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Conserved domains on  [gi|74730631|sp|Q8WTU0|]
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RecName: Full=Protein DDI1 homolog 1

Protein Classification

DNA damage-inducible protein 1; ubiquitin family protein( domain architecture ID 12922302)

DNA damage-inducible protein 1 (DDI1) is a probable aspartic protease that may be involved in the regulation of exocytosis| ubiquitin family protein belongs to a diverse class of protein modifier and gene expression regulatory proteins that participate in a number of cellular processes; has an N-terminal domain with similarity to the N-terminus of ubiquitin fusion degradation UFD1 which functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RP_DDI cd05479
RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the ...
 229-351 4.26e-80

RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.


:

Pssm-ID: 133146  Cd Length: 124  Bit Score: 241.69  E-value: 4.26e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631 229 IAIEEAPESFGQVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQ 308
Cdd:cd05479   2 NAMEHHPESFGKVPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVK 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 74730631 309 IEGDFLQCSFSILEDQPMDMLLGLDMLRRHQCSIDLKKNVLVI 351
Cdd:cd05479  82 IGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQCVIDLKENVLRI 124
Ubl_Ddi1_like cd01796
ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, ...
 1-76 5.37e-23

ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, including yeast aspartyl protease DNA-damage inducible 1 (Ddi1) and Ddi1-like proteins from vertebrates and other eukaryotes, has been characterized by containing an N-terminal ubiquitin-like (Ubl) domain and a conserved retroviral aspartyl-protease-like domain (RVP) that is important in cell-cycle control. Yeast Ddi1 and many family members also contain a C-terminal ubiquitin-association (UBA) domain, however, Ddi1-like proteins from all vertebrates lack the UBA domain. Ddi1, also termed v-SNARE-master 1 (Vsm1), is an ubiquitin receptor involved in the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as an UBA-Ubl shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. For instance, Ddi1 plays an essential role in the final stages of proteasomal degradation of Ho endonuclease and of its cognate FBP, Ufo1. Moreover, Ddi1 and its associated protein Rad23p play a cooperative role as negative regulators in yeast PHO pathway. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also termed transporter regulator RS1 (RS1), which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1. Ddi1-like proteins play a significant role in cell cycle control, growth control, and trafficking in yeast and may play a crucial role in embryogenesis in higher eukaryotes.


:

Pssm-ID: 340494 [Multi-domain]  Cd Length: 73  Bit Score: 91.46  E-value: 5.37e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 74730631   1 MLITVYCVRRDlseVTFSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLIEDHCSLGSYGLKDGDIVVLLQ 76
Cdd:cd01796   1 MKLTVTTEDDD---RLFSLEVSPDMTLEDLKALCEAETGIPAAEQVLLHNGQPLTDDKKTLEALGLKDGDLLLLRP 73
rad23 super family cl36702
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
 1-215 6.66e-05

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR00601:

Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 44.50  E-value: 6.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631     1 MLITVycvrRDLSEVTFSLQVSPDFELRNFKVLCEAE---SRVPVEEIQIIHMERLLiEDHCSLGSYGLKDGD-IVVLLQ 76
Cdd:TIGR00601   1 MTLTF----KTLQQQKFKIDMEPDETVKELKEKIEAEqgkDAYPVAQQKLIYSGKIL-SDDKTVKEYKIKEKDfVVVMVS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631    77 KDNVGPRAPGRAPNQPRvdfsgiAVPGTSSSRPQHPGQQQQRTPAAQRSQGLASGEKVAglqglgSPALiRSMLLSNPhd 156
Cdd:TIGR00601  76 KPKTGTGKVAPPAATPT------SAPTPTPSPPASPASGMSAAPASAVEEKSPSEESAT------ATAP-ESPSTSVP-- 140

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 74730631   157 lsllkERNPPLAEALLSGS-LETFSQVLME-----QQREKALR------EQERLRLYTADPLDREAQAKIE 215
Cdd:TIGR00601 141 -----SSGSDAASTLVVGSeRETTIEEIMEmgyerEEVERALRaafnnpDRAVEYLLTGIPEDPEQPEPVQ 206
 
Name Accession Description Interval E-value
RP_DDI cd05479
RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the ...
 229-351 4.26e-80

RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.


