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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR0060 IGR0065 IGR0061 IGR0059 IGR0058.1 IGR0064 IGR0063 IGR0062 NG0073 avtA, - NG0082 dnaE, - NG0078 NG0074 NG0079 tonB, - NG0075 NG0077 NG0081 NG0073 avtA, - NG0082 dnaE, - NG0078 NG0074 NG0079 tonB, - NG0075 NG0077 NG0081 NG0073 avtA, - NG0082 dnaE, - NG0078 tonB, - NG0075 NG0081 NG0080 NG0076 NG0079 NG0077 NG0074 NG0080 NG0076
* Calculated from Protein Sequence

Gene ID: NG0078

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
dnaE  

Definition:
DNA-dependent DNA polymerase III alpha chain

Gene Start:
85423

Gene Stop:
81992

Gene Length:
3432

Molecular Weight*:
127001

pI*:
5.20

Net Charge*:
-25.65

EC:
2.7.7.7  

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

Pathway: pathway table
DNA polymerase
Purine metabolism
Pyrimidine metabolism

Secondary Evidence:
Fijalkowska,I.J. and Schaaper,R.M.
Antimutator mutations in the alpha subunit of Escherichia coli DNA
polymerase III: identification of the responsible mutations and
alignment with other DNA polymerases
Genetics 134 (4), 1039-1044 (1993)
Medline: 93387658.

Pritchard AE, McHenry CS.
Identification of the acidic residues in the active site of DNA polymerase III.
J Mol Biol. 1999 Jan 22;285(3):1067-80.
PMID: 9887268

Jonczyk P, Nowicka A, Fijalkowska IJ, Schaaper RM, Ciesla Z.
In vivo protein interactions within the Escherichia coli DNA polymerase III core.
J Bacteriol. 1998 Mar;180(6):1563-6.
PMID: 9515927


Comment:
From GenBANK (gi:118808): 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 tau chain serves as a scaffold to help in the dimerizaton of the core complex. The gamma chain seems to interact with the delta subunit to transfer the beta subunit on the DNA. The reaction: N deoxynucleoside triphosphate = N pyrophosphate + DNA(N). The enzyme contains a core (composed of alpha, epsilon, and theta chains) that associates with a tau subunit which allow the core dimerization to form the PolIII' complex. PolIII' associates with the gamma complex (composed of chains gamma, delta, delta', psi, and chi) and with the beta chain. The final composition of the complex is: (alpha,epsilon,theta)[2]-tau[2]-(gamma,delta,delta', psi,chi)[2]-beta[4]. The production of the two protein products from this region is due to programmed ribosomal frameshifting. Partial similarity to phage T4 DNA polymerase accessory protein 44 and to human activator 1, 37 and 40 kda subunits.

For a review of DNA Pol III, see O'Donnell,M. Accessory protein function in the DNA polymerase III holoenzyme from E. coli. Bioessays 14 (2), 105-111 (1992) Medline: 92246902.

For other 'dna' genes, see NG0002 (dnaN), NG0001 (dnaA), NG0235 (dnaJ), NG0451 (dnaB), NG0485 (dnaB), NG0551 (dnaJ), NG0973 (dnaQ), NG0998 (dnaG), NG1110 (dnaC), NG1429 (dnaK), NG1636 (dnaC) and NG1901 (dnaJ). For other pol III subunits, see NG0002 (beta), NG0283 (delta), NG0347 (delta prime), NG0743 (gamma-tau), NG0973 (epsilon), NG1226 (chi).

Oklahoma ID: NGO.78c

Blast Summary:  PSI-Blast Search
Numerous hits in gapped BLAST to polIII alpha chain sequences, e.g. residues 1-1144 are 47% similar to the E.coli polIII alpha subunit.

Residues 1-1144 are virtually identical to NMA0632 in N.meningitidis (11261608).

