Gene

KWMTBOMO05803

Pre Gene Modal

BGIBMGA006939

Annotation

DNA_polymerase_delta_catalytic_subunit_[Bombyx_mori]

Location

Bomo_Chr10(+):10451911-10455384      View in EpiBrowser

Full name

DNA polymerase       + More
DNA polymerase delta catalytic subunit      

Location in the cell

Nuclear   Reliability : 3.79

CDS

ATGGACAGGAATAAAACTAAAGGTCCTCCTCCAAAGAGGTTTAAATCTGGCGACGATGACGATGAAAACGATACTCCATTTAGTTTCGAAGAACAACTGGCTTGTATGGACACTGGTGATATTGACAGCCAAGAAATATTTGAAGGTGAAGGACCTGAAAATCAATCTTCGAATATGAAATGGTCTCGTCCTCCACCGCCTATACTGACTCCAAACCGAGAAACATTAATATTTCAACAACTCGACATTGATCATTATTATGGCTCACCAATGAATGGCATGCCTGGCTCCCAATTGGCTCCCGTACCTATAATGAGGATGTACGGGATAACTTCAGAGGGAAACTCTGTTTGCTGTCATGTACATGGTTTTACACCATATTTTTATGTCACTGTACCAGTAAATTTTACAGAATCTTCTTGTAACGAAATGAAAACAAATCTTAACAAAGCAATATTAGAAGATTTAAGAGGGAATAAAGATAATATTAAAGAATGTGTCCTTGAAGTGCGTTTAGTACAGGCCAAATCAATTATGTATTACAAAGGTGATTCCAATATTACATTTGCAAGAGTTTCAGTAGCACTGCCAAAATTAATTGCTGCTGCCAAAAGACTGATCGAAAGGCAACCTCTATCTTTTGGATTGATGGATCCTCAATTTTATGAAACAAACATCGATTTTGATATACGTTTCATGGTTGATACTTCAATTGTTGGATGCAGTTGGATTGAACTACCTGTTGGGAAGTGGTTTTTAAGAACAATAGATTCAAAAGTGAAGCCTGAATCTAGATGTCAGATTGAAGTGGATGTGGCATGGAATGCTTTCATATTTCATCCACCAGAAGGAGAGTGGTCAAAAGTGGCACCATTCAGAATATTAAGTTTTGATATTGAATGTGCTGGTAGAAAAGGTATTTTCCCAGAAGCTAAACATGACCCTGTAATTCAAATTGCATCCATGGTCATAAGACAAGGTGAAACAGAACCATATTTAAGAAACGTATTTACATTGAATACATGTGCTCCTATTGTAGGTTCACAAGTACTTAGTTTTCAATCAGAGTCTGAAATGTTATCTAAGTGGTCTGATTTTTTTCGCAAATTAGATCCTGATATCATTACTGGATATAATATTAGCAATTTCGACTGGCCATATCTTATAAATCGTGCTAAACATTTAAATGTGCAAAAATTTGATTTTCTGGGACGAATAAAAAATGTAAGATCTGTTATAAAAGATACAGTCTTGCAATCGAAACAGATGGGTCGAAGAGAAAATAAAACCATTAATTTTGAAGGACGAGTTCCTTTTGATTTATTGTTGGTATTAGTTCGTGATTACAAATTAAGGTCATATACTCTGAATGCTGTCAGTTACCATTTCCTTCAAGAGCAGAAAGAAGATGTGCATCACAGTATAATCACAGATTTACAAAATGAAAGTGAACAAACCAGAAGGAGATTGGCAATGTACTGTCTTAAAGATGCTTACCTCCCACTAAAACTTTTAAACAAATTAATGTGTATCATTAATCACATGGAAATGGCTAGAGTTACTGGTGTTCCTTTACTTTGTTTACTAACAAGAGGGCAACAAATAAAAGTTGTCAGTCAGCTACTACGCAAAGCAAAAGAAGCTGGATATTTAATGCCAGTATACCATAGCCAAGGTTCTGATGATCAGTATGAAGGAGCCACAGTTATTGAACCCAAAAGAGGATACTATGCCGACCCTATTTCAACCTTAGATTTTGCATCTTTGTACCCGAGCATCATGATGGCACATAATTTATGTTATACAACTTTAGTTCCCCCTAATGCTCAAAACCAATTTAATGTTGCTGACAATGATGTTACTATAACACCTTCAAAAAACATGTTTGTAAAAAATCACATCAGAAAGGGCCTACTACCAGAAATTCTAGAATCACTACTCGCAGCAAGAAAAAAAGCAAAGGCAGACTTGAAGGATGAAAAAGACCCATTTAAAAGGTCAGTTCTGGATGGTAGACAACTGGCTTTGAAAATAAGTGCAAACTCTGTTTATGGATTTACAGGTGCTCAAGTAGGAAAATTACCATGCTTAGAAATATCTGGTAGTGTCACTGCTTATGGCAGAACTATGATTGAATTCACTAAGTCAGAAGTAGAAAAGAAATACACTAAAGCTAATGGATATAAAGAAGATGCTGTTGTTATATATGGAGATACTGATTCTGTAATGGTTAAGTTTGGAGTGAAAACTCTTGAAGAGAGTATGGAATTAGGAAAAGAAGCAGCTGAATTTGTTACAGCAAAGTTTGTAAAACCTATAAAATTAGAATTTGAGAAAGTATACTACCCATACTTACTCATTAATAAGAAACGATATGCTGGCCTTTATTTTACTAGACCAGATAAATATGACAAAATGGATTGCAAGGGTATTGAAACTGTTCGAAGAGACAATTGTCCTCTTGTTTCTAATGTAATGAGCACTTGTTTACAGAAGTTGCTCATAGACAGAGACCCAGATGGAGCTATTAATTATGCTAAACAAATTATAGCTGATTTATTATGCAATCGAATTGATATATCACAACTTGTTATTACTAAAGAACTCACAAAAAATGATTATGCTGCTAAACAGGCTCATGTAGAACTTGCTAAGAAAATGAAAAAGCGTGATGAGGGAACTGCACCGAAATTAGGAGACAGGGTTCCGTATGTGTTATGCTGTGCAACAAAAAATACACCTGCTTATATGAAAGCCGAAGATCCTATTTATGTATTAGAAAATAGCGTTCCTATTGATTTTAATTACTATTTGGAAAATCAGTTATCGAAACCCCTTTTAAGGATATTTGAACCAATTCTAGGTGAGAAAGCAGAATCTCTACTTCTTAAGGGTGAACATACCAGAACCAAAGCTATGGTCACTTCCAAAGTTGGGGCACTTGCTGCTTTCACTAAAAAGAAAGAAAAATGTCTAGGTTGTAAAACTGTCATGCCTAGTGAAACAAAAAAAGCGTTATGTGATCACTGCATGAAAAAAGAAGGCCAGTTATACATTACAGAAGTATTCAAATTACGGCAGCTTCAACAAAATTTTTCCAGATTATGGACAGAATGTCAAAGATGCCAAGGTAGTTTACATGAAGAAGTGCTTTGTACCAATCGAGATTGTACTATTTTTTACATGAGAAAGAAAATGGGTATGGAGCTTGACACTCAAGAAAATACAATTTTAAGGTTTGGGCAGCCGATTTGGTGA

