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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap tRNA-Leu-3 IGR932 IGR930 IGR931 IGR936 IGR933 IGR934 fhs, - HD1282 secG, - HD1277 mepA, - HD1275 aroC, - HD1274 nisP, - HD1278 nisP, - HD1280 topB, - HD1276 aefA,kefA, - HD1273 fhs, - HD1282 secG, - HD1277 mepA, - HD1275 aroC, - HD1274 nisP, - HD1278 nisP, - HD1280 topB, - HD1276 aefA,kefA, - HD1273 fhs, - HD1282 secG, - HD1277 mepA, - HD1275 aroC, - HD1274 nisP, - HD1278 nisP, - HD1280 topB, - HD1276 aefA,kefA, - HD1273
* Calculated from Protein Sequence

Gene ID: HD1276

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
topB  

Definition:
DNA topoisomerase III

Gene Start:
1038165

Gene Stop:
1040084

Gene Length:
1920

Molecular Weight*:
72965

pI*:
9.50

Net Charge*:
18.82

EC:
5.99.1.2  

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

Pathway: pathway table

Secondary Evidence:
Wang JC.
Cellular roles of DNA topoisomerases: a molecular perspective.
Nat Rev Mol Cell Biol. 2002 Jun;3(6):430-40. Review.
PMID: 12042765

DiGate,R.J. and Marians,K.J.
Molecular cloning and DNA sequence analysis of Escherichia coli topB, the gene encoding topoisomerase III.
J. Biol. Chem. 264(30):17924-17930.
Medline: 90036864.

Comment:
For other "top" genes, see HD1385 (top1) and HD0954 (topA).

Blast Summary:  PSI-Blast Search
Matches in gapped BLAST to DNA topoisomerase III. Residues 2-605 are 72% similar to this protein from Pasteurella multocida (18202830|) and residues 2-622 are 69% similar to this protein from Haemophilus influenzae (1174743|).

HD1276 is similar to DNA topoisomerase I from C. trachomatis (CT643), T. pallidum (TP0394), U. urealyticum (UU590), C. pneumoniae (CPn0769), M. genitalium (MG122), and M. pneumoniae (MP0572).

COGS Summary:  COGS Search
BeTs to 17 clades of COG0550
COG name: Topoisomerase IA
Functional Class: L
The phylogenetic pattern of COG0550 is amtkyqvcEBrHUJgpolinx
Number of proteins in this genome belonging to this COG is 3

Blocks Summary:  Blocks Search
***** IPB000380 (Prokaryotic DNA topoisomerase I) with a combined E-value of 2.8e-92.
    IPB000380A    4-16
    IPB000380B    32-49
    IPB000380C    99-116
    IPB000380D    132-143
    IPB000380E    160-183
    IPB000380F    194-225
    IPB000380G    293-323
    IPB000380H    326-342
    IPB000380I    376-390
    IPB000380J    404-421
    IPB000380K    504-543
    IPB000380L    564-582


ProDom Summary:  Protein Domain Search
Residues 240-354 are 72% similar to a (TOPOISOMERASE DNA ENZYME DNA-BINDING PROTEOME COMPLETE) protein domain (PD001593) which is seen in TOP3_ECOLI.

Residues 6-77 are 80% similar to a (TOPOISOMERASE PLASMID DNA ENZYME) protein domain (PD352542) which is seen in Q9CP53_PASMU.

Residues 98-145 are 75% similar to a (TOPOISOMERASE III PLASMID DNA) protein domain (PD384511) which is seen in Q9CP53_PASMU.

Residues 398-460 are 52% similar to a (TOPOISOMERASE III B PROTEOME) protein domain (PD406571) which is seen in TOP3_VIBCH.

Residues 356-444 are 66% similar to a (TOPOISOMERASE DNA III COMPLETE) protein domain (PD017178) which is seen in Q9CP53_PASMU.

Residues 475-605 are 60% similar to a (TOPOISOMERASE ENZYME DNA DNA-BINDING) protein domain (PD242953) which is seen in TOP3_VIBCH.

Residues 150-194 are 86% similar to a (TOPOISOMERASE PLASMID DNA ENZYME) protein domain (PD235718) which is seen in Q9CP53_PASMU.

Residues 447-597 are 80% similar to a (TOPOISOMERASE DNA ENZYME DNA-BINDING PROTEOME COMPLETE) protein domain (PD001411) which is seen in TOP3_HAEIN.

Residues 195-229 are 88% similar to a (TOPOISOMERASE DNA ENZYME DNA-BINDING COMPLETE PROTEOME) protein domain (PD011342) which is seen in Q9CP53_PASMU.



Paralogs:  Local Blast Search


HD1276 is paralogously related to HD0954 (5e-94) and HD1385 (2e-28).


Pfam Summary:  Pfam Search
Residues 2 to 136 (E-value = 3.9e-28) place HD1276 in the Toprim family which is described as Toprim domain (PF01751)
Residues 154 to 566 (E-value = 5.2e-160) place HD1276 in the Topoisom_bac family which is described as DNA topoisomerase (PF01131)

PDB Hit:
pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomer... 781 0.0
pdb|1CY7|A Chain A, Complex Of E.Coli Dna Topoisomerase I With ... 101 2e-022
pdb|1ECL| Amino Terminal 67kda Domain Of Escherichia Coli Dn... 101 2e-022

