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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR679 IGR678 IGR686 IGR675 IGR687 IGR680 IGR684 IGR677 IGR674 IGR683 IGR682 IGR676 IGR685 IGR688 IGR681 HD0948 HD0952 HD0958 HD0963 HD0947 HD0946 HD0957 ssb, - HD0962 HD0951 HD0950 radC, - HD0945 HD0960 HD0961 HD0944 topA, - HD0954 HD0959 HD0953 HD0956 HD0948 HD0952 HD0958 HD0963 HD0947 HD0946 HD0957 ssb, - HD0962 HD0951 HD0950 radC, - HD0945 HD0960 HD0961 HD0944 topA, - HD0954 HD0959 HD0953 HD0956 HD0952 HD0946 HD0957 ssb, - HD0962 HD0950 HD0961 HD0944 topA, - HD0954 HD0955 HD0955 HD0958 HD0963 HD0947 HD0951 radC, - HD0945 HD0960 HD0948 HD0959 HD0953 HD0956
* Calculated from Protein Sequence

Gene ID: HD0954

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
topA  

Definition:
topoisomerase I

Gene Start:
756690

Gene Stop:
755179

Gene Length:
1512

Molecular Weight*:
56379

pI*:
10.00

Net Charge*:
18.76

EC:
5.99.1.2  

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

Pathway: pathway table

Secondary Evidence:
Zhu Q, Pongpech P, DiGate RJ.
Type I topoisomerase activity is required for proper chromosomal segregation in Escherichia coli.
Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9766-71.
PMID: 11493711

Comment:
For other "top" genes, see HD1276 (topB) and HD1385 (top1).

Blast Summary:  PSI-Blast Search
Numerous significant hits using gapped BLAST to DNA topoisomerases from Salmonella typhimurium (6513858), H. influenzae (1174743), E. coli (136000), among others.

HD0954 is similar to DNA topoisomerase I proteins from C. pneumoniae (CPn0769), C. trachomatis (CT643), M. pneumoniae (MP0572), M. genitalium (MG122), T. pallidum (TP0394), and U. urealyticum (UU590).

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 1.9e-55.
    IPB000380A    3-15
    IPB000380B    31-48
    IPB000380C    98-115
    IPB000380E    155-178
    IPB000380F    190-221
    IPB000380G    285-315
    IPB000380H    318-334
    IPB000380I    368-382
    IPB000380J    397-414


ProDom Summary:  Protein Domain Search
Residues 242-331 are 50% similar to a (TOPOISOMERASE DNA ENZYME DNA-BINDING PROTEOME COMPLETE) protein domain (PD001593) which is seen in Q9RHF5_SALTI.

Residues 337-390 are 51% similar to a (TOPOISOMERASE PLASMID B PROTEOME) protein domain (PD246620) which is seen in Q9RHF5_SALTI.

Residues 3-75 are 56% similar to a (TOPOISOMERASE PLASMID DNA ENZYME) protein domain (PD352542) which is seen in Q9RHF5_SALTI.

Residues 87-141 are 63% similar to a (TOPOISOMERASE DNA ENZYME III) protein domain (PD331069) which is seen in Q9RHF5_SALTI.

Residues 73-140 are 39% similar to a (TOPOISOMERASE III PLASMID DNA) protein domain (PD384511) which is seen in P71196_ECOLI.

Residues 352-434 are 49% similar to a (TOPOISOMERASE DNA III COMPLETE) protein domain (PD017178) which is seen in Q9PCK3_XYLFA.

Residues 142-187 are 63% similar to a (TOPOISOMERASE PLASMID DNA ENZYME) protein domain (PD235718) which is seen in Q9PCK3_XYLFA.

Residues 80-134 are 51% similar to a (TOPOISOMERASE ENZYME PLASMID RELAXING) protein domain (PD379406) which is seen in Q9RMV8_BACAN.

Residues 369-437 are 36% similar to a (TOPOISOMERASE DNA DNA-BINDING III PROTEOME COMPLETE) protein domain (PD337468) which is seen in P96583_BACSU.



Paralogs:  Local Blast Search
HD0954 is paralogously related to HD1276 (4e-94), HD1385 (7e-28) and HD0413 (1e-04).


