NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|147859158|emb|CAN82540|]
View 

hypothetical protein VITISV_015270 [Vitis vinifera]

Protein Classification

gag-polypeptide of LTR copia-type domain-containing protein( domain architecture ID 707859)

gag-polypeptide of LTR copia-type domain-containing protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Retrotran_gag_2 super family cl26047
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 132-234 2.17e-14

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


The actual alignment was detected with superfamily member pfam14223:

Pssm-ID: 464108  Cd Length: 130  Bit Score: 69.96  E-value: 2.17e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147859158  132 FSALLGAISVSLQPHIARTTTSLDAWQTLANTYAKPSRGHIKQLKEQL---KWctKGSKSISEYMQVIKTHADELALLGK 208
Cdd:pfam14223   1 LALIVLSLSDSLLRLVRNADTAKEAWDKLESTYERKSPANKLTLRRQLhslKM--KEGESVLEHINKFEELVNKLSALGV 78

                          90       100
                  ....*....|....*....|....*.
gi 147859158  209 LVDDEDLIDRVLEGLSDEYKSIIDAI 234
Cdd:pfam14223  79 EISDEDLVVKLLRSLPESYENFVTAI 104
transpos_IS481 super family cl41329
IS481 family transposase; null
 440-478 3.59e-04

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 42.58  E-value: 3.59e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 147859158 440 DNGGEYQA----LDNFLSTNGISHLTTPPHAPEHNGLFERRHR 478
Cdd:NF033577 194 DNGSEFRSrahgFELALAELGIEHRRTRPYHPQTNGKVERFHR 236
 
Name Accession Description Interval E-value
Retrotran_gag_2 pfam14223
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 132-234 2.17e-14

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


Pssm-ID: 464108  Cd Length: 130  Bit Score: 69.96  E-value: 2.17e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147859158  132 FSALLGAISVSLQPHIARTTTSLDAWQTLANTYAKPSRGHIKQLKEQL---KWctKGSKSISEYMQVIKTHADELALLGK 208
Cdd:pfam14223   1 LALIVLSLSDSLLRLVRNADTAKEAWDKLESTYERKSPANKLTLRRQLhslKM--KEGESVLEHINKFEELVNKLSALGV 78

                          90       100
                  ....*....|....*....|....*.
gi 147859158  209 LVDDEDLIDRVLEGLSDEYKSIIDAI 234
Cdd:pfam14223  79 EISDEDLVVKLLRSLPESYENFVTAI 104
transpos_IS481 NF033577
IS481 family transposase; null
 440-478 3.59e-04

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 42.58  E-value: 3.59e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 147859158 440 DNGGEYQA----LDNFLSTNGISHLTTPPHAPEHNGLFERRHR 478
Cdd:NF033577 194 DNGSEFRSrahgFELALAELGIEHRRTRPYHPQTNGKVERFHR 236
 
Name Accession Description Interval E-value
Retrotran_gag_2 pfam14223
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 132-234 2.17e-14

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


Pssm-ID: 464108  Cd Length: 130  Bit Score: 69.96  E-value: 2.17e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147859158  132 FSALLGAISVSLQPHIARTTTSLDAWQTLANTYAKPSRGHIKQLKEQL---KWctKGSKSISEYMQVIKTHADELALLGK 208
Cdd:pfam14223   1 LALIVLSLSDSLLRLVRNADTAKEAWDKLESTYERKSPANKLTLRRQLhslKM--KEGESVLEHINKFEELVNKLSALGV 78

                          90       100
                  ....*....|....*....|....*.
gi 147859158  209 LVDDEDLIDRVLEGLSDEYKSIIDAI 234
Cdd:pfam14223  79 EISDEDLVVKLLRSLPESYENFVTAI 104
transpos_IS481 NF033577
IS481 family transposase; null
 440-478 3.59e-04

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 42.58  E-value: 3.59e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 147859158 440 DNGGEYQA----LDNFLSTNGISHLTTPPHAPEHNGLFERRHR 478
Cdd:NF033577 194 DNGSEFRSrahgFELALAELGIEHRRTRPYHPQTNGKVERFHR 236
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 129-225 1.03e-03

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: 38.47  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147859158  129 CLIFSALLGAISVSLQPHIARTTTSLDAWQTLANTYAKP--SRGHIKQLKEQLKWCTKGSKSISEYMQVIKTHADELALL 206
Cdd:pfam03732   1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRffPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                          90
                  ....*....|....*....
gi 147859158  207 GklVDDEDLIDRVLEGLSD 225
Cdd:pfam03732  81 G--RDEEALISAFLRGLRP 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH