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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR609 IGR607 IGR608 IGR605 IGR611 IGR606 IGR610 recF, - HD0849 dnaN, - HD0850 asd, - HD0847 lpxB, - HD0846 dnaA, - HD0851 sodC, - HD0848 prfA, - HD0853 HD0852 recF, - HD0849 dnaN, - HD0850 asd, - HD0847 lpxB, - HD0846 dnaA, - HD0851 sodC, - HD0848 prfA, - HD0853 HD0852 recF, - HD0849 dnaN, - HD0850 asd, - HD0847 lpxB, - HD0846 dnaA, - HD0851 sohB, - HD0845 sohB, - HD0845 sodC, - HD0848 prfA, - HD0853 HD0852
* Calculated from Protein Sequence

Gene ID: HD0850

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
dnaN  

Definition:
DNA polymerase III beta chain, dnaN

Gene Start:
678408

Gene Stop:
677305

Gene Length:
1104

Molecular Weight*:
41386

pI*:
4.90

Net Charge*:
-9.53

EC:
2.7.7.7  

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

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism

Secondary Evidence:
Ohmori,H., Kimura,M., Nagata,T. and Sakakibara,Y.
Structural analysis of the dnaA and dnaN genes of Escherichia coli
Gene 28 (2), 159-170 (1984)
Medline: 84237568

Armengod,M.E., Garcia-Sogo,M. and Lambies,E.
Transcriptional organization of the dnaN and recF genes of
Escherichia coli K-12
J. Biol. Chem. 263 (24), 12109-12114 (1988)
Medline: 88298898

Armengod,M.E. and Lambies,E.
Overlapping arrangement of the recF and dnaN operons of Escherichia coli; positive and negative control sequences
Gene 43 (3), 183-196 (1986)
Medline: 86301872

Kong,X.P., Onrust,R., O"Donnell,M. and Kuriyan,J.
Three-dimensional structure of the beta subunit of E. coli DNA
polymerase III holoenzyme: a sliding DNA clamp
Cell 69 (3), 425-437 (1992)
Medline: 92257585

O"Donnell,M.
Accessory protein function in the DNA polymerase III holoenzyme
from E. coli
Bioessays 14 (2), 105-111 (1992)
Medline: 92246902


Comment:
For other "dna" genes, see HD1372 (dnaB), HD1771 (dnaJ), HD1819 (dnaX), HD0189 (dnaK), HD1935 (dnaX), HD0551 (dnaE), HD0690 (dnaG), HD0973 (dnaB), HD0851 (dnaA)

Blast Summary:  PSI-Blast Search
Many significant hits using gapped BLAST to DNA polymerase III beta chain from H. influenzae (1169393), Salmonella typhimurium (3915668), E. coli (118798), among others. HD0850 is 67% similar to residues 1-366 from DP3B_HAEIN.

HD0850 is similar to DNA polymerase III beta chain from C. trachomatis (CT075), C. pneumoniae (CPn0338), T. pallidum (TP0002), U. urealyticum (UU079), and M. genitalium (MG001).
No similarities to M. pneumoniae.

COGS Summary:  COGS Search
BeTs to 12 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
***** IPB001001 (DNA polymerase III, beta chain) with a combined E-value of 1.5e-84.
    IPB001001A    5-53
    IPB001001B    67-81
    IPB001001C    100-118
    IPB001001D    136-159
    IPB001001E    170-180
    IPB001001F    194-204
    IPB001001G    235-250
    IPB001001H    313-332


ProDom Summary:  Protein Domain Search
Residues 1-120 are 31% similar to a (DNA POLYMERASE BETA TRANSFERASE) protein domain (PD290125) which is seen in DP3B_SYNY3.

Residues 238-366 are 44% similar to a (DNA POLYMERASE III BETA) protein domain (PD373027) which is seen in Q9JXS8_NEIMB.

Residues 1-147 are 67% similar to a (DNA POLYMERASE III BETA) protein domain (PD328536) which is seen in Q9CLQ5_PASMU.

Residues 1-147 are 55% similar to a (DNA POLYMERASE III BETA) protein domain (PD343696) which is seen in DP3B_PROMI.

Residues 148-367 are 77% similar to a (DNA POLYMERASE III BETA) protein domain (PD003062) which is seen in Q9CLQ5_PASMU.