Pssm-ID: 133146  Cd Length: 124  Bit Score: 241.69  E-value: 4.26e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631 229 IAIEEAPESFGQVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQ 308
Cdd:cd05479   2 NAMEHHPESFGKVPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVK 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 74730631 309 IEGDFLQCSFSILEDQPMDMLLGLDMLRRHQCSIDLKKNVLVI 351
Cdd:cd05479  82 IGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQCVIDLKENVLRI 124
Asp_protease pfam09668
Aspartyl protease; This family of eukaryotic aspartyl proteases have a fold similar to ...
 220-343 1.15e-76

Aspartyl protease; This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover.


Pssm-ID: 312981  Cd Length: 124  Bit Score: 233.01  E-value: 1.15e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631   220 QQNIEENMNIAIEEAPESFGQVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRII 299
Cdd:pfam09668   1 QENIDENLEHAMEHHPEVFGRVTMLYINCEINGVPVKAFVDSGAQTSIMSPRCAERCGIMRLVDTRFAGIAKGVGTARIL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 74730631   300 GRVHLAQIQIEGDFLQCSFSILEDQPMDMLLGLDMLRRHQCSID 343
Cdd:pfam09668  81 GRIHMADVKIGGLFLPCSFSVIEGQDMDLLLGLDMLKRHQCCID 124
Ubl_Ddi1_like cd01796
ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, ...
 1-76 5.37e-23

ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, including yeast aspartyl protease DNA-damage inducible 1 (Ddi1) and Ddi1-like proteins from vertebrates and other eukaryotes, has been characterized by containing an N-terminal ubiquitin-like (Ubl) domain and a conserved retroviral aspartyl-protease-like domain (RVP) that is important in cell-cycle control. Yeast Ddi1 and many family members also contain a C-terminal ubiquitin-association (UBA) domain, however, Ddi1-like proteins from all vertebrates lack the UBA domain. Ddi1, also termed v-SNARE-master 1 (Vsm1), is an ubiquitin receptor involved in the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as an UBA-Ubl shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. For instance, Ddi1 plays an essential role in the final stages of proteasomal degradation of Ho endonuclease and of its cognate FBP, Ufo1. Moreover, Ddi1 and its associated protein Rad23p play a cooperative role as negative regulators in yeast PHO pathway. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also termed transporter regulator RS1 (RS1), which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1. Ddi1-like proteins play a significant role in cell cycle control, growth control, and trafficking in yeast and may play a crucial role in embryogenesis in higher eukaryotes.


Pssm-ID: 340494 [Multi-domain]  Cd Length: 73  Bit Score: 91.46  E-value: 5.37e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 74730631   1 MLITVYCVRRDlseVTFSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLIEDHCSLGSYGLKDGDIVVLLQ 76
Cdd:cd01796   1 MKLTVTTEDDD---RLFSLEVSPDMTLEDLKALCEAETGIPAAEQVLLHNGQPLTDDKKTLEALGLKDGDLLLLRP 73
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
245-351 1.30e-08

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 53.41  E-value: 1.30e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631 245 YINCKVNGHPLKAFVDSGAQMTIMSQACAERCNI--MRLVDRRWAGVAKGVGTQRiigRVHLAQIQIeGDFL--QCSFSI 320
Cdd:COG3577  43 VVEGTINGQPVRFLVDTGASTVVLSESDARRLGLdpEDLGRPVRVQTANGVVRAA---RVRLDSVRI-GGITlrNVRAVV 118

                        90       100       110
                ....*....|....*....|....*....|..
gi 74730631 321 LEDQPM-DMLLGLDMLRRHQCSIDlkKNVLVI 351
Cdd:COG3577 119 LPGGELdDGLLGMSFLGRLDFEID--GDRLTL 148
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 1-77 1.06e-07

