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Conserved domains on  [gi|569010276|ref|XP_006528164|]
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retrotransposon Gag-like protein 5 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Retrotrans_gag super family cl46289
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 157-234 1.12e-10

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


The actual alignment was detected with superfamily member pfam16297:

Pssm-ID: 480629  Cd Length: 112  Bit Score: 59.16  E-value: 1.12e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 569010276  157 PDIEPFSGDPVYLAEFLMQLETFIADHEDHFPGGAERVAFLISFFTGEARDWAISVTQEGSSLHANFPRFLDEIRKEF 234
Cdd:pfam16297  26 PFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
 
Name Accession Description Interval E-value
DUF4939 pfam16297
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ...
 157-234 1.12e-10

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.


Pssm-ID: 465086  Cd Length: 112  Bit Score: 59.16  E-value: 1.12e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 569010276  157 PDIEPFSGDPVYLAEFLMQLETFIADHEDHFPGGAERVAFLISFFTGEARDWAISVTQEGSSLHANFPRFLDEIRKEF 234
Cdd:pfam16297  26 PFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
 
Name Accession Description Interval E-value
DUF4939 pfam16297
Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around ...
 157-234 1.12e-10

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.


Pssm-ID: 465086  Cd Length: 112  Bit Score: 59.16  E-value: 1.12e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 569010276  157 PDIEPFSGDPVYLAEFLMQLETFIADHEDHFPGGAERVAFLISFFTGEARDWAISVTQEGSSLHANFPRFLDEIRKEF 234
Cdd:pfam16297  26 PFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQYF 103
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 151-294 1.51e-07

Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements.


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 52.09  E-value: 1.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569010276  151 LPPLERPDIEPFSG--DPVYLAEFLMQLETFIADHEdhFPGGAERVAFLISFFTGEARDWAISVTQEGSSLHANFPRFLD 228
Cdd:pfam19259   6 LPNFMIQVILPFRGrkDVLKLKSFISEIMLQMSMIF--WPNDAERIVFCARHLTGPAAQWFHDFVQEQGILDATFDTFIK 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 569010276  229 EIRKEFCGPIPSRVAKKAIRKLKQGNCTLGSYADAFQFLAQFL---SWDDCRLQNQFLKGLSEIFRKEL 294
Cdd:pfam19259  84 AFKQHFYGKPDINKLFNDIVNLSEAKLGIERYNSHFNRLWDLLppdFLSEKAAIMFYIRGLKPETYIIV 152
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 195-288 7.38e-07

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 47.71  E-value: 7.38e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569010276  195 AFLISFFTGEARDWAISVTQEGSSLHANFPRFLDEIRKEFCGPIPSRVAKKAIRKLKQGNCTLGSYADAFQFLAQFL--- 271
Cdd:pfam03732   1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLphh 80

                          90
                  ....*....|....*..
gi 569010276  272 SWDDCRLQNQFLKGLSE 288
Cdd:pfam03732  81 GRDEEALISAFLRGLRP 97
 
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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