COGS Summary:  COGS Search
BeTs to 12 clades of COG0587
COG name: DNA-dependent DNA polymerase III alpha chain
Functional Class:  L
The phylogenetic pattern of COG0587 is -----qvCeBRhujgpolinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB003141 (PHP domain N-terminal region) with a combined E-value of 2.3e-33.
    IPB003141A    7-44
    IPB003141B    392-407
    IPB003141C    747-757


ProDom Summary:  Protein Domain Search
Residues 394-742 are 51% similar to a (DNA POLYMERASE III ALPHA) protein domain (PD004180) which is seen in DP3A_ECOLI.

Residues 744-1134 are 39% similar to a (DNA POLYMERASE III ALPHA) protein domain (PD004426) which is seen in DP3A_VIBCH.

Residues 362-393 are 90% similar to a (DNA III POLYMERASE ALPHA) protein domain (PD005473) which is seen in DP3A_VIBCH.

Residues 6-65 are 51% similar to a (DNA POLYMERASE ALPHA PROTEIN) protein domain (PD001693) which is seen in DP3A_AQUAE.

Residues 90-359 are 48% similar to a (DNA POLYMERASE ALPHA III) protein domain (PD003212) which is seen in DP3A_ECOLI.



Paralogs:  Local Blast Search


NG0078 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 7 to 72 (E-value = 1.1e-16) place NG0078 in the PHP_N family which is described as PHP domain N-terminal region (PF02231)
Residues 979 to 1059 (E-value = 5.6e-09) place NG0078 in the tRNA_anti family which is described as OB-fold nucleic acid binding domain (PF01336)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
453  
528

PDB Hit:
No hits to the PDB database.

Gene Protein Sequence:
MTEPTYIPLRLHTEFSITDGMVRIKKLIAKAQEYGLPALGISDLMNEFGL
VKFYKACRGAGIKPVGAADVWIGNPNAPDKPFRAMLVIRNDAGYLRLSEL
LTEAYVGQDRNIHHAELNPEWLENGDNSGLICLSGAHYGEVGVNLLNGNE
DAARAAALKYAAWFPDTFYLELQRLPERPEWEACVSGSVKLAEELGLPVV
ATHPTQFMNRDDFNAHEARVCIAGGWVLTDKKRPRDFTPSQFFIPPETML
ERFADLPEALENTVEIAKRCNLHITLGKNFLPLFPTPDGLSLDDCLIKLS
NEGLQERMVQLYPDEAERAAKMPEYQERLDFELNIIIQMKFPGYFLIVQD
FINWAKTHGCPVGPGRGSGAGSLVAYSLKITDLDPLKYALLFERFLNPER
VSMPDFDVDFCQANRGRVIEYVREKYGAQAVSQIVTFGTMSSKAVIRDVG
RVLELPFMLCDKLSKLIPLEANKPLSLDDAMKAQPQIQELLEAEEADELI
TLAKKLEDLTRGLGMHAGGVLIAPGKISDYSPVYQADESASPVSMYDKGD
VEDVGLVKFDFLGLRNLTIIEMAQNNIKNTAGDIVDVGKIPLDDQTAYQI
FRDANTTAVFQFESTGMKKMLKTAHTTKFEELIAFVSLYRPGPMDNIPDF
VARMKGQEFQYIHPLLEGILAPTYGIMVYQEQVMQAAQIIGGYSLGGADL
LRRAMGKKKPEEMVKHREIFAEGAAKQGISREKSDEIFNYMEKFAGYGFN
KSHAAAYALISYQTAWLKAHYPAEFMAATMSSELDNTDQLKHFYDDCRAN
GIEFLPPDINESDYRFTPYPDMKIRYALGAIKGTGEAAVESIIAARQSGG
KFTGLLDFCERVGKEHMNRRTLEALIRGGAFDSIEPNRAMLLANIDLAMD
NADQKAANANQGGLFDMMEDAIEPVRLIDAPMWSESEKLAEEKTVIGFYL
SGHPFGPYAQEVRQIAPTKLGRLKPQDSVRLAGFVTAVRTMMGKRGKIAF
VSLEDSSGQAEIMVGGQTLENCADCLKADQVLIIESKVSRDDYGGGDGLR
IMANQVMTLQTARERYARSLSLALAPHHDIGGLVRLLAAHQLPDTPRIPL
QLSYANEKASGRLQVPPKWTVTPSSALFGELETLLGSRSVRVNW