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 48.79  E-value: 1.06e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 74730631      1 MLITVycvrRDLSEVTFSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLiEDHCSLGSYGLKDGDIVVLLQK 77
Cdd:smart00213   1 IELTV----KTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVL-EDDRTLADYGIQDGSTIHLVLR 72
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 16-77 1.96e-06

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 45.24  E-value: 1.96e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 74730631    16 TFSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLiEDHCSLGSYGLKDGDIVVLLQK 77
Cdd:pfam00240  10 KITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVL-EDDQTLGEYGIEDGSTIHLVLR 70
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
 1-215 6.66e-05

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 44.50  E-value: 6.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631     1 MLITVycvrRDLSEVTFSLQVSPDFELRNFKVLCEAE---SRVPVEEIQIIHMERLLiEDHCSLGSYGLKDGD-IVVLLQ 76
Cdd:TIGR00601   1 MTLTF----KTLQQQKFKIDMEPDETVKELKEKIEAEqgkDAYPVAQQKLIYSGKIL-SDDKTVKEYKIKEKDfVVVMVS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631    77 KDNVGPRAPGRAPNQPRvdfsgiAVPGTSSSRPQHPGQQQQRTPAAQRSQGLASGEKVAglqglgSPALiRSMLLSNPhd 156
Cdd:TIGR00601  76 KPKTGTGKVAPPAATPT------SAPTPTPSPPASPASGMSAAPASAVEEKSPSEESAT------ATAP-ESPSTSVP-- 140

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 74730631   157 lsllkERNPPLAEALLSGS-LETFSQVLME-----QQREKALR------EQERLRLYTADPLDREAQAKIE 215
Cdd:TIGR00601 141 -----SSGSDAASTLVVGSeRETTIEEIMEmgyerEEVERALRaafnnpDRAVEYLLTGIPEDPEQPEPVQ 206
clan_AA_DTGA TIGR02281
clan AA aspartic protease, TIGR02281 family; This family consists of predicted aspartic ...
 245-337 3.09e-03

clan AA aspartic protease, TIGR02281 family; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Sequences in the seed alignment and those scoring above the trusted cutoff are Proteobacterial; homologs scroing between trusted and noise are found in Pyrobaculum aerophilum str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and Nostoc sp. PCC 7120 (Cyanobacteria). [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 131334  Cd Length: 121  Bit Score: 37.25  E-value: 3.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631   245 YINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRiIGRVHLAQIQIEGDFLQ-CSFSILED 323
Cdd:TIGR02281  13 YATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIK-AARVTLDRVAIGGIVVNdVDAMVAEG 91

                          90
                  ....*....|....*
gi 74730631   324 QPMD-MLLGLDMLRR 337
Cdd:TIGR02281  92 GALSeSLLGMSFLNR 106
 
Name Accession Description Interval E-value
RP_DDI cd05479
RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the ...
 229-351 4.26e-80

RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.


Pssm-ID: 133146  Cd Length: 124  Bit Score: 241.69  E-value: 4.26e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631 229 IAIEEAPESFGQVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIIGRVHLAQIQ 308
Cdd:cd05479   2 NAMEHHPESFGKVPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRIHLAQVK 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 74730631 309 IEGDFLQCSFSILEDQPMDMLLGLDMLRRHQCSIDLKKNVLVI 351
Cdd:cd05479  82 IGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQCVIDLKENVLRI 124
Asp_protease pfam09668
Aspartyl protease; This family of eukaryotic aspartyl proteases have a fold similar to ...
 220-343 1.15e-76

Aspartyl protease; This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover.


Pssm-ID: 312981  Cd Length: 124  Bit Score: 233.01  E-value: 1.15e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631   220 QQNIEENMNIAIEEAPESFGQVTMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRII 299
Cdd:pfam09668   1 QENIDENLEHAMEHHPEVFGRVTMLYINCEINGVPVKAFVDSGAQTSIMSPRCAERCGIMRLVDTRFAGIAKGVGTARIL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 74730631   300 GRVHLAQIQIEGDFLQCSFSILEDQPMDMLLGLDMLRRHQCSID 343
Cdd:pfam09668  81 GRIHMADVKIGGLFLPCSFSVIEGQDMDLLLGLDMLKRHQCCID 124
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 246-337 3.82e-31

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.


