MMSYN1 0825 veeral

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Author Information

Veeral Patel

Basic Information

  • ID: MMSYN1_0825
  • Name: uvrb: excinuclease ABC subunit B
  • Organism: JCVI-Syn3.0
  • Description: The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA2B2 complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage. UniProtKB
  • DNA Length: 1998 base pairs.
  • DNA sequence:

ATG TTC ATT GCC AAT AAC AAG TAT AAG CTT GTT ACC AAA TAT AAG CCT AGC GGT GAT CAA AAC CAG GCA ATT GAA AAA CTT AAT AAG GGC ATC ATT GAA AAT AAG AAA CAC CAA GTA CTT CTG GGC GCA ACA GGC ACG GGT AAA ACC TTT ACG ATC GCT AAC ATT ATC GCC AAG CAT AAC AAG CAG GCG TTA GTG ATT GCA CAT AAT AAA ACT CTG GCC ATG CAG TTA TAC TAC GAA TTG AAA GAA ATG TTC CCC GAG AAC CGC GTA GAG TAT TTT GTC AGT AAC TTC GAC TTT TTC CAA CCA GAA GCT TAC ATC CCG TCA AAA GAC TTG TAT ATC GAC AAG GAT TCA CGC CAA AAT ATG GAA CTG GAT ATG ATG CGT TTG TCT GCC TGC AAT GCA CTT TTA ACC CGC AAC GAC ACC ATC GTT GTA GCT TCG GTC GCC GCC CTT TTC GCT TTG CAG AAT CCT TTG GAA TAC TCA TCA GCG TTC ATC GAG CTG AAA GTC GGA CAG AAG ATT AAG CGC AAT GAA CTT TTA ACG TGG CTT GTA CGC TCT GGC TAC ACA CGC AAT GAC ATC GAG AAC CAG TTG GGG TCC TTC AGC GCA AAA GGC GAC GTG GTG AAG ATC GTG CCA GGA TGG GTT AAC AAT ATT ATG TTC CGT ATT TCG TTA TTC GAC GAT GAA ATT GAG TCC ATC CAC ACC CTG AAC ACT ATT ACA AAC AGC ATC TTG GAC AAT ATC ACG ACG GTC ACG ATT CAC CCC GCT CAG TCA TAC ATT ACC CCT CAA GAC AAG TTG AAG ACC ATC TGT AAC AAC ATT CGT AAT GAG CTT GTG