like 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: 467247 [Multi-domain]  Cd Length: 81  Bit Score: 43.15  E-value: 4.79e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 7657261   384 RLMTLTKPSREapLPFILLGGSEKGfgIFVDSVDSGSKATEA-GLKRGDQILEVNGQNFENIQLSKA-MEILR 454
Cdd:cd06766    3 RLVFLKKSQVE--LGIQLCGGNLHG--IFVEDVEDDSPAKGPdGLVPGDLILEYNSVDMRNKTAEEAyLEMLK 71
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
 410-464 5.07e-05

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: 43.24  E-value: 5.07e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN--NTHLSITVK 464
Cdd:cd06782   15 YLVVVSPIPGGPAEKAGIKPGDVIVAVDGESVRGMSLDEVVKLLRGpkGTKVKLTIR 71
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
 404-528 5.13e-05

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273938 [Multi-domain]  Cd Length: 428  Bit Score: 47.60  E-value: 5.13e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     404 GSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFEN-------IQLSKA-----MEILRNNTHLSITVKtnlfvfk 471
Cdd:TIGR02037  252 GLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSfadlrraIGTLKPgkkvtLGILRKGKEKTITVT------- 324

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 7657261     472 elLTRLSEEKRNGAPHLPKI--GDIKKASRYSIPDlaVDVEQVIGLEKVNKKSKANTVG 528
Cdd:TIGR02037  325 --LGASPEEQASSSNPFLGLtvANLSPEIRKELRL--KGDVKGVVVTKVVSGSPAARAG 379
cpPDZ_BsHtra-like cd06781
circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and ...
 410-464 5.83e-05

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: 43.39  E-value: 5.83e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENI-QLSKAM-----------EILRNNTHLSITVK 464
Cdd:cd06781   31 GVYVAQVQSNSPAEKAGLKKGDVITKLDGKKVESSsDLRQILyshkvgdtvkvTIYRDGKEKTLNIK 97
PDZ_ARHGEF11-12-like cd23069
PDZ domain of ARHGEF11, ARHGEF12, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 406-464 8.59e-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: 42.38  E-value: 8.59e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 7657261   406 EKGFG--------IFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITVK 464
Cdd:cd23069   10 ENGYGltvsgdnpVFVQSVKEGGAAYRAGVQEGDRIIKVNGTLVTHSNHLEVVKLIKSGSYVALTLL 76
PDZ2_L-delphilin-like cd06744
PDZ domain 2 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 ...
 407-453 9.54e-05

PDZ domain 2 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of delphilin (also known as glutamate receptor, ionotropic, delta 2-interacting protein 1, L-delphilin). Delphilin, a postsynaptic protein which it is selectively expressed at cerebellar Purkinje cells, links the glutamate receptor delta 2 subunit (GluRdelta2) with the actin cytoskeleton and various signaling molecules. Two alternatively spliced isoforms of delphilin have been characterized: L-delphilin has two PDZ domains, PDZ1 and PDZ2, and S-delphilin has a single PDZ domain (PDZ2). These two isoforms are differently palmitoylated and may be involved in controlling GluRdelta2 signaling in Purkinje cells. 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 delphilin-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: 467226 [Multi-domain]  Cd Length: 75  Bit Score: 42.26  E-value: 9.54e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 7657261   407 KGFG--------IFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEIL 453
Cdd:cd06744    9 GSFGftlrghapVYIESVDPGSAAERAGLKPGDRILFLNGLDVRNCSHDKVVSLL 63
PDZ1_PTPN13-like cd23072
PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related ...
 397-455 9.78e-05

PDZ domain 1 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 1 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 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: 467285 [Multi-domain]  Cd Length: 92  Bit Score: 42.48  E-value: 9.78e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 7657261   397 LPFILLGGSEKG---FGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd23072   15 LGFQIVGGEKSGrldLGIFISSITPGGPADLDGrLKPGDRLISVNDVSLEGLSHDAAVEILQN 77
PDZ_SNX27-like cd23070
PDZ domain of sorting nexin-27 (SNX27), and related domains; PDZ (PSD-95 (Postsynaptic density ...
 413-463 1.57e-04