Gene Nucleotide Sequence:  Sequence Viewer
ATGACCGAGCCGACCTACATCCCCCTGCGCCTGCATACCGAATTCTCCAT
TACCGACGGTATGGTGCGGATTAAAAAACTGATTGCCAAAGCGCAAGAAT
ACGGTTTGCCTGCTTTGGGCATCAGCGATTTGATGAACGAATTCGGTTTG
GTGAAATTCTATAAAGCCTGCCGCGGCGCAGGGATTAAGCCCGTCGGCGC
GGCGGACGTGTGGATAGGCAATCCGAATGCGCCCGACAAGCCGTTCCGCG
CCATGCTGGTTATCCGCAACGATGCGGGTTATCTGCGCTTGAGCGAGCTT
TTGACGGAGGCTTATGTCGGCCAAGACCGCAATATCCATCATGCGGAACT
CAATCCCGAATGGCTGGAAAACGGCGACAACAGCGGCTTGATTTGTTTGA
GCGGCGCGCATTACGGCGAAGTGGGCGTGAATCTGTTGAACGGCAATGAA
GACGCGGCGCGTGCGGCGGCGTTGAAATATGCGGCATGGTTTCCCGATAC
GTTTTATTTAGAGCTGCAACGCCTGCCCGAACGCCCCGAATGGGAGGCTT
GCGTTTCCGGCAGCGTGAAGCTGGCGGAGGAACTGGGTTTGCCGGTGGTA
GCAACGCATCCGACACAGTTTATGAACCGCGACGATTTCAACGCGCACGA
GGCGCGGGTGTGCATCGCGGGCGGCTGGGTGCTGACGGACAAGAAACGTC
CGCGCGATTTCACGCCGAGCCAGTTTTTCATTCCGCCGGAAACGATGCTG
GAGCGTTTCGCCGACTTGCCCGAAGCCTTGGAAAACACGGTGGAAATCGC
CAAACGCTGCAACTTGCACATCACATTGGGCAAAAACTTCCTACCCCTTT
TCCCCACGCCCGACGGTTTATCACTCGATGACTGTCTCATCAAACTCTCC
AACGAGGGTTTGCAGGAACGCATGGTTCAGCTTTATCCCGACGAGGCGGA
ACGGGCGGCAAAAATGCCGGAATATCAGGAGCGGCTGGACTTTGAGCTGA
ACATCATCATCCAAATGAAATTCCCCGGCTATTTCCTTATCGTACAAGAC
TTTATCAACTGGGCGAAAACGCACGGCTGTCCGGTCGGGCCGGGACGCGG
TTCGGGCGCGGGTTCGCTGGTGGCGTATTCGCTGAAGATTACCGACCTCG
ACCCGCTGAAATACGCGCTGCTGTTCGAGCGTTTCCTAAACCCCGAACGC
GTTTCCATGCCCGACTTTGACGTGGACTTCTGTCAGGCAAACCGCGGCCG
CGTGATTGAATACGTGCGCGAAAAATACGGCGCTCAGGCGGTCAGCCAGA
TTGTGACTTTCGGCACGATGTCGTCCAAAGCGGTCATCCGCGACGTGGGG
CGTGTGCTGGAACTGCCGTTTATGCTGTGCGACAAACTGTCCAAGCTGAT
TCCGTTGGAAGCCAACAAACCCCTGAGTTTGGACGACGCGATGAAGGCGC
AGCCGCAGATTCAGGAATTGCTTGAAGCGGAAGAAGCGGACGAACTGATT
ACGCTGGCGAAAAAACTGGAAGACCTGACGCGCGGTTTGGGTATGCACGC
AGGCGGCGTGTTGATTGCGCCGGGCAAGATTTCCGATTACAGCCCCGTGT
ATCAGGCGGACGAATCCGCCTCGCCCGTATCCATGTACGACAAGGGCGAC
GTGGAAGACGTGGGTTTGGTGAAGTTCGACTTTTTGGGCCTGCGCAACCT
