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Conserved domains on  [gi|404325416|gb|AFR58499|]
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interphotoreceptor retinoid-binding protein 2, partial [Moxostoma sp. 'sicklefin redhorse']

Protein Classification

S41 family peptidase( domain architecture ID 10165999)

S41 family peptidase similar to vertebrate retinol-binding protein 3 (Rbp3), the major soluble component of the interphotoreceptor matrix and is critical to the function, integrity, and development of the retina

CATH:  3.90.226.10|3.30.750.44
EC:  3.4.-.-
Gene Ontology:  GO:0006508|GO:0008236
MEROPS:  S41

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 ...
 3-269 2.05e-67

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: 217.54  E-value: 2.05e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   3 EAIEAASSNTEILSIPDPATLSSVLTDGVKNtIGDSRVQITYepgyipaappampdippehlaavikstvgvevldgnIA 82
Cdd:cd07563   24 DALAARLRAQVYLDITSPEELAAVLTADLQE-LGDGHLNVSY------------------------------------IG 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  83 YLKIQHIIGEEMAqkVGPLLLEYIWDKVLPTSAMILDFRYAVSGELSGIPYIVSYFTDSEPLIHIDSVYDRPSDTTTELW 162
Cdd:cd07563   67 YLRIDSFGGFEIA--AAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTELW 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 163 SMPTLLGKRYGTSKPLIILTSKNTIGIAEDVAYCLKNLKRATIVGENTAGGTVKTDKIKVGDtDFYVSVPVAKSVNPITG 242
Cdd:cd07563  145 TLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSVDPITG 223

                        250       260
                 ....*....|....*....|....*..
gi 404325416 243 KSWEINGVAPDVEVTAEDALDTAIAII 269
Cdd:cd07563  224 TNWEGVGVPPDIEVPATPGYDDALERA 250
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 280-514 1.05e-65

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: 212.92  E-value: 1.05e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 280 QAAATLIDDNYAFPSVGAIVAEKLEAVVASGEYNFVSTKEELEAKLSADLLKLsGDKCLKttsnipalppmnptpemfie 359
Cdd:cd07563    3 EALAKLLEENYAFPEAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQEL-GDGHLN-------------------- 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 360 likVSFhtdvfennIGYLRFDMFGDFEhvAAIAQIIVEHVWNKVVDTDALILDLRNNIGGATTSIAGFCSYFFDGDKQIV 439
Cdd:cd07563   62 ---VSY--------IGYLRIDSFGGFE--IAAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVH 128

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 404325416 440 LDQLYDRPSNTTRGVLTLTKLTGRRYGSKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSGGCHPPENFR 514
Cdd:cd07563  129 LYTIYKRPGNTTTELWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFP 203
 
Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 3-269 2.05e-67

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: 217.54  E-value: 2.05e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   3 EAIEAASSNTEILSIPDPATLSSVLTDGVKNtIGDSRVQITYepgyipaappampdippehlaavikstvgvevldgnIA 82
Cdd:cd07563   24 DALAARLRAQVYLDITSPEELAAVLTADLQE-LGDGHLNVSY------------------------------------IG 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  83 YLKIQHIIGEEMAqkVGPLLLEYIWDKVLPTSAMILDFRYAVSGELSGIPYIVSYFTDSEPLIHIDSVYDRPSDTTTELW 162
Cdd:cd07563   67 YLRIDSFGGFEIA--AAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTELW 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 163 SMPTLLGKRYGTSKPLIILTSKNTIGIAEDVAYCLKNLKRATIVGENTAGGTVKTDKIKVGDtDFYVSVPVAKSVNPITG 242
Cdd:cd07563  145 TLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSVDPITG 223

                        250       260
                 ....*....|....*....|....*..
gi 404325416 243 KSWEINGVAPDVEVTAEDALDTAIAII 269
Cdd:cd07563  224 TNWEGVGVPPDIEVPATPGYDDALERA 250
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 280-514 1.05e-65

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: 212.92  E-value: 1.05e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 280 QAAATLIDDNYAFPSVGAIVAEKLEAVVASGEYNFVSTKEELEAKLSADLLKLsGDKCLKttsnipalppmnptpemfie 359
Cdd:cd07563    3 EALAKLLEENYAFPEAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQEL-GDGHLN-------------------- 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 360 likVSFhtdvfennIGYLRFDMFGDFEhvAAIAQIIVEHVWNKVVDTDALILDLRNNIGGATTSIAGFCSYFFDGDKQIV 439
Cdd:cd07563   62 ---VSY--------IGYLRIDSFGGFE--IAAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVH 128