PDZ domain of sorting nexin-27 (SNX27), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SNX27, and related domains. SNX27 is involved in retrograde transport from endosome to plasma membrane. The PDZ domain of SNX27 links cargo identification to retromer-mediated transport. SNX27 binds to the retromer complex (vacuolar protein sorting 26(VPS26)-VPS29-VPS35), via its PDZ domain binding to VPS26. The SNX27 PDZ domain also binds to cargo including the G-protein-coupled receptors (GPCRs): beta2-adrenergic receptor (beta2AR), beta1AR, parathyroid hormone receptor (PTHR), alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), NMDA receptors, 5-hydroxytryptamine 4a receptors, frizzled receptors, and somatostatin receptor subtype 5 (SSTR5). Additional binding partners of the SNX27 PDZ domain include G protein-gated inwardly rectifying potassium (Kir3) channels, angiotensin-converting enzyme 2 (ACE2), and PTEN (phosphatase and tensin homolog deleted on chromosome 10); PTEN binding to SNX27 prevents SNX27's association with the retromer complex. SNX27 has been reported to be a host factor needed for efficient entry of an engineered SARS-CoV-2 variant, the spike protein of which contains a deletion at the S1/S2 subunit cleavage site; the PDZ domain of SNX27 binds angiotensin-converting enzyme 2 (ACE2), and may be involved in recycling ACE2 to the plasma membrane, thereby promoting viral entry. 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 SNX27-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: 467283 [Multi-domain]  Cd Length: 93  Bit Score: 42.01  E-value: 1.57e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 7657261   413 VDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTH-LSITV 463
Cdd:cd23070   40 VSAVLEGGAADKAGVRKGDRILEVNGVNVEGATHKQVVDLIKSGGDeLTLTV 91
PDZ_RGS3-like cd06711
PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 ...
 407-463 1.61e-04

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: 41.61  E-value: 1.61e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 7657261   407 KGFG--------IFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN-NTHLSITV 463
Cdd:cd06711   10 DGFGfticddspVRVQAVDPGGPAEQAGLQQGDTVLQINGQPVERSKCVELAHAIRNcPSEIILLV 75
PDZ_MYO18-like cd06747
PDZ domain of MYO18A protein, and related domains; PDZ (PSD-95 (Postsynaptic density protein ...
 411-455 1.73e-04

PDZ domain of MYO18A protein, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MYO18 protein and related domains. MYO18 (also known as myosin XVIIIA, KIAA0216, MysPDZ), a member of the myosin superfamily, is involved in regulating cell protrusion and migration, and Golgi trafficking and morphology, and is required for myoblast adhesion and muscle integrity. The MYO18A/MRCK/LRAP35a complex regulates actomyosin retrograde flow in cell protrusion and migration; the PtdIns(4)P/GOLPH3/MYO18A/F-actin complex is a hub for signals that regulate Golgi trafficking function. The MYO18A PDZ domain binds p190Rho-guanine nucleotide exchange factor (p190RhoGEF), Golgin45, and leucine repeat adaptor protein 1 (Lurap1, also known as Lrap35a). 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 MYO18-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: 467229 [Multi-domain]  Cd Length: 90  Bit Score: 41.91  E-value: 1.73e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 7657261   411 IFVDSVDsGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06747   37 HFAEPGA-GTKNLATGLLPGDRLIEVNGVNVENASRDEIIEMIRK 80
PDZ3_GRIP1-2-like cd06684
PDZ domain 3 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related ...
 410-457 2.00e-04

PDZ domain 3 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 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: 467172 [Multi-domain]  Cd Length: 87  Bit Score: 41.47  E-value: 2.00e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 7657261   410 GIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRNNT 457
Cdd:cd06684   29 VIVIDSIKPASIADRCGaLHVGDHILSIDGTSVEHCSLAEATQLLASNS 77
PDZ_Dishevelled-like cd06717
PDZ domain of segment polarity protein dishevelled homolog DVL1, DVL2, DVL3, and related ...
 410-458 2.19e-04

