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

Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR906 IGR901 IGR902 IGR904 IGR905 IGR903 IGR907 HD1239 lolA, - HD1237 rimK, - HD1238 sapB, - HD1231 citC, - HD1240 sapD, - HD1235 sapA, - HD1230 polA, - HD1236 HD1239 lolA, - HD1237 rimK, - HD1238 sapB, - HD1231 citC, - HD1240 sapD, - HD1235 sapA, - HD1230 polA, - HD1236 HD1239 lolA, - HD1237 rimK, - HD1238 sapB, - HD1231 citC, - HD1240 sapD, - HD1235 sapA, - HD1230 polA, - HD1236 sapC, - HD1232 sapC, - HD1232
* Calculated from Protein Sequence

Gene ID: HD1236

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
polA  

Definition:
DNA polymerase I (polA)

Gene Start:
1001514

Gene Stop:
1004402

Gene Length:
2889

Molecular Weight*:
107031

pI*:
5.70

Net Charge*:
-18.26

EC:
2.7.7.7  

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

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism

Secondary Evidence:
Joyce,C.M., Kelley,W.S. and Grindley,N.D.
Nucleotide sequence of the Escherichia coli polA gene and primary
structure of DNA polymerase I
J. Biol. Chem. 257 (4), 1958-1964 (1982)
Medline: 82120160

Joyce,C.M. and Grindley,N.D.
Identification of two genes immediately downstream from the polA
gene of Escherichia coli
J. Bacteriol. 152 (3), 1211-1219 (1982)
Medline: 83056713

Brown,W.E., Stump,K.H. and Kelley,W.S.
Escherichia coli DNA polymerase I. Sequence characterization and
secondary structure prediction
J. Biol. Chem. 257 (4), 1965-1972 (1982)
Medline: 82120161

Ollis,D.L., Brick,P., Hamlin,R., Xuong,N.G. and Steitz,T.A.
Structure of large fragment of Escherichia coli DNA polymerase I
complexed with dTMP
Nature 313 (6005), 762-766 (1985)
Medline: 85137890


Comment:
From Genbank:[gi:1169402]
In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity.



Blast Summary:  PSI-Blast Search
Numerous significant hits using gapped BLAST to DNA polymerase I from H. influenzae (1169402), E. coli (118825), Neisseria meningitidis (7379209), among others.

HD1236 is similar to DNA polymerase I from T. pallidum (TP0105), C. trachomatis (CT493), C. pneumoniae (CPn0612), U. urealyticum (UU414), M. pneumoniae (MP0458), and similar to 5"-3" exonuclease (including N-terminal domain of PolI) from M. genitalium (MG262).

COGS Summary:  COGS Search
BeTs to 10 clades of COG0749
COG name: DNA polymerase I - 3'-5' exonuclease and polymerase domains
Functional Class: L
The phylogenetic pattern of COG0749 is ----yqvcebrhuj--olinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB001098 (Replicative DNA polymerase) with a combined E-value of 4.4e-100.
    IPB001098A    13-24
    IPB001098B    566-579
    IPB001098C    608-627
    IPB001098D    689-715
    IPB001098E    740-751
    IPB001098F    764-774
    IPB001098G    789-802
    IPB001098H    878-896
    IPB001098I    907-926
    IPB001098J    946-958


ProDom Summary:  Protein Domain Search
Residues 540-610 are 46% similar to a (DNA I POLYMERASE REPLICATION) protein domain (PD389899) which is seen in Q9CLY4_PASMU.

Residues 7-285 are 77% similar to a (DNA POLYMERASE I EXONUCLEASE) protein domain (PD002066) which is seen in Q9CLY4_PASMU.

Residues 456-609 are 36% similar to a (DNA POLYMERASE I TRANSFERASE) protein domain (PD011729) which is seen in Q9WWL5_METSP.

Residues 612-962 are 74% similar to a (DNA POLYMERASE I TRANSFERASE) protein domain (PD001497) which is seen in Q9CLY4_PASMU.

Residues 540-601 are 48% similar to a (DNA I POLYMERASE TRANSFERASE) protein domain (PD243491) which is seen in DPO1_HAEIN.

Residues 342-522 are 54% similar to a (DNA POLYMERASE I DNA-DIRECTED) protein domain (PD249324) which is seen in Q9CLY4_PASMU.

Residues 338-455 are 43% similar to a (I TRANSFERASE POLYMERASE DNA) protein domain (PD245742) which is seen in Q9WWL5_METSP.

Residues 909-962 are 50% similar to a (DNA POLYMERASE I TRANSFERASE) protein domain (PD335608) which is seen in DPO1_ECOLI.

Residues 665-903 are 48% similar to a (DNA POLYMERASE TRANSFERASE DNA-DIRECTED) protein domain (PD264287) which is seen in Q9F191_TREHY.

Residues 540-610 are 43% similar to a (DNA I POLYMERASE PROTEOME) protein domain (PD283676) which is seen in DPO1_ECOLI.