Pfam Summary:  Pfam Search
Residues 1 to 131 (E-value = 1.3e-25) place HD0954 in the Toprim family which is described as Toprim domain (PF01751)
Residues 147 to 501 (E-value = 5.7e-52) place HD0954 in the Topoisom_bac family which is described as DNA topoisomerase (PF01131)
Residues 446 to 478 (E-value = 1.5e-06) place HD0954 in the zf-C4_Topoisom family which is described as Topoisomerase DNA binding C4 zinc finger (PF01396)

PDB Hit:
pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomer... 329 6e-091
pdb|1CY7|A Chain A, Complex Of E.Coli Dna Topoisomerase I With ... 98 2e-021
pdb|1ECL| Amino Terminal 67kda Domain Of Escherichia Coli Dn... 98 2e-021

Gene Protein Sequence:
MRLFLCEKPSQGNDIAKVLGATKRGDGCLSSGNGQVFVTWGIGHLVEQLN
PEQYHPEWKKWSLETLPIIPGQWQLAPKKETKKQYNIVIKLIKQASEVII
ATDIDREGETIARELLELAGFKGKIQRLWLSALDDASIRKALALLKPNHE
TLPLYYAGLGRSRADWLIGMNFSRLFTLLAQQQGYQGKPLSVGRVQSPTL
ALVVNRDREIQNFVPKNHFTLSALLYSGQQNFTAQYVIPEQYCDEDGLCL
SQQTIQAVNQQVQQAGVMKVESVETKREKQSAPLLFALSDLQSEANRLYG
LGAQQVLDIAQSLYETHKATTYPRTDCGYLPESQLAEAPQVIKSLISSDS
RLQPLTSKLNLTQKSRAWNDKKITAHHGIIPTAVKVDIGKMSEEEFRLYD
LIRRRYLAQFLPVSQSDKTQIVLKCGVHTFISRGNVLIATGWKMLCGAPM
TKRNGKNGQFWGCTAYPDCQHIENIGKSTARRKGTANSQNISQQIANLRK
LVQ$

Gene Nucleotide Sequence:  Sequence Viewer
ATGAGATTATTTCTTTGTGAAAAACCTTCCCAAGGCAATGATATTGCCAA
AGTATTAGGTGCAACTAAGCGTGGTGACGGTTGTCTCTCCTCCGGCAACG
GGCAAGTTTTTGTCACTTGGGGGATTGGCCATTTAGTTGAGCAATTAAAT
CCGGAACAATATCATCCGGAATGGAAAAAGTGGTCTTTAGAAACACTTCC
TATTATCCCGGGACAATGGCAACTTGCCCCCAAGAAAGAAACTAAAAAGC
AATACAACATTGTTATCAAGCTCATCAAGCAAGCGAGTGAGGTCATTATT
GCAACGGATATTGATAGAGAAGGTGAAACCATCGCCCGGGAATTATTAGA
GTTAGCAGGTTTCAAAGGTAAGATTCAACGCCTCTGGTTGTCCGCTTTGG
ATGATGCCAGTATTCGCAAAGCCCTAGCCTTATTGAAACCCAATCATGAA
ACCCTACCGTTATACTATGCCGGATTAGGACGTAGCCGGGCGGATTGGCT
TATTGGCATGAATTTTTCCCGGTTATTTACCTTGCTGGCACAACAACAAG
GTTACCAAGGCAAACCGCTTTCCGTGGGACGGGTGCAAAGTCCAACCCTT
GCTTTAGTCGTCAATCGAGACAGAGAAATTCAAAACTTTGTCCCCAAAAA
TCACTTTACCTTATCCGCACTCCTCTATTCCGGACAGCAGAATTTCACAG
CTCAATATGTTATTCCCGAGCAATATTGCGATGAGGACGGACTTTGTTTA
TCCCAACAAACAATACAAGCGGTTAATCAACAAGTGCAACAAGCCGGAGT
AATGAAAGTCGAGTCGGTCGAGACCAAACGTGAAAAACAAAGTGCACCGT
TATTATTTGCACTCAGTGATTTGCAAAGTGAAGCAAATCGTCTGTACGGA
TTAGGCGCCCAACAGGTATTAGATATTGCTCAATCATTGTACGAAACCCA
TAAAGCGACGACTTACCCTAGAACGGATTGCGGTTATTTACCGGAGTCAC
AACTGGCTGAAGCACCACAAGTAATTAAAAGCTTAATATCTTCAGACAGT
CGATTACAGCCTCTTACCTCTAAGCTAAATCTAACGCAAAAATCCCGCGC
CTGGAATGATAAAAAAATTACCGCACACCATGGCATCATTCCCACCGCAG
TTAAAGTAGATATCGGCAAAATGTCCGAAGAAGAATTTAGGCTTTATGAC
TTAATCCGTCGTCGTTATCTGGCACAATTTTTACCGGTCAGTCAAAGTGA
TAAAACGCAGATAGTGTTGAAATGTGGTGTTCATACCTTTATTTCACGCG
GTAACGTATTAATTGCGACCGGCTGGAAAATGCTGTGCGGCGCACCGATG
ACTAAACGTAACGGCAAAAACGGACAATTTTGGGGCTGTACCGCCTATCC
GGATTGTCAGCATATTGAGAACATCGGCAAATCCACGGCACGACGAAAAG
GTACCGCTAATTCTCAAAATATTAGCCAACAAATTGCCAATTTAAGAAAG
TTGGTTCAATGA


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