ASFVdb The African Swine Fever Virus Database
Strain
China_ASFV-SY18_2018 (Region: China;  Strain: ASFV-SY18;  Date: 2018)
Gene
pNP419L
Description
Annoated by sequence mapping,  protein synthesis: early
GenBank Accession
Full name
DNA ligase      
Alternative Name
Polydeoxyribonucleotide synthase [ATP]
 

Sequence

CDS
ATGCTAAATCAATTTCCTGGGCAATATTCAAACAACATTTTTTGTTTTCCTCCGATTGAGTCTGAAACGAAAAGCGGAAAAAAGGCCTCATGGATTATTTGTGTGCAAGTGGTGCAGCACAACACGATCATTCCCATCACAGATGAGATGTTTTCCACAGATGTAAAAGACGCCGTTGCTGAAATTTTCACAAAATTTTTTGTGGAAGAAGGGGCGGTGCGGATATCAAAAATGACACGTGTTACCGAGGGAAAAAACTTGGGTAAAAAAAATGCCACAACGGTAGTCCATCAGGCATTCAAGGACGCCCTTAGTAAATATAATCGCCATGCCAGACAAAAGCGGGGAGCCCACACAAATAGAGGAATTATCCCCCCTATGCTGGTAAAATATTTTAATATAATTCCTAAGACATTTTTTGAAGAAGAAACAGATCCCATCGTGCAGCGCAAGCGTAATGGCGTTCGAGCTGTGGCCTGCCAGCAGGGCGATGGTAGCATTCTCTTGTATTCGCGCACGAAAAAGGAATTTTTAGGTCTTGACAATATTAAAAAAGAGCTCAAACAGCTTTATTTATTTATAGACGTGAGAGTATATTTGGATGGTGAGCTTTATTTACACCGCAAACCTCTGCAATGGATCGCGGGGCAGGCGAATGCGAAGACAGATTCCTCCGAGCTGCACTTTTACGTGTTTGACTGTTTTTGGAGTGATCAGCTTCAAATGCCTTCCAACAAGAGACAACAGCTATTAACAAATATTTTTAAACAGAAGGAAGATCTTACCTTTATCCACCAAGTTGAAAATTTTAGCGTGAAGAATGTGGATGAGGCCCTTAGGCTTAAGGCGCAGTTTATTAAGGAGGGCTACGAGGGAGCCATCGTACGCAATGCCAATGGGCCCTATGAGCCGGGATACAACAACTACCACTCAGCGCATCTTGCCAAGCTGAAACCGCTGCTAGACGCTGAATTTATTTTAGTGGACTATACTCAGGGAAAAAAGGGAAAGGACTTAGGCGCCATTTTATGGGTTTGCGAATTGCCAAACAAAAAGCGGTTTGTAGTCACTCCTAAGCATTTGACGTACGCGGATCGTTATGCTCTTTTTCAAAAACTCACGCCCGCCTTATTTAAAAAACATCTTTATGGAAAAGAGCTTACCGTGGAATATGCCGAGCTTTCCCCCAAAACTGGCATTCCTCTTCAGGCCCGTGCGGTAGGTTTTCGTGAACCGATAAGTGTTTTAGAAATCATTTAA
Protein
MLNQFPGQYSNNIFCFPPIESETKSGKKASWIICVQVVQHNTIIPITDEMFSTDVKDAVAEIFTKFFVEEGAVRISKMTRVTEGKNLGKKNATTVVHQAFKDALSKYNRHARQKRGAHTNRGIIPPMLVKYFNIIPKTFFEEETDPIVQRKRNGVRAVACQQGDGSILLYSRTKKEFLGLDNIKKELKQLYLFIDVRVYLDGELYLHRKPLQWIAGQANAKTDSSELHFYVFDCFWSDQLQMPSNKRQQLLTNIFKQKEDLTFIHQVENFSVKNVDEALRLKAQFIKEGYEGAIVRNANGPYEPGYNNYHSAHLAKLKPLLDAEFILVDYTQGKKGKDLGAILWVCELPNKKRFVVTPKHLTYADRYALFQKLTPALFKKHLYGKELTVEYAELSPKTGIPLQARAVGFREPISVLEII