PDZ domain of segment polarity protein dishevelled homolog DVL1, DVL2, DVL3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of DVL1-3, and related domains. The dishevelleds (DVL1, 2 and 3 in humans) act downstream of Frizzled (FZD) receptors in both the canonical and non-canonical WNT signaling pathway; they bind the cytoplasmic C-terminus of frizzled family members and transduce the Wnt signal to down-stream effectors. They bind to several proteins known to modulate Wnt signaling. Binding partners of the DVL1 PDZ domain include nucleoredoxin (NXN), Van Gogh-like (VANGL1), Wnt receptor RYK, Dapper 1 (DACT1), Frizzled7 (FZD7), transmembrane protein 88 (TMEM88), Daple (dishevelled-associating protein with a high frequency of leucines), also known as Ccdc88c), and cysteine-rich protein Idax. The DVL2 PDZ domain has been shown to bind the nuclear export signal sequence of the DVL2 protein. 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 DVL-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: 467201 [Multi-domain]  Cd Length: 87  Bit Score: 41.58  E-value: 2.19e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 7657261   410 GIFVDSV-DSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTH 458
Cdd:cd06717   27 GIYVGSImKGGAVAADGRIEPGDMILQVNDISFENMSNDDAVRVLREAVH 76
PDZ4_LNX1_2-like cd06680
PDZ domain 4 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ ...
 386-455 2.26e-04

PDZ domain 4 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2)and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467168 [Multi-domain]  Cd Length: 89  Bit Score: 41.56  E-value: 2.26e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 7657261   386 MTLTKpSREAPLPFILLGGSEKGFG---IFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06680    3 ITLRR-SSSGSLGFSIVGGYEESHGnqpFFVKSIVPGTPAYNDGrLKCGDIILAVNGVSTVGMSHAALVPLLKE 75
RA1_DAGK-theta cd17111
Ras-associating (RA) domain 1 found in diacylgylcerol kinase theta (DAGK-theta) and similar ...
 607-655 2.48e-04

Ras-associating (RA) domain 1 found in diacylgylcerol kinase theta (DAGK-theta) and similar proteins; DAGK phosphorylates the second messenger diacylglycerol to phosphatidic acid as part of a protein kinase C pathway. DAGK-theta is characterized as a type V DAGK that has three cysteine-rich domains (all other isoforms have two), a proline/glycine-rich domain at its N-terminal, and a proposed Ras-associating (RA) domain. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has a beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. Ten mammalian isoforms of DAGK have been identified to date which are organized into five categories based on the domain architecture. DAGK-theta also contains a pleckstrin homology (PH) domain. The subcellular localization and the activity of DAGK-theta are regulated in a complex (stimulation- and cell type-dependent) manner. This family corresponds to the first RA domain of DAGK-theta.


Pssm-ID: 340631  Cd Length: 91  Bit Score: 41.42  E-value: 2.48e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 7657261   607 DQVLRVFKAD-----QQSRYIMISKDTTAKEVVIQAIREFAVTATPDQYSLCEV 655
Cdd:cd17111    1 KEIVKVFDGNaslkrNQFRLITVPRNASVEQVLEAALRAFHIPDDPENYYLTDA 54
PDZ_AFDN-like cd06789
PDZ domain of afadin (AFDN), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95) ...
 403-453 2.55e-04

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: 41.50  E-value: 2.55e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 7657261   403 GGSEKGFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEIL 453
Cdd:cd06789   24 GAGQDKLGIYIKSVVKGGAADLDGrLQAGDQLLSVDGHSLVGLSQERAAELM 75
PDZ_MAST cd06705
PDZ domain of the microtubule-associated serine-threonine (MAST) protein kinase family; PDZ ...
 413-463 2.89e-04

PDZ domain of the microtubule-associated serine-threonine (MAST) protein kinase family; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MAST family kinases, including MAST1-4. These MAST proteins contain a DUF1908 domain, a serine/threonine kinase domain, a AGC-kinase C-terminal domain, and a PDZ domain; MAST family member MASTL is a shorter protein lacking the PDZ domain. The PDZ domain gives the MAST family the capacity to scaffold its own kinase activity. These kinases are implicated in the inhibition of neurite outgrowth and regeneration in cultured cells. Their binding partners include microtubules, beta2-syntrophin, TNF receptor-associated factor 6 (TRAF6), cAMP-regulated phosphoprotein (ARPP-16), and PTEN. This family also includes Caenorhabditis elegans KIN-4 MAST kinase, a key longevity factor acting through binding PTEN phosphatase, and Drosophila Drop out which regulates dynein-dependent transport during embryonic development. 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 MAST-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: 467189 [Multi-domain]  Cd Length: 93  Bit Score: 41.46  E-value: 2.89e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 7657261   413 VDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAME-ILRNNTHLSITV 463
Cdd:cd06705   37 VTAVEEGSPAYEAGLRPGDLITHVNGEPVQGLLHTQVVQlILKGGNKVSIRA 88
PDZ_RGS12-like cd06710
PDZ domain of regulator of G-protein signaling 12 (RGS12), and related domains; PDZ (PSD-95 ...
 408-440 3.24e-04

