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Conserved domains on  [gi|37595963|gb|AAQ94648|]
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interphotoreceptor retinoid-binding protein, partial [Grammomys macmillani]

Protein Classification

interphotoreceptor retinoid-binding protein( domain architecture ID 10166016)

interphotoreceptor retinoid-binding protein (IRBP) is a large glycoprotein known to bind retinoids and found primarily in the interphotoreceptor matrix of the retina between the retinal pigment epithelium and the photoreceptor cells

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 ...
3-274 6.04e-68

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: 215.62  E-value: 6.04e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963   3 GMQAAIEQAMKSHEILGISDPQTLAHVLTAGVQSsLNDPRLFISYepstleapqqapaftnltreellaqiqknirhevl 82
Cdd:cd07563  21 IDWDALAARLRAQVYLDITSPEELAAVLTADLQE-LGDGHLNVSY----------------------------------- 64
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963  83 egnVGYLRVDBLPGQEVlsELEEFLVSHVWEQLMGTSSLVLDLRHCAGGHVSGIPYVISYLHPGNTVMHVDTIYDRPSNT 162
Cdd:cd07563  65 ---IGYLRIDSFGGFEI--AAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNT 139
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963 163 TTEIWTLPKVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTEGGALDLQKLRIGQsNFFLTVPVSRSL 242
Cdd:cd07563 140 TTELWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSV 218
                       250       260       270
                ....*....|....*....|....*....|..
gi 37595963 243 GPLggGGQTWEGSGVLPCVGTPAEQALEKALA 274
Cdd:cd07563 219 DPI--TGTNWEGVGVPPDIEVPATPGYDDALE 248
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
265-390 4.74e-57

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: 183.29  E-value: 4.74e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963   265 AEQALEKALAILTLRRALPGVVLRLQEALQDYYTLVDRVPGLLHHLASM----DYSAVVSEEDLVTKLNAGLQAVSEDPR 340
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLlasgDYSSVVSEEDLASKLNADLQALSGDPR 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 37595963   341 LLVRVTGPRETSSRPETGPNdPPAATPEVPKEEDARRALVESVFQVSVLP 390
Cdd:pfam11918  81 LKVRYIRPEPASDEPEAADN-IPGLVPMQPPSPEMLEALIKSSFKVDVLP 129
 
Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
3-274 6.04e-68

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: 215.62  E-value: 6.04e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963   3 GMQAAIEQAMKSHEILGISDPQTLAHVLTAGVQSsLNDPRLFISYepstleapqqapaftnltreellaqiqknirhevl 82
Cdd:cd07563  21 IDWDALAARLRAQVYLDITSPEELAAVLTADLQE-LGDGHLNVSY----------------------------------- 64
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963  83 egnVGYLRVDBLPGQEVlsELEEFLVSHVWEQLMGTSSLVLDLRHCAGGHVSGIPYVISYLHPGNTVMHVDTIYDRPSNT 162
Cdd:cd07563  65 ---IGYLRIDSFGGFEI--AAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNT 139
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963 163 TTEIWTLPKVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTEGGALDLQKLRIGQsNFFLTVPVSRSL 242
Cdd:cd07563 140 TTELWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSV 218
                       250       260       270
                ....*....|....*....|....*....|..
gi 37595963 243 GPLggGGQTWEGSGVLPCVGTPAEQALEKALA 274
Cdd:cd07563 219 DPI--TGTNWEGVGVPPDIEVPATPGYDDALE 248
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
265-390 4.74e-57

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: 183.29  E-value: 4.74e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963   265 AEQALEKALAILTLRRALPGVVLRLQEALQDYYTLVDRVPGLLHHLASM----DYSAVVSEEDLVTKLNAGLQAVSEDPR 340
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLlasgDYSSVVSEEDLASKLNADLQALSGDPR 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 37595963   341 LLVRVTGPRETSSRPETGPNdPPAATPEVPKEEDARRALVESVFQVSVLP 390
Cdd:pfam11918  81 LKVRYIRPEPASDEPEAADN-IPGLVPMQPPSPEMLEALIKSSFKVDVLP 129
TSPc smart00245
tail specific protease; tail specific protease
65-264 3.38e-53

