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Treponema pallidum Search Results

Record: 1 of 1  
MiniMap IGR771 IGR1 IGR770 IGR772 IGR2 IGR4 IGR3 IGR769 IGR1.1 TpF1, - TP1038 clpP, - TP1041 lysS, - TP1040 Tp75, - TP0006 apt, - TP1039 recF, - TP0003 dnaA, - TP0001 gyrA, - TP0005 TpF1, - TP1038 clpP, - TP1041 lysS, - TP1040 Tp75, - TP0006 apt, - TP1039 recF, - TP0003 dnaA, - TP0001 gyrA, - TP0005 Type: tandem, Name:  - 4 Type: tandem, Name:  - 1 Type: tandem, Name:  - 2 Type: tandem, Name:  - 3 Type: tandem, Name:  - 5 TpF1, - TP1038 clpP, - TP1041 lysS, - TP1040 Tp75, - TP0006 apt, - TP1039 recF, - TP0003 dnaA, - TP0001 gyrA, - TP0005 TP0004 dnaN, - TP0002 TP0004 dnaN, - TP0002
* Calculated from Protein Sequence

Gene ID: TP0002

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
dnaN  

Definition:
DNA polymerase III, subunit beta

Gene Start:
1641

Gene Stop:
2753

Gene Length:
1113

Molecular Weight*:
41278

pI*:
6.08

Net Charge*:
-5.23

EC:
2.7.7.7  

Functional Class:
Replication; DNA replication, restriction, modification, recombination, and repair  

Pathway: pathway table
Nucleotide metabolism; Purine Metabolism
Nucleotide metabolism; Pyrimidine Metabolism

Secondary Evidence:
Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH 1999.
Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases.
Nucleic Acids Res. Apr 1;27(7):1642-9. Medline: 10075995.

Comment:
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiaton of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA. It contains a core (of alpha, epsilon, and theta) chains that can repair short gaps created by nuclease in duplex DNA. For efficient replication of the long, single-stranded templates, Pol III requires the auxiliary chains beta, gamma and delta.

Reaction:
N DEOXYNUCLEOSIDE TRIPHOSPHATE = N PYROPHOSPHATE + DNA(N).

Blast Summary:  PSI-Blast Search
Gapped BLAST revealed several significant hits to DNA polymerase III,
subunit beta. For example residues 1-369 are 29% similar to DP3B_PSEPU,
dnaN protein of Pseudomonas putida,(X14791).

This sequence is equivalent to TD1197, a predicted dnaN protein.

COGS Summary:  COGS Search
BeTs to 11 clades of COG0592
COG name: DNA polymerase III beta subunit
Functional Class: L
The phylogenetic pattern of COG0592 is amtKyqvcebrhujgpolinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
None.

ProDom Summary:  Protein Domain Search
Residues 1-346 are 30% similar to DNA polymerase III, subunit beta of
DP3B_PSEPU. Residues 314-368 also support this match.

Paralogs:  Local Blast Search
There is no evidence of paralogs in T. pallidum.

Pfam Summary:  Pfam Search
Residues 1 to 120 (E-value = 6.7e-20) place TP0002 in the DNA_pol3_beta family which is described as DNA polymerase III beta subunit, N-terminal domain (PF00712)
Residues 129 to 243 (E-value = 1.7e-22) place TP0002 in the DNA_pol3_beta_2 family which is described as DNA polymerase III beta subunit, central domain (PF02767)
Residues 245 to 369 (E-value = 1.1e-28) place TP0002 in the DNA_pol3_beta_3 family which is described as DNA polymerase III beta subunit, C-terminal domain (PF02768)

PDB Hit:
gi494833pdb2POLA Escherichia coli

Gene Protein Sequence:
MKILCEKEAFLKEISTAQEVISNKKNTSIFSNVLLAAQGALLTIRATDTK
VTFETSIPVNVLAEGTTTVFCDKLVNVVSALPTKEIELTLCEEQLVITPP
NKKISFQLRTLSHESFPCFPQNEGGVSLAVPTSDLRNMINHTVFAVSEDS
TRHFINGVHVDFQYGNIICVSTDGKRLAYIEKKGESSPQSFSGVIVPTKI
LGIVNRKLTPEGSVTLCITSQHVYFFFGGYKFSSVLIEGQFPNYKRVIPD
HQERSFCVGRVELMEALKRVSLLVEQKSHRIFITIQQGLLTLSSKAHTQE
NEIGDAQEEIACAYTGESEVIALNYLYLEEPLKVFTSKEVQVEFTDPAKA
LTLRAVPNTDCFHIIMPMQTE

Gene Nucleotide Sequence:  Sequence Viewer
GTGAAAATCCTATGCGAGAAAGAAGCCTTTCTGAAGGAAATAAGCACAGC
ACAAGAGGTTATTTCAAATAAAAAAAACACGTCTATTTTTTCGAACGTCC
TATTAGCTGCTCAAGGAGCCCTGCTTACCATCAGAGCAACCGACACAAAA
GTTACCTTTGAAACTAGCATTCCCGTCAATGTTCTCGCCGAAGGCACAAC
GACAGTTTTTTGCGACAAACTTGTGAATGTTGTTTCTGCCCTTCCAACAA
AAGAAATCGAATTAACGTTATGTGAAGAACAACTTGTCATTACCCCTCCA
AACAAAAAGATAAGCTTTCAGCTCAGAACCCTCTCGCATGAGAGTTTTCC
ATGTTTCCCTCAAAATGAAGGAGGCGTCTCTCTTGCTGTGCCTACCTCCG
ATCTTAGAAACATGATTAACCATACCGTTTTTGCAGTTTCAGAAGACAGT
ACGCGCCATTTTATCAATGGCGTACACGTTGATTTTCAGTATGGAAATAT
TATTTGTGTTTCAACAGATGGAAAGCGGCTCGCCTATATAGAAAAAAAGG
GAGAATCCTCTCCCCAATCCTTTTCGGGTGTTATTGTGCCAACTAAGATC
TTAGGCATAGTAAACCGTAAGCTTACCCCTGAAGGATCAGTGACGCTATG
CATTACGTCGCAGCACGTTTACTTTTTTTTCGGTGGATATAAGTTTTCTT
CTGTGCTTATTGAGGGGCAATTTCCTAATTACAAAAGAGTAATCCCTGAT
CATCAGGAGCGTTCTTTTTGTGTTGGACGTGTGGAGCTAATGGAGGCACT
TAAACGAGTCTCGTTGTTGGTAGAACAAAAATCTCACAGGATATTTATTA
CCATACAGCAGGGTTTGTTGACTTTAAGCTCAAAAGCTCACACTCAAGAA
AATGAAATAGGTGATGCTCAGGAAGAAATAGCCTGTGCTTATACAGGAGA
AAGTGAGGTCATAGCTCTTAACTATCTATACCTTGAAGAACCGCTTAAGG
TTTTTACTTCGAAGGAGGTTCAAGTGGAATTTACCGATCCTGCAAAAGCA
CTCACGCTTCGTGCTGTACCAAACACGGACTGCTTTCACATCATTATGCC
TATGCAAACGGAG


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