Summary

Function
Very low-fidelity DNA ligase that seals, during DNA repair, nicks in double-stranded DNA. Together with the viral repair DNA polymerase X, fills the single nucleotide gaps generated by the AP endonuclease. It is not essential for viral replication and recombination.
Catalytic Activity
ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.
Cofactor
a divalent metal cation
Miscellaneous
Consistent with its intracellular location, ASFV encodes its own replicative DNA polymerase and three base excision repair enzymes: a class II AP endonuclease, the repair polymerase Pol X, and an ATP-dependent DNA ligase.
Similarity
Belongs to the ATP-dependent DNA ligase family.
Keywords
ATP-binding   Cell cycle   Cell division   Complete proteome   DNA damage   DNA recombination   DNA repair   DNA replication   Ligase   Metal-binding   Nucleotide-binding   Reference proteome  
Feature
chain  DNA ligase
EC Number
6.5.1.1
Pfam
PF01068   DNA_ligase_A_M
Interpro
IPR012340   NA-bd_OB-fold
IPR016059   DNA_ligase_ATP-dep_CS
IPR012310   DNA_ligase_ATP-dep_cent
SUPFAM
SSF50249   SSF50249
PDB
6IMK     E-value=0,     Score=2234

Ontologies

KEGG

Subcellular Location

From MSLVP
Capsid

Topology

Length:
419
Number of predicted TMHs:
0
Exp number of AAs in TMHs:
0.0029
Exp number, first 60 AAs:
0.00075
Total prob of N-in:
0.00248
outside
1  -  419
 
 

Population Genetic Test Statistics

Pi
0.0314289
Theta
0.0319709
Tajima's D
0.0840635
CLR
0
Interpretation
Possibly Balancing Selection

Multiple alignment of Orthologues

 
 

Gene Tree

 
 

Orthologous in Strains

Strain Availability Status Gene
Spain_BA71_1971 Protein
AKO62781.1
China_AnhuiXCGQ_2018 Protein
AYW34071.1
China_ASFV-SY18_2018 Protein
AKO62781.1
Poland_Pol16_20186_o7_2016-2017 Protein
AXZ95874.1
Poland_Pol16_20538_o9_2016-2017 Protein
CAN10199.1
Poland_Pol16_20540_o10_2016-2017 Protein
CAN10199.1
Poland_Pol16_29413_o23_2016-2017 Protein
CAN10199.1
Poland_Pol17_03029_C201_2016-2017 Protein
CAN10199.1
Poland_Pol17_04461_C210_2016-2017 Protein
AXZ96157.1
Poland_Pol17_05838_C220_2016-2017 Protein
CAN10199.1
Poland_ASFV_POL_Podlaskie_2015 Protein
CAN10199.1
Uganda_R8_2015 Protein
AXB49328.1
Uganda_R7_2015 Protein
AXB49502.1
Uganda_R25_2015 Protein
AXB49674.1
Uganda_N10_2015 Protein
AXB49845.1
Uganda_R35_2015 Protein
AXB50018.1
Estonia_2014 Protein
SPS73523.1
Italy_26544_OG10_2010 Protein
AJZ77074.1
Italy_47_Ss_2008_2008 Protein
AOO54457.1
Portugal_OURT_88.3_1988 Protein
CAN10449.1
Spain_E75_1975 Protein
CBH29200.1
Russia_Georgia_2007 Protein
CBW46766.1
Kenya_Tk1_2005 Protein
AJL34113.1
Kenya_Bus_2006 Protein
AJL34278.1
Russia_Odintsovo_2014 Protein
CAN10199.1
Portugal_L60_1960 Protein
AIY22291.1
Portugal_NHV_1968 Protein
AIY22449.1
Russia_Kashino_2013 Protein
CAN10199.1
Benin_1997 Protein
Protein
CAN10199.1
CAN10199.1
South_Africa_KNP_Pretorisuskop_1996 Protein
CAN10199.1
South_Africa_MGR_Mkuzi_1979 Protein
CAN10199.1
Malawi_Lil_1983 Protein
CAN10199.1
Kenya_1950 Protein
CAN10199.1
Namibia_Warthog_1980 Protein
CAN10199.1
South_Africa_Warmbaths_1987 Protein
CAN10199.1
Malawi_Tengani_1962 Protein
CAN10199.1
China_HLJ_2018 Protein
QBH90588.1
China_LN_2018 Protein
QBH90773.1
China_wbBS01_2018 Protein
QDL88131.1
Ukraine_Kyiv_2014 Protein
Protein
QED21697.1
QED21698.1
Belgium_Etalle_wb_2018 Protein
QED90543.1
Lithuania_LT14_2014 Protein
QEY87906.1
South_Africa_1985 Protein
CAN10199.1
South_Africa_2_2008 Protein
CAN10199.1
Zambia_LIV_1983 Protein
CAN10199.1
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