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 175.52  E-value: 3.38e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963     65 TREELLAQIQKNIRHEVLEGNVGYLRVDbLPGQEVL---SELEEFLVSHVWEQLMGT--SSLVLDLRHCAGGHVSGIPYV 139
Cdd:smart00245   1 SKERTIALIRDKIKIETLEGNVGYLRFG-FIGYIRIpefSEHTSNLVEKAWKKLEKTnvEGLILDLRNNPGGLLSAAIDV 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963    140 ISYLHPGNTvmHVDTIYDRpsntTTEIWTLPKVLGERYSadKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTEGGA 219
Cdd:smart00245  80 SSLFLDKGV--IVYTVYRR----TGELWTYPANLGRKYS--KPLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKG 151
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 37595963    220 LDLQKLRIGqSNFFLTVPVSRSLGPlggGGQTWEGSGVLPCVGTP 264
Cdd:smart00245 152 LVQQTVPLG-DGSGLKLTVAKYYTP---SGKSIEKKGVEPDIQVP 192
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
63-259 3.32e-18

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: 84.92  E-value: 3.32e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963  63 NLTREEllaqIQ-KNIRHEVLEGNVGYLRVDBL---PGQEVLSELEEFlvshvweQLMGTSSLVLDLRHCAGGHVSGIPY 138
Cdd:COG0793 139 TLTRAE----IKlPSVEAKLLEGKIGYIRIPSFgenTAEEFKRALKEL-------KKQGAKGLILDLRNNPGGLLDEAVE 207
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963 139 VISYLHPGNTVMhvdtiYDRPSNTTTEIWtlpKVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTEGG 218
Cdd:COG0793 208 LADLFLPKGPIV-----YTRGRNGKVETY---KATPGGALYDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGK 279
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 37595963 219 AldlqklrIGQSNF------FLTVPVSRSLGPlggGGQTWEGSGVLP 259
Cdd:COG0793 280 G-------SVQTVFplpdggALKLTTARYYTP---SGRSIQGKGVEP 316
Peptidase_S41 pfam03572
Peptidase family S41;
85-259 7.94e-14

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 68.79  E-value: 7.94e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963    85 NVGYLRV---DBLPGQEVLSELEEFLVSHVweqlmgtSSLVLDLRHCAGGHVSGIPYVISYLHPGNTVMHVDtiyDRPSN 161
Cdd:pfam03572   1 KIGYIRIpsfSEKTAKELAEALKELKKQGV-------KGLILDLRGNPGGLLSAAVEIASLFLPDGTIVSTR---GRDGS 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963   162 TTTEIWTLPkvlGERYSADKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTeGGALDLQKLRIGQSNFFLTVPVSRS 241
Cdd:pfam03572  71 KEVYFAAGK---ADEVLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVGERT-FGKGTVQTVYPLPDGSALKLTIAKY 146
                         170
                  ....*....|....*...
gi 37595963   242 LGPlggGGQTWEGSGVLP 259
Cdd:pfam03572 147 YTP---DGRSIEGKGIEP 161
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
285-347 3.61e-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: 41.89  E-value: 3.61e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 37595963 285 VVLRLQEALQDYY----TLVDRVPGLLHHLASMDYSAVVSEEDLVTKLNAGLQAVsEDPRLLVRVTG 347
Cdd:cd07563   1 VFEALAKLLEENYafpeAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQEL-GDGHLNVSYIG 66
 
Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
3-274 6.04e-68

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: 215.62  E-value: 6.04e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963   3 GMQAAIEQAMKSHEILGISDPQTLAHVLTAGVQSsLNDPRLFISYepstleapqqapaftnltreellaqiqknirhevl 82
Cdd:cd07563  21 IDWDALAARLRAQVYLDITSPEELAAVLTADLQE-LGDGHLNVSY----------------------------------- 64
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963  83 egnVGYLRVDBLPGQEVlsELEEFLVSHVWEQLMGTSSLVLDLRHCAGGHVSGIPYVISYLHPGNTVMHVDTIYDRPSNT 162
Cdd:cd07563  65 ---IGYLRIDSFGGFEI--AAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNT 139
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963 163 TTEIWTLPKVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTEGGALDLQKLRIGQsNFFLTVPVSRSL 242
Cdd:cd07563 140 TTELWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSV 218
                       250       260       270
                ....*....|....*....|....*....|..
gi 37595963 243 GPLggGGQTWEGSGVLPCVGTPAEQALEKALA 274
Cdd:cd07563 219 DPI--TGTNWEGVGVPPDIEVPATPGYDDALE 248
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
265-390 4.74e-57

