Basic Search | Intermediate Search | Advanced SQL Search | Gene Image Map |  Home

Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1018 IGR1016 IGR1019 IGR1015 IGR1020 IGR1012 IGR1017 IGR1013 IGR1014 moaD, - HD1390 moaE, - HD1389 HD1387 moaC, - HD1391 moaA, - HD1392 HD1386 serC, - HD1382 aroF,aroA, - HD1383 argA, - HD1384 topA, - HD1385 moaD, - HD1390 moaE, - HD1389 HD1387 moaC, - HD1391 moaA, - HD1392 HD1386 serC, - HD1382 aroF,aroA, - HD1383 argA, - HD1384 topA, - HD1385 moaE, - HD1389 HD1387 moaA, - HD1392 HD1386 moaC, - HD1391 moaD, - HD1390 serC, - HD1382 aroF,aroA, - HD1383 argA, - HD1384 topA, - HD1385
* Calculated from Protein Sequence

Gene ID: HD1385

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
topA  

Definition:
DNA topoisomerase I (omega-protein) (relaxing enzyme)

Gene Start:
1132308

Gene Stop:
1134911

Gene Length:
2604

Molecular Weight*:
97715

pI*:
8.90

Net Charge*:
17.96

EC:
5.99.1.2  

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

Pathway: pathway table

Secondary Evidence:
Tse-Dinh,Y.C. and Wang,J.C.
Complete nucleotide sequence of the topA gene encoding Escherichia
coli DNA topoisomerase I
J. Mol. Biol. 191 (3), 321-331 (1986)
Medline: 87141163

Lima,C.D., Wang,J.C. and Mondragon,A.
Three-dimensional structure of the 67K N-terminal fragment of E.
coli DNA topoisomerase I
Nature 367 (6459), 138-146 (1994)
Medline: 94159070



Comment:


Blast Summary:  PSI-Blast Search
Numerous significant hits using gapped BLAST to DNA topoisomerase I from H. influenzae (1174735), E. coli (730966), Bacillus subtilis (730965), among others. HD1385 is 80% similar to residues 1-868 from TOP1_HAEIN.

HD1385 is similar to DNA topoisomerase I from C. pneumoniae (CPn0769), C. trachomatis (CT643), T. pallidum (TP0394), M. pneumoniae (MP0572), M. genitalium (MG122), and U. urealyticum (UU590).

COGS Summary:  COGS Search
BeTs to 16 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 1.7e-182.
    IPB000380A    5-17
    IPB000380B    20-37
    IPB000380C    112-129
    IPB000380D    142-153
    IPB000380E    168-191
    IPB000380F    197-228
    IPB000380G    288-318
    IPB000380H    320-336
    IPB000380I    362-376
    IPB000380J    394-411
    IPB000380K    476-515
    IPB000380L    539-557


ProDom Summary:  Protein Domain Search
Residues 341-379 are 84% similar to a (TOPOISOMERASE ENZYME DNA DNA-BINDING) protein domain (PD114071) which is seen in TOP1_HAEIN.

Residues 709-795 are 94% similar to a (TOPOISOMERASE DNA ENZYME COMPLETE PROTEOME DNA-BINDING) protein domain (PD003328) which is seen in Q9CN30_PASMU.

Residues 109-154 are 91% similar to a (TOPOISOMERASE ENZYME DNA DNA-BINDING) protein domain (PD001285) which is seen in Q9CN30_PASMU.

Residues 255-336 are 79% similar to a (TOPOISOMERASE DNA ENZYME DNA-BINDING PROTEOME COMPLETE) protein domain (PD001593) which is seen in Q9CN30_PASMU.

Residues 796-862 are 83% similar to a (TOPOISOMERASE ENZYME DNA RELAXING) protein domain (PD035074) which is seen in Q9CN30_PASMU.

Residues 77-108 are 93% similar to a (TOPOISOMERASE ENZYME DNA RELAXING) protein domain (PD330454) which is seen in TOP1_HAEIN.

Residues 156-192 are 75% similar to a (TOPOISOMERASE GYRASE REVERSE COMPLETE) protein domain (PD301358) which is seen in TOP1_VIBCH.

Residues 5-42 are 89% similar to a (TOPOISOMERASE ENZYME DNA DNA-BINDING) protein domain (PD338116) which is seen in Q9HZJ5_PSEAE.

Residues 572-708 are 84% similar to a (TOPOISOMERASE ENZYME DNA RELAXING) protein domain (PD037841) which is seen in Q9CN30_PASMU.

Residues 154-193 are 90% similar to a (TOPOISOMERASE ENZYME DNA DNA-BINDING) protein domain (PD329190) which is seen in TOP1_HAEIN.

Residues 96-193 are 36% similar to a (TOPOISOMERASE DNA DNA-BINDING III PROTEOME COMPLETE) protein domain (PD363138) which is seen in Q59046_METJA.

Residues 94-153 are 58% similar to a (TOPOISOMERASE ENZYME PLASMID RELAXING) protein domain (PD379406) which is seen in TOP1_STRCO.