Pssm-ID: 464060  Cd Length: 92  Bit Score: 113.83  E-value: 3.82e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631   246 INCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRiIGRVHLAQIQIEGDFLQ-CSFSILEDQ 324
Cdd:pfam13975   1 VDVTINGRPVRFLVDTGASVTVISEALAERLGLDRLVDAYPVTVRTANGTVR-AARVRLDSVKIGGIELRnVPAVVLPGD 79

                          90
                  ....*....|...
gi 74730631   325 PMDMLLGLDMLRR 337
Cdd:pfam13975  80 LDDVLLGMDFLKR 92
Ubl_Ddi1_like cd01796
ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, ...
 1-76 5.37e-23

ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, including yeast aspartyl protease DNA-damage inducible 1 (Ddi1) and Ddi1-like proteins from vertebrates and other eukaryotes, has been characterized by containing an N-terminal ubiquitin-like (Ubl) domain and a conserved retroviral aspartyl-protease-like domain (RVP) that is important in cell-cycle control. Yeast Ddi1 and many family members also contain a C-terminal ubiquitin-association (UBA) domain, however, Ddi1-like proteins from all vertebrates lack the UBA domain. Ddi1, also termed v-SNARE-master 1 (Vsm1), is an ubiquitin receptor involved in the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as an UBA-Ubl shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. For instance, Ddi1 plays an essential role in the final stages of proteasomal degradation of Ho endonuclease and of its cognate FBP, Ufo1. Moreover, Ddi1 and its associated protein Rad23p play a cooperative role as negative regulators in yeast PHO pathway. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also termed transporter regulator RS1 (RS1), which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1. Ddi1-like proteins play a significant role in cell cycle control, growth control, and trafficking in yeast and may play a crucial role in embryogenesis in higher eukaryotes.


Pssm-ID: 340494 [Multi-domain]  Cd Length: 73  Bit Score: 91.46  E-value: 5.37e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 74730631   1 MLITVYCVRRDlseVTFSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLIEDHCSLGSYGLKDGDIVVLLQ 76
Cdd:cd01796   1 MKLTVTTEDDD---RLFSLEVSPDMTLEDLKALCEAETGIPAAEQVLLHNGQPLTDDKKTLEALGLKDGDLLLLRP 73
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 246-336 2.21e-16

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133136  Cd Length: 92  Bit Score: 73.91  E-value: 2.21e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631 246 INCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQ-RIIGRVHLAQIQIEGDFLQCSFSILEDQ 324
Cdd:cd00303   1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSvKTLGVILPVTIGIGGKTFTVDFYVLDLL 80

                        90
                ....*....|..
gi 74730631 325 PMDMLLGLDMLR 336
Cdd:cd00303  81 SYDVILGRPWLE 92
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 246-333 8.72e-10

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 54.98  E-value: 8.72e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631   246 INCKVNGHPLKAFVDSGAQMTIMSQACAERCNImRLVDRRWAGVAKGVGTQRIIGRVHLAQIQIeGDFL--QCSFSILED 323
Cdd:pfam13650   1 VPVTINGKPVRFLVDTGASGTVISPSLAERLGL-KVRGLAYTVRVSTAGGRVSAARVRLDSLRL-GGLTleNVPALVLDL 78

                          90
                  ....*....|.
gi 74730631   324 QPM-DMLLGLD 333
Cdd:pfam13650  79 GDLiDGLLGMD 89
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 10-75 1.63e-09

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 53.75  E-value: 1.63e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 74730631  10 RDLSEVTFSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLiEDHCSLGSYGLKDGDIVVLL 75
Cdd:cd17039   4 KTLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKEL-KDDKTLSDYGIKDGSTIHLV 68
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
245-351 1.30e-08

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 53.41  E-value: 1.30e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631 245 YINCKVNGHPLKAFVDSGAQMTIMSQACAERCNI--MRLVDRRWAGVAKGVGTQRiigRVHLAQIQIeGDFL--QCSFSI 320
Cdd:COG3577  43 VVEGTINGQPVRFLVDTGASTVVLSESDARRLGLdpEDLGRPVRVQTANGVVRAA---RVRLDSVRI-GGITlrNVRAVV 118

                        90       100       110
                ....*....|....*....|....*....|..
gi 74730631 321 LEDQPM-DMLLGLDMLRRHQCSIDlkKNVLVI 351
Cdd:COG3577 119 LPGGELdDGLLGMSFLGRLDFEID--GDRLTL 148
NRIP_C cd05480
NRIP_C; putative nuclear receptor interacting protein; Proteins in this family have been ...
 246-346 3.06e-08

NRIP_C; putative nuclear receptor interacting protein; Proteins in this family have been described as probable nuclear receptor interacting proteins. The C-terminal domain of this family is homologous to the retroviral aspartyl protease domain. The domain is structurally related to one lobe of the pepsin molecule. The conserved active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133147  Cd Length: 103  Bit Score: 51.01  E-value: 3.06e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631 246 INCKVNGHPLKAFVDSGAQMTIMSQACAERCNIM-RLVDRRWAGVAKGVGTQ-RIIGRVHLAQIQIEGDFLQCSFSILED 323
Cdd:cd05480   1 VSCQCAGKELRALVDTGCQYNLISAACLDRLGLKeRVLKAKAEEEAPSLPTSvKVIGQIERLVLQLGQLTVECSAQVVDD 80

                        90       100
                ....*....|....*....|...
gi 74730631 324 QPMDMLLGLDMLRRHQCSIDLKK 346
Cdd:cd05480  81 NEKNFSLGLQTLKSLKCVINLEK 103
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 1-77 1.06e-07

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 48.79  E-value: 1.06e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 74730631      1 MLITVycvrRDLSEVTFSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLiEDHCSLGSYGLKDGDIVVLLQK 77
Cdd:smart00213   1 IELTV----KTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVL-EDDRTLADYGIQDGSTIHLVLR 72
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 243-336 5.62e-07

Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133150  Cd Length: 96  Bit Score: 47.24  E-value: 5.62e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631 243 MLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNI-MRLVDRRWAGVAKGVGTQRiigRVHLAQIQIeGD--FLQCSFS 319
Cdd:cd05483   2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLpLTLGGKVTVQTANGRVRAA---RVRLDSLQI-GGitLRNVPAV 77

                        90
                ....*....|....*....
gi 74730631 320 ILEDQPM--DMLLGLDMLR 336
Cdd:cd05483  78 VLPGDALgvDGLLGMDFLR 96
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 16-77 1.96e-06

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 45.24  E-value: 1.96e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 74730631    16 TFSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLiEDHCSLGSYGLKDGDIVVLLQK 77
Cdd:pfam00240  10 KITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVL-EDDQTLGEYGIEDGSTIHLVLR 70
Ubl_Dsk2p_like cd16106
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein ...
 17-76 1.46e-05

ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein Dsk2p and similar proteins; The family contains several fungal multiubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (Ubl) and with ubiquitin (Ub) through their C-terminal Ub-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is an ubiquitin (Ub0 receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect Ub chains against disassembly by deubiquitinating enzymes.


Pssm-ID: 340523 [Multi-domain]  Cd Length: 73  Bit Score: 42.63  E-value: 1.46e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631  17 FSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLiEDHCSLGSYGLKDGDIVVLLQ 76
Cdd:cd16106  13 FTVEVEPDATVLELKELIAEKSDIPAEQQRLIYKGKIL-KDEETLSSYKIQDGHTVHLVK 71
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
 1-215 6.66e-05

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 44.50  E-value: 6.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631     1 MLITVycvrRDLSEVTFSLQVSPDFELRNFKVLCEAE---SRVPVEEIQIIHMERLLiEDHCSLGSYGLKDGD-IVVLLQ 76
Cdd:TIGR00601   1 MTLTF----KTLQQQKFKIDMEPDETVKELKEKIEAEqgkDAYPVAQQKLIYSGKIL-SDDKTVKEYKIKEKDfVVVMVS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631    77 KDNVGPRAPGRAPNQPRvdfsgiAVPGTSSSRPQHPGQQQQRTPAAQRSQGLASGEKVAglqglgSPALiRSMLLSNPhd 156
Cdd:TIGR00601  76 KPKTGTGKVAPPAATPT------SAPTPTPSPPASPASGMSAAPASAVEEKSPSEESAT------ATAP-ESPSTSVP-- 140

