Protein : Qrob_P0078600.2 Q. robur
Protein Identifier  ? Qrob_P0078600.2 Organism . Name  Quercus robur
Score  99.1 Score Type  egn
Protein Description  (M=2) 6.5.1.1 - DNA ligase (ATP). Code Enzyme  EC:6.5.1.1
Gene Prediction Quality  validated Protein length 

Sequence

Length: 94  
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0 Synonyms

7 GO Terms

Identifier Name Description
GO:0003677 DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0005524 ATP binding Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0006281 DNA repair The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
GO:0006310 DNA recombination Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
GO:0003909 DNA ligase activity Catalysis of the formation of a phosphodiester bond between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of another. This reaction requires an energy source such as ATP or NAD+.
GO:0051103 DNA ligation involved in DNA repair The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair.
GO:0003910 DNA ligase (ATP) activity Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m).

33 Blast

Analysis Hit Start End Strand Length Note Hit Coverage Hit Length Hit Pident E Val Hit Description
blastp_kegg lcl|sly:101266429 22 93 + 72 none 6.14 1172 88.89 2e-38 DNA ligase 4-like
blastp_kegg lcl|sot:102578397 22 93 + 72 none 6.14 1172 88.89 3e-38 DNA ligase 4-like
blastp_kegg lcl|mtr:MTR_2g038030 22 93 + 72 none 5.79 1244 83.33 1e-36 DNA ligase
blastp_kegg lcl|brp:103845154 22 93 + 72 none 6.03 1195 83.33 1e-35 DNA ligase 4
blastp_kegg lcl|pvu:PHAVU_009G235800g 22 93 + 72 none 6.14 1172 83.33 2e-35 hypothetical protein
blastp_kegg lcl|mus:103995944 22 93 + 72 none 6.23 1155 81.94 2e-34 DNA ligase 4 isoform X1
blastp_kegg lcl|atr:s00025p00149970 22 93 + 72 none 6.43 1120 77.78 3e-32 AMTR_s00025p00149970 hypothetical protein
blastp_kegg lcl|pda:103701483 22 93 + 72 none 6.16 1169 77.78 1e-31 DNA ligase 4
blastp_kegg lcl|zma:103645969 22 93 + 72 none 11.94 603 77.78 2e-30 putative DNA ligase 4
blastp_kegg lcl|pper:PRUPE_ppa018049mg 22 92 + 71 none 13.17 539 92.96 1e-29 hypothetical protein
blastp_pdb 3l2p_A 22 80 + 59 Gaps:5 10.36 579 41.67 3e-09 mol:protein length:579 DNA ligase 3
blastp_pdb 4eq5_A 21 80 + 60 Gaps:4 9.81 571 44.64 1e-08 mol:protein length:571 DNA ligase
blastp_pdb 3rr5_A 21 80 + 60 Gaps:4 9.82 570 46.43 1e-07 mol:protein length:570 DNA ligase
blastp_pdb 2cfm_A 21 80 + 60 Gaps:4 9.98 561 42.86 4e-07 mol:protein length:561 THERMOSTABLE DNA LIGASE
blastp_pdb 1x9n_A 22 80 + 59 Gaps:3 9.01 688 38.71 2e-06 mol:protein length:688 DNA ligase I
blastp_uniprot_sprot sp|Q9LL84|DNLI4_ARATH 22 93 + 72 none 5.91 1219 81.94 7e-25 DNA ligase 4 OS Arabidopsis thaliana GN LIG4 PE 1 SV 1
blastp_uniprot_sprot sp|Q7X7E9|DNLI4_ORYSJ 22 93 + 72 none 5.45 1322 77.78 1e-22 Putative DNA ligase 4 OS Oryza sativa subsp. japonica GN LIG4 PE 2 SV 2
blastp_uniprot_sprot sp|Q90YB1|DNLI4_CHICK 22 91 + 70 Gaps:1 7.79 912 52.11 1e-17 DNA ligase 4 OS Gallus gallus GN LIG4 PE 2 SV 2
blastp_uniprot_sprot sp|Q54CR9|DNLI4_DICDI 22 81 + 60 Gaps:6 6.07 1088 51.52 2e-15 DNA ligase 4 OS Dictyostelium discoideum GN lig4 PE 3 SV 1
blastp_uniprot_sprot sp|Q5R6L3|DNLI4_PONAB 22 91 + 70 Gaps:1 7.79 911 47.89 4e-15 DNA ligase 4 OS Pongo abelii GN DNL4 PE 2 SV 1
blastp_uniprot_sprot sp|P49917|DNLI4_HUMAN 22 91 + 70 Gaps:1 7.79 911 47.89 5e-15 DNA ligase 4 OS Homo sapiens GN LIG4 PE 1 SV 2
blastp_uniprot_sprot sp|Q8BTF7|DNLI4_MOUSE 22 91 + 70 Gaps:1 7.79 911 49.30 7e-15 DNA ligase 4 OS Mus musculus GN Lig4 PE 2 SV 2
blastp_uniprot_sprot sp|Q1DKE7|DNLI4_COCIM 22 81 + 60 Gaps:1 6.19 985 52.46 4e-13 DNA ligase 4 OS Coccidioides immitis (strain RS) GN LIG4 PE 3 SV 1
blastp_uniprot_sprot sp|Q5BH83|DNLI4_EMENI 22 81 + 60 Gaps:1 6.05 1009 49.18 2e-12 DNA ligase 4 OS Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN lig4 PE 3 SV 1
blastp_uniprot_sprot sp|Q7SB49|DNLI4_NEUCR 22 81 + 60 Gaps:1 5.83 1046 47.54 2e-12 DNA ligase 4 OS Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN lig-4 PE 3 SV 1
rpsblast_cdd gnl|CDD|188065 22 83 + 62 Gaps:1 12.26 514 49.21 7e-14 TIGR00574 dnl1 DNA ligase I ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair DNA replication and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999 Ph.D. Thesis Stanford University).
rpsblast_cdd gnl|CDD|185713 22 50 + 29 none 12.89 225 62.07 1e-09 cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication recombination and repair. ATP-dependent ligases are present in many organisms such as viruses bacteriophages eukarya archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4 a nuclear phosphoprotein which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic unit comprises six conserved sequence motifs (I III IIIa IV V and VI) that define this family of related nucleotidyltransferases.
rpsblast_cdd gnl|CDD|153437 53 93 + 41 none 29.29 140 58.54 2e-09 cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication recombination and repair. ATP-dependent ligases are present in many organisms such as viruses bacteriohages eukarya archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4 a nuclear phosphoprotein which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I III IIIa IV V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI) which is essential for ATP hydrolysis is located in the OB-fold domain.
rpsblast_cdd gnl|CDD|31978 22 80 + 59 Gaps:6 11.94 444 37.74 2e-08 COG1793 CDC9 ATP-dependent DNA ligase [DNA replication recombination and repair].
rpsblast_cdd gnl|CDD|178660 22 79 + 58 Gaps:3 8.20 744 39.34 5e-08 PLN03113 PLN03113 DNA ligase 1 Provisional.