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 404325416 440 LDQLYDRPSNTTRGVLTLTKLTGRRYGSKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSGGCHPPENFR 514
Cdd:cd07563  129 LYTIYKRPGNTTTELWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFP 203
TSPc smart00245
tail specific protease; tail specific protease
 60-256 1.44e-50

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 171.28  E-value: 1.44e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416    60 PPEHLAAVIKSTVGVEVLDGNIAYLKIqHIIGEEMAQKVGPL---LLEYIWDKVLPT--SAMILDFRYAVSGELSGIPYI 134
Cdd:smart00245   1 SKERTIALIRDKIKIETLEGNVGYLRF-GFIGYIRIPEFSEHtsnLVEKAWKKLEKTnvEGLILDLRNNPGGLLSAAIDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   135 VSYFTDSEplIHIDSVYDRpsdtTTELWSMPTLLGKRYgtSKPLIILTSKNTIGIAEDVAYCLKNLKRATIVGENTAGGT 214
Cdd:smart00245  80 SSLFLDKG--VIVYTVYRR----TGELWTYPANLGRKY--SKPLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKG 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 404325416   215 VKTDKIKVGDtDFYVSVPVAKSVNPiTGKSWEINGVAPDVEV 256
Cdd:smart00245 152 LVQQTVPLGD-GSGLKLTVAKYYTP-SGKSIEKKGVEPDIQV 191
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 258-371 2.51e-43

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: 149.78  E-value: 2.51e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  258 AEDALDTAIAIIKLRAEIPGLAQAAATLIDDNYAFPSVGAIVAEKLEAVVASGEYNFVSTKEELEAKLSADLLKLSGDKC 337
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLLASGDYSSVVSEEDLASKLNADLQALSGDPR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 404325416  338 LKTT--------------SNIPALPPM-NPTPEMFIELIKVSFHTDVFE 371
Cdd:pfam11918  81 LKVRyirpepasdepeaaDNIPGLVPMqPPSPEMLEALIKSSFKVDVLP 129
TSPc smart00245
tail specific protease; tail specific protease
 353-514 1.65e-39

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 142.01  E-value: 1.65e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   353 TPEMFIELIKVSFHTDVFENNIGYLRFdMFGDFEHVAAIAQ---IIVEHVWNKVVDT--DALILDLRNNIGGATTSIAGF 427
Cdd:smart00245   1 SKERTIALIRDKIKIETLEGNVGYLRF-GFIGYIRIPEFSEhtsNLVEKAWKKLEKTnvEGLILDLRNNPGGLLSAAIDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   428 CSYFFDGDkqIVLDQLYDRpsntTRGVLTLTKLTGRRYgsKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSGGC 507
Cdd:smart00245  80 SSLFLDKG--VIVYTVYRR----TGELWTYPANLGRKY--SKPLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKG 151


                   ....*..
gi 404325416   508 HPPENFR 514
Cdd:smart00245 152 LVQQTVP 158
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 71-268 5.56e-16

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: 79.14  E-value: 5.56e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  71 TVGVEVLDGNIAYLKIQhiigeEMAQKVGPLLLEYIWD-KVLPTSAMILDFRYAVSGELSGIPYIVSYFTDSEPLihids 149
Cdd:COG0793  149 SVEAKLLEGKIGYIRIP-----SFGENTAEEFKRALKElKKQGAKGLILDLRNNPGGLLDEAVELADLFLPKGPI----- 218

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 150 VYDRPSDTTTELWSMPtllGKRYGTSKPLIILTSKNTIGIAEDVAYCLKNLKRATIVGENTAG-GTVKTDkIKVGDTDFy 228
Cdd:COG0793  219 VYTRGRNGKVETYKAT---PGGALYDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGkGSVQTV-FPLPDGGA- 293

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 404325416 229 VSVPVAKSVNPiTGKSWEINGVAPDVEV--------TAEDA-LDTAIAI 268
Cdd:COG0793  294 LKLTTARYYTP-SGRSIQGKGVEPDIEVpltpedllKGRDPqLEKALEL 341
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 369-506 1.12e-12