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 74730631   157 lsllkERNPPLAEALLSGS-LETFSQVLME-----QQREKALR------EQERLRLYTADPLDREAQAKIE 215
Cdd:TIGR00601 141 -----SSGSDAASTLVVGSeRETTIEEIMEmgyerEEVERALRaafnnpDRAVEYLLTGIPEDPEQPEPVQ 206
clan_AA_DTGA TIGR02281
clan AA aspartic protease, TIGR02281 family; This family consists of predicted aspartic ...
 245-337 3.09e-03

clan AA aspartic protease, TIGR02281 family; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Sequences in the seed alignment and those scoring above the trusted cutoff are Proteobacterial; homologs scroing between trusted and noise are found in Pyrobaculum aerophilum str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and Nostoc sp. PCC 7120 (Cyanobacteria). [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 131334  Cd Length: 121  Bit Score: 37.25  E-value: 3.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631   245 YINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRiIGRVHLAQIQIEGDFLQ-CSFSILED 323
Cdd:TIGR02281  13 YATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIK-AARVTLDRVAIGGIVVNdVDAMVAEG 91

                          90
                  ....*....|....*
gi 74730631   324 QPMD-MLLGLDMLRR 337
Cdd:TIGR02281  92 GALSeSLLGMSFLNR 106
Ubl2_FAT10 cd17053
ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 ...
 16-75 4.67e-03

ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins; FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the second Ubl domain of FAT10. Some family members contain only one Ubl domain.


Pssm-ID: 340573  Cd Length: 71  Bit Score: 35.40  E-value: 4.67e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 74730631  16 TFSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLIEDHCSLGSYGLKDGDIVVLL 75
Cdd:cd17053  12 VHTLQVSRSTTVAQVKAMIEDQSGVPPNEQILVYNGKRLEDGDKTLGEYGIKTGDTLYLL 71
Ubl_UBL4A_like cd01807
ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins; UBL4A, ...
 1-77 6.74e-03

ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins; UBL4A, also termed GdX, is a ubiquitously expressed ubiquitin-like (Ubl) protein that forms a complex with partner proteins and participates in the protein processing through endoplasmic reticulum (ER), acting as a chaperone. As a key component of the BCL2-associated athanogene 6 (BAG6) chaperone complex, UBL4A plays a role in mediating DNA damage signaling and cell death. UBL4A also regulates insulin-induced Akt plasma membrane translocation through promotion of Arp2/3-dependent actin branching. Moreover, UBL4A specifically stabilizes the TC45/STAT3 association and promotes dephosphorylation of STAT3 to repress tumorigenesis. UBL4B is testis-specific, and encoded by an X-derived retrogene Ubl4b, which is specifically expressed in post-meiotic germ cells in mammals. As a germ cell-specific cytoplasmic protein, UBL4B is not present in somatic cells. Moreover, UBL4B is present in elongated spermatids, but not in spermatocytes and round spermatids, suggesting its function is restricted to late spermiogenesis. The function of UBL4A may be compensated by either UBL4B or other Ubl proteins in normal conditions. Both UBL4A and UBL4B contain a conserved Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340505 [Multi-domain]  Cd Length: 72  Bit Score: 35.03  E-value: 6.74e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 74730631   1 MLITVycvrRDLSEVTFSLQVSPDFELRNFKVLCEAESRVPVEEIQIIHMERLLIEDHCsLGSYGLKDGDIVVLLQK 77
Cdd:cd01807   1 MLITV----KILQGKECTIEVSPTESVLTVKQLVAEQLNVPVSQQRLVFKGKTLADEHS-LSDYSIGPGSKIHLVVK 72
 
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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