Residues 610-687 are 57% similar to a (DNA POLYMERASE I TRANSFERASE) protein domain (PD354859) which is seen in Q9HT80_PSEAE.



Paralogs:  Local Blast Search


HD1236 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 7 to 169 (E-value = 1.9e-88) place HD1236 in the 5_3_exonuc_N family which is described as 5'-3' exonuclease, N-terminal resolvase-like domain (PF02739)
Residues 171 to 277 (E-value = 1.2e-46) place HD1236 in the 5_3_exonuc family which is described as 5'-3' exonuclease, C-terminal SAM fold (PF01367)
Residues 342 to 551 (E-value = 1.3e-45) place HD1236 in the 3_5_exonuc family which is described as 3'-5' exonuclease (PF01612)
Residues 581 to 961 (E-value = 4.3e-197) place HD1236 in the DNA_pol_A family which is described as DNA polymerase family A (PF00476)

PDB Hit:
pdb|2KFN|A Chain A, Klenow Fragment With Bridging-Sulfur Substr... 683 0.0
pdb|1KFD| Dna Polymerase I (Klenow Fragment) (E.C.2.7.7.7) C... 683 0.0
pdb|1KLN|A Chain A, Dna Polymerase I (Klenow Fragment) (E.C.2.7... 680 0.0

Gene Protein Sequence:
MAQIAQNPLVLVDGSSYLYRAFHVFNYLTNSGGEPTGAMYGVLNMLRSLV
NQVNPSHIAVVFDAKGKTFRDDLFEQYKSHRPPMPDELRAQIQPLHNIIR
ALGIPLISIEGVEADDVIGTLAVQAAQDGKEVLISTGDKDMAQLVNQHIM
LINTMNDSLLDREGVIEKYGIPPELIIDYLALQGDASDNIPGVKGIGEKT
ALALLQGIGSLQTIYANLDRVATLSVRGAKTLATKLVAEKQAADLSYLLA
TIKTDVALDMTHHQLTPSAQRREELIALFERYEFKRWLNDVMNDINPILK
NVSDNDKKTTLNHSTDLQAVQNTVFDVPNKKIATVKIDRSQYQTITTELQ
LTEWMAKIEQAKLVAVDTETDNVDAMSAHLVGISFSLSNGEACYIPLAHT
QQISVQPQQEDLFAETDNDAITQFQLASNQLNLTACLAQLKPLLENVEIK
KVGQNIKYDLTVFANHGIELQGVAFDTMLESYTLNSTGRHNMDELAERYL
DHKTIAFEDIAGKGKNQLTFDKIAIETATEYAAEDADITMKLHQQLITSL
AKTPSLIKLFNEIEMPLVNVLARVEQNGVLIDSDKLLAQSKEMEQRLAEV
EIAVHTAAGQAFNLASTKQLQEILFEKLALPVLKKTPKGAPSTNEEVLEQ
LAQQGHLVPKLLSEHRALSKLKSTYTDKLPKMINQHTGRVHTSYHQAVTT
TGRLSSSDPNLQNIPIRTEAGRRIRQAFIARDGYKIVAADYSQIELRIMA
HLANDEGMITAFANGQDIHQATAAEIFGLSLAEVTSEQRRSAKAINFGLI
YGMSDFGLANQLAISRDEAKEYMARYFQRYPNVQQFMRDIRESASVKGYV
ETLFGRRLYLPEIKSNNAIRRKAAERLAINAPMQGTAADIIKIAMISIDK
QIRADQNIKMIMQVHDELIFEVKQECIEYYTGLIKTEMEKAIAMKVPLIA
EVGVGANWDEAH$