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: 69.13  E-value: 1.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 369 VFENNIGYLRFDMFGD--FEHV-AAIAQIIVEHVwnkvvdtDALILDLRNNIGGATTSIAGFCSYFFDGDKqIVLDQLYD 445
Cdd:COG0793  154 LLEGKIGYIRIPSFGEntAEEFkRALKELKKQGA-------KGLILDLRNNPGGLLDEAVELADLFLPKGP-IVYTRGRN 225

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 404325416 446 RPSNTTRGVLTLTKLTGRrygskksLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSGG 506
Cdd:COG0793  226 GKVETYKATPGGALYDGP-------LVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGK 279
Peptidase_S41 pfam03572
Peptidase family S41;
80-256 1.18e-12

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 66.09  E-value: 1.18e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   80 NIAYLKIQhiigeEMAQKVGPLLLEYIWDkvLPTSAM---ILDFRYAVSGELSGIPYIVSYFTDSEPlihIDSVYDRPSD 156
Cdd:pfam03572   1 KIGYIRIP-----SFSEKTAKELAEALKE--LKKQGVkglILDLRGNPGGLLSAAVEIASLFLPDGT---IVSTRGRDGS 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  157 TTTELwsmPTLLGKRYGTSKPLIILTSKNTIGIAEDVAYCLKNLKRATIVGENTAGGTVKTDKIKVGDtDFYVSVPVAKS 236
Cdd:pfam03572  71 KEVYF---AAGKADEVLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVGERTFGKGTVQTVYPLPD-GSALKLTIAKY 146

                         170       180
                  ....*....|....*....|
gi 404325416  237 VNPItGKSWEINGVAPDVEV 256
Cdd:pfam03572 147 YTPD-GRSIEGKGIEPDIEV 165
prc TIGR00225
C-terminal peptidase (prc); A C-terminal peptidase with different substrates in different ...
 358-505 9.18e-08

C-terminal peptidase (prc); A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database. [Protein fate, Degradation of proteins, peptides, and glycopeptides, Protein fate, Protein modification and repair]


Pssm-ID: 272970 [Multi-domain]  Cd Length: 334  Bit Score: 53.90  E-value: 9.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  358 IELIKVSFhTDVFENNIGYLRFDMFgdFEHVAAIAQIIVEHVWNKVVDtdALILDLRNNIGGATTSIAGFCSYFFDGDKq 437
Cdd:TIGR00225 138 LETVKASV-KKVGGHSVGYIRISSF--SEHTAEDVAKALDKLEKKNAK--GYILDLRGNPGGLLQSAVDISRLFITKGP- 211

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 404325416  438 IVldQLYDRpsnttRGVLTLTKLTGRRYgSKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSG 505
Cdd:TIGR00225 212 IV--QTKDR-----NGSKRHYKANGRQK-YNLPLVVLVNRGSASASEILAGALQDNGRATIVGEKTFG 271
PLN00049 PLN00049
carboxyl-terminal processing protease; Provisional
 374-505 1.18e-03

carboxyl-terminal processing protease; Provisional


Pssm-ID: 177681 [Multi-domain]  Cd Length: 389  Bit Score: 41.26  E-value: 1.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 374 IGYLRFDMFGDFEhVAAIAQIIVEHVWNKVvdtDALILDLRNNIGG---ATTSIAGFcsYFFDGDKQIVLDQLYDRPSNT 450
Cdd:PLN00049 196 IGYIKLTTFNQNA-SSAVKEAIETLRANGV---DAFVLDLRDNSGGlfpAGIEIAKL--WLDKGVIVYIADSRGVRDIYD 269

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 404325416 451 TRGVLTLTkltgrrygSKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSG 505
Cdd:PLN00049 270 ADGSSAIA--------TSEPLAVLVNKGTASASEILAGALKDNKRAVVLGEPTFG 316
PLN00049 PLN00049
carboxyl-terminal processing protease; Provisional
 114-253 3.90e-03

carboxyl-terminal processing protease; Provisional


Pssm-ID: 177681 [Multi-domain]  Cd Length: 389  Bit Score: 39.72  E-value: 3.90e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 114 SAMILDFRYAVSGELSGIPYIVSYFTDSEPLIHI-DS-----VYDrpSDTTTELwsmptllgkryGTSKPLIILTSKNTI 187
Cdd:PLN00049 225 DAFVLDLRDNSGGLFPAGIEIAKLWLDKGVIVYIaDSrgvrdIYD--ADGSSAI-----------ATSEPLAVLVNKGTA 291

