Protein : Qrob_P0082880.2 Q. robur
Protein Identifier  ? Qrob_P0082880.2 Organism . Name  Quercus robur
Score  60.1 Score Type  egn
Protein Description  (M=1) PTHR18867 - RAD50 Code Enzyme  EC:3.6.3.25
Gene Prediction Quality  validated Protein length 

Sequence

Length: 178  
Kegg Orthology  K10866
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0 Synonyms

5 GO Terms

Identifier Name Description
GO:0005634 nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
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:0016887 ATPase activity Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
GO:0000723 telomere maintenance Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins and the length of telomeric DNA. These processes includes those that shorten and lengthen the telomeric DNA sequences.
GO:0030870 Mre11 complex Trimeric protein complex that possesses endonuclease activity; involved in meiotic recombination, DNA repair and checkpoint signaling. In Saccharomyces cerevisiae, the complex comprises Mre11p, Rad50p, and Xrs2p; complexes identified in other species generally contain proteins orthologous to the Saccharomyces cerevisiae proteins.

31 Blast

Analysis Hit Start End Strand Length Note Hit Coverage Hit Length Hit Pident E Val Hit Description
blastp_kegg lcl|aly:ARALYDRAFT_920987 18 176 + 159 none 85.48 186 95.60 9e-110 hypothetical protein
blastp_kegg lcl|pper:PRUPE_ppa001176mg 18 176 + 159 none 17.93 887 97.48 3e-105 hypothetical protein
blastp_kegg lcl|pda:103702580 18 176 + 159 none 17.61 903 96.86 8e-105 DNA repair protein RAD50
blastp_kegg lcl|gmx:100818545 18 176 + 159 none 12.08 1316 98.11 1e-104 DNA repair protein RAD50-like
blastp_kegg lcl|cmo:103483462 18 176 + 159 none 12.08 1316 98.74 3e-104 DNA repair protein RAD50
blastp_kegg lcl|csv:101209902 18 176 + 159 none 12.08 1316 98.11 6e-104 DNA repair protein RAD50-like
blastp_kegg lcl|pvu:PHAVU_001G266800g 18 176 + 159 none 12.08 1316 96.86 1e-103 hypothetical protein
blastp_kegg lcl|cit:102616752 18 176 + 159 none 12.08 1316 98.11 2e-103 DNA repair protein RAD50-like
blastp_kegg lcl|cic:CICLE_v10004166mg 18 176 + 159 none 12.08 1316 98.11 2e-103 hypothetical protein
blastp_kegg lcl|pop:POPTR_0001s32760g 18 176 + 159 none 12.08 1316 97.48 2e-103 POPTRDRAFT_829809 DNA repair-recombination family protein
blastp_uniprot_sprot sp|Q9SL02|RAD50_ARATH 18 176 + 159 none 12.08 1316 95.60 2e-103 DNA repair protein RAD50 OS Arabidopsis thaliana GN RAD50 PE 1 SV 2
blastp_uniprot_sprot sp|P70388|RAD50_MOUSE 18 175 + 158 Gaps:5 12.42 1312 66.87 2e-68 DNA repair protein RAD50 OS Mus musculus GN Rad50 PE 1 SV 1
blastp_uniprot_sprot sp|Q9JIL8|RAD50_RAT 19 175 + 157 Gaps:5 12.35 1312 67.28 2e-68 DNA repair protein RAD50 OS Rattus norvegicus GN Rad50 PE 1 SV 1
blastp_uniprot_sprot sp|Q92878|RAD50_HUMAN 18 175 + 158 Gaps:5 12.42 1312 65.64 5e-68 DNA repair protein RAD50 OS Homo sapiens GN RAD50 PE 1 SV 1
blastp_uniprot_sprot sp|Q9UTJ8|RAD50_SCHPO 19 175 + 157 none 12.22 1285 64.97 7e-62 DNA repair protein rad50 OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN rad50 PE 1 SV 3
blastp_uniprot_sprot sp|Q54CS9|RAD50_DICDI 18 175 + 158 none 11.70 1351 58.23 4e-61 DNA repair protein RAD50 OS Dictyostelium discoideum GN rad50 PE 3 SV 1
blastp_uniprot_sprot sp|P12753|RAD50_YEAST 19 177 + 159 Gaps:2 12.27 1312 56.52 5e-55 DNA repair protein RAD50 OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN RAD50 PE 1 SV 1
blastp_uniprot_sprot sp|Q9W252|RAD50_DROME 19 177 + 159 Gaps:8 12.22 1318 55.90 2e-51 DNA repair protein RAD50 OS Drosophila melanogaster GN rad50 PE 2 SV 4
blastp_uniprot_sprot sp|Q8SRK6|RAD50_ENCCU 18 176 + 159 Gaps:3 12.51 1247 52.56 6e-48 DNA repair protein RAD50 OS Encephalitozoon cuniculi (strain GB-M1) GN RAD50 PE 1 SV 1
blastp_uniprot_sprot sp|C6KSQ6|RAD50_PLAF7 18 176 + 159 Gaps:6 7.38 2236 50.30 3e-46 Probable DNA repair protein RAD50 OS Plasmodium falciparum (isolate 3D7) GN PFF0285c PE 3 SV 1
rpsblast_cdd gnl|CDD|129694 19 175 + 157 Gaps:5 12.36 1311 66.05 3e-57 TIGR00606 rad50 rad50. All proteins in this family for which functions are known are involvedin recombination recombinational repair and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999 Ph.D. Thesis Stanford University).
rpsblast_cdd gnl|CDD|72999 78 177 + 100 Gaps:9 44.61 204 70.33 5e-32 cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs the Q loop a histidine residue in the switch region a D-loop and a conserved LSGG sequence. This conserved sequence LSGG is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence..
rpsblast_cdd gnl|CDD|30768 26 177 + 152 Gaps:16 15.42 908 27.14 2e-15 COG0419 SbcC ATPase involved in DNA repair [DNA replication recombination and repair].
rpsblast_cdd gnl|CDD|72985 84 163 + 80 Gaps:11 33.66 205 37.68 2e-09 cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria archaea and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component the cobalt-binding periplasmic protein and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems..
rpsblast_cdd gnl|CDD|205736 64 132 + 69 Gaps:8 97.47 79 31.17 9e-09 pfam13558 SbcCD_C Putative exonuclease SbcCD C subunit. Possible exonuclease SbcCD C subunit on AAA proteins.
rpsblast_cdd gnl|CDD|72986 80 159 + 80 Gaps:7 45.06 162 36.99 1e-08 cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterised by the fact that the ABC subunit is made up of duplicated fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins..
rpsblast_cdd gnl|CDD|72971 85 163 + 79 Gaps:11 43.31 157 41.18 2e-08 cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds like sugars ions peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif Q-loop and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins..
rpsblast_cdd gnl|CDD|72984 85 163 + 79 Gaps:11 32.23 211 35.29 5e-07 cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria archaea and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component the cobalt-binding periplasmic protein and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems..
rpsblast_cdd gnl|CDD|200215 85 154 + 70 Gaps:12 10.96 529 37.93 7e-07 TIGR02857 CydD thiol reductant ABC exporter CydD subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Unfortunately the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name CydD.
rpsblast_cdd gnl|CDD|31331 85 158 + 74 Gaps:10 28.32 226 34.38 9e-07 COG1136 SalX ABC-type antimicrobial peptide transport system ATPase component [Defense mechanisms].

