ASFVdb The African Swine Fever Virus Database
Strain
Ukraine_Kyiv_2014 (Region: Ukraine;  Strain: ASFV/Kyiv/2016/131;  Date: 2014)
Gene
EP1242L
Description
Annotated in NCBI,  ASFV_Kyiv_2016_131_00079
GenBank Accession
Full name
DNA-directed RNA polymerase subunit 2       + More
DNA-directed RNA polymerase subunit beta      
 

Sequence

CDS
ATGCGGGGCAGCAACCGCTGCCACACTCATCACCTATCAAAAACCGCAAAAAAAGAAATAGGAGAAGACCCTAATGAACCCGGCGGCTACTTTATAGCCCGAGGCGGGGAATGGGTCGTAGACCTCTTAGAAAACATCCGCTTTAACACGCTTCACATCCATTACCATACCATGCAACAAGGGAATAATGAAATCATTCGCGGCGAGTTTATCTCCCAACCGGGAGGTGCCTTCGAAAATAGCTCTCAAATTATTATACGCTACATGACCACCGGCGCCATTACCATTGAAATCAATAGCACCAAGTTCTCAAAACTTCGCATACCTTGGTATCTCATCTTTCGCATGTTTGGAATGACAGGCGATGACAGCATCATTGAGCAAGTGGTATTTGATCTAGAATCCAACTCCCTTGTGAATACCTTCATGATAGAAATTCTGGAAAAATCCATTCATGTTTTAGACCCCATATTTCAACCGGTCCAACACGAGCTGAACCGAGAAAAAATTATCCAGTTTTTATCCGAGAAGGTTTCCAAATTTGTCTCAAACCCATCTGCTTACAAAAGCGATGAAAATGCGGTACAATACTTAAATGAAAGACAACTTACTATTTTAGACAAAATATTGCTGCCACACATGGGCCAAACCGCAGATACACGTGTACGAAAGCTGCGCTTTTTAGGCCTGCTTATTCATAAAATACTTCTTGTCATTATGAATGTGTTTCCACCCACGGACCGTGATAGCTACCGCACCAAGCGGGTGCACGGCTCAGGGGTCTCACTCGCCAAGGCCTTTAAGGCTATTTTTAATACTTCCGTGATAGCACCCATCATCAATGGGTTCAAAGAACTTCTTAAACAAACAGCCTTTGAGGAGCTTACTCAGCGAAACATTATCGAGGCATTTTCTGCCGCTTTATCAAAAAATACCGCCTCCGATCTTAATCGCAGTATGGAACAGTCTATCATTTCAGGAAATAAAACCATCATGGTGCGACAGCGCCCCATTGTAAACAGAGTATCTACTCAAAGTTTGGAAAGAAAAAATTTATTAAATACCATTTCAGCATTGCGTACGGTAAATACTCATAACACCACCAACGCATCCAAACAAACAGAAAGGGCTGACATGATGCGTCGCGTGCACGCATCCTATCCTGGATACATCTGCGTAGCCCAGTCAGCCGATACTGGTGAAAAAGTAGGCATGTCTAAACAGTTAGCCATCACTGCCAATGTCTGCACCGCCGGAGAAGTACTTTCGTTAAAACAACGCCTTCTATCAGATCCGGCCATTCAACAGTTAGCCGATGTTTCCAACAAGGACATTGTACGAAAGGGCCTAGCGCGCGTATTTATCAACGGAGAATGGATCGGCTGCTGCACCAATGCCTTTGAGCTTGCTCAGCGGTATAGAATGCTTCGCCGTGAGGGCAAGGTTGTGCATCCCCATACCACCATCTACTGGGATAGCATGGTAGACGAAGTAGAATTTTGGTTGGACGTCGGTAGGCTGACCCGCCCCCTACTCATTGTAGATAATAATATTGAAAAATACAATCAAGCCTGCTACAAGGCCGCAGAGGCCAGAAAAAAGGCGATAAAGACTGGGAAAAACATAAAATCCCTTTCATTCAAAATACGCGATTTACGCCTCAAATGGCAAAAGACATTTTAG
Protein
MRGSNRCHTHHLSKTAKKEIGEDPNEPGGYFIARGGEWVVDLLENIRFNTLHIHYHTMQQGNNEIIRGEFISQPGGAFENSSQIIIRYMTTGAITIEINSTKFSKLRIPWYLIFRMFGMTGDDSIIEQVVFDLESNSLVNTFMIEILEKSIHVLDPIFQPVQHELNREKIIQFLSEKVSKFVSNPSAYKSDENAVQYLNERQLTILDKILLPHMGQTADTRVRKLRFLGLLIHKILLVIMNVFPPTDRDSYRTKRVHGSGVSLAKAFKAIFNTSVIAPIINGFKELLKQTAFEELTQRNIIEAFSAALSKNTASDLNRSMEQSIISGNKTIMVRQRPIVNRVSTQSLERKNLLNTISALRTVNTHNTTNASKQTERADMMRRVHASYPGYICVAQSADTGEKVGMSKQLAITANVCTAGEVLSLKQRLLSDPAIQQLADVSNKDIVRKGLARVFINGEWIGCCTNAFELAQRYRMLRREGKVVHPHTTIYWDSMVDEVEFWLDVGRLTRPLLIVDNNIEKYNQACYKAAEARKKAIKTGKNIKSLSFKIRDLRLKWQKTF