PDZ domain of regulator of G-protein signaling 12 (RGS12), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS12, and related domains. RGS12 downregulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. The RGS12 PDZ domain can bind selectively to C-terminal (A/S)-T-X-(L/V) motifs as found within both the CXCR2 IL-8 receptor, and the alternative 3' exon form of RGS12. 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 RGS12-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: 467194 [Multi-domain]  Cd Length: 76  Bit Score: 40.69  E-value: 3.24e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 7657261   408 GFGI------FVDSVDSGSKATEAGLKRGDQILEVNGQN 440
Cdd:cd06710   13 GFTIsgqapcVLSCVVRGSPADVAGLKAGDQILAVNGIN 51
PDZ1_ZO1-like cd06727
PDZ domain 1 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ ...
 411-464 3.38e-04

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: 41.11  E-value: 3.38e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 7657261   411 IFVDSVDSGSKAtEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLS-ITVK 464
Cdd:cd06727   33 IVISDVLKGGPA-EGKLQENDRVVSVNGVSMENVEHSFAVQILRKCGKTAnITVK 86
PDZ2_ZO1-like_ds cd06728
PDZ domain 2 of Zonula Occludens-1 (ZO-1), ZO-2 and ZO-3, and related domains; form ...
 408-455 3.59e-04

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: 40.67  E-value: 3.59e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 7657261   408 GFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06728   19 GSRIFVKEITPDSLAAKDGnLQEGDIILKINGTPVENLSLSEAKKLIEK 67
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
405-464 4.33e-04

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


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 44.81  E-value: 4.33e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   405 SEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRNNTHLSITVK 464
Cdd:COG3975  490 SADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVTADNLDDALAAYKPGDPIELLVF 549
PulC COG3031
Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular ...
 403-487 5.99e-04

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


Pssm-ID: 442267 [Multi-domain]  Cd Length: 220  Bit Score: 43.05  E-value: 5.99e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   403 GGSEKGFGIFvdSVDSGSKATEAGLKRGDQILEVNGQNFENIQlsKAMEI---LRNNTHLSITVktnlfvfkelltrlse 479
Cdd:COG3031  147 DGKLVGYRVN--PGRPGSLFSKLGLQPGDVITSINGQDLTDPA--QALELlqqLRDASEVTLTV---------------- 206


                 ....*...
gi 7657261   480 eKRNGAPH 487
Cdd:COG3031  207 -ERNGQPV 213
PDZ1-PDZRN4-like cd06715
PDZ domain 1 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related ...
 410-449 7.17e-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: 40.07  E-value: 7.17e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 7657261   410 GIFVDSV-DSGSKATEAGLKRGDQILEVNGQNfeniqLSKA 449
Cdd:cd06715   35 GIYVSKIvENGPAADEGGLQVHDRIIEVNGKD-----LSKA 70
PRK10942 PRK10942
serine endoprotease DegP;
410-459 7.35e-04

serine endoprotease DegP;


Pssm-ID: 236802 [Multi-domain]  Cd Length: 473  Bit Score: 43.99  E-value: 7.35e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261    410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENI-QLSK---------AMEILRNNTHL 459
Cdd:PRK10942  409 GVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIaELRKildskpsvlALNIQRGDSSI 468
PDZ1_INAD-like cd23063
PDZ domain 1 of inactivation-no-after-potential D (INAD), and related domains; PDZ (PSD-95 ...
 403-455 7.61e-04

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: 39.80  E-value: 7.61e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 7657261   403 GGSEKGFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd23063   24 SPNTKTTGIFIKGIIPDSPAHKCGrLKVGDRILSVNGNDVRNSTEQAAIDLIKE 77
cNMP_binding pfam00027
Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, ...
 158-237 8.26e-04