Residues 389-436 are 77% similar to a (TOPOISOMERASE DNA ENZYME DNA-BINDING) protein domain (PD238848) which is seen in Q9CN30_PASMU.

Residues 438-561 are 82% similar to a (TOPOISOMERASE DNA ENZYME DNA-BINDING PROTEOME COMPLETE) protein domain (PD001411) which is seen in TOP1_HAEIN.

Residues 198-251 are 73% similar to a (TOPOISOMERASE DNA ENZYME DNA-BINDING COMPLETE PROTEOME) protein domain (PD011342) which is seen in Q9CN30_PASMU.



Paralogs:  Local Blast Search

HD1385 is paralogously related to HD1276 (3e-28) and HD0954 (1e-27).


Pfam Summary:  Pfam Search
Residues 3 to 146 (E-value = 6.4e-35) place HD1385 in the Toprim family which is described as Toprim domain (PF01751)
Residues 160 to 558 (E-value = 3.2e-172) place HD1385 in the Topoisom_bac family which is described as DNA topoisomerase (PF01131)
Residues 601 to 644 (E-value = 5.4e-11) place HD1385 in the zf-C4_Topoisom family which is described as Topoisomerase DNA binding C4 zinc finger (PF01396)
Residues 712 to 747 (E-value = 2.2e-11) place HD1385 in the zf-C4_Topoisom family which is described as Topoisomerase DNA binding C4 zinc finger (PF01396)

PDB Hit:
pdb|1CY7|A Chain A, Complex Of E.Coli Dna Topoisomerase I With ... 822 0.0
pdb|1ECL| Amino Terminal 67kda Domain Of Escherichia Coli Dn... 811 0.0
pdb|1CYY|B Chain B, Crystal Structure Of The 30 Kda Fragment Of... 332 1e-091

Gene Protein Sequence:
MGKSLVIVESPAKAKTINKYLGSDYIVKSSVGHIRDLPKSGSEKAEKVKP
ISTKGLTAEQKAKVKADKARAALVKRMGIDPYHDWKANYQILPDKDKVVS
ELKSLAKKADHIYLATDLDREGEAIAWHLREVIGGKEEHFSRVVFNEITK
NAIQKAFEKPEQLNLDRVNAQQTRRFLDRIVGFMVSPLLWKKVARGLSAG
RVQSVAVKLLVEREREIKAFQPEEYWDILANTLAENGRLPLALTSYKGKK
FVAKNQTEADNAVKALQCCEFVVSDIDKKPTSSKANAPFITSTLQQTAST
RLSFGVKKTMMLAQRLYEAGYITYMRTDSTNLSQDALTMVREYVENHFGT
DYLPAKPNFYSSKENAQEAHEAIRPSDVRVKMSDLKGMEKDAERLYDLIW
RRFVACQMPPARYDSTSLTITAGDYELKAKGRVLRFDGWTKVLPIQGKTA
EDQELPAVMLNEKLTLAEIIPSQHFTKPPAHFSEAALVKELEKRGIGRPS
TYATIISTIQERGYVRTENRRFYAEKMGEIVTDRLDESFSDLMNYDFTAN
MEETLDQIAKGNKNWKEALNSFFSDFSEQLSKAELDELEGGMKPNSLVVT
DIDCPTCARKMAIRTASTGVFLGCTGYALPPKERCKTTMNLILEAELFNV
LDEESEAKALLARKRCPKCGSAMDSYIIDPTRKLHICGNNPNCDGHIVEQ
GSFKIKGYDGPIVECDKCGADMHLKLGRFGKYMACTACDNTSKILKNGEV
APPREEPTHFPELKCEKSDAYFVLRDGASGVFMSAHNFPKSRETRAPKVA
ELALYRDRLPAKLQYLADAPQQDPEGNQAIIRFSRKEKRQYVTSEKEGKA
TKWIVDFIDGKWLERHK$