Paralogs:  Local Blast Search
HD0850 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 1 to 121 (E-value = 3.3e-52) place HD0850 in the DNA_pol3_beta family which is described as DNA polymerase III beta subunit, N-terminal domain (PF00712)
Residues 130 to 244 (E-value = 4e-54) place HD0850 in the DNA_pol3_beta_2 family which is described as DNA polymerase III beta subunit, central domain (PF02767)
Residues 246 to 366 (E-value = 7.6e-57) place HD0850 in the DNA_pol3_beta_3 family which is described as DNA polymerase III beta subunit, C-terminal domain (PF02768)

PDB Hit:
pdb|2POL|A Chain A, Pol Iii (Beta Subunit) (E.C.2.7.7.7) >gi|49... 461 7e-131

Gene Protein Sequence:
MQLTITREQLLKPLQQVCGVLSSRPTLPVINNILLDINGSRLSLTGTDLE
VELTTQAELEQAVDFSGKFTLPAKKWLDICRSLPENSLISIQFEQDRALI
RADRSKFNLATLPASDYPNLMDWKPEVDFSMEQSTLSRLIDATQFSMANQ
DARYFLNGMKFETEGNLLRTVATDGHRLAVCTMALSQELTTHSVIVPRKA
VLELSRILSMTADPVRLEIGTNNLRISMNGVVFTSKLIDGRFPDYRRVLP
RNADRILEAETEMLKRALMRAAILSNEKFHGVRLALSENMLKITANNPEQ
EEAEEIIDVAYQNTAMEIGFNVSYLLDVLNTLKCERVRFNLVDASSSCLI
EDCENSTAEYVIMPMRL$

Gene Nucleotide Sequence:  Sequence Viewer
ATGCAACTTACGATTACCAGAGAACAGTTACTTAAACCTTTACAACAAGT
CTGTGGCGTATTAAGCAGCCGCCCTACCTTGCCTGTCATTAATAATATTT
TACTCGACATTAACGGATCTCGCTTGTCATTAACGGGCACAGACCTGGAA
GTAGAATTAACAACTCAAGCTGAACTTGAACAAGCGGTTGATTTTAGTGG
CAAATTTACTCTTCCAGCCAAGAAATGGCTTGATATTTGTCGCAGTTTAC
CTGAAAACAGCCTCATTTCTATTCAGTTTGAACAAGATCGTGCATTAATC
CGAGCTGATCGTAGCAAATTTAACTTAGCGACTTTACCCGCTAGCGATTA
TCCAAATTTAATGGATTGGAAACCTGAAGTTGATTTTAGTATGGAACAAT
CAACACTTTCTCGTTTAATTGATGCCACACAATTCTCAATGGCAAATCAA
GACGCTCGCTATTTCTTAAACGGTATGAAATTTGAAACAGAAGGTAATTT
ATTACGTACTGTAGCAACTGATGGCCACCGCTTAGCCGTATGTACTATGG
CTCTCAGCCAAGAACTGACAACCCATTCAGTGATTGTCCCCCGCAAAGCC
GTATTAGAATTATCACGGATATTATCTATGACGGCTGATCCTGTCCGCTT
AGAAATAGGCACGAATAATTTACGAATATCAATGAATGGCGTTGTCTTTA
CTTCAAAATTAATTGATGGTCGTTTCCCTGATTACCGCAGAGTATTACCA
CGTAATGCAGATCGTATTTTAGAGGCCGAAACCGAAATGTTAAAACGCGC
ATTAATGCGAGCGGCTATTCTTTCTAATGAAAAATTCCACGGTGTACGTT
TAGCCTTAAGTGAAAATATGCTGAAAATCACGGCTAACAATCCAGAACAA
GAAGAAGCAGAAGAAATTATTGACGTGGCATACCAGAATACCGCAATGGA
AATAGGCTTTAATGTAAGCTATTTATTAGACGTACTAAATACGCTGAAAT
GTGAACGCGTACGTTTTAACTTAGTCGATGCAAGCTCAAGCTGTTTAATT
GAAGATTGTGAGAACAGCACAGCAGAATATGTCATTATGCCAATGCGCTT
ATAA


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