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 404325416 188 GIAEDVAYCLKNLKRATIVGENTAG-GTVKTdKIKVGDTDfYVSVPVAKSVNPiTGKswEIN--GVAPD 253
Cdd:PLN00049 292 SASEILAGALKDNKRAVVLGEPTFGkGLIQS-VFELSDGS-GLAVTVARYQTP-AGT--DIDkvGITPD 355
 
Name Accession Description Interval E-value
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 3-269 2.05e-67

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: 217.54  E-value: 2.05e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   3 EAIEAASSNTEILSIPDPATLSSVLTDGVKNtIGDSRVQITYepgyipaappampdippehlaavikstvgvevldgnIA 82
Cdd:cd07563   24 DALAARLRAQVYLDITSPEELAAVLTADLQE-LGDGHLNVSY------------------------------------IG 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  83 YLKIQHIIGEEMAqkVGPLLLEYIWDKVLPTSAMILDFRYAVSGELSGIPYIVSYFTDSEPLIHIDSVYDRPSDTTTELW 162
Cdd:cd07563   67 YLRIDSFGGFEIA--AAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTELW 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 163 SMPTLLGKRYGTSKPLIILTSKNTIGIAEDVAYCLKNLKRATIVGENTAGGTVKTDKIKVGDtDFYVSVPVAKSVNPITG 242
Cdd:cd07563  145 TLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFPLPN-GLYLTVPTSRSVDPITG 223

                        250       260
                 ....*....|....*....|....*..
gi 404325416 243 KSWEINGVAPDVEVTAEDALDTAIAII 269
Cdd:cd07563  224 TNWEGVGVPPDIEVPATPGYDDALERA 250
Peptidase_S41_IRBP cd07563
Interphotoreceptor retinoid-binding protein; serine protease family S41; Interphotoreceptor ...
 280-514 1.05e-65

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: 212.92  E-value: 1.05e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 280 QAAATLIDDNYAFPSVGAIVAEKLEAVVASGEYNFVSTKEELEAKLSADLLKLsGDKCLKttsnipalppmnptpemfie 359
Cdd:cd07563    3 EALAKLLEENYAFPEAKGIDWDALAARLRAQVYLDITSPEELAAVLTADLQEL-GDGHLN-------------------- 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 360 likVSFhtdvfennIGYLRFDMFGDFEhvAAIAQIIVEHVWNKVVDTDALILDLRNNIGGATTSIAGFCSYFFDGDKQIV 439
Cdd:cd07563   62 ---VSY--------IGYLRIDSFGGFE--IAAAEALLDEALDKLADTDALIIDLRYNGGGSDSLVAYLASYFTDEDKPVH 128

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 404325416 440 LDQLYDRPSNTTRGVLTLTKLTGRRYGSKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSGGCHPPENFR 514
Cdd:cd07563  129 LYTIYKRPGNTTTELWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAGGASPVLPFP 203
TSPc smart00245
tail specific protease; tail specific protease
 60-256 1.44e-50

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 171.28  E-value: 1.44e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416    60 PPEHLAAVIKSTVGVEVLDGNIAYLKIqHIIGEEMAQKVGPL---LLEYIWDKVLPT--SAMILDFRYAVSGELSGIPYI 134
Cdd:smart00245   1 SKERTIALIRDKIKIETLEGNVGYLRF-GFIGYIRIPEFSEHtsnLVEKAWKKLEKTnvEGLILDLRNNPGGLLSAAIDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   135 VSYFTDSEplIHIDSVYDRpsdtTTELWSMPTLLGKRYgtSKPLIILTSKNTIGIAEDVAYCLKNLKRATIVGENTAGGT 214
Cdd:smart00245  80 SSLFLDKG--VIVYTVYRR----TGELWTYPANLGRKY--SKPLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKG 151

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 404325416   215 VKTDKIKVGDtDFYVSVPVAKSVNPiTGKSWEINGVAPDVEV 256
Cdd:smart00245 152 LVQQTVPLGD-GSGLKLTVAKYYTP-SGKSIEKKGVEPDIQV 191
Peptidase_S41_N pfam11918
N-terminal domain of Peptidase_S41 in eukaryotic IRBP; Peptidase_S41_N is a family found at ...
 258-371 2.51e-43

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: 149.78  E-value: 2.51e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  258 AEDALDTAIAIIKLRAEIPGLAQAAATLIDDNYAFPSVGAIVAEKLEAVVASGEYNFVSTKEELEAKLSADLLKLSGDKC 337
Cdd:pfam11918   1 AEEALEKALEILALRRAIPALVQTLGKLLADNYAFPERVPAVAAHLASLLASGDYSSVVSEEDLASKLNADLQALSGDPR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 404325416  338 LKTT--------------SNIPALPPM-NPTPEMFIELIKVSFHTDVFE 371
Cdd:pfam11918  81 LKVRyirpepasdepeaaDNIPGLVPMqPPSPEMLEALIKSSFKVDVLP 129
TSPc smart00245
tail specific protease; tail specific protease
 353-514 1.65e-39

tail specific protease; tail specific protease


Pssm-ID: 214582  Cd Length: 192  Bit Score: 142.01  E-value: 1.65e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   353 TPEMFIELIKVSFHTDVFENNIGYLRFdMFGDFEHVAAIAQ---IIVEHVWNKVVDT--DALILDLRNNIGGATTSIAGF 427
Cdd:smart00245   1 SKERTIALIRDKIKIETLEGNVGYLRF-GFIGYIRIPEFSEhtsNLVEKAWKKLEKTnvEGLILDLRNNPGGLLSAAIDV 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   428 CSYFFDGDkqIVLDQLYDRpsntTRGVLTLTKLTGRRYgsKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSGGC 507
Cdd:smart00245  80 SSLFLDKG--VIVYTVYRR----TGELWTYPANLGRKY--SKPLVVLVNKGTASASEIFAGALKDLGRATIVGERTFGKG 151


                   ....*..
gi 404325416   508 HPPENFR 514
Cdd:smart00245 152 LVQQTVP 158
Peptidase_S41 cd06567
C-terminal processing peptidase family S41; Peptidase family S41 (C-terminal processing ...
 52-256 3.36e-31

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: 120.09  E-value: 3.36e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  52 APPAMPDIPPEHLAAVIKSTVGvEVLDG-----NIAYLKIQHIIGEEMAQkvgpLLLEYIWDKVLPTSAMILDFRYAVSG 126
Cdd:cd06567   28 VDLLDAVDDRELLAGALNGMLG-ELGDPhsrylTIGYIRIPSFSAESTAE----ELREALAELKKGVKGLILDLRNNPGG 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 127 ELSGIPYIVSYFTDSEPLIHIDSVYDRPsdtttelWSMPTLLGKRYGTSKPLIILTSKNTIGIAEDVAYCLKNLKRATIV 206
Cdd:cd06567  103 LLSAAVELASLFLPKGKIVVTTRRRGGN-------ETEYVAPGGGSLYDGPLVVLVNEGSASASEIFAGALQDLGRATLV 175

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 404325416 207 GENTAGGTVKTDKIKVGDtDFYVSVPVAKSVNPiTGKSWEINGVAPDVEV 256
Cdd:cd06567  176 GERTFGKGSVQTVFPLLD-GSALKLTTAKYYTP-SGRSIEGKGVEPDIEV 223
Peptidase_S41 cd06567
C-terminal processing peptidase family S41; Peptidase family S41 (C-terminal processing ...
 281-506 2.03e-27

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: 109.69  E-value: 2.03e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 281 AAATLIDDNYAFPSVGAIVAEKLEAVVasgEYNFVSTKEELEAKLSADLLKLsGDKclkttsnipalppmnptpemfiel 360
Cdd:cd06567    3 EAWRLLRENYYDPHGVDWDALRDRYVD---LLDAVDDRELLAGALNGMLGEL-GDP------------------------ 54

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 361 ikvsfHTDVFenNIGYLRFDMFGDfehvAAIAQIIVEHVWNKVVDTDALILDLRNNIGGATTSIAGFCSYFFDGDKQIVL 440
Cdd:cd06567   55 -----HSRYL--TIGYIRIPSFSA----ESTAEELREALAELKKGVKGLILDLRNNPGGLLSAAVELASLFLPKGKIVVT 123

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 404325416 441 DQLYDRPSNTTrgvltltKLTGRRYGSKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSGG 506
Cdd:cd06567  124 TRRRGGNETEY-------VAPGGGSLYDGPLVVLVNEGSASASEIFAGALQDLGRATLVGERTFGK 182
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 71-268 5.56e-16

