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Conserved domains on  [gi|588284345|gb|AHK22713|]
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interphotoreceptor retinoid binding protein, partial [Muriculus imberbis]

Protein Classification

Peptidase_S41_IRBP and Peptidase_S41_N domain-containing protein( domain architecture ID 10869334)

Peptidase_S41_IRBP and Peptidase_S41_N domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 1-269 2.05e-66

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


:

Pssm-ID: 143479 [Multi-domain]  Cd Length: 250  Bit Score: 211.38  E-value: 2.05e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345   1 AAIEQAMKSHEILGISDPQTLARVLTAGVQSsLSDPRLFISYepntleapqqapaltnltqeellaqiqrnirhevlegn 80
Cdd:cd07563   24 DALAARLRAQVYLDITSPEELAAVLTADLQE-LGDGHLNVSY-------------------------------------- 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  81 VGYLRVDDLPGQEVlsELGEFLVSHVWKKLMGTSSLVLDLRHCTGGHVSGIPYVISYLYPGNTVMHVDTVYDRPSNTTTE 160
Cdd:cd07563   65 IGYLRIDSFGGFEI--AAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTE 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345 161 IWTLPEVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTEGGALDLQKLRIGQsNFFLTVPVSRSLGPL 240
Cdd:cd07563  143 LWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSVDPI 221

                        250       260
                 ....*....|....*....|....*....
gi 588284345 241 ggGGQTWEGSGVLPCVGIPAEQALEKALA 269
Cdd:cd07563  222 --TGTNWEGVGVPPDIEVPATPGYDDALE 248
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 260-385 3.70e-56

N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterized as a serine-peptidase, pfam03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B.


:

Pssm-ID: 463396  Cd Length: 129  Bit Score: 180.98  E-value: 3.70e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  260 AEQALEKALAILTLRRALPGVVLRLQEALQDYYTLVDRVPGLLHHLASM----DYSAVVSEEDLVTKLNAGLQAVSEDPR 335
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLlasgDYSSVVSEEDLASKLNADLQALSGDPR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 588284345  336 LLVRVTGPRDSSLRPETGPNeAPAATPELPTEEDALRALVNSVFQVSVLP 385
Cdd:pfam11918  81 LKVRYIRPEPASDEPEAADN-IPGLVPMQPPSPEMLEALIKSSFKVDVLP 129
Peptidase_S41_N super family cl12052
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 15-78 5.14e-03

N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterized as a serine-peptidase, pfam03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B.


The actual alignment was detected with superfamily member pfam11918:

Pssm-ID: 463396  Cd Length: 129  Bit Score: 36.92  E-value: 5.14e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 588284345   15 ISDPQTLARVLTAGVQSSLSDPRLFISY--------EPNTLEAPQQAPALTNLTQEELLAQIQRNIRHEVLE 78
Cdd:pfam11918  58 VVSEEDLASKLNADLQALSGDPRLKVRYirpepasdEPEAADNIPGLVPMQPPSPEMLEALIKSSFKVDVLP 129
 
Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 1-269 2.05e-66

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


Pssm-ID: 143479 [Multi-domain]  Cd Length: 250  Bit Score: 211.38  E-value: 2.05e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345   1 AAIEQAMKSHEILGISDPQTLARVLTAGVQSsLSDPRLFISYepntleapqqapaltnltqeellaqiqrnirhevlegn 80
Cdd:cd07563   24 DALAARLRAQVYLDITSPEELAAVLTADLQE-LGDGHLNVSY-------------------------------------- 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  81 VGYLRVDDLPGQEVlsELGEFLVSHVWKKLMGTSSLVLDLRHCTGGHVSGIPYVISYLYPGNTVMHVDTVYDRPSNTTTE 160
Cdd:cd07563   65 IGYLRIDSFGGFEI--AAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTE 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345 161 IWTLPEVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTEGGALDLQKLRIGQsNFFLTVPVSRSLGPL 240
Cdd:cd07563  143 LWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSVDPI 221

                        250       260
                 ....*....|....*....|....*....
gi 588284345 241 ggGGQTWEGSGVLPCVGIPAEQALEKALA 269
Cdd:cd07563  222 --TGTNWEGVGVPPDIEVPATPGYDDALE 248
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 260-385 3.70e-56

N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterized as a serine-peptidase, pfam03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B.