Protein

MDRNKTKGPPPKRFKSGDDDDENDTPFSFEEQLACMDTGDIDSQEIFEGEGPENQSSNMKWSRPPPPILTPNRETLIFQQLDIDHYYGSPMNGMPGSQLAPVPIMRMYGITSEGNSVCCHVHGFTPYFYVTVPVNFTESSCNEMKTNLNKAILEDLRGNKDNIKECVLEVRLVQAKSIMYYKGDSNITFARVSVALPKLIAAAKRLIERQPLSFGLMDPQFYETNIDFDIRFMVDTSIVGCSWIELPVGKWFLRTIDSKVKPESRCQIEVDVAWNAFIFHPPEGEWSKVAPFRILSFDIECAGRKGIFPEAKHDPVIQIASMVIRQGETEPYLRNVFTLNTCAPIVGSQVLSFQSESEMLSKWSDFFRKLDPDIITGYNISNFDWPYLINRAKHLNVQKFDFLGRIKNVRSVIKDTVLQSKQMGRRENKTINFEGRVPFDLLLVLVRDYKLRSYTLNAVSYHFLQEQKEDVHHSIITDLQNESEQTRRRLAMYCLKDAYLPLKLLNKLMCIINHMEMARVTGVPLLCLLTRGQQIKVVSQLLRKAKEAGYLMPVYHSQGSDDQYEGATVIEPKRGYYADPISTLDFASLYPSIMMAHNLCYTTLVPPNAQNQFNVADNDVTITPSKNMFVKNHIRKGLLPEILESLLAARKKAKADLKDEKDPFKRSVLDGRQLALKISANSVYGFTGAQVGKLPCLEISGSVTAYGRTMIEFTKSEVEKKYTKANGYKEDAVVIYGDTDSVMVKFGVKTLEESMELGKEAAEFVTAKFVKPIKLEFEKVYYPYLLINKKRYAGLYFTRPDKYDKMDCKGIETVRRDNCPLVSNVMSTCLQKLLIDRDPDGAINYAKQIIADLLCNRIDISQLVITKELTKNDYAAKQAHVELAKKMKKRDEGTAPKLGDRVPYVLCCATKNTPAYMKAEDPIYVLENSVPIDFNYYLENQLSKPLLRIFEPILGEKAESLLLKGEHTRTKAMVTSKVGALAAFTKKKEKCLGCKTVMPSETKKALCDHCMKKEGQLYITEVFKLRQLQQNFSRLWTECQRCQGSLHEEVLCTNRDCTIFYMRKKMGMELDTQENTILRFGQPIW

Description

Possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. Required with its accessory proteins (proliferating cell nuclear antigen (PCNA) and replication factor C (RFC) or activator 1) for leading strand synthesis. Also involved in completing Okazaki fragments initiated by the DNA polymerase alpha/primase complex (By similarity).

Catalytic Activity

a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)

Cofactor

[4Fe-4S] cluster

Subunit

Heterodimer with subunits of 125 kDa and 50 kDa. The 125 kDa subunit contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity (By similarity).

Miscellaneous

In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis.

Similarity

Belongs to the DNA polymerase type-B family.

Keywords

4Fe-4S   Complete proteome   DNA replication   DNA-binding   DNA-directed DNA polymerase   Exonuclease   Hydrolase   Iron   Iron-sulfur   Metal-binding   Nuclease   Nucleotidyltransferase   Nucleus   Reference proteome   Transferase   Zinc   Zinc-finger  

Feature

chain  DNA polymerase delta catalytic subunit

Uniprot

W6AQI8   A0A2H1VM28   A0A2W1C0S0   A0A194Q8C6   E9RHR8   A0A182LS03   + More
A0A182P6X9   A0A182WEC8   E9RHR9   A0A182QPB6   A0A182JZP9   A0A182HH42   B0XFN1   A0A182R4E9   A0A182UD51   A0A182X6N7   A0A182V2S9   A0A084VIP1   A0A182NPQ0   A0A1Q3EX65   A0A182J4N4   A0A1J1HT32   A0A182FKP2   W5JF03   E9RHS0   A0A336LTL5   A0A182YL44   E9RHQ3   B4KYH9   E9RHN3   A0A0Q9XQJ5   E9RHP0   B4LDZ6   A0A0M4EIY0   Q29D92   E9RHN4   T1PJY7   A0A3B0JTW6   A0A0J9RW00   B4QLS3   P54358   B4ITV6   B3M9U0   B3NDQ0   A0A1W4VB36   E9RHP3   A0A0L0CRF6   A0A154NXW2   B4J3N9   E9RHN9   E9RHN6   E9RHP4   B4N725   A0A1I8Q9D8   E9RHQ4   A0A034V7P1   A0A0A1XEY8   A0A0C9QV42   E0VUR3   E9RHP5   E9RHR1   W8C0Q7   A0A1B0CA08   E9RHS1   A0A2J7PQM5   K7J8R6   E9RHQ2   A0A2A3EKA9   A0A0M9A481   A0A067QVI5   A0A3L8DT86   K7J2W7   A0A087ZVU5   A0A1A9VAR4   A0A1B6GS87   E9RHQ0   A0A232F0F7   A0A1B0AIE3   A0A1B0GNL4   A0A0L7R5U0   E9RHP6   A0A026WGY9   E9RHQ1   A0A1A9WGG8   A0A1A9XT21   A0A195F7Z8   A0A0J7KKJ4   A0A0C9Q128   A0A1B0B962   A0A1B6KBW9   A0A2J7PQM4   A0A158N9D0   A0A151I399   E9IA59   E9RHR0   A0A2J7PQM9   E9RHQ7   Q16H29   E9RHQ5   A0A151XG24  

