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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap tRNA-Lys-2 IGR1415 IGR1420 IGR1425 IGR1426 IGR1418 IGR1421 IGR1422 IGR1423 IGR1417 IGR1424 IGR1414 IGR1416 IGR1419 HD1930 HD1926 HD1927 HD1941 xerC, - HD1940 glyS, - HD1942 acpP, - HD1931 HD1939 HD1937 dod, - HD1929 HD1938 HD1936 menB, - HD1925 holB, - HD1935 HD1932 HD1930 HD1926 HD1927 HD1941 xerC, - HD1940 glyS, - HD1942 acpP, - HD1931 HD1939 HD1937 dod, - HD1929 HD1938 HD1936 menB, - HD1925 holB, - HD1935 HD1932 Type: tandem, Name:  - 19 HD1930 HD1927 xerC, - HD1940 glyS, - HD1942 HD1926 HD1941 acpP, - HD1931 HD1939 HD1937 dod, - HD1929 HD1938 HD1936 menB, - HD1925 holB, - HD1935 HD1932 tmk, - HD1933 tmk, - HD1933
* Calculated from Protein Sequence

Gene ID: HD1935

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
holB  

Definition:
DNA polymerase III, delta' subunit

Gene Start:
1624935

Gene Stop:
1625921

Gene Length:
987

Molecular Weight*:
37355

pI*:
7.60

Net Charge*:
3.18

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:
Dong,Z., Onrust,R., Skangalis,M. and O"Donnell,M. 1993.
DNA polymerase III accessory proteins. I. holA and holB encoding delta and delta".
J. Biol. Chem. 268(16): 11758-11765.
Medline: 93280136.

Carter,J.R., Franden,M.A., Aebersold,R. and McHenry,C.S.
Identification, isolation, and characterization of the structural
gene encoding the delta' subunit of Escherichia coli DNA polymerase III holoenzyme
J. Bacteriol. 175 (12), 3812-3822 (1993)
Medline: 93285995

Onrust,R. and O'Donnell,M.
DNA polymerase III accessory proteins. II. Characterization of
delta and delta'
J. Biol. Chem. 268 (16), 11766-11772 (1993)
Medline: 93280137

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

Guenther,B., Onrust,R., Sali,A., O'Donnell,M. and Kuriyan,J.
Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III
Cell 91 (3), 335-345 (1997)
Medline: 98028572


Comment:
For other "dna" genes, see HD1372 (dnaB), HD1771 (dnaJ), HD1819 (dnaX), HD0189 (dnaK), HD0973 (dnaB), HD0551 (dnaE), HD0690 (dnaG), HD0850 (dnaN), HD0851 (dnaA).

For other "hol" genes, see HD1130 (holA)and HD0667 (holC).

Blast Summary:  PSI-Blast Search
Many significant hits using gapped BLAST to DNA polymerase III delta" subunit from H. influenzae (2506369, 1074027), Yersinia pestis (6016239), E. coli (145799, 2506368), Pseudomonas aeruginosa (1708282), among others.

HD1935 is similar to DNA polymerase III subunits gamma and tau from C. trachomatis (CT334), U. urealyticum (UU087), C. pneumoniae (CPn0040), M. genitalium (MG420), T. pallidum (TP1005 DNA), and M. pneumoniae (MP0224, MP0147).

COGS Summary:  COGS Search
BeTs to 16 clades of COG0470
COG name: ATPase involved in DNA replication
Functional Class: L
The phylogenetic pattern of COG0470 is AMTKYQVCEBRHUJGPOLINX
Number of proteins in this genome belonging to this COG is 2

Blocks Summary:  Blocks Search
No significant hits to the Blocks database.

ProDom Summary:  Protein Domain Search
Residues 166-312 are 43% similar to a (DNA POLYMERASE DELTA' III) protein domain (PD036054) which is seen in Q9CKE8_PASMU.