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: 79.14  E-value: 5.56e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  71 TVGVEVLDGNIAYLKIQhiigeEMAQKVGPLLLEYIWD-KVLPTSAMILDFRYAVSGELSGIPYIVSYFTDSEPLihids 149
Cdd:COG0793  149 SVEAKLLEGKIGYIRIP-----SFGENTAEEFKRALKElKKQGAKGLILDLRNNPGGLLDEAVELADLFLPKGPI----- 218

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 150 VYDRPSDTTTELWSMPtllGKRYGTSKPLIILTSKNTIGIAEDVAYCLKNLKRATIVGENTAG-GTVKTDkIKVGDTDFy 228
Cdd:COG0793  219 VYTRGRNGKVETYKAT---PGGALYDGPLVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGkGSVQTV-FPLPDGGA- 293

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 404325416 229 VSVPVAKSVNPiTGKSWEINGVAPDVEV--------TAEDA-LDTAIAI 268
Cdd:COG0793  294 LKLTTARYYTP-SGRSIQGKGVEPDIEVpltpedllKGRDPqLEKALEL 341
Peptidase_S41 pfam03572
Peptidase family S41;
373-506 1.47e-14

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 71.48  E-value: 1.47e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  373 NIGYLRFDMFGdfEHVAA-IAQIIVEhvwNKVVDTDALILDLRNNIGGATTSIAGFCSYFFDGDKqIVLDQLYDRPSNTT 451
Cdd:pfam03572   1 KIGYIRIPSFS--EKTAKeLAEALKE---LKKQGVKGLILDLRGNPGGLLSAAVEIASLFLPDGT-IVSTRGRDGSKEVY 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 404325416  452 RgvltlTKLTGRRYGSKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSGG 506
Cdd:pfam03572  75 F-----AAGKADEVLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVGERTFGK 124
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
 369-506 1.12e-12

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: 69.13  E-value: 1.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 369 VFENNIGYLRFDMFGD--FEHV-AAIAQIIVEHVwnkvvdtDALILDLRNNIGGATTSIAGFCSYFFDGDKqIVLDQLYD 445
Cdd:COG0793  154 LLEGKIGYIRIPSFGEntAEEFkRALKELKKQGA-------KGLILDLRNNPGGLLDEAVELADLFLPKGP-IVYTRGRN 225

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 404325416 446 RPSNTTRGVLTLTKLTGRrygskksLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSGG 506
Cdd:COG0793  226 GKVETYKATPGGALYDGP-------LVVLVNEGSASASEIFAGALQDYGRGVIVGTRTFGK 279
Peptidase_S41 pfam03572
Peptidase family S41;
80-256 1.18e-12

Peptidase family S41;


Pssm-ID: 460977  Cd Length: 165  Bit Score: 66.09  E-value: 1.18e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416   80 NIAYLKIQhiigeEMAQKVGPLLLEYIWDkvLPTSAM---ILDFRYAVSGELSGIPYIVSYFTDSEPlihIDSVYDRPSD 156
Cdd:pfam03572   1 KIGYIRIP-----SFSEKTAKELAEALKE--LKKQGVkglILDLRGNPGGLLSAAVEIASLFLPDGT---IVSTRGRDGS 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  157 TTTELwsmPTLLGKRYGTSKPLIILTSKNTIGIAEDVAYCLKNLKRATIVGENTAGGTVKTDKIKVGDtDFYVSVPVAKS 236
Cdd:pfam03572  71 KEVYF---AAGKADEVLWKGPLVVLVNEGSASASEIFAGALQDNGRATLVGERTFGKGTVQTVYPLPD-GSALKLTIAKY 146

                         170       180
                  ....*....|....*....|
gi 404325416  237 VNPItGKSWEINGVAPDVEV 256
Cdd:pfam03572 147 YTPD-GRSIEGKGIEPDIEV 165
Peptidase_S41_TRI cd07562
Tricorn protease; serine protease family S41; The tricorn protease (TRI), a member of the S41 ...
 65-270 2.86e-11

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: 64.14  E-value: 2.86e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  65 AAVIKSTVGVEVL-DGNIAYLKIQhiigeEMaqkvGPLLLEYIWDKVLPTS---AMILDFRYAVSGELSGipYIVSYFTd 140
Cdd:cd07562   72 DWVESNREYVEELsDGRIGYVHIP-----DM----GDDGFAEFLRDLLAEVdkdGLIIDVRFNGGGNVAD--LLLDFLS- 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 141 SEPLIhidsvYDRPSDTTtELWSMPtllgkRYGTSKPLIILTSKNTIGIAEDVAYCLKNLKRATIVGENTAGGTVKTDKI 220
Cdd:cd07562  140 RRRYG-----YDIPRGGG-KPVTYP-----SGRWRGPVVVLVNEGSASDAEIFAYGFRALGLGPVVGTRTAGGVIISGRY 208