Gene Nucleotide Sequence:  Sequence Viewer
ATGGCTCAAATTGCACAAAACCCACTGGTTCTCGTGGATGGTTCTTCTTA
TTTATACCGTGCTTTTCATGTATTCAATTACTTAACCAATAGTGGCGGCG
AGCCTACAGGGGCAATGTATGGTGTGTTAAATATGTTGAGAAGCCTAGTC
AATCAAGTCAATCCGAGCCATATTGCGGTCGTATTTGATGCAAAAGGAAA
AACTTTCCGTGATGATTTATTTGAACAATATAAATCGCATAGACCACCTA
TGCCAGATGAATTACGTGCACAAATCCAGCCATTACATAATATTATCAGA
GCCTTAGGTATTCCGTTGATTTCGATTGAAGGTGTAGAAGCTGATGATGT
GATTGGTACCTTAGCAGTACAAGCCGCCCAAGATGGCAAAGAGGTATTGA
TTAGTACCGGTGATAAAGATATGGCACAGCTAGTTAATCAGCATATTATG
CTGATTAATACGATGAATGACAGTTTATTAGATCGTGAAGGCGTGATCGA
AAAATACGGTATTCCACCAGAGTTGATTATTGATTATTTAGCTTTACAAG
GCGATGCTTCGGATAATATTCCCGGTGTAAAAGGCATTGGTGAGAAAACG
GCATTAGCTTTATTGCAAGGAATTGGTTCGTTACAAACGATTTATGCAAA
CCTAGATCGTGTTGCGACACTTTCTGTTCGGGGAGCCAAAACATTAGCCA
CCAAATTAGTGGCAGAAAAACAAGCGGCTGATTTATCTTATTTATTAGCA
ACAATTAAAACTGATGTGGCATTAGACATGACGCATCATCAATTAACGCC
AAGCGCGCAACGGCGCGAGGAATTAATCGCATTATTTGAGCGTTATGAAT
TTAAACGTTGGCTAAATGATGTGATGAACGATATCAATCCGATCTTAAAA
AATGTTTCAGATAATGATAAAAAAACAACATTAAACCATTCAACGGATCT
ACAAGCGGTGCAAAATACCGTTTTTGATGTCCCTAATAAAAAAATAGCAA
CAGTTAAAATTGATCGCAGTCAGTATCAGACGATAACCACTGAATTACAG
TTAACGGAATGGATGGCCAAAATTGAGCAAGCTAAATTAGTTGCTGTAGA
TACTGAAACTGATAATGTAGATGCAATGTCAGCCCATTTAGTCGGCATCT
CATTTAGTTTATCAAATGGTGAAGCGTGTTATATTCCGCTAGCGCATACC
CAACAAATCAGTGTTCAGCCCCAACAAGAAGATTTATTTGCTGAAACAGA
CAATGATGCGATTACACAGTTCCAATTAGCGTCAAATCAGCTAAATCTAA
CCGCTTGTTTAGCTCAATTAAAGCCATTATTAGAAAACGTTGAGATTAAA
AAGGTCGGGCAGAATATCAAGTACGATCTGACTGTTTTTGCTAATCATGG
CATTGAACTACAAGGAGTCGCTTTTGACACAATGCTTGAATCTTATACGT
TAAATAGCACCGGACGGCACAATATGGACGAGTTAGCGGAACGTTATTTA
GATCATAAGACAATTGCTTTTGAAGATATTGCGGGCAAAGGAAAAAATCA
ACTGACATTTGATAAAATTGCCATTGAAACTGCGACAGAATATGCTGCGG
AAGATGCTGATATAACGATGAAATTACATCAACAGCTTATTACATCCTTA
GCTAAGACTCCATCATTAATCAAATTATTTAATGAAATTGAAATGCCATT
AGTCAATGTATTAGCCAGAGTTGAGCAGAATGGAGTATTAATTGATTCTG
ACAAATTATTAGCACAATCAAAAGAAATGGAACAGCGTCTTGCTGAAGTA
GAAATCGCAGTTCATACAGCAGCAGGTCAAGCATTTAACCTTGCATCAAC
CAAACAACTGCAAGAAATATTATTTGAAAAATTAGCATTACCCGTATTAA
AGAAAACCCCGAAAGGTGCGCCATCGACGAATGAAGAAGTATTAGAGCAA
TTGGCACAACAAGGGCATCTCGTACCTAAATTACTCAGTGAACATCGCGC
GTTAAGCAAGTTAAAATCAACTTATACTGATAAATTACCGAAGATGATTA
ATCAGCATACAGGTCGAGTGCACACTTCTTATCATCAGGCAGTTACCACC
ACAGGTCGACTTTCTTCAAGTGATCCTAATTTACAAAATATTCCCATTCG
TACAGAAGCGGGACGGCGTATTCGTCAAGCATTTATCGCACGTGATGGTT
ATAAAATCGTGGCGGCTGATTATTCCCAAATTGAATTGCGGATTATGGCA
CATTTAGCAAATGATGAAGGAATGATTACCGCTTTTGCTAATGGCCAAGA
TATTCATCAAGCAACAGCAGCAGAAATTTTTGGTTTAAGCTTAGCTGAGG
TAACGAGTGAACAGCGGCGCAGTGCGAAAGCAATAAATTTTGGACTAATT
TATGGTATGTCAGATTTTGGGCTAGCAAATCAGCTAGCTATCTCACGCGA
TGAAGCGAAAGAATATATGGCGCGTTATTTCCAACGTTATCCAAATGTTC
AGCAATTTATGCGCGATATTCGTGAATCTGCAAGTGTAAAAGGTTATGTC
GAAACATTGTTTGGCCGTCGATTGTATTTGCCGGAGATTAAATCAAATAA
TGCTATACGCCGTAAAGCTGCTGAACGGCTAGCGATCAACGCACCAATGC
AAGGCACCGCCGCTGATATCATTAAAATCGCGATGATAAGTATCGATAAG
CAAATTCGTGCTGACCAGAATATAAAAATGATTATGCAAGTGCACGATGA
ATTAATATTTGAAGTTAAACAAGAATGTATAGAGTACTACACTGGCTTAA
TCAAAACGGAAATGGAAAAAGCTATTGCGATGAAGGTGCCACTGATTGCT
GAAGTGGGCGTAGGTGCTAATTGGGATGAAGCGCATTAG


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