Pssm-ID: 463396  Cd Length: 129  Bit Score: 180.98  E-value: 3.70e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  260 AEQALEKALAILTLRRALPGVVLRLQEALQDYYTLVDRVPGLLHHLASM----DYSAVVSEEDLVTKLNAGLQAVSEDPR 335
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLlasgDYSSVVSEEDLASKLNADLQALSGDPR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 588284345  336 LLVRVTGPRDSSLRPETGPNeAPAATPELPTEEDALRALVNSVFQVSVLP 385
Cdd:pfam11918  81 LKVRYIRPEPASDEPEAADN-IPGLVPMQPPSPEMLEALIKSSFKVDVLP 129
TSPc smart00245
tail specific protease; tail specific protease
 60-259 1.66e-53

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 176.29  E-value: 1.66e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345    60 TQEELLAQIQRNIRHEVLEGNVGYLRVDDLpGQEVLSELGE---FLVSHVWKKLMGT--SSLVLDLRHCTGGHVSGIPYV 134
Cdd:smart00245   1 SKERTIALIRDKIKIETLEGNVGYLRFGFI-GYIRIPEFSEhtsNLVEKAWKKLEKTnvEGLILDLRNNPGGLLSAAIDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345   135 ISYLYPGNTvmHVDTVYDRpsntTTEIWTLPEVLGERYSadKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTEGGA 214
Cdd:smart00245  80 SSLFLDKGV--IVYTVYRR----TGELWTYPANLGRKYS--KPLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKG 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 588284345   215 LDLQKLRIGqSNFFLTVPVSRSLGPlggGGQTWEGSGVLPCVGIP 259
Cdd:smart00245 152 LVQQTVPLG-DGSGLKLTVAKYYTP---SGKSIEKKGVEPDIQVP 192
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 72-254 1.30e-15

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: 77.22  E-value: 1.30e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  72 IRHEVLEGNVGYLRVDDL---PGQEVLSELGEFlvshvwkKLMGTSSLVLDLRHCTGGHVSGIPYVISYLYPGNTVmhvd 148
Cdd:COG0793  150 VEAKLLEGKIGYIRIPSFgenTAEEFKRALKEL-------KKQGAKGLILDLRNNPGGLLDEAVELADLFLPKGPI---- 218

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345 149 tVYDRPSNTTTEIWTlpeVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTEGGAldlqklrIGQSNF- 227
Cdd:COG0793  219 -VYTRGRNGKVETYK---ATPGGALYDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGKG-------SVQTVFp 287

                        170       180       190
                 ....*....|....*....|....*....|..
gi 588284345 228 -----FLTVPVSRSLGPlggGGQTWEGSGVLP 254
Cdd:COG0793  288 lpdggALKLTTARYYTP---SGRSIQGKGVEP 316
Peptidase_S41 pfam03572
Peptidase family S41;
80-254 5.40e-13

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 66.48  E-value: 5.40e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345   80 NVGYLRVDDLpGQEVLSELGEFLvshvwKKLM--GTSSLVLDLRHCTGGHVSGIPYVISYLYPGNTVMhvdTVYDRPSNT 157
Cdd:pfam03572   1 KIGYIRIPSF-SEKTAKELAEAL-----KELKkqGVKGLILDLRGNPGGLLSAAVEIASLFLPDGTIV---STRGRDGSK 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  158 TTEIWTLPevlGERYSADKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTeGGALDLQKLRIGQSNFFLTVPVSRSL 237
Cdd:pfam03572  72 EVYFAAGK---ADEVLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVGERT-FGKGTVQTVYPLPDGSALKLTIAKYY 147

                         170
                  ....*....|....*..
gi 588284345  238 GPlggGGQTWEGSGVLP 254
Cdd:pfam03572 148 TP---DGRSIEGKGIEP 161
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 280-342 4.53e-04

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


Pssm-ID: 143479 [Multi-domain]  Cd Length: 250  Bit Score: 41.51  E-value: 4.53e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 588284345 280 VVLRLQEALQDYY----TLVDRVPGLLHHLASMDYSAVVSEEDLVTKLNAGLQAVsEDPRLLVRVTG 342
Cdd:cd07563    1 VFEALAKLLEENYafpeAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQEL-GDGHLNVSYIG 66
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 15-78 5.14e-03

N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterized as a serine-peptidase, pfam03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B.