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 404325416 221 KVGDTDfYVSVPVAKSVNPiTGKSWEINGVAPDVEV--TAED-------ALDTAIAIIK 270
Cdd:cd07562  209 RLPDGG-SLTVPEFGVYLP-DGGPLENRGVAPDIEVenTPEDvaagrdpQLEAAIEELL 265
Peptidase_S41_TRI cd07562
Tricorn protease; serine protease family S41; The tricorn protease (TRI), a member of the S41 ...
 374-507 3.44e-10

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: 60.68  E-value: 3.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 374 IGYLRFDMFGDFEHVAAIAQIIVEhvwnkvVDTDALILDLRNNIGGattSIAGFcsyffdgdkqiVLDQLYDRPSNT--T 451
Cdd:cd07562   89 IGYVHIPDMGDDGFAEFLRDLLAE------VDKDGLIIDVRFNGGG---NVADL-----------LLDFLSRRRYGYdiP 148

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 404325416 452 RGVLTLTKLTGRRYgsKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSGGC 507
Cdd:cd07562  149 RGGGKPVTYPSGRW--RGPVVVLVNEGSASDAEIFAYGFRALGLGPVVGTRTAGGV 202
prc TIGR00225
C-terminal peptidase (prc); A C-terminal peptidase with different substrates in different ...
 358-505 9.18e-08

C-terminal peptidase (prc); A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database. [Protein fate, Degradation of proteins, peptides, and glycopeptides, Protein fate, Protein modification and repair]


Pssm-ID: 272970 [Multi-domain]  Cd Length: 334  Bit Score: 53.90  E-value: 9.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416  358 IELIKVSFhTDVFENNIGYLRFDMFgdFEHVAAIAQIIVEHVWNKVVDtdALILDLRNNIGGATTSIAGFCSYFFDGDKq 437
Cdd:TIGR00225 138 LETVKASV-KKVGGHSVGYIRISSF--SEHTAEDVAKALDKLEKKNAK--GYILDLRGNPGGLLQSAVDISRLFITKGP- 211

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 404325416  438 IVldQLYDRpsnttRGVLTLTKLTGRRYgSKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSG 505
Cdd:TIGR00225 212 IV--QTKDR-----NGSKRHYKANGRQK-YNLPLVVLVNRGSASASEILAGALQDNGRATIVGEKTFG 271
Peptidase_S41_CPP cd07560
C-terminal processing peptidase; serine protease family S41; The C-terminal processing ...
 366-505 1.79e-07

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: 51.64  E-value: 1.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 366 HTdVFENNIGYLRFDMFG-----DFEhvAAIAQIIVEHVwnkvvdtDALILDLRNNIGGATTSIAGFCSYFFDGdKQIVl 440
Cdd:cd07560   43 YS-RYLTPIGYIRITSFSentaeELK--KALKELKKQGM-------KGLILDLRNNPGGLLDEAVEIADLFLPG-GPIV- 110

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 404325416 441 dQLYDRPSNTTrgvltlTKLTGRRYGSKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSG 505
Cdd:cd07560  111 -STKGRNGKRE------AYASDDGGLYDGPLVVLVNGGSASASEIVAGALQDNGRAVLVGERTFG 168
Peptidase_S41_CPP_like cd07561
C-terminal processing peptidase-like; serine protease family S41; Bacterial protease homologs ...
 344-505 2.04e-04

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: 43.01  E-value: 2.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 344 IPALPPMN--PTPEMFIELIKV--------SFHTDVFENnIGYLRFDMFG---DFEHVAAIAQIIVEHVwnkvvdtDALI 410
Cdd:cd07561   27 IPALDDLDyfDDPEDFLESLLSekdgkdrfSYIVDGGKK-VGYLVYNSFTsgyDDELNQAFAEFKAQGV-------TELV 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 411 LDLRNNIGGATTS-------IAG-------FCSYFFDgDKQIVLDQLYDRPSNTTRGVLTLtkltgrrygSKKSLIILTS 476
Cdd:cd07561   99 LDLRYNGGGLVSSanllaslLAPavalgqvFATLEYN-DKRSANNEDLLFSSKTLAGGNSL---------NLSKVYVLTS 168