EC Number

2.7.7.7

Pubmed

28756777    26354079    21075208    24438588    20920257    23761445    + More
25244985    17994087    15632085    25315136    22936249    8543168    10731132    12537572    12537569    17550304    26108605    25348373    25830018    20566863    24495485    20075255    24845553    30249741    28648823    24508170    21347285    21282665    17510324   

EMBL

KF878074    AHI59988.1    ODYU01003034    SOQ41304.1    KZ149900    PZC78556.1    + More
KQ459302    KPJ01778.1    AB598732    BAJ78772.1    AXCM01000779    AB598733    BAJ78773.1    AXCN02001661    APCN01002384    DS232946    EDS26912.1    ATLV01013376    KE524854    KFB37835.1    GFDL01015257    JAV19788.1    CVRI01000012    CRK89353.1    ADMH02001696    ETN61394.1    AB598734    BAJ78774.1    UFQT01000115    SSX20301.1    AB598717    BAJ78757.1    CH933809    EDW18790.1    AB598697    BAJ78737.1    KRG06360.1    AB598704    BAJ78744.1    CH940647    EDW70039.1    CP012525    ALC44790.1    CH379070    EAL30522.2    AB598698    BAJ78738.1    KA648974    AFP63603.1    OUUW01000002    SPP76796.1    CM002912    KMY99891.1    CM000363    EDX10622.1    X88928    AE014296    AY113526    CH891734    EDW99819.1    CH902618    EDV40131.1    CH954178    EDV52183.1    AB598707    BAJ78747.1    JRES01000005    KNC34945.1    KQ434772    KZC03868.1    CH916366    EDV97270.1    AB598703    BAJ78743.1    AB598700    BAJ78740.1    AB598708    BAJ78748.1    CH964168    EDW80164.1    AB598718    BAJ78758.1    GAKP01019651    JAC39301.1    GBXI01004338    JAD09954.1    GBYB01007619    JAG77386.1    DS235787    EEB17119.1    AB598709    BAJ78749.1    AB598725    BAJ78765.1    GAMC01007329    JAB99226.1    AJWK01003155    AB598735    BAJ78775.1    NEVH01022635    PNF18639.1    AB598716    BAJ78756.1    KZ288219    PBC32243.1    KQ435737    KOX76910.1    KK853201    KDR09904.1    QOIP01000005    RLU23109.1    GECZ01004474    JAS65295.1    AB598714    BAJ78754.1    NNAY01001399    OXU24105.1    AJVK01029539    AJVK01029540    KQ414648    KOC66245.1    AB598710    BAJ78750.1    KK107211    EZA55332.1    AB598715    BAJ78755.1    KQ981727    KYN36740.1    LBMM01006107    KMQ90933.1    GBYB01007618    JAG77385.1    JXJN01010286    GEBQ01031029    JAT08948.1    PNF18641.1    ADTU01009386    KQ976484    KYM83690.1    GL761987    EFZ22529.1    AB598724    BAJ78764.1    PNF18640.1    AB598721    BAJ78761.1    CH478211    EAT33548.1    AB598719    BAJ78759.1    KQ982174    KYQ59301.1   

Proteomes

UP000053268    UP000075883    UP000075885    UP000075920    UP000075886    UP000075881    + More
UP000075840    UP000002320    UP000075900    UP000075902    UP000076407    UP000075903    UP000030765    UP000075884    UP000075880    UP000183832    UP000069272    UP000000673    UP000076408    UP000009192    UP000008792    UP000092553    UP000001819    UP000095301    UP000268350    UP000000304    UP000000803    UP000002282    UP000007801    UP000008711    UP000192221    UP000037069    UP000076502    UP000001070    UP000007798    UP000095300    UP000009046    UP000092461    UP000235965    UP000002358    UP000242457    UP000053105    UP000027135    UP000279307    UP000005203    UP000078200    UP000215335    UP000092445    UP000092462    UP000053825    UP000053097    UP000091820    UP000092443    UP000078541    UP000036403    UP000092460    UP000005205    UP000078540    UP000008820    UP000075809   