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: 183.29  E-value: 4.74e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963   265 AEQALEKALAILTLRRALPGVVLRLQEALQDYYTLVDRVPGLLHHLASM----DYSAVVSEEDLVTKLNAGLQAVSEDPR 340
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLlasgDYSSVVSEEDLASKLNADLQALSGDPR 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 37595963   341 LLVRVTGPRETSSRPETGPNdPPAATPEVPKEEDARRALVESVFQVSVLP 390
Cdd:pfam11918  81 LKVRYIRPEPASDEPEAADN-IPGLVPMQPPSPEMLEALIKSSFKVDVLP 129
TSPc smart00245
tail specific protease; tail specific protease
65-264 3.38e-53

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 175.52  E-value: 3.38e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963     65 TREELLAQIQKNIRHEVLEGNVGYLRVDbLPGQEVL---SELEEFLVSHVWEQLMGT--SSLVLDLRHCAGGHVSGIPYV 139
Cdd:smart00245   1 SKERTIALIRDKIKIETLEGNVGYLRFG-FIGYIRIpefSEHTSNLVEKAWKKLEKTnvEGLILDLRNNPGGLLSAAIDV 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963    140 ISYLHPGNTvmHVDTIYDRpsntTTEIWTLPKVLGERYSadKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTEGGA 219
Cdd:smart00245  80 SSLFLDKGV--IVYTVYRR----TGELWTYPANLGRKYS--KPLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKG 151
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 37595963    220 LDLQKLRIGqSNFFLTVPVSRSLGPlggGGQTWEGSGVLPCVGTP 264
Cdd:smart00245 152 LVQQTVPLG-DGSGLKLTVAKYYTP---SGKSIEKKGVEPDIQVP 192
Peptidase_S41 cd06567
C-terminal processing peptidase family S41; Peptidase family S41 (C-terminal processing ...
85-261 1.09e-30

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: 117.40  E-value: 1.09e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963  85 NVGYLRVDBLPGQEVLSELEEFLVshvwEQLMGTSSLVLDLRHCAGGHVSGIPYVISYLHPGNTVMHVDTIYDRPsnttt 164
Cdd:cd06567  60 TIGYIRIPSFSAESTAEELREALA----ELKKGVKGLILDLRNNPGGLLSAAVELASLFLPKGKIVVTTRRRGGN----- 130
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963 165 eiWTLPKVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTEGGALDlQKLRIGQSNFFLTVPVSRSLGP 244
Cdd:cd06567 131 --ETEYVAPGGGSLYDGPLVVLVNEGSASASEIFAGALQDLGRATLVGERTFGKGSV-QTVFPLLDGSALKLTTAKYYTP 207
                       170
                ....*....|....*..
gi 37595963 245 lggGGQTWEGSGVLPCV 261
Cdd:cd06567 208 ---SGRSIEGKGVEPDI 221
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
63-259 3.32e-18

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: 84.92  E-value: 3.32e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963  63 NLTREEllaqIQ-KNIRHEVLEGNVGYLRVDBL---PGQEVLSELEEFlvshvweQLMGTSSLVLDLRHCAGGHVSGIPY 138
Cdd:COG0793 139 TLTRAE----IKlPSVEAKLLEGKIGYIRIPSFgenTAEEFKRALKEL-------KKQGAKGLILDLRNNPGGLLDEAVE 207
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963 139 VISYLHPGNTVMhvdtiYDRPSNTTTEIWtlpKVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTEGG 218
Cdd:COG0793 208 LADLFLPKGPIV-----YTRGRNGKVETY---KATPGGALYDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGK 279
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 37595963 219 AldlqklrIGQSNF------FLTVPVSRSLGPlggGGQTWEGSGVLP 259
Cdd:COG0793 280 G-------SVQTVFplpdggALKLTTARYYTP---SGRSIQGKGVEP 316
Peptidase_S41_TRI cd07562
Tricorn protease; serine protease family S41; The tricorn protease (TRI), a member of the S41 ...
73-276 2.57e-14

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: 72.62  E-value: 2.57e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963  73 IQKNIR--HEVLEGNVGYLRVDBLpGQEVLSELeeflvshvWEQLMGTSS---LVLDLRHCAGGHVSGipYVISYLHPGN 147
Cdd:cd07562  74 VESNREyvEELSDGRIGYVHIPDM-GDDGFAEF--------LRDLLAEVDkdgLIIDVRFNGGGNVAD--LLLDFLSRRR 142
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963 148 TVMHVDTIYDRPSNTTTEIWTLPkvlgerysadkdVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTEGGALDLQKLR- 226
Cdd:cd07562 143 YGYDIPRGGGKPVTYPSGRWRGP------------VVVLVNEGSASDAEIFAYGFRALGLGPVVGTRTAGGVIISGRYRl 210
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 37595963 227 IGQSnfFLTVPVSRSLGPLGGGGqtwEGSGVLPCV---GTPAEQA------LEKALAIL 276
Cdd:cd07562 211 PDGG--SLTVPEFGVYLPDGGPL---ENRGVAPDIeveNTPEDVAagrdpqLEAAIEEL 264
Peptidase_S41 pfam03572
Peptidase family S41;
85-259 7.94e-14