Residues 4-130 are 48% similar to a (DNA POLYMERASE III SUBUNIT) protein domain (PD345569) which is seen in HOLB_HAEIN.

Residues 161-328 are 31% similar to a (DNA POLYMERASE III TRANSFERASE) protein domain (PD399168) which is seen in HOLB_HAEIN.

Residues 8-143 are 33% similar to a (ATP-BINDING PROTEASE SUBUNIT PROTEOME COMPLETE) protein domain (PD000092) which is seen in Q9JTS1_NEIMA.



Paralogs:  Local Blast Search

HD1935 is paralogously related to HD1819 (1e-14).


Pfam Summary:  Pfam Search
No significant hits to the Pfam 11.0 database

PDB Hit:
pdb|1A5T| Crystal Structure Of The Delta Prime Subunit Of The... 165 8e-042

Gene Protein Sequence:
MALYPWLEQHYQQLTATFSNGRGHHALLFKSDVGLGTEKLIAQFAAWLLC
QTPKQGHACDQCKSCLLLKNGNHPDLHILESIDGKDIGIEQIRETNTKLQ
NFAQQGGNTVVYIKNAECLTAASGNALLKTLEEPNDKVYFLLAAPQQTAI
LPTIASRCQTWLIHSPEMALTLAWLQAQAPTATREACEIAMRLCHQRPLI
CKTFLEKDRLTARKTFLRTFWRFFNNRDVFLLFSQFDKEKALILEQLEWL
ESFFSDSIKAKLAITNGWINHDLHNGILQFSQQLDIKRLLIGHQLIQQTK
WDLLAVNAINQELILLACLTKLTLNVFE$

Gene Nucleotide Sequence:  Sequence Viewer
ATGGCATTATATCCTTGGCTTGAACAACATTATCAACAACTGACAGCAAC
CTTTTCAAATGGGCGGGGGCATCACGCCTTATTATTTAAAAGTGATGTTG
GCTTAGGCACAGAGAAATTAATAGCACAATTTGCTGCTTGGCTACTTTGC
CAAACACCAAAGCAAGGTCACGCTTGTGATCAATGCAAAAGCTGTTTATT
GCTTAAAAATGGCAATCATCCCGACTTACACATTCTGGAATCAATAGATG
GCAAAGATATCGGCATTGAGCAAATCCGCGAAACAAATACTAAATTGCAA
AATTTCGCCCAACAAGGCGGAAATACGGTTGTCTATATTAAAAACGCCGA
ATGCCTAACCGCAGCAAGCGGCAACGCCTTATTGAAAACATTAGAAGAAC
CAAATGATAAAGTTTACTTCCTATTAGCAGCACCACAACAAACAGCTATC
TTGCCAACCATTGCAAGCCGTTGCCAAACGTGGTTAATACATTCACCAGA
AATGGCACTTACATTAGCTTGGCTACAAGCACAGGCACCCACTGCCACTC
GTGAAGCCTGTGAGATTGCAATGCGTTTATGCCACCAACGTCCACTCATT
TGCAAAACTTTTCTTGAAAAAGACCGCTTAACCGCACGTAAAACCTTTTT
ACGTACTTTTTGGCGTTTTTTTAACAATCGTGATGTTTTTCTACTGTTTA
GCCAATTTGATAAAGAAAAAGCGCTTATTTTAGAACAATTGGAATGGTTA
GAAAGCTTCTTCAGTGATAGCATCAAAGCAAAGTTAGCCATTACTAATGG
TTGGATAAACCACGATTTACATAATGGCATTCTGCAATTCAGCCAACAAC
TTGATATAAAACGATTATTAATAGGCCATCAATTAATTCAACAAACAAAA
TGGGATTTACTCGCGGTGAATGCAATTAATCAGGAGTTAATATTATTAGC
TTGTCTGACTAAATTAACGTTAAATGTATTTGAATAA


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