GACCATTATCGAAATGGCGCAGAACAACATCAAAAACACCGCCGGCGATA
TCGTCGATGTCGGCAAGATTCCGCTTGACGACCAGACTGCCTACCAAATC
TTCCGCGATGCGAACACCACCGCCGTCTTCCAGTTCGAGTCGACCGGCAT
GAAAAAAATGCTGAAAACGGCGCATACGACCAAGTTTGAAGAACTCATCG
CCTTCGTATCGCTCTACCGACCCGGCCCGATGGACAACATTCCCGACTTC
GTCGCACGCATGAAGGGACAGGAATTCCAATACATCCACCCGCTGCTGGA
AGGCATCCTCGCGCCGACCTACGGCATTATGGTGTATCAGGAACAAGTGA
TGCAGGCGGCGCAGATTATCGGCGGCTACTCGCTCGGCGGCGCGGACCTG
CTGCGCCGCGCCATGGGTAAGAAAAAGCCCGAAGAGATGGTGAAACACCG
CGAAATCTTCGCCGAAGGTGCGGCAAAACAAGGCATTTCGCGCGAAAAAT
CCGACGAAATCTTCAACTACATGGAAAAATTCGCCGGCTACGGTTTCAAC
AAATCCCACGCCGCCGCCTACGCCCTGATTTCCTACCAGACCGCATGGCT
CAAAGCCCACTATCCCGCCGAATTTATGGCGGCGACGATGTCGTCCGAAT
TGGACAACACCGACCAGCTCAAACATTTCTACGACGACTGCCGCGCCAAC
GGCATCGAGTTCCTGCCGCCCGACATTAACGAATCCGACTACCGCTTCAC
GCCGTATCCGGACATGAAAATCCGCTACGCACTCGGCGCGATTAAAGGCA
CGGGCGAAGCCGCCGTCGAATCCATCATCGCCGCGCGGCAAAGCGGCGGC
AAATTTACCGGCCTGTTGGACTTCTGCGAGCGCGTCGGCAAAGAACACAT
GAACCGCCGCACCCTCGAAGCCCTGATACGCGGCGGCGCGTTCGACAGCA
TCGAACCCAACCGCGCCATGCTCTTGGCGAACATCGACCTTGCCATGGAC
AACGCCGACCAAAAAGCCGCCAACGCCAATCAGGGCGGGCTGTTTGACAT
GATGGAAGACGCCATCGAACCGGTGCGGCTCATCGACGCACCCATGTGGA
GCGAATCGGAAAAACTCGCCGAAGAAAAAACCGTCATCGGCTTTTACCTG
TCCGGCCACCCGTTCGGCCCGTATGCCCAAGAAGTCCGCCAAATCGCCCC
GACCAAATTAGGCCGTCTGAAACCGCAAGACAGCGTGCGCCTCGCCGGAT
TCGTTACCGCCGTGCGCACCATGATGGGCAAACGCGGCAAAATCGCCTTC
GTCAGCCTCGAAGATTCGAGCGGGCAGGCTGAAATCATGGTCGGCGGACA
AACGCTGGAAAACTGCGCCGACTGCCTCAAAGCCGACCAAGTGCTGATTA
TCGAATCCAAAGTCAGCCGCGACGATTACGGCGGCGGCGACGGGCTGCGC
ATCATGGCAAACCAAGTCATGACCCTGCAAACGGCGCGCGAACGCTACGC
CCGCAGCCTCAGCCTCGCCCTTGCCCCGCATCACGACATCGGCGGACTGG
TACGGCTGCTCGCCGCCCACCAACTGCCCGACACGCCGCGCATCCCGCTT
CAATTGTCGTATGCCAACGAAAAAGCGTCGGGCAGGCTTCAAGTGCCTCC
GAAATGGACGGTTACACCGAGTTCCGCATTGTTCGGCGAACTGGAAACAT
TGCTCGGCAGCCGGTCGGTGCGCGTGAATTGG


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