Gene Protein Sequence:
MMRVFLAEKPSLARAIAEVLPKPHIRGDGYIQCGEHDYVTWCIGHLLEQA
EPDAYDERFKTWRMEHLPIIPQQWKLIAKKQTAKQLKVVEKLVKKAEILV
NAGDPDREGQLLVDEVFNYLNVPASKKSQIQRCLVSDLNPTAVSKAINKL
QNNCDFIPLATSALARARADWLYGINMTRAYTLQGRWVGYQGVLSVGRVQ
TPVLGLIVRRDLEIEHFTPKDYFEVLAHIIVPTTQERFTAHWQPSKACED
YQDEEGRVLSRALVENVVKRISDQTACVTDYQDKTESEIAPLPYSLSALQ
IDAARRYGLSAQAVLDICQTLYETHKLITYPRSDNRYLPNEHYNERFNVV
AAIAHHLTEYQQKPEVVNLALRGRCWNDKKIEAHHAIIPTARQGNLRLTE
NEKRIYRLIACQYLMQFCPDAEYSKRKITLDIAGGTFIAQARNLVTAGWK
ALLGKEDCDEMIEPLLPAVQKAQRLHCEKREIISKKTQLPRHFTDASLLS
AMTGIARFVQDKQLKKILRETDGLGTEATRAGIIELLFKRGFVTKKGRNI
QSTETGRVLISALPDIATQPDMTAQWEMQLKQISQKQVSYQQFMHQLTTK
LPELLHTDRQKLQKLNIITPLKLPAKRTHTKASIMADEK$

Gene Nucleotide Sequence:  Sequence Viewer
ATGATGCGAGTGTTTTTAGCCGAAAAACCGAGTTTAGCCCGTGCGATTGC
TGAAGTATTGCCTAAACCTCATATCCGAGGCGATGGTTATATTCAATGTG
GTGAACATGATTATGTGACTTGGTGTATAGGCCATTTACTTGAACAGGCA
GAGCCAGATGCATATGATGAACGTTTTAAAACTTGGCGAATGGAGCATTT
ACCGATTATTCCACAGCAATGGAAATTAATTGCTAAAAAACAAACCGCTA
AACAGCTTAAAGTGGTCGAAAAATTAGTTAAGAAAGCAGAAATATTAGTC
AATGCGGGCGACCCTGATAGAGAAGGCCAATTATTAGTTGATGAAGTATT
TAATTATTTAAATGTGCCAGCGAGTAAAAAAAGCCAAATACAACGCTGTC
TAGTTAGTGACCTTAATCCAACTGCAGTCAGTAAGGCGATCAATAAATTA
CAAAATAATTGTGATTTTATACCGCTTGCCACTTCTGCGTTAGCACGCGC
AAGAGCGGATTGGTTGTATGGCATTAATATGACTAGGGCCTATACTCTAC
AAGGCCGTTGGGTTGGTTATCAAGGCGTGCTTTCAGTCGGGCGCGTACAA
ACGCCTGTATTAGGTTTGATTGTACGGCGTGATCTTGAGATCGAACATTT
TACACCTAAAGATTATTTTGAAGTTTTAGCACATATCATTGTGCCAACCA
CACAAGAAAGATTTACCGCCCACTGGCAGCCAAGTAAAGCGTGTGAAGAT
TACCAAGATGAAGAAGGAAGAGTACTCTCGCGCGCATTGGTGGAAAATGT
TGTTAAACGTATCAGTGATCAAACCGCTTGCGTGACTGATTATCAAGATA
AAACCGAAAGTGAAATAGCGCCTTTACCTTATTCGCTTTCAGCATTACAG
ATTGATGCCGCACGCCGTTATGGTCTATCGGCTCAAGCAGTATTAGATAT
TTGCCAAACCTTATATGAAACCCACAAATTAATTACTTATCCTCGTTCAG
ATAATCGTTATTTACCAAATGAACATTATAATGAACGATTTAACGTCGTG
GCAGCGATTGCACATCATCTAACAGAATATCAACAAAAACCCGAAGTCGT
TAACTTAGCATTACGTGGCCGTTGTTGGAATGATAAAAAAATAGAAGCAC
ATCACGCCATTATTCCGACCGCTAGGCAAGGCAATCTGCGACTCACTGAA
AATGAAAAAAGGATTTATCGCTTGATCGCTTGTCAATATTTAATGCAATT
TTGCCCAGATGCAGAATATAGCAAAAGAAAAATTACTTTAGATATTGCGG
GAGGCACGTTTATTGCTCAAGCTAGAAATTTAGTGACTGCAGGTTGGAAA
GCCTTATTAGGTAAGGAAGACTGCGATGAAATGATTGAACCATTGTTACC
CGCAGTACAGAAAGCACAACGACTGCATTGTGAGAAAAGGGAAATTATCA
GTAAAAAAACACAACTGCCACGCCATTTCACTGATGCAAGTTTGTTATCC
GCTATGACAGGTATTGCACGTTTTGTGCAAGATAAACAGCTTAAAAAAAT
ACTACGTGAAACAGATGGTTTGGGTACAGAAGCCACTCGTGCAGGTATTA
TTGAATTGCTCTTTAAACGCGGTTTTGTTACCAAAAAAGGGCGTAATATT
CAAAGTACTGAAACAGGACGAGTTTTAATTAGCGCCTTGCCAGATATAGC
GACTCAACCAGATATGACTGCCCAATGGGAAATGCAACTGAAACAAATTA
GCCAAAAACAAGTCTCTTACCAACAATTTATGCACCAATTAACGACTAAA
TTACCCGAGCTACTGCATACAGACCGACAAAAATTGCAAAAACTCAACAT
AATTACACCGCTTAAGCTACCTGCTAAGCGAACACATACTAAAGCATCAA
TAATGGCTGATGAAAAATAA


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