Pssm-ID: 463396  Cd Length: 129  Bit Score: 36.92  E-value: 5.14e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 588284345   15 ISDPQTLARVLTAGVQSSLSDPRLFISY--------EPNTLEAPQQAPALTNLTQEELLAQIQRNIRHEVLE 78
Cdd:pfam11918  58 VVSEEDLASKLNADLQALSGDPRLKVRYirpepasdEPEAADNIPGLVPMQPPSPEMLEALIKSSFKVDVLP 129
 
Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 1-269 2.05e-66

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


Pssm-ID: 143479 [Multi-domain]  Cd Length: 250  Bit Score: 211.38  E-value: 2.05e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345   1 AAIEQAMKSHEILGISDPQTLARVLTAGVQSsLSDPRLFISYepntleapqqapaltnltqeellaqiqrnirhevlegn 80
Cdd:cd07563   24 DALAARLRAQVYLDITSPEELAAVLTADLQE-LGDGHLNVSY-------------------------------------- 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  81 VGYLRVDDLPGQEVlsELGEFLVSHVWKKLMGTSSLVLDLRHCTGGHVSGIPYVISYLYPGNTVMHVDTVYDRPSNTTTE 160
Cdd:cd07563   65 IGYLRIDSFGGFEI--AAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTE 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345 161 IWTLPEVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTEGGALDLQKLRIGQsNFFLTVPVSRSLGPL 240
Cdd:cd07563  143 LWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSVDPI 221

                        250       260
                 ....*....|....*....|....*....
gi 588284345 241 ggGGQTWEGSGVLPCVGIPAEQALEKALA 269
Cdd:cd07563  222 --TGTNWEGVGVPPDIEVPATPGYDDALE 248
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 260-385 3.70e-56

N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterized as a serine-peptidase, pfam03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B.


Pssm-ID: 463396  Cd Length: 129  Bit Score: 180.98  E-value: 3.70e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  260 AEQALEKALAILTLRRALPGVVLRLQEALQDYYTLVDRVPGLLHHLASM----DYSAVVSEEDLVTKLNAGLQAVSEDPR 335
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLlasgDYSSVVSEEDLASKLNADLQALSGDPR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 588284345  336 LLVRVTGPRDSSLRPETGPNeAPAATPELPTEEDALRALVNSVFQVSVLP 385
Cdd:pfam11918  81 LKVRYIRPEPASDEPEAADN-IPGLVPMQPPSPEMLEALIKSSFKVDVLP 129
TSPc smart00245
tail specific protease; tail specific protease
 60-259 1.66e-53

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 176.29  E-value: 1.66e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345    60 TQEELLAQIQRNIRHEVLEGNVGYLRVDDLpGQEVLSELGE---FLVSHVWKKLMGT--SSLVLDLRHCTGGHVSGIPYV 134
Cdd:smart00245   1 SKERTIALIRDKIKIETLEGNVGYLRFGFI-GYIRIPEFSEhtsNLVEKAWKKLEKTnvEGLILDLRNNPGGLLSAAIDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345   135 ISYLYPGNTvmHVDTVYDRpsntTTEIWTLPEVLGERYSadKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTEGGA 214
Cdd:smart00245  80 SSLFLDKGV--IVYTVYRR----TGELWTYPANLGRKYS--KPLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKG 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 588284345   215 LDLQKLRIGqSNFFLTVPVSRSLGPlggGGQTWEGSGVLPCVGIP 259
Cdd:smart00245 152 LVQQTVPLG-DGSGLKLTVAKYYTP---SGKSIEKKGVEPDIQVP 192
Peptidase_S41 cd06567
C-terminal processing peptidase family S41; Peptidase family S41 (C-terminal processing ...
 80-259 2.52e-28