Summary

Function
Component of the DNA-dependent RNA polymerase that catalyzes the transcription in the cytoplasm of viral DNA into RNA using the four ribonucleoside triphosphates as substrates. Subunit 2 is the second largest component of RNA polymerase. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. DNA-dependent RNA polymerase is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template (By similarity).
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
Catalytic Activity
a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1)
a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1)
Subunit
Component of the RNA polymerase that consists of at least 6 subunits.
Component of the RNA polymerase that consists of at least 6 subunits.
Miscellaneous
The binding of ribonucleoside triphosphate to the RNA polymerase transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion coordinated by three conserved aspartate residues of the two largest RNA Pol subunits (By similarity).
The binding of ribonucleoside triphosphate to the RNA polymerase transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion coordinated by three conserved aspartate residues of the two largest RNA Pol subunits (By similarity).
Similarity
Belongs to the RNA polymerase beta chain family.
Keywords
Complete proteome   DNA-directed RNA polymerase   Host cytoplasm   Metal-binding   Nucleotidyltransferase   Transcription   Transferase   Zinc   Zinc-finger   Reference proteome  
Feature
chain  DNA-directed RNA polymerase subunit 2
EC Number
2.7.7.6
2.7.7.6
EMBL
MN194591    QED21615.1    AY261366    AY261363    AM712239    CAN10153.1    + More
FN557520    CBH29154.1    AM712240    CAN10401.1    KM262844    KM262845    KP055815    AIY22244.1    AIY22403.1    AKO62735.1    KM102979    KX354450    AJZ77042.1    AOO54384.1    FR682468    CBW46719.1    MG939583    MG939587    MG939588    LS478113    AXZ95829.1    AXZ96017.1    AXZ96112.1    SPS73476.1    Z21490    U18466    AY261361    KM111294    AJL34067.1    KM111295    AJL34232.1    AY261360    MH025916    MH025917    MH025918    MH025919    MH025920    AXB49282.1    AXB49456.1    AXB49628.1    AXB49799.1    AXB49972.1    CZDJ02000003    SMH63388.1    KU702949    KU702951    KU556803    AMN83870.1    AMN84468.1    AMP44390.1    KU702948    KU702952    AMN82980.1    AMN84950.1    KJ614390    KU702950    AIB51752.1    AMN83967.1    LT706986    SIP85761.1    LT839607    SME64703.1    KX552040    ARA72182.1    FRFC01000001    SHO42515.1    VBPS01000081    TLX83474.1    MNFB01000064    OLC33654.1    MNGX01000149    OLD28660.1    MNED01000043    OLB90768.1    MNFZ01000037    OLC93301.1    VBPD01000024    TLY08475.1    VBPZ01000130    TLX69971.1    CABMJN010000025    VVC05246.1    VBPL01000040    TLX94524.1    AEXL02000008    EIJ67011.1    LT841358    SMH72468.1    PFCM01000353    PIN96807.1    LN890280    CUR51077.1    CP003843    AFS82146.1    BGKI01000002    GBH33780.1    CP011070    AJW71582.1    PFRJ01000106    PJC50142.1    PFGA01000294    PIW35501.1    PCWH01000304    PIN83041.1    AFPU01000001    EGP93080.1    QQVT01000007    QQVN01000004    QQVH01000002    QQVA01000001    RDJ31631.1    RDJ33574.1    RDJ38103.1    RDJ39128.1    PFLV01000304    PIY88190.1    AEGP01000040    EGG42088.1    BGOU01000002    GBL41117.1    BJHR01000001    GDY15239.1    AHJG01000013    EPA06703.1    SCUP01000060    TAK26642.1    NSIR01000002    PHY09505.1    SCVP01000042    TBR26002.1    CBTY010000006    CDI05204.1    SCVO01000126    TBR06709.1    QZIM01000013    RJQ21012.1    DP000238    ABK78187.1    JPUE01000079    KPU81155.1    CABMGU010000092    VVB81924.1   
Pfam
PF04566   RNA_pol_Rpb2_4
PF04565   RNA_pol_Rpb2_3
PF04561   RNA_pol_Rpb2_2
PF00562   RNA_pol_Rpb2_6
PF04560   RNA_pol_Rpb2_7
PF04563   RNA_pol_Rpb2_1
PF04567   RNA_pol_Rpb2_5
PF14528   LAGLIDADG_3
Interpro
IPR015712   DNA-dir_RNA_pol_su2
IPR007642   RNA_pol_Rpb2_2
IPR007645   RNA_pol_Rpb2_3
IPR037034   RNA_pol_Rpb2_2_sf
IPR007646   RNA_pol_Rpb2_4
IPR037033   DNA-dir_RNAP_su2_hyb_sf
IPR007120   DNA-dir_RNAP_su2_dom
IPR007641   RNA_pol_Rpb2_7
IPR007121   RNA_pol_bsu_CS
IPR007644   RNA_pol_bsu_protrusion
IPR014724   RNA_pol_RPB2_OB-fold
IPR007647   RNA_pol_Rpb2_5
IPR004042   Intein_endonuc
IPR006142   INTEIN
IPR027434   Homing_endonucl
IPR036844   Hint_dom_sf
IPR004860   LAGLIDADG_2
IPR019969   RNAP_B
SUPFAM
SSF55608   SSF55608
SSF51294   SSF51294
PDB
6GML     E-value=7.92573e-32,     Score=344

