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Conserved domains on  [gi|395864079|gb|AFN80584|]
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capsid protein [Paspalum striate mosaic virus]

Protein Classification

capsid/nuclear shuttle family protein( domain architecture ID 10467201)

geminivirus capsid/nuclear shuttle family protein such as capsid (or coat) protein that encapsidates the viral DNA into characteristic twinned ('geminate') particles, and nuclear shuttle protein (NSP) that binds to the genomic viral ssDNA and shuttles it into and out of the cell nucleus

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Gemini_coat pfam00844
Geminivirus coat protein/nuclear export factor BR1 family; It has been shown that the 104 ...
 3-239 7.39e-54

Geminivirus coat protein/nuclear export factor BR1 family; It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus.


:

Pssm-ID: 307130  Cd Length: 244  Bit Score: 173.26  E-value: 7.39e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 395864079    3 ASSKRKRGSTSATKRRKKPRYTKWTSARSSNRDALQVQTFTW---GEDQAFNAGGRAILLTAFTRGSAENQRKSQETITY 79
Cdd:pfam00844  13 ARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRSPPLKVQSFEInqfGPDFVVSNTGKVSLISDPTRGKGETNRVRKYIKLK 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 395864079   80 KVSINLGVSASATVLKYCCKSQPLCWLVYDKSPTGITDLTPSDIFDVpsgLQNWPSTWKVKREASHRFVVKRRWPFTLSC 159
Cdd:pfam00844  93 SLYFKGTVWIDENIKDKNMTGVFSFWLVRDRRPHGNTPGTFDELFGM---YDNEPGTLTVKRDLRDRFVVKRKWKRVVSS 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 395864079  160 NGSTfqkdYTNLPVCNtdNLVSVTRFAKGLGVRTEWKDTTTAEASDIKGGALYLV----VAPANGLVFTargVIKVYFKS 235
Cdd:pfam00844 170 EGDT----NMVDFPGK--NQLSVRRFFKWLGVKDEWNNSETGKYGNIKKNALLLYycwmSAPNSGASTT---KIRVYFKL 240


                  ....
gi 395864079  236 VGNQ 239
Cdd:pfam00844 241 SYNG 244
 
Name Accession Description Interval E-value
Gemini_coat pfam00844
Geminivirus coat protein/nuclear export factor BR1 family; It has been shown that the 104 ...
 3-239 7.39e-54

Geminivirus coat protein/nuclear export factor BR1 family; It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus.


Pssm-ID: 307130  Cd Length: 244  Bit Score: 173.26  E-value: 7.39e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 395864079    3 ASSKRKRGSTSATKRRKKPRYTKWTSARSSNRDALQVQTFTW---GEDQAFNAGGRAILLTAFTRGSAENQRKSQETITY 79
Cdd:pfam00844  13 ARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRSPPLKVQSFEInqfGPDFVVSNTGKVSLISDPTRGKGETNRVRKYIKLK 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 395864079   80 KVSINLGVSASATVLKYCCKSQPLCWLVYDKSPTGITDLTPSDIFDVpsgLQNWPSTWKVKREASHRFVVKRRWPFTLSC 159
Cdd:pfam00844  93 SLYFKGTVWIDENIKDKNMTGVFSFWLVRDRRPHGNTPGTFDELFGM---YDNEPGTLTVKRDLRDRFVVKRKWKRVVSS 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 395864079  160 NGSTfqkdYTNLPVCNtdNLVSVTRFAKGLGVRTEWKDTTTAEASDIKGGALYLV----VAPANGLVFTargVIKVYFKS 235
Cdd:pfam00844 170 EGDT----NMVDFPGK--NQLSVRRFFKWLGVKDEWNNSETGKYGNIKKNALLLYycwmSAPNSGASTT---KIRVYFKL 240


                  ....
gi 395864079  236 VGNQ 239
Cdd:pfam00844 241 SYNG 244
 
Name Accession Description Interval E-value
Gemini_coat pfam00844
Geminivirus coat protein/nuclear export factor BR1 family; It has been shown that the 104 ...
 3-239 7.39e-54

Geminivirus coat protein/nuclear export factor BR1 family; It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus.


Pssm-ID: 307130  Cd Length: 244  Bit Score: 173.26  E-value: 7.39e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 395864079    3 ASSKRKRGSTSATKRRKKPRYTKWTSARSSNRDALQVQTFTW---GEDQAFNAGGRAILLTAFTRGSAENQRKSQETITY 79
Cdd:pfam00844  13 ARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRSPPLKVQSFEInqfGPDFVVSNTGKVSLISDPTRGKGETNRVRKYIKLK 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 395864079   80 KVSINLGVSASATVLKYCCKSQPLCWLVYDKSPTGITDLTPSDIFDVpsgLQNWPSTWKVKREASHRFVVKRRWPFTLSC 159
Cdd:pfam00844  93 SLYFKGTVWIDENIKDKNMTGVFSFWLVRDRRPHGNTPGTFDELFGM---YDNEPGTLTVKRDLRDRFVVKRKWKRVVSS 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 395864079  160 NGSTfqkdYTNLPVCNtdNLVSVTRFAKGLGVRTEWKDTTTAEASDIKGGALYLV----VAPANGLVFTargVIKVYFKS 235
Cdd:pfam00844 170 EGDT----NMVDFPGK--NQLSVRRFFKWLGVKDEWNNSETGKYGNIKKNALLLYycwmSAPNSGASTT---KIRVYFKL 240


                  ....
gi 395864079  236 VGNQ 239
Cdd:pfam00844 241 SYNG 244
 
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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