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 459637 [Multi-domain]  Cd Length: 89  Bit Score: 39.90  E-value: 8.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261     158 RAGTIVLNDGEELDSWSVILNGSVEV--TYPDGKAEILCM---GNSFGVSPTMDKEYMKGVMRTkVDDCQFVCIAQQDYC 232
Cdd:pfam00027    5 KAGEVIFREGDPADSLYIVLSGKVKVyrTLEDGREQILAVlgpGDFFGELALLGGEPRSATVVA-LTDSELLVIPREDFL 83


                   ....*
gi 7657261     233 RILNQ 237
Cdd:pfam00027   84 ELLER 88
PDZ11_MUPP1-PDZ9_PATJ-like cd06674
PDZ domain 11 of MUPP1 of multi-PDZ-domain protein 1 (MUPP1), domain 9 of PATJ ...
 404-455 8.76e-04

PDZ domain 11 of MUPP1 of multi-PDZ-domain protein 1 (MUPP1), domain 9 of 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 11 of MUPP1, PDZ domain 9 of 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 PDZ11 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: 467162 [Multi-domain]  Cd Length: 87  Bit Score: 39.57  E-value: 8.76e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 7657261   404 GSEKGFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06674   22 GKRNDTGVFVSDIVKGGAADADGrLMQGDQILSVNGEDVRNASQEAAAALLKC 74
PDZ9_MUPP1-like cd10817
PDZ domain 9 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 ...
 410-454 9.86e-04

PDZ domain 9 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 9 of MUPP1. 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. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ9 domain is therefore absent from PATJ. 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). 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 PDZ9 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: 467263 [Multi-domain]  Cd Length: 79  Bit Score: 39.25  E-value: 9.86e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 7657261   410 GIFVDSV-DSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILR 454
Cdd:cd10817   23 GIVIKSLtEGGPAAKDGRLKVGDQILAVDDESVVGCPYEKAISLLK 68
PDZ_rhophilin-like cd06712
PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 384-463 1.04e-03

PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of rhophilin-1, rhophilin-2, and related domains. Rhophilin-1 (RHPN1, also known as GTP-Rho-binding protein 1) and rhophilin-2 (RHPN2, also known as GTP-Rho-binding protein 2) are Rho-GTP binding proteins involved in cytoskeletal dynamics. Rhophilin-2 inhibits RhoA's activity to induce F-actin stress fibers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This rhophilin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467196 [Multi-domain]  Cd Length: 78  Bit Score: 39.10  E-value: 1.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7657261   384 RLMTLTKpsREAPLPFILLGGSEkgfgIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILR--NNTHLSI 461
Cdd:cd06712    2 RTVHLTK--EEGGFGFTLRGDSP----VQVASVDPGSCAAEAGLKEGDYIVSVGGVDCKWSKHSEVVKLLKsaGEEGLEL 75


                 ..
gi 7657261   462 TV 463
Cdd:cd06712   76 QV 77
RA_ARAPs cd17113
Ras-associating (RA) domain found in Arf-GAP with Rho-GAP domain, ANK repeat and PH ...
 612-655 1.11e-03

Ras-associating (RA) domain found in Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing proteins ARAP1, ARAP2, ARAP3, and similar proteins; ARAPs are phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P(3))-dependent Arf Rap-activated guanosine triphosphatase (GTPase)-activating proteins (GAPs). They contain multiple functional domains, including ArfGAP and RhoGAP domains, as well as a sterile alpha motif (Sam) domain, five PH domains, and a RA domain. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub); Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes.


Pssm-ID: 340633  Cd Length: 95  Bit Score: 39.54  E-value: 1.11e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 7657261   612 VFKADQQSRYIMISKDTTAKEVVIQAIREFAVTATPDQYSLCEV 655
Cdd:cd17113   10 IEEKEGTSVNIKVTPTMTAEEVVEQALNKKNLGGPEGNWALFEV 53
cpPDZ_DegS cd06777
circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density ...
 401-463 1.14e-03

circularly permuted PDZ domain of DegS serine endoprotease; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Escherichia coli DegS and related domains. DegS (also known as Site-1 protease DegS, S1P protease DegS, and Site-1-type intramembrane protease) participates in the activation of the sigma(E) extracytoplasmic stress response. Initially, there is an accumulation of misfolded membrane proteins (OMPs) in the periplasm which bind by their YXF motif to the DegS PDZ domain, activating DegS-catalyzed cleavage of the RseA periplasmic domain and making RseA a substrate for cleavage by another membrane protease RseP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegS family PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467620 [Multi-domain]  Cd Length: 93  Bit Score: 39.68  E-value: 1.14e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 7657261   401 LLGGSEKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENI-----QLSKA-------MEILRNNTHLSITV 463
Cdd:cd06777   17 RGGGIDQLQGALVKGVSPDSPAAKAGIQVGDIILQFDNKPVISVlelmdLVAEIrpgtvipVVVLRDGKQLTLEV 91
cpPDZ2_EcRseP-like cd23083
circularly permuted PDZ domain 2 (PDZ-C) of Escherichia coli Regulator of sigma-E protease ...
 416-463 1.33e-03

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: 39.03  E-value: 1.33e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 7657261   416 VDSGSKATEAGLKRGDQILEVNGQNFE-----------NIQLSKAMEILRNNTHLSITV 463
Cdd:cd23083    6 VQPNSAAEKAGLQAGDRIVKVDGQPLTqwqtfvmavrdNPGKPLALEIERQGSPLSLTL 64
PDZ_2 pfam13180
PDZ domain;
410-465 1.59e-03

PDZ domain;


Pssm-ID: 433015 [Multi-domain]  Cd Length: 74  Bit Score: 38.79  E-value: 1.59e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 7657261     410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQ------NFENIQLSKA------MEILRNNTHLSITVKT 465
Cdd:pfam13180    7 GVVVVSVKSSGPAAKAGLKAGDVILSIDGRkindltDLESALYGHKpgdtvtLQVYRDGKLLTVEVKL 74
PDZ_Radil-like cd06690
PDZ domain of Ras-associating and dilute domain-containing protein (Radil) and related domains; ...
 410-455 1.73e-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: 38.81  E-value: 1.73e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 7657261   410 GIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06690   31 GIYIRTLVPDSPAARDGrLRLGDRILAVNGTSLVGADYQSAMDLIRT 77
PDZ_tamalin_CYTIP-like cd06713
PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains; PDZ ...
 412-442 1.86e-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: 38.76  E-value: 1.86e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 7657261   412 FVDSVDSGSKATEAGLKRGDQILEVNGQNFE 442
Cdd:cd06713   38 YVCRVHEDSPAYLAGLTAGDVILSVNGVSVE 68
PDZ1_LNX1_2-like cd06677
PDZ domain 1 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ ...
 388-454 1.94e-03

PDZ domain 1 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family 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: 467165 [Multi-domain]  Cd Length: 89  Bit Score: 38.77  E-value: 1.94e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 7657261   388 LTKPSREAPLPFILLGGSEKGFG-IFVDSV-DSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILR 454
Cdd:cd06677    8 IHRSDPYEELGISIVGGNDTPLInIVIQEVyRDGVIARDGRLLPGDQILEVNGVDISNVTHSQARSVLR 76
PDZ4_Scribble-like cd06701
PDZ domain 4 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...
 410-458 2.43e-03

PDZ domain 4 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 4 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 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: 467185 [Multi-domain]  Cd Length: 98  Bit Score: 38.75  E-value: 2.43e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 7657261   410 GIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRNNTH 458
Cdd:cd06701   39 GIFISKINPDGAAARDGrLKVGQRILEVNGQSLLGATHQEAVRILRSVGD 88
PDZ_GOPC-like cd06800
PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and ...
 384-453 2.51e-03

PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GOPC and related domains. GOPC, also known as PIST (PDZ domain protein interacting specifically with TC10), FIG (fused in glioblastoma), and CAL (CFTR-associated ligand), regulates the trafficking of a wide array of proteins, including small GTPases, receptors, and cell surface molecules such as cadherin 23 and CFTR. It may regulate CFTR chloride currents and acid-sensing ASIC3 currents by modulating cell surface expression of both channels, and may play a role in autophagy. Interaction partners of the GOPC PDZ domains include: FZD5, FZD8, ASIC3, CFTR, MUC3, ARFRP1, Ggamma13, neuroligin, and Stargazin. 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 GOPC-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: 467261 [Multi-domain]  Cd Length: 83  Bit Score: 38.51  E-value: 2.51e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7657261   384 RLMTLTKPSREApLPFILLGGSEKGFGIFVDSVDSGSKATE-AGLKRGDQILEVNGQNFENIQLSKAMEIL 453
Cdd:cd06800    1 RKVLLSKEPHEG-LGISITGGKEHGVPILISEIHEGQPADRcGGLYVGDAILSVNGIDLRDAKHKEAVTIL 70
PDZ3_harmonin cd06739
PDZ domain 3 of harmonin isoforms a and b, and related domains; PDZ (PSD-95 (Postsynaptic ...
 393-455 2.54e-03