5 Domain Motifs

Analysis Begin End Length Domain Identifier Cross Ref Description Inter Pro
PANTHER 18 177 160 PTHR18867 none none IPR004584
PANTHER 18 177 160 PTHR18867:SF12 none none none
Gene3D 22 163 142 G3DSA:3.40.50.300 none none IPR027417
SUPERFAMILY 21 168 148 SSF52540 none none IPR027417
Pfam 64 132 69 PF13558 none Putative exonuclease SbcCD, C subunit none

0 Localization

16 Qtllist

Qtl Name Chromosome Name Linkage Group Prox Marker Dist Marker Position QTL Pos One Pos Two Test Type Test Value R 2
Bourran2_2014_nLBD*_A4 Qrob_Chr08 8 v_12498_318 v_12364_308 34,91 16,12 53,62 lod 2,4961 5,2
Bourran2_2014_nSecLBD_3P Qrob_Chr08 8 s_1BN2OD_551 s_1B5AYF_599 17,17 0 43,51 lod 1,9229 4,4
Bourran2_2014_rEpiBC*_A4 Qrob_Chr08 8 v_12498_318 v_12364_308 35,77 14,11 55,31 lod 2,9413 6,2
Bourran2_2015_nEpiBC_3P Qrob_Chr12 12 s_1B73S5_217 v_7050_211 28,31 26,37 28,45 lod 4.5 11.6
Bourran_2000_2002_QTL3_Delta.F Qrob_Chr08 8 s_1A3EF7_1406 s_1AIWYC_607 30.17 21,01 40,21 lod 6.8553 0.055
Bourran2_2014_aSeqBC_A4 Qrob_Chr08 8 v_15999_278 v_AP13YL15_395 32,52 4,22 57,22 lod 2,7561 6,7
Bourran2_2014_nFork*_A4 Qrob_Chr08 8 PIE175 s_1CD7GJ_1398 31,22 5,24 57,24 lod 2,6724 6,8
Bourran2_2014_nLBD*_3P Qrob_Chr08 8 v_5216_549 v_11837_70 12,25 0 35,55 lod 2,5951 6
Bourran2_2014_nP*_3P Qrob_Chr08 8 v_5216_549 v_11837_70 12,19 0 31,97 lod 2,8472 6
Bourran2_2014_nPriLBD_3P Qrob_Chr08 8 v_5216_549 v_11837_70 12,36 0 30,43 lod 2,5806 5,1
Bourran2_2014_nPriLBD_A4 Qrob_Chr08 8 PIE175 v_9164_159 31,85 15,39 48,29 lod 2,8308 6,8
Bourran2_2015_rEpiBC_3P Qrob_Chr08 8 s_A9TNV_543 v_11837_70 9,93 9,83 11,15 lod 3.3 7.3
Champenoux_2015_nSeqBC_A4 Qrob_Chr08 8 v_AD7YD13_501 s_1A7IED_780 43,44 43,42 43,99 lod 3.7 8.9
NancyGreenhouseCO2_2001_ambient_elevated_leaf_cellulose_QTL3_d13Cf Qrob_Chr08 8 v_5216_549 v_11625_20 37.08 12,26 54,9 lod 6.5888 0.04
Bourran2_2014_nEpis*_3P Qrob_Chr08 8 s_1DA4QW_688 s_1DNI7D_820 17,96 0 37,75 lod 2,9745 7,5
Bourran2_2014_nPriBD_3P Qrob_Chr11 11 v_11486_194 s_1AT3E_2335 5,54 0,4 20,6 lod 2,6345 5,9

0 Targeting