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 68.79  E-value: 7.94e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963    85 NVGYLRV---DBLPGQEVLSELEEFLVSHVweqlmgtSSLVLDLRHCAGGHVSGIPYVISYLHPGNTVMHVDtiyDRPSN 161
Cdd:pfam03572   1 KIGYIRIpsfSEKTAKELAEALKELKKQGV-------KGLILDLRGNPGGLLSAAVEIASLFLPDGTIVSTR---GRDGS 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963   162 TTTEIWTLPkvlGERYSADKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTeGGALDLQKLRIGQSNFFLTVPVSRS 241
Cdd:pfam03572  71 KEVYFAAGK---ADEVLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVGERT-FGKGTVQTVYPLPDGSALKLTIAKY 146
                         170
                  ....*....|....*...
gi 37595963   242 LGPlggGGQTWEGSGVLP 259
Cdd:pfam03572 147 YTP---DGRSIEGKGIEP 161
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
285-347 3.61e-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: 41.89  E-value: 3.61e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 37595963 285 VVLRLQEALQDYY----TLVDRVPGLLHHLASMDYSAVVSEEDLVTKLNAGLQAVsEDPRLLVRVTG 347
Cdd:cd07563   1 VFEALAKLLEENYafpeAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQEL-GDGHLNVSYIG 66
Peptidase_S41_CPP_like cd07561
C-terminal processing peptidase-like; serine protease family S41; Bacterial protease homologs ...
85-217 3.73e-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: 38.77  E-value: 3.73e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963  85 NVGYLRVDBLP---GQEVLSELEEFlvshvweQLMGTSSLVLDLRHCAGGHVSGIPYVISYLHPGNT---VMHVdTIY-- 156
Cdd:cd07561  65 KVGYLVYNSFTsgyDDELNQAFAEF-------KAQGVTELVLDLRYNGGGLVSSANLLASLLAPAVAlgqVFAT-LEYnd 136
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 37595963 157 DRPSNTTTEIWTLPKVLGERYSADKDVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERTEG 217
Cdd:cd07561 137 KRSANNEDLLFSSKTLAGGNSLNLSKVYVLTSGSTASASELVINSLKPYMDVVLIGETTYG 197
Peptidase_S41_CPP cd07560
C-terminal processing peptidase; serine protease family S41; The C-terminal processing ...
86-215 5.43e-03

C-terminal processing peptidase; serine protease family S41; The C-terminal processing peptidase (CPP, EC 3.4.21.102) also known as tail-specific protease (tsp), the photosystem II D1 C-terminal processing protease (D1P), and other related S41 protease family members are present in this CD. CPP is synthesized as a precursor form with a carboxyl-terminal extension. It specifically recognizes a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. The C-terminal carboxylate group is essential, and proteins where this group is amidated are not substrates. This family of proteases contains the PDZ domain that promotes protein-protein interactions and is important for substrate recognition. The active site consists of a serine/lysine catalytic dyad. The bacterial CCP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. In E. coli, it is involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3 (PBP3). In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II, allowing the light-driven assembly of the tetranuclear manganese cluster, which is responsible for photosynthetic water oxidation.


Pssm-ID: 143476 [Multi-domain]  Cd Length: 211  Bit Score: 37.78  E-value: 5.43e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 37595963  86 VGYLRV---DBLPGQEVLSELEEFLvshvwEQLMgtSSLVLDLRHCAGGHV-SGIPyVISYLHPGNTVMHV---DTIYDR 158
Cdd:cd07560  50 IGYIRItsfSENTAEELKKALKELK-----KQGM--KGLILDLRNNPGGLLdEAVE-IADLFLPGGPIVSTkgrNGKREA 121
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 37595963 159 PSNTTTEIWTLPkvlgerysadkdVVVLTSGHTGGVAEDIAYILKQMRRAIVVGERT 215
Cdd:cd07560 122 YASDDGGLYDGP------------LVVLVNGGSASASEIVAGALQDNGRAVLVGERT 166
 
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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