SGID Silkworm Genome Informatics Database
Gene
KWMTBOMO05632
Pre Gene Modal
BGIBMGA002957
Annotation
PREDICTED:_zinc_finger_CCHC_domain-containing_protein_13-like_[Bombyx_mori]
Full name
Gag polyprotein      
Location in the cell
Nuclear   Reliability : 2.146
 

Sequence

CDS
ATGCCAGGCCCATGCATTGACGGATTTGAGACCGCTGAGAAACACAGGCGATACAAAATGCGACGTGTCACCCAAACCGATGCGGAGGTTATTCCAACGTTCCGGCCGGATGAAAAATCTAACAACGTCAAGGGATGGCTGCACAAGATCGACCAGTTGGATCACGTATATGGATGGGACAACAAAGACTGCCAGTTCATCATGCAGATATGTCTTCGTGGGTCGGCTAGGGATTGTGCGATACACCACCGCAACTATACTACACATCCGCGAATGGCTACCACATGGAGAAGAGAAGGTGCTGTTGCTCCAGTTGCAAGAGGGACCGACTTTCAACCAAAGAAATGTTACGCCTGCCGAAGAGAAGGTCATGAAACAAAGAACTGCAAAGAGCCGCGCTGCGAGATGTGCCATCGCCCGGGACACACGTCGGTCAGCTGA
Protein
MPGPCIDGFETAEKHRRYKMRRVTQTDAEVIPTFRPDEKSNNVKGWLHKIDQLDHVYGWDNKDCQFIMQICLRGSARDCAIHHRNYTTHPRMATTWRREGAVAPVARGTDFQPKKCYACRREGHETKNCKEPRCEMCHRPGHTSVS

Summary

Catalytic Activity
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)
Cofactor
Mg(2+)
Similarity
Belongs to the primate lentivirus group gag polyprotein family.
Pfam
PF00540   Gag_p17        + More
PF00607   Gag_p24
PF00098   zf-CCHC
PF00552   IN_DBD_C
PF06815   RVT_connect
PF06817   RVT_thumb
PF00077   RVP
PF00665   rve
PF02022   Integrase_Zn
PF00075   RNase_H
PF00078   RVT_1
PF08705   Gag_p6
Interpro
IPR036875   Znf_CCHC_sf        + More
IPR001878   Znf_CCHC       
IPR010999   Retrovr_matrix       
IPR000071   Lentvrl_matrix_N       
IPR000721   Gag_p24       
IPR008919   Retrov_capsid_N       
IPR008916   Retrov_capsid_C       
IPR012344   Matrix_HIV/RSV_N       
IPR010659   RVT_connect       
IPR012337   RNaseH-like_sf       
IPR036862   Integrase_C_dom_sf_retrovir       
IPR001969   Aspartic_peptidase_AS       
IPR001584   Integrase_cat-core       
IPR003308   Integrase_Zn-bd_dom_N       
IPR001995   Peptidase_A2_cat       
IPR000477   RT_dom       
IPR010661   RVT_thumb       
IPR002156   RNaseH_domain       
IPR018061   Retropepsins       
IPR036397   RNaseH_sf       
IPR021109   Peptidase_aspartic_dom_sf       
IPR001037   Integrase_C_retrovir       
IPR034170   Retropepsin-like_cat_dom       
IPR017856   Integrase-like_N       
IPR014817   Gag_p6       
SUPFAM
SSF57756   SSF57756        + More
SSF47836   SSF47836       
SSF47943   SSF47943       
SSF50630   SSF50630       
SSF46919   SSF46919       
SSF53098   SSF53098       
SSF50122   SSF50122       
PDB
5O2U     E-value=0.0147317,     Score=84

Ontologies

Topology

Subcellular location
Virion  
Host nucleus  
Host cytoplasm  
Host cell membrane  
Length:
146
Number of predicted TMHs:
0
Exp number of AAs in TMHs:
0
Exp number, first 60 AAs:
0
Total prob of N-in:
0.02330
outside
1  -  146
 
 

Population Genetic Test Statistics

Pi
284.339781
Theta
230.454557
Tajima's D
-2.136596
CLR
0.632859
CSRT
0.00854957252137393
Interpretation
Uncertain

Multiple alignment of Orthologues

 
 

Gene Tree

 
 
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