Gene Nucleotide Sequence:  Sequence Viewer
ATGGGAAAATCATTAGTCATCGTTGAGTCGCCAGCTAAAGCTAAAACGAT
TAATAAGTACTTAGGCAGCGATTATATAGTGAAGTCGAGTGTTGGACATA
TTCGCGATTTACCCAAAAGCGGTAGTGAAAAAGCGGAAAAAGTCAAACCA
ATCTCAACTAAAGGTTTAACAGCAGAGCAGAAAGCAAAAGTAAAAGCGGA
TAAAGCGCGAGCGGCATTAGTTAAACGGATGGGCATTGATCCATATCACG
ATTGGAAAGCAAATTATCAAATTCTACCGGATAAAGATAAAGTGGTTTCC
GAATTGAAATCCTTAGCCAAAAAAGCTGACCATATTTATCTTGCGACCGA
CTTGGATAGAGAAGGGGAAGCAATTGCTTGGCATTTGCGTGAAGTGATTG
GCGGTAAAGAAGAGCATTTTAGTCGAGTTGTCTTTAATGAAATCACTAAA
AATGCCATTCAAAAAGCATTCGAAAAGCCAGAGCAGCTCAATTTAGATCG
TGTTAATGCACAGCAAACTCGGCGATTTTTAGATCGTATCGTTGGTTTTA
TGGTATCACCATTGCTATGGAAAAAAGTGGCTAGAGGCTTATCTGCAGGC
CGTGTTCAATCGGTTGCGGTGAAATTACTCGTTGAGCGTGAACGTGAAAT
TAAAGCGTTTCAACCGGAAGAATATTGGGATATTTTAGCCAATACGTTAG
CTGAAAATGGCAGATTGCCATTAGCCTTAACAAGCTATAAAGGCAAAAAG
TTTGTGGCAAAAAACCAGACTGAAGCGGATAATGCGGTAAAAGCGTTACA
ATGTTGCGAATTTGTTGTGTCGGATATTGATAAAAAACCCACATCCTCTA
AAGCGAATGCACCTTTTATTACGTCAACACTGCAACAAACAGCCAGTACG
CGCTTAAGTTTTGGGGTAAAGAAAACAATGATGTTAGCACAGCGTCTATA
TGAAGCGGGCTACATTACTTATATGCGCACAGATTCAACAAATTTAAGTC
AAGATGCATTAACAATGGTACGAGAGTATGTTGAAAACCACTTTGGCACA
GACTATTTGCCAGCCAAGCCAAATTTCTACTCAAGTAAGGAAAACGCACA
AGAAGCACACGAAGCCATTCGCCCTTCAGATGTTAGGGTAAAAATGAGTG
ATCTTAAAGGAATGGAAAAGGATGCTGAACGTTTATATGATTTAATTTGG
CGTCGCTTTGTCGCGTGTCAAATGCCCCCAGCAAGATATGATTCGACCAG
TTTAACTATTACGGCTGGCGACTATGAATTAAAAGCAAAAGGGCGTGTAT
TACGCTTTGATGGTTGGACGAAAGTATTACCTATACAAGGAAAAACTGCA
GAAGATCAAGAATTACCAGCCGTGATGTTGAATGAAAAATTAACACTAGC
AGAAATAATCCCTAGTCAACATTTTACGAAACCACCTGCGCATTTCAGTG
AAGCCGCATTAGTTAAAGAGCTTGAAAAACGTGGTATTGGTCGTCCTTCA
ACGTATGCGACCATTATTTCGACCATTCAAGAACGAGGTTATGTGCGTAC
TGAAAACCGGCGTTTTTATGCTGAGAAAATGGGGGAAATTGTTACTGATC
GGTTAGATGAATCCTTTAGTGATTTAATGAATTACGATTTCACCGCTAAC
ATGGAAGAAACCTTAGATCAGATCGCCAAAGGTAATAAAAATTGGAAAGA
GGCGTTAAATAGCTTCTTTAGTGATTTTTCTGAACAATTGAGCAAAGCAG
AATTAGATGAGCTTGAAGGTGGAATGAAGCCAAATAGCTTAGTTGTGACG
GATATAGATTGTCCAACTTGTGCAAGAAAAATGGCGATTCGTACCGCTTC
TACTGGTGTCTTTTTAGGTTGTACAGGCTATGCATTACCGCCTAAAGAAC
GTTGTAAAACGACAATGAACCTAATTTTAGAAGCGGAATTATTTAATGTG
CTTGATGAAGAATCTGAAGCAAAAGCATTATTAGCGCGCAAACGTTGTCC
TAAATGCGGTTCTGCAATGGATAGCTATATTATTGATCCAACAAGAAAAT
TACATATTTGTGGTAATAATCCAAATTGTGATGGCCATATTGTTGAGCAA
GGAAGCTTCAAAATAAAAGGCTATGATGGGCCTATTGTTGAATGTGATAA
ATGCGGTGCAGATATGCACCTAAAATTAGGTCGTTTTGGTAAATATATGG
CCTGTACTGCTTGCGATAATACCAGTAAAATTTTAAAAAATGGTGAAGTT
GCTCCACCACGTGAAGAACCAACACATTTCCCTGAATTGAAATGTGAAAA
ATCAGATGCTTATTTTGTGTTACGTGATGGTGCTAGTGGGGTATTTATGT
CTGCACATAACTTCCCTAAATCACGAGAAACGCGTGCACCCAAAGTTGCT
GAGTTAGCGTTATACCGTGATCGATTACCTGCTAAATTGCAATATTTAGC
AGATGCGCCACAGCAAGATCCGGAGGGTAATCAAGCTATTATTCGCTTTA
GTCGTAAAGAGAAACGTCAATATGTGACCTCAGAAAAAGAGGGAAAAGCA
ACAAAATGGATTGTTGATTTTATTGATGGAAAATGGTTAGAACGACATAA
ATAA


Los Alamos National Laboratory     
Operated by the University of California for the National Nuclear Security Administration,
of the US Department of Energy.     Copyright © 2001 UC | Disclaimer/Privacy