PDZ domain 3 of harmonin isoforms a and b, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of harmonin isoforms a and b, 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 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: 467221 [Multi-domain]  Cd Length: 94  Bit Score: 38.83  E-value: 2.54e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 7657261   393 REAPLPFILLGGSEKGFG--IFVDSV-DSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06739   10 KNGPLDLALEGGIDSPLGgkIVVSAVyEGGAADKHGGIVKGDQIMMVNGKSLTDVTLAEAEAALQR 75
cpPDZ_HtrA-like cd06785
circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine ...
 410-463 2.70e-03

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: 38.63  E-value: 2.70e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 7657261   410 GIFVDSVDSGSKATEAGLKRGDQILEVNGQ---NFENIQlskamEILRNNTHLSITV 463
Cdd:cd06785   32 GVYVHKVIPGSPAQRAGLKDGDVIISINGKpvkSSSDVY-----EAVKSGSSLLVVV 83
PDZ3_Scribble-like cd06702
PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...
 396-458 2.85e-03

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: 38.39  E-value: 2.85e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7657261   396 PLPFILLGGS--------EKGFGIFVDSVDSGSKATEAGLKRGDQILEVNGQNfeniqlskameiLRNNTH 458
Cdd:cd06702   11 PLGLSIVGGSdhsshpfgVDEPGIFISKVIPDGAAAKSGLRIGDRILSVNGKD------------LRHATH 69
PDZ1_FRMPD2-like cd23071
PDZ domain 1 of FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains; PDZ ...
 399-455 2.89e-03

PDZ domain 1 of 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 1 of FRMPD2 (also known as PDZ domain-containing protein 4, and related domains. 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. 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 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: 467284 [Multi-domain]  Cd Length: 92  Bit Score: 38.63  E-value: 2.89e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 7657261   399 FILLGGSEKG---FGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd23071   17 FVIVGGENTGkldLGIFIASIIPGGPAEKDGrIKPGGRLISLNNISLEGVTFNTAVKILQN 77
PDZ4_PTPN13-like cd06696
PDZ domain 4 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related ...
 387-455 3.10e-03

PDZ domain 4 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 4 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 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: 467182 [Multi-domain]  Cd Length: 85  Bit Score: 38.06  E-value: 3.10e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 7657261   387 TLTKPSREApLPFILLGGSEKGfGIFVDSVDSGSKATEAGLKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06696    7 TLTKSEKGS-LGFTVTKGKDDN-GCYIHDIVQDPAKSDGRLRPGDRLIMVNGVDVTNMSHTEAVSLLRA 73
PDZ_syntrophin-like cd06801
PDZ domain of syntrophins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), ...
 403-464 6.07e-03

