Score = 42.7 bits (99), Expect = 7e-04, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 33/55 (60%)
Query: 33 LYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYED 87
++ A G FR L+ YK++RPP PD + ++ L A +KAM + ++ V+ + D
Sbjct: 61 VFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEAD 115
In addition to polymerase activity, this DNA polymerase 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.
Escherichia coli (strain K12) (taxid: 83333)
EC: 2
EC: .
EC: 7
EC: .
EC: 7
EC: .
EC: 7
>sp|Q9F173|DPO1_SALTY DNA polymerase I OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=polA PE=3 SV=2
Score = 42.7 bits (99), Expect = 7e-04, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 33/55 (60%)
Query: 33 LYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYED 87
++ A G FR L+ YK++RPP PD + ++ L A +KAM + ++ V+ + D
Sbjct: 61 VFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEAD 115
In addition to polymerase activity, this DNA polymerase 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.
>gi|255579458|ref|XP_002530572.1| DNA polymerase I, putative [Ricinus communis] gi|223529871|gb|EEF31802.1| DNA polymerase I, putative [Ricinus communis]
Score = 99 (39.9 bits), Expect = 0.00057, P = 0.00057
Identities = 21/59 (35%), Positives = 35/59 (59%)
Query: 33 LYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVN-VMYEDAYG 90
++ A G FR L+ YK++RPP PD + ++ L A +KAM + ++ V+ V +D G
Sbjct: 61 VFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEADDVIG 119
Parameters:
V=100
filter=SEG
E=0.001
ctxfactor=1.00
Query ----- As Used ----- ----- Computed ----
Frame MatID Matrix name Lambda K H Lambda K H
+0 0 BLOSUM62 0.322 0.139 0.431 same same same
Q=9,R=2 0.244 0.0300 0.180 n/a n/a n/a
Query
Frame MatID Length Eff.Length E S W T X E2 S2
+0 0 90 90 0.00091 102 3 11 22 0.47 29
29 0.39 31
Statistics:
Database: /share/blast/go-seqdb.fasta
Title: go_20130330-seqdb.fasta
Posted: 5:47:42 AM PDT Apr 1, 2013
Created: 5:47:42 AM PDT Apr 1, 2013
Format: XDF-1
# of letters in database: 169,044,731
# of sequences in database: 368,745
# of database sequences satisfying E: 5
No. of states in DFA: 559 (59 KB)
Total size of DFA: 115 KB (2075 KB)
Time to generate neighborhood: 0.00u 0.00s 0.00t Elapsed: 00:00:00
No. of threads or processors used: 24
Search cpu time: 10.00u 0.13s 10.13t Elapsed: 00:00:01
Total cpu time: 10.00u 0.13s 10.13t Elapsed: 00:00:01
Start: Fri May 10 07:10:03 2013 End: Fri May 10 07:10:04 2013
GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA;IDA
GO:0090305 "nucleic acid phosphodiester bond hydrolysis" evidence=IEA
GO:0006261 "DNA-dependent DNA replication" evidence=IDA
The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 16 residues in 53EXO PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA/RNA binding. The active site includes a set of conserved acidic residues that are essential for binding divalent metal ions required for nuclease activity. Length = 174
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional
All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 887
rad2 DNA excision repair protein (rad2). All prote
81.1
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities
The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes
They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases
XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