C-terminal processing peptidase family S41; Peptidase family S41 (C-terminal processing peptidase or CTPase family) contains very different subfamilies; it includes photosystem II D1 C-terminal processing protease (CTPase), interphotoreceptor retinoid-binding protein IRBP and tricorn protease (TRI). CTPase and TRI both contain the PDZ domain while IRBP, although being very similar to the tail-specific protease domain, lacks the PDZ insertion domain and hydrolytic activity. These serine proteases have distinctly different active sites: in CTPase, the active site consists of a serine/lysine catalytic dyad while in tricorn core protease, it is a tetrad (serine, histidine, serine, glutamate). CPases with different substrate specificities in different species include processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein; and others such as tricorn protease (TRI) act as a carboxypeptidase, involved in the degradation of proteasomal products. CTPase homolog IRBP, secreted by photoreceptors into the interphotoreceptor matrix, having arisen in the early evolution of the vertebrate eye, promotes the release of all-trans retinol from photoreceptors and facilitates its delivery to the retinal pigment epithelium.


Pssm-ID: 143475 [Multi-domain]  Cd Length: 224  Bit Score: 110.85  E-value: 2.52e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  80 NVGYLRVDDLPGQEVLSELGEFLVshvwKKLMGTSSLVLDLRHCTGGHVSGIPYVISYLYPGNTVMHVDTVYDRPsnttt 159
Cdd:cd06567   60 TIGYIRIPSFSAESTAEELREALA----ELKKGVKGLILDLRNNPGGLLSAAVELASLFLPKGKIVVTTRRRGGN----- 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345 160 eiWTLPEVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTEGGALDlQKLRIGQSNFFLTVPVSRSLGP 239
Cdd:cd06567  131 --ETEYVAPGGGSLYDGPLVVLVNEGSASASEIFAGALQDLGRATLVGERTFGKGSV-QTVFPLLDGSALKLTTAKYYTP 207

                        170       180
                 ....*....|....*....|
gi 588284345 240 lggGGQTWEGSGVLPCVGIP 259
Cdd:cd06567  208 ---SGRSIEGKGVEPDIEVP 224
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 72-254 1.30e-15

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: 77.22  E-value: 1.30e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  72 IRHEVLEGNVGYLRVDDL---PGQEVLSELGEFlvshvwkKLMGTSSLVLDLRHCTGGHVSGIPYVISYLYPGNTVmhvd 148
Cdd:COG0793  150 VEAKLLEGKIGYIRIPSFgenTAEEFKRALKEL-------KKQGAKGLILDLRNNPGGLLDEAVELADLFLPKGPI---- 218

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345 149 tVYDRPSNTTTEIWTlpeVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTEGGAldlqklrIGQSNF- 227
Cdd:COG0793  219 -VYTRGRNGKVETYK---ATPGGALYDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGKG-------SVQTVFp 287

                        170       180       190
                 ....*....|....*....|....*....|..
gi 588284345 228 -----FLTVPVSRSLGPlggGGQTWEGSGVLP 254
Cdd:COG0793  288 lpdggALKLTTARYYTP---SGRSIQGKGVEP 316
Peptidase_S41 pfam03572
Peptidase family S41;
80-254 5.40e-13

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 66.48  E-value: 5.40e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345   80 NVGYLRVDDLpGQEVLSELGEFLvshvwKKLM--GTSSLVLDLRHCTGGHVSGIPYVISYLYPGNTVMhvdTVYDRPSNT 157
Cdd:pfam03572   1 KIGYIRIPSF-SEKTAKELAEAL-----KELKkqGVKGLILDLRGNPGGLLSAAVEIASLFLPDGTIV---STRGRDGSK 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  158 TTEIWTLPevlGERYSADKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTeGGALDLQKLRIGQSNFFLTVPVSRSL 237
Cdd:pfam03572  72 EVYFAAGK---ADEVLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVGERT-FGKGTVQTVYPLPDGSALKLTIAKYY 147