Ontologies

KEGG

Subcellular Location

From MSLVP
Single-Pass Membrane
From Uniprot
Host cytoplasm  
Host cytoplasm  

Topology

Length:
560
Number of predicted TMHs:
0
Exp number of AAs in TMHs:
9.14161999999999
Exp number, first 60 AAs:
0.0002
Total prob of N-in:
0.41994
Length:
560
Number of predicted TMHs:
0
Exp number of AAs in TMHs:
9.14161999999999
Exp number, first 60 AAs:
0.0002
Total prob of N-in:
0.41994
outside
1  -  560
outside
1  -  560
 
 

Population Genetic Test Statistics

Pi
0.0369717
Theta
0.0455105
Tajima's D
-0.8991158
CLR
0.135421
Interpretation
No evidence of Selection

Multiple alignment of Orthologues

 
 

Gene Tree

 
 

Orthologous in Strains

Strain Availability Status Gene
Spain_BA71_1971    
China_AnhuiXCGQ_2018    
China_ASFV-SY18_2018    
Poland_Pol16_20186_o7_2016-2017    
Poland_Pol16_20538_o9_2016-2017    
Poland_Pol16_20540_o10_2016-2017    
Poland_Pol16_29413_o23_2016-2017    
Poland_Pol17_03029_C201_2016-2017    
Poland_Pol17_04461_C210_2016-2017    
Poland_Pol17_05838_C220_2016-2017    
Poland_ASFV_POL_Podlaskie_2015    
Uganda_R8_2015    
Uganda_R7_2015    
Uganda_R25_2015    
Uganda_N10_2015    
Uganda_R35_2015    
Estonia_2014    
Italy_26544_OG10_2010    
Italy_47_Ss_2008_2008    
Portugal_OURT_88.3_1988    
Spain_E75_1975    
Russia_Georgia_2007    
Kenya_Tk1_2005    
Kenya_Bus_2006    
Russia_Odintsovo_2014    
Portugal_L60_1960    
Portugal_NHV_1968    
Russia_Kashino_2013    
Benin_1997    
South_Africa_KNP_Pretorisuskop_1996    
South_Africa_MGR_Mkuzi_1979    
Malawi_Lil_1983    
Kenya_1950    
Namibia_Warthog_1980    
South_Africa_Warmbaths_1987    
Malawi_Tengani_1962    
China_HLJ_2018    
China_LN_2018    
China_wbBS01_2018    
Ukraine_Kyiv_2014 Protein
Protein
QED21615.1
QED21615.1
Belgium_Etalle_wb_2018    
Lithuania_LT14_2014    
South_Africa_1985    
South_Africa_2_2008    
Zambia_LIV_1983    
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