PDZ domain of syntrophins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of syntrophins (including alpha-1-syntrophin, beta-1-syntrophin, beta-2-syntrophin, gamma-1-syntrophin, and gamma-2-syntrophin), and related domains. Syntrophins play a role in recruiting various signaling molecules into signaling complexes and help provide appropriate spatiotemporal regulation of signaling pathways. They function in cytoskeletal organization and maintenance; as components of the dystrophin-glycoprotein complex (DGC), they help maintain structural integrity of skeletal muscle fibers. They link voltage-gated sodium channels to the actin cytoskeleton and the extracellular matrix, and control the localization and activity of the actin reorganizing proteins such as PI3K, PI(3,4)P2 and TAPP1. Through association with various cytoskeletal proteins within the cells, they are involved in processes such as regulation of focal adhesions, myogenesis, calcium homeostasis, and cell migration. They also have roles in synapse formation and in the organization of utrophin, acetylcholine receptor, and acetylcholinesterase at the neuromuscular synapse. 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 syntrophin-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: 467262 [Multi-domain]  Cd Length: 83  Bit Score: 37.17  E-value: 6.07e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 7657261   403 GGSEKGFGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN-NTHLSITVK 464
Cdd:cd06801   19 GGAEHKMPILISKIFKGQAADQTGqLFVGDAILSVNGENLEDATHDEAVQALKNaGDEVTLTVK 82
PDZ4_GRIP1-2-like cd06686
PDZ domain 4 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related ...
 400-454 6.49e-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: 37.71  E-value: 6.49e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 7657261   400 ILLGGSEKGFGI----------------FVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILR 454
Cdd:cd06686   11 ILRGDPLKGFGIqlqggvfatetlssppLISFIEPDSPAERCGvLQVGDRVLSINGIPTEDRTLEEANQLLR 82
RA_RASSF1_like cd01778
Ras-associating (RA) domain found in Ras-association domain family members, RASSF1, RASSF3, ...
 619-670 9.20e-03

Ras-associating (RA) domain found in Ras-association domain family members, RASSF1, RASSF3, and RASSF5; The RASSF family of proteins shares a conserved RalGDS/AF6 Ras association (RA) domain which is located either at the C-terminus (RASSF1-6, the classical group) or at the N-terminus (RASSF7-10). RASSF1-6 contains a conserved SARAH (Salvador/RASSF/Hpo) motif adjacent to the RA domain that functions in scaffolding and regulatory interactions. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. Classical RASSF members interact either directly or indirectly with activated Ras. Ras proteins are small GTPases that are involved in cellular signal transduction. The classical RASSF proteins seem to modulate some of the growth inhibitory responses mediated by Ras and may serve as tumor suppressor genes. This family contains RASSF1, RASSF3, and RASSF5.


Pssm-ID: 340476  Cd Length: 130  Bit Score: 38.04  E-value: 9.20e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 7657261   619 SRYIMISKDTTAKEVVIQAIREFAVTATPDQYSLCEVSVTPEGVIKQRRLPD 670
Cdd:cd01778   54 VKALHITSDTTAREVIEALLKKFKITDNPRKFALYERTHEEEGKVKLRKLSD 105
PDZ_ARHGAP21_23-like cd06756
PDZ domain of ARHGAP21 and ARHGAP23, and related domains; PDZ (PSD-95 (Postsynaptic density ...
 411-439 9.48e-03

PDZ domain of ARHGAP21 and ARHGAP23, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ARHGAP21, ARHGAP23, and related domains. This subfamily includes the GAPs (GTPase activating proteins): ARHGAP21 (Rho GTPase-activating protein 21; also known as Rho GTPase-activating protein 10, Rho-type GTPase-activating protein 21) and ARHGAP23 (Rho GTPase-activating protein 23; also known as Rho-type GTPase-activating protein 23). GAPs deactivate Rho GTPases by accelerating GTP hydrolysis. ARHGAP21/23 interact with a planar cell polarity (PCP) protein Pk1 to regulate a lateral signaling pathway in migrating cells. The ARHGAP21 PDZ domain binds claudin-2. 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 ARHGAP21-23-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: 467238 [Multi-domain]  Cd Length: 109  Bit Score: 37.44  E-value: 9.48e-03
                         10        20
                 ....*....|....*....|....*....
gi 7657261   411 IFVDSVDSGSKATEAGLKRGDQILEVNGQ 439
Cdd:cd06756   55 IFVKQVKEGGPAHQAGLCTGDRIVKVNGE 83
PDZ5_MAGI-1_3-like cd06735
PDZ domain 5 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, ...
 399-455 9.53e-03

PDZ domain 5 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5, and belongs to this MAGI1,2,3-like family. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. 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 MAGI family PDZ5 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: 467217 [Multi-domain]  Cd Length: 84  Bit Score: 36.79  E-value: 9.53e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 7657261   399 FILLGGSEKG-FGIFVDSVDSGSKATEAG-LKRGDQILEVNGQNFENIQLSKAMEILRN 455
Cdd:cd06735   15 FSIRGGREYNnMPLYVLRLAEDGPAQRDGrLRVGDQILEINGESTQGMTHAQAIELIRS 73
 
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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