PRIDE

W6AQI8    P54358   

Pfam

PF00136   DNA_pol_B        + More
PF14260   zf-C4pol
PF03104   DNA_pol_B_exo1

Interpro

IPR042087   DNA_pol_B_C        + More
IPR023211   DNA_pol_palm_dom_sf       
IPR012337   RNaseH-like_sf       
IPR006133   DNA-dir_DNA_pol_B_exonuc       
IPR017964   DNA-dir_DNA_pol_B_CS       
IPR036397   RNaseH_sf       
IPR025687   Znf-C4pol       
IPR006134   DNA-dir_DNA_pol_B_multi_dom       
IPR006172   DNA-dir_DNA_pol_B       

SUPFAM

SSF53098   SSF53098       

Gene 3D

1.10.132.60     3.30.420.10     3.90.1600.10    

ProteinModelPortal

W6AQI8   A0A2H1VM28   A0A2W1C0S0   A0A194Q8C6   E9RHR8   A0A182LS03   + More
A0A182P6X9   A0A182WEC8   E9RHR9   A0A182QPB6   A0A182JZP9   A0A182HH42   B0XFN1   A0A182R4E9   A0A182UD51   A0A182X6N7   A0A182V2S9   A0A084VIP1   A0A182NPQ0   A0A1Q3EX65   A0A182J4N4   A0A1J1HT32   A0A182FKP2   W5JF03   E9RHS0   A0A336LTL5   A0A182YL44   E9RHQ3   B4KYH9   E9RHN3   A0A0Q9XQJ5   E9RHP0   B4LDZ6   A0A0M4EIY0   Q29D92   E9RHN4   T1PJY7   A0A3B0JTW6   A0A0J9RW00   B4QLS3   P54358   B4ITV6   B3M9U0   B3NDQ0   A0A1W4VB36   E9RHP3   A0A0L0CRF6   A0A154NXW2   B4J3N9   E9RHN9   E9RHN6   E9RHP4   B4N725   A0A1I8Q9D8   E9RHQ4   A0A034V7P1   A0A0A1XEY8   A0A0C9QV42   E0VUR3   E9RHP5   E9RHR1   W8C0Q7   A0A1B0CA08   E9RHS1   A0A2J7PQM5   K7J8R6   E9RHQ2   A0A2A3EKA9   A0A0M9A481   A0A067QVI5   A0A3L8DT86   K7J2W7   A0A087ZVU5   A0A1A9VAR4   A0A1B6GS87   E9RHQ0   A0A232F0F7   A0A1B0AIE3   A0A1B0GNL4   A0A0L7R5U0   E9RHP6   A0A026WGY9   E9RHQ1   A0A1A9WGG8   A0A1A9XT21   A0A195F7Z8   A0A0J7KKJ4   A0A0C9Q128   A0A1B0B962   A0A1B6KBW9   A0A2J7PQM4   A0A158N9D0   A0A151I399   E9IA59   E9RHR0   A0A2J7PQM9   E9RHQ7   Q16H29   E9RHQ5   A0A151XG24  

PDB

3IAY     E-value=0,     Score=2400

KEGG

101735729    K02327 DNA polymerase delta subunit 1 [EC:2.7.7.7] | (RefSeq) DNA polymerase delta catalytic subunit

PATHWAY

03030    DNA replication - Bombyx mori (domestic silkworm)
03410    Base excision repair - Bombyx mori (domestic silkworm)
03420    Nucleotide excision repair - Bombyx mori (domestic silkworm)
03430    Mismatch repair - Bombyx mori (domestic silkworm)
03440    Homologous recombination - Bombyx mori (domestic silkworm)

GO

GO:0051539   GO:0000166   GO:0003887   GO:0006260   GO:0003677   GO:0046872   GO:0005634   GO:0008296   GO:0043625   GO:0003676   GO:0008408   GO:0005216   GO:0006811   GO:0006541   GO:0016812   GO:0016597  

Subcellular location

Nucleus  

Length:

1085

Number of predicted TMHs:

0

Exp number of AAs in TMHs:

0.0543800000000002

Exp number, first 60 AAs:

0

Total prob of N-in:

0.00256

outside

1  -  1085

 

 

Pi

3.62607

Theta

233.006337

Tajima's D

-1.070618

CLR

33.954858

CSRT

0.126443677816109

Interpretation

Uncertain