                        170       180
                 ....*....|....*....|....*....
gi 404325416 477 GATAGAAEEFVFIMKRLGRAMIIGETTSG 505
Cdd:cd07561  169 GSTASASELVINSLKPYMDVVLIGETTYG 197
Peptidase_S41_CPP cd07560
C-terminal processing peptidase; serine protease family S41; The C-terminal processing ...
 134-256 4.44e-04

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: 41.63  E-value: 4.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 134 IVSYFTDSEPLIHI---DSVYDRPSDTTTELWSMPtllgkrygtskpLIILTSKNTIGIAEDVAYCLKNLKRATIVGENT 210
Cdd:cd07560   99 IADLFLPGGPIVSTkgrNGKREAYASDDGGLYDGP------------LVVLVNGGSASASEIVAGALQDNGRAVLVGERT 166

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 404325416 211 AG-GTVKTdkikVGDTDF--YVSVPVAKSVNPiTGKSweIN--GVAPDVEV 256
Cdd:cd07560  167 FGkGSVQT----VFPLSDgsALKLTTAKYYTP-SGRS--IQkkGIEPDIEV 210
PLN00049 PLN00049
carboxyl-terminal processing protease; Provisional
 374-505 1.18e-03

carboxyl-terminal processing protease; Provisional


Pssm-ID: 177681 [Multi-domain]  Cd Length: 389  Bit Score: 41.26  E-value: 1.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 374 IGYLRFDMFGDFEhVAAIAQIIVEHVWNKVvdtDALILDLRNNIGG---ATTSIAGFcsYFFDGDKQIVLDQLYDRPSNT 450
Cdd:PLN00049 196 IGYIKLTTFNQNA-SSAVKEAIETLRANGV---DAFVLDLRDNSGGlfpAGIEIAKL--WLDKGVIVYIADSRGVRDIYD 269

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 404325416 451 TRGVLTLTkltgrrygSKKSLIILTSGATAGAAEEFVFIMKRLGRAMIIGETTSG 505
Cdd:PLN00049 270 ADGSSAIA--------TSEPLAVLVNKGTASASEILAGALKDNKRAVVLGEPTFG 316
Peptidase_S41_CPP_like cd07561
C-terminal processing peptidase-like; serine protease family S41; Bacterial protease homologs ...
 117-257 1.77e-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: 40.32  E-value: 1.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 117 ILDFRYAVSGELSGIPYIVSYFTdsePLIHIDSVY-------DRPSDTTTELWSMPTLLGKRYGTSKPLIILTSKNTIGI 189
Cdd:cd07561   98 VLDLRYNGGGLVSSANLLASLLA---PAVALGQVFatleyndKRSANNEDLLFSSKTLAGGNSLNLSKVYVLTSGSTASA 174

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 404325416 190 AEDVAYCLKNLKRATIVGENTAGgtvKTdkikVGDTDFYVSVPVAKSVNPITGKSWE-------INGVAPDVEVT 257
Cdd:cd07561  175 SELVINSLKPYMDVVLIGETTYG---KN----VGSLTFEDDRKHKWALQPVVFKVVNadgqgdySNGLTPDIEVN 242
PLN00049 PLN00049
carboxyl-terminal processing protease; Provisional
 114-253 3.90e-03

carboxyl-terminal processing protease; Provisional


Pssm-ID: 177681 [Multi-domain]  Cd Length: 389  Bit Score: 39.72  E-value: 3.90e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 404325416 114 SAMILDFRYAVSGELSGIPYIVSYFTDSEPLIHI-DS-----VYDrpSDTTTELwsmptllgkryGTSKPLIILTSKNTI 187
Cdd:PLN00049 225 DAFVLDLRDNSGGLFPAGIEIAKLWLDKGVIVYIaDSrgvrdIYD--ADGSSAI-----------ATSEPLAVLVNKGTA 291

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 404325416 188 GIAEDVAYCLKNLKRATIVGENTAG-GTVKTdKIKVGDTDfYVSVPVAKSVNPiTGKswEIN--GVAPD 253
Cdd:PLN00049 292 SASEILAGALKDNKRAVVLGEPTFGkGLIQS-VFELSDGS-GLAVTVARYQTP-AGT--DIDkvGITPD 355
 
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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