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Treponema pallidum Search Results

Record: 1 of 1  
MiniMap IGR83 IGR82 IGR81 IGR84 pfpA, - TP0108 lps,lic, - TP0107 ushA, - TP0104 recQ, - TP0103 polA, - TP0105 pfpA, - TP0108 lps,lic, - TP0107 ushA, - TP0104 recQ, - TP0103 polA, - TP0105 Type: tandem, Name:  - 30 Type: tandem, Name:  - 27 Type: tandem, Name:  - 231 Type: tandem, Name:  - 28 Type: tandem, Name:  - 29 Type: tandem, Name:  - 31 pfpA, - TP0108 lps,lic, - TP0107 TP0106 TP0106 ushA, - TP0104 recQ, - TP0103 polA, - TP0105
* Calculated from Protein Sequence

Gene ID: TP0105

DNA Molecule Name:
1  

Genbank ID:
3322368

Gene Name:
polA  

Definition:
DNA polymerase I

Gene Start:
115806

Gene Stop:
118796

Gene Length:
2991

Molecular Weight*:
112214

pI*:
6.81

Net Charge*:
-3.90

EC:
2.7.7.7  

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

Pathway: pathway table
Nucleotide metabolism; Purine Metabolism

Secondary Evidence:
Marfin AA, Liu H, Sutton MY, Steiner B, Pillay A, Markowitz LE.
Amplification of the DNA polymerase I gene of Treponema pallidum from whole blood of persons with syphilis.
Diagn Microbiol Infect Dis. 2001 Aug;40(4):163-6.
PMID: 11576788

Al Mamun AA, Yadava RS, Ren L, Humayun MZ.
The Escherichia coli UVM response is accompanied by an SOS-independent error-prone DNA replication activity demonstrable in vitro.
Mol Microbiol. 2000 Oct;38(2):368-80.
PMID: 11069662

Moolenaar GF, Moorman C, Goosen N.
Role of the Escherichia coli nucleotide excision repair proteins in DNA replication.
J Bacteriol. 2000 Oct;182(20):5706-14.
PMID: 11004168

Kayser MF, Stumpp MT, Vuilleumier S.
DNA polymerase I is essential for growth of Methylobacterium dichloromethanicum DM4 with dichloromethane.
J Bacteriol. 2000 Oct;182(19):5433-9.
PMID: 10986246

Comment:
In addition to polymerase activity, PolA exhibits 3' to 5' and 5' to
3' exonuclease activity. It is able to utilize nicked circular duplex
DNA as a template and can unwind the parental DNA strand from its
template.

Reaction:
N DEOXYNUCLEOSIDE TRIPHOSPHATE = N PYROPHOSPHATE + DNA(N).

Blast Summary:  PSI-Blast Search
Gapped BLAST revealed this protein is almost identical to PolA of
Treponema pallidum,(U57757). In addition there were several other
significant hits to PolA proteins. For example residues 3-997
are 34% similar to DPO1_ECOLI, DNA polymerase I of Escherichia
coli,(AE000461).

COGS Summary:  COGS Search
BeTs to 11 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
Residues 569-574, 112-117, 725-749, 794-808, and 823- 836 represent
significant (99%) hits to blocks (BL00447A,B,C,D), DNA polymerase
family A proteins. In addition residues 270-281 are a significant
(96%) hit to blocks (BL00567C), Phosphoribulokinase proteins.

ProDom Summary:  Protein Domain Search
Residues 758-961 are 52% similar to DNA polymerase I of DPO1_BACCA.
Residues 9-253, 368-424, 516-564, 600-749, and 602-930 are also well
matched to DNA polymerase I proteins.

Paralogs:  Local Blast Search
There is no evidence of paralogs in T. pallidum.

Pfam Summary:  Pfam Search
Residues 5 to 172 (E-value = 5.3e-94) place TP0105 in the 5_3_exonuc_N family which is described as 5'-3' exonuclease, N-terminal resolvase-like domain (PF02739)
Residues 174 to 273 (E-value = 1.1e-48) place TP0105 in the 5_3_exonuc family which is described as 5'-3' exonuclease, C-terminal SAM fold (PF01367)
Residues 409 to 589 (E-value = 2.7e-60) place TP0105 in the 3_5_exonuc family which is described as 3'-5' exonuclease (PF01612)
Residues 618 to 996 (E-value = 1.5e-150) place TP0105 in the DNA_pol_A family which is described as DNA polymerase family A (PF00476)

