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Conserved domains on  [gi|6689600|emb|CAB65503|]
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capsid protein [Watermelon chlorotic stunt virus-[IR]]

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 ...
 18-258 1.01e-104

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: 303.45  E-value: 1.01e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6689600     18 RRKLNFDSpYMSRALAPTVLVTSKRRQWANRPMYRKPRMYRMYRSPdvpkgcegPCKVQSYE-----QRDDVKHTGIVRC 92
Cdd:pfam00844   1 RRRLNFDS-RRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRSP--------PLKVQSFEinqfgPDFVVSNTGKVSL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6689600     93 VSDVTRGSGITHRVGKRFCVKSIYILGKIWMDENIKKQNHTNQVMFFLVRDRRPYGSSPMDFGQVFNMFDNEPSTATVKN 172
Cdd:pfam00844  72 ISDPTRGKGETNRVRKYIKLKSLYFKGTVWIDENIKDKNMTGVFSFWLVRDRRPHGNTPGTFDELFGMYDNEPGTLTVKR 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6689600    173 DLRDRFQVMRKFHATVVGGPS------GMKEQALVKRFYR-VYNHVVYNHQETAKYENHTENAMLLYMACTHASNPVYAT 245
Cdd:pfam00844 152 DLRDRFVVKRKWKRVVSSEGDtnmvdfPGKNQLSVRRFFKwLGVKDEWNNSETGKYGNIKKNALLLYYCWMSAPNSGAST 231

                         250
                  ....*....|...
gi 6689600    246 LKIRIYFYDSVTN 258
Cdd:pfam00844 232 TKIRVYFKLSYNG 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 ...
 18-258 1.01e-104

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: 303.45  E-value: 1.01e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6689600     18 RRKLNFDSpYMSRALAPTVLVTSKRRQWANRPMYRKPRMYRMYRSPdvpkgcegPCKVQSYE-----QRDDVKHTGIVRC 92
Cdd:pfam00844   1 RRRLNFDS-RRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRSP--------PLKVQSFEinqfgPDFVVSNTGKVSL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6689600     93 VSDVTRGSGITHRVGKRFCVKSIYILGKIWMDENIKKQNHTNQVMFFLVRDRRPYGSSPMDFGQVFNMFDNEPSTATVKN 172
Cdd:pfam00844  72 ISDPTRGKGETNRVRKYIKLKSLYFKGTVWIDENIKDKNMTGVFSFWLVRDRRPHGNTPGTFDELFGMYDNEPGTLTVKR 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6689600    173 DLRDRFQVMRKFHATVVGGPS------GMKEQALVKRFYR-VYNHVVYNHQETAKYENHTENAMLLYMACTHASNPVYAT 245
Cdd:pfam00844 152 DLRDRFVVKRKWKRVVSSEGDtnmvdfPGKNQLSVRRFFKwLGVKDEWNNSETGKYGNIKKNALLLYYCWMSAPNSGAST 231

                         250
                  ....*....|...
gi 6689600    246 LKIRIYFYDSVTN 258
Cdd:pfam00844 232 TKIRVYFKLSYNG 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 ...
 18-258 1.01e-104

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: 303.45  E-value: 1.01e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6689600     18 RRKLNFDSpYMSRALAPTVLVTSKRRQWANRPMYRKPRMYRMYRSPdvpkgcegPCKVQSYE-----QRDDVKHTGIVRC 92
Cdd:pfam00844   1 RRRLNFDS-RRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRSP--------PLKVQSFEinqfgPDFVVSNTGKVSL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6689600     93 VSDVTRGSGITHRVGKRFCVKSIYILGKIWMDENIKKQNHTNQVMFFLVRDRRPYGSSPMDFGQVFNMFDNEPSTATVKN 172
Cdd:pfam00844  72 ISDPTRGKGETNRVRKYIKLKSLYFKGTVWIDENIKDKNMTGVFSFWLVRDRRPHGNTPGTFDELFGMYDNEPGTLTVKR 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6689600    173 DLRDRFQVMRKFHATVVGGPS------GMKEQALVKRFYR-VYNHVVYNHQETAKYENHTENAMLLYMACTHASNPVYAT 245
Cdd:pfam00844 152 DLRDRFVVKRKWKRVVSSEGDtnmvdfPGKNQLSVRRFFKwLGVKDEWNNSETGKYGNIKKNALLLYYCWMSAPNSGAST 231

                         250
                  ....*....|...
gi 6689600    246 LKIRIYFYDSVTN 258
Cdd:pfam00844 232 TKIRVYFKLSYNG 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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