                         170
                  ....*....|....*..
gi 588284345  238 GPlggGGQTWEGSGVLP 254
Cdd:pfam03572 148 TP---DGRSIEGKGIEP 161
Peptidase_S41_TRI cd07562
Tricorn protease; serine protease family S41; The tricorn protease (TRI), a member of the S41 ...
 68-271 2.37e-12

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


Pssm-ID: 143478 [Multi-domain]  Cd Length: 266  Bit Score: 66.84  E-value: 2.37e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  68 IQRNIR--HEVLEGNVGYLRVDDLpGQEVLSELGEFLVSHVWKKlmgtsSLVLDLRHCTGGHVSGipYVISYLYPGNTVM 145
Cdd:cd07562   74 VESNREyvEELSDGRIGYVHIPDM-GDDGFAEFLRDLLAEVDKD-----GLIIDVRFNGGGNVAD--LLLDFLSRRRYGY 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345 146 HVDTVYDRPSNTTTEIWTLPevlgerysadkdVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTEGGALDLQKLR-IGQ 224
Cdd:cd07562  146 DIPRGGGKPVTYPSGRWRGP------------VVVLVNEGSASDAEIFAYGFRALGLGPVVGTRTAGGVIISGRYRlPDG 213

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 588284345 225 SnfFLTVPVSRSLGPLGGGGqtwEGSGVLPCVGIPAE---------QALEKALAIL 271
Cdd:cd07562  214 G--SLTVPEFGVYLPDGGPL---ENRGVAPDIEVENTpedvaagrdPQLEAAIEEL 264
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 280-342 4.53e-04

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


Pssm-ID: 143479 [Multi-domain]  Cd Length: 250  Bit Score: 41.51  E-value: 4.53e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 588284345 280 VVLRLQEALQDYY----TLVDRVPGLLHHLASMDYSAVVSEEDLVTKLNAGLQAVsEDPRLLVRVTG 342
Cdd:cd07563    1 VFEALAKLLEENYafpeAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQEL-GDGHLNVSYIG 66
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 15-78 5.14e-03

N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterized as a serine-peptidase, pfam03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B.


Pssm-ID: 463396  Cd Length: 129  Bit Score: 36.92  E-value: 5.14e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 588284345   15 ISDPQTLARVLTAGVQSSLSDPRLFISY--------EPNTLEAPQQAPALTNLTQEELLAQIQRNIRHEVLE 78
Cdd:pfam11918  58 VVSEEDLASKLNADLQALSGDPRLKVRYirpepasdEPEAADNIPGLVPMQPPSPEMLEALIKSSFKVDVLP 129
Peptidase_S41_CPP_like cd07561
C-terminal processing peptidase-like; serine protease family S41; Bacterial protease homologs ...
 80-212 6.59e-03

C-terminal processing peptidase-like; serine protease family S41; Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP). CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at variable distance from the C-terminus. The CPP active site consists of a serine/lysine catalytic dyad. Conservation of these residues is seen in the CPP-like proteins of this group. CPP proteins contain a PDZ domain that promotes protein-protein interactions and is important for substrate recognition however, most of CPP-like proteins only have an internal fragment or lack the PDZ domain.


Pssm-ID: 143477 [Multi-domain]  Cd Length: 256  Bit Score: 38.00  E-value: 6.59e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345  80 NVGYLRVDDLP---GQEVLSELGEFlvshvwkKLMGTSSLVLDLRHCTGGHVSGIPYVISYLYPGNTVMHVDTVY----D 152
Cdd:cd07561   65 KVGYLVYNSFTsgyDDELNQAFAEF-------KAQGVTELVLDLRYNGGGLVSSANLLASLLAPAVALGQVFATLeyndK 137

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 588284345 153 RPSNTTTEIWTLPEVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQIRHAIVVGERTEG 212
Cdd:cd07561  138 RSANNEDLLFSSKTLAGGNSLNLSKVYVLTSGSTASASELVINSLKPYMDVVLIGETTYG 197
 
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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