PDB Hit:
gi|809180|pdb|1KLN|A Escherichia coli

Gene Protein Sequence:
MQEKKTLYLLDAYGLIYRSYHAFARAPLINDSGANVSAVYGFFRSLHTLL
CHYRPRYFVAVFDSLTPTFRHVQYPAYKAKRDKTSAELYAQIPLIEEILC
ALGITVLRHDGFEADDLIATLAKRVAAEHCHVVIISSDKDVLQLVCDTVQ
VLRLDIDHKWTCCDAAYVQQRWTVMPTQLLDLFSLMGDSSDNVPGVRGIG
PKTAAHLLHCFGTLDGIYRHTYSLKEALRTKIVCGKKDAFFSRSLIELRD
DVPCVFSLEDSCCIPLDVTSAARIFVREGLHALAQQYRACVQEIDTEATN
DTLQMTESSVLTSGRCANECFLSQVEGRASTPEVNSVLKSELKTSAVSGA
IPIENRDLRQDVMLARSAGHYRGVTDPVELKRIIDCACANGVVAFDCETD
GLHPHDTRLVGFSICFQEAEAFYVPLIVPDVSLHTESTQCTCARSTNVET
EKECTEQHGVSASAVQDPAYVQAVMHQLRRLWNDETLTLVMHNGKFDYHV
MHRAGVFEHCACNIFDTMVAAWLLDPDRGTYGMDVLAASFFQIRTITFEE
VVAKGQTFAHVPYECAVRYAAEDADITFRLYHYLKLRLETAGLLSVFETI
EMPLLPILARMEEVGIFLRKDVVQQLTRSFSDLIQQYEHDIFSLAGHEFN
IGSPKQLQTVLFQELHLPPGKKNTQGYSTDHSVLKKLARKHPIAEKILLF
RDLSKLRSTYTESLAKLADQTGRVHTSFVQIGTATGRLSSRNPNLQNIPI
KSTEGRKIRQAFQATVGHELISADYTQIELVVLAHLSQDRNLLNAFRQHI
DIHALTAAYIFNVSIDDVQPAMRRIAKTINFGIVYGMSAFRLSDELKISQ
KEAQSFIYRYFETYPGVYAFSTQVAEQTRKTGYVTSLAGRRRYIRTIDSR
NTLERARAERMALNTQIQSSAADIVKIAMIAIQRAFARRPLRAQLLLQVH
DELIFEAPAAETAIVKEILFAEMEHAVELSIPLRIHVESGNSWGDFH

Gene Nucleotide Sequence:  Sequence Viewer
ATGCAAGAGAAAAAAACGCTTTACCTTCTTGATGCCTACGGACTTATTTA
TCGGAGTTACCACGCGTTCGCGCGTGCGCCGTTGATTAACGACAGCGGTG
CGAATGTTTCTGCCGTATATGGTTTTTTTCGGAGTTTGCACACGCTCCTG
TGTCACTATCGACCCCGTTATTTTGTTGCTGTTTTTGATTCTCTCACGCC
TACCTTTCGGCACGTACAGTACCCAGCCTATAAGGCAAAAAGGGATAAGA
CTTCTGCAGAGCTTTATGCGCAAATTCCCCTTATCGAAGAAATCCTGTGT
GCACTGGGCATTACAGTTTTGCGTCATGACGGCTTTGAAGCTGACGACCT
CATTGCAACCCTAGCAAAACGAGTTGCGGCTGAGCACTGTCATGTTGTGA
TTATCTCCTCAGATAAAGATGTACTTCAGCTTGTGTGTGATACGGTGCAA
GTGCTCAGACTTGACATAGATCATAAGTGGACATGTTGCGACGCTGCGTA
CGTACAGCAACGGTGGACGGTCATGCCAACACAATTACTTGATTTGTTCT
CTCTCATGGGAGATTCCTCCGACAATGTGCCTGGTGTGAGAGGGATTGGT
CCTAAGACGGCTGCACATCTTCTCCACTGTTTTGGCACACTTGATGGTAT
TTATCGTCATACCTATTCCTTAAAAGAAGCGCTGCGCACGAAGATAGTGT
GTGGGAAGAAAGATGCATTTTTTTCTCGTTCACTCATTGAGTTGCGTGAC
GATGTACCATGTGTTTTTTCGCTCGAAGATTCCTGTTGTATTCCGCTCGA
TGTAACGTCTGCTGCACGTATTTTTGTGCGAGAAGGATTGCATGCGCTTG
CACAACAATATCGTGCTTGTGTGCAAGAAATAGATACAGAAGCAACAAAC
GATACATTACAAATGACAGAGTCTTCTGTGCTCACGTCTGGTCGATGTGC
AAATGAGTGTTTCTTATCTCAGGTAGAAGGGAGGGCTAGTACACCGGAGG
TGAACTCCGTATTGAAGTCGGAGTTGAAGACGAGTGCTGTGTCTGGCGCC
ATACCTATAGAAAATAGAGATCTTAGGCAGGATGTTATGCTTGCACGCAG
TGCAGGTCATTATCGTGGTGTTACTGACCCTGTAGAACTTAAACGTATTA
TTGATTGCGCGTGTGCGAATGGTGTGGTCGCGTTTGATTGTGAAACGGAT
GGATTGCATCCGCACGATACACGTCTGGTCGGATTTTCGATCTGCTTTCA
GGAAGCAGAGGCTTTTTATGTTCCTCTTATTGTTCCGGACGTTTCTCTTC
ATACCGAGTCAACTCAGTGTACATGTGCACGTAGCACTAATGTCGAGACT
GAAAAGGAGTGCACAGAACAGCATGGGGTATCTGCATCTGCTGTGCAGGA
TCCGGCATATGTCCAAGCTGTCATGCACCAGCTTCGACGTCTTTGGAATG
ATGAGACGCTCACACTTGTTATGCATAATGGAAAGTTTGATTATCACGTT
ATGCATCGTGCAGGCGTTTTTGAGCACTGTGCATGTAATATTTTCGATAC
GATGGTTGCAGCTTGGTTGCTGGATCCCGATCGCGGTACATACGGTATGG
ATGTACTTGCCGCATCATTCTTTCAGATCAGAACGATTACATTTGAAGAA
GTGGTAGCAAAAGGGCAAACCTTTGCGCACGTCCCTTATGAGTGTGCAGT
CCGCTATGCAGCGGAGGATGCAGATATTACTTTTCGTTTATACCATTATT
TAAAACTCCGCTTGGAAACAGCAGGATTGCTTTCTGTGTTTGAGACCATA
GAAATGCCGCTTTTGCCTATCCTAGCACGTATGGAAGAAGTGGGGATTTT
TTTACGTAAGGATGTTGTGCAGCAGCTCACTCGATCTTTTTCAGATTTGA
TCCAGCAGTACGAGCACGATATTTTTTCTCTTGCCGGTCATGAATTTAAT
ATTGGTTCTCCGAAGCAACTGCAGACAGTCCTTTTTCAAGAATTACATTT
ACCGCCCGGTAAAAAGAATACTCAAGGTTATTCTACTGATCATTCTGTAT
TGAAGAAACTTGCACGTAAGCATCCCATTGCAGAAAAAATATTGCTCTTT
AGAGATCTTTCAAAGTTACGTTCGACGTATACCGAATCGCTTGCAAAACT
TGCTGATCAAACAGGGCGTGTACATACTAGCTTTGTGCAAATTGGTACCG
CAACTGGAAGGCTTTCGAGTAGAAATCCAAATTTACAAAACATTCCCATT
AAAAGCACAGAAGGAAGAAAAATAAGGCAGGCGTTTCAAGCTACTGTTGG
GCATGAGTTAATTTCGGCAGACTATACACAAATAGAGCTGGTCGTGTTGG
CCCATCTATCTCAAGATAGAAATCTTCTCAATGCATTTCGACAGCACATT
GATATTCATGCATTGACTGCTGCATATATTTTCAATGTGTCTATAGACGA
TGTACAACCTGCAATGAGAAGAATCGCAAAAACTATTAACTTTGGAATCG
TGTATGGAATGAGCGCTTTTAGATTGAGTGACGAACTTAAAATTTCTCAG
AAGGAAGCGCAGAGCTTCATTTACCGTTATTTTGAAACGTACCCGGGGGT
GTATGCTTTTAGTACACAGGTTGCAGAGCAGACACGTAAAACCGGCTATG
TGACTAGCTTGGCTGGAAGACGACGCTACATCCGTACTATCGATAGTCGC
AATACGCTTGAGCGCGCGCGTGCCGAACGTATGGCGTTGAATACTCAAAT
TCAGAGTTCTGCGGCGGATATTGTGAAAATTGCCATGATAGCAATCCAGC
GTGCGTTTGCGCGCCGACCGTTACGTGCACAATTGTTGCTGCAGGTACAC
GATGAATTGATTTTTGAGGCGCCAGCTGCTGAGACAGCGATAGTGAAAGA
AATTCTCTTTGCTGAGATGGAACATGCTGTTGAGCTCTCGATCCCGCTGC
GTATACACGTGGAGTCTGGAAATAGTTGGGGTGATTTTCAT


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