7 Domain Motifs

Analysis Begin End Length Domain Identifier Cross Ref Description Inter Pro
ProSitePatterns 22 46 25 PS00333 "Reactome:REACT_216" ATP-dependent DNA ligase signature 2. IPR016059
Gene3D 21 51 31 G3DSA:3.30.1490.70 none none none
PANTHER 22 83 62 PTHR10459 none none none
ProSiteProfiles 22 83 62 PS50160 "Reactome:REACT_216" ATP-dependent DNA ligase family profile. IPR012310
SUPERFAMILY 19 47 29 SSF56091 none none none
Gene3D 55 82 28 G3DSA:2.40.50.140 none none IPR012340
PANTHER 22 83 62 PTHR10459:SF7 none none IPR029710

0 Localization

11 Qtllist

Qtl Name Chromosome Name Linkage Group Prox Marker Dist Marker Position QTL Pos One Pos Two Test Type Test Value R 2
Bourran1_2003_QTL2_peak_Bud_burst_A4 Qrob_Chr02 2 s_1B0H8U_259 s_1CB1VL_554 17 0 87 lod 3,3 8,7
Bourran2_2004_QTL9_peak_Bud_burst_3P Qrob_Chr02 2 s_1C34E9_788 v_12238_322 50 25 75 lod 4,4 10,1
NancyGreenhouseCO2_2001_ambient_elevated_leaf_cellulose_QTL2_d13Cf Qrob_Chr02 2 s_1AQA4Z_1644 s_1AK5QX_947 53.67 14,01 79,68 lod 5.6594 0.03
Bourran1_2004_QTL2_peak_Bud_burst_3P Qrob_Chr02 2 s_1AW12F_382 s_1A77MR_223 42 6 64 lod 3,6 9,6
Bourran_2000_2002_QTL2_Delta.F Qrob_Chr02 2 s_1CSO13_1244 s_1AVEUF_1540 55.44 46,71 63,68 lod 7.3232 0.058
Bourran2_2002_QTL9_peak_Bud_burst_A4 Qrob_Chr02 2 s_1BFNDA_375 s_1A3VA1_2139 32,5 17 62 lod 3,1 4,2
Bourran2_2003_QTL8_peak_Bud_burst_3P Qrob_Chr02 2 s_1ANG6_1446 v_11270_161 40 0 72 lod 4,4 9,9
Bourran2_2014_nP_A4 Qrob_Chr11 11 s_1B58GB_1413 s_1A5BYY_1671 11,15 0 42,38 lod 1,8913 4,5
Bourran2_2015_nP_A4 Qrob_Chr02 2 s_1A0FUE_1868 s_1A1UAI_500 20,64 20,47 21,36 lod 5.8 10.9
Bourran2_2015_nPriLBD_A4 Qrob_Chr02 2 s_1CP5DI_1183 s_1A63ZX_1277 24,87 24,63 26,18 lod 3.8 7
NancyGreenhouseCO2_2001_ambient_elevated_leaf_cellulose_QTL6_d13Cf Qrob_Chr02 2 s_1AEP21_172 v_6048_204 46.33 22,5 65,23 lod 4.972 0.03

1 Targeting

Analysis Start End Length Location Reliability Signal Peptide Cut Off Mitochondrion Cut Off Network Signal Peptide Length
TargetP 1 26   Secretory pathway 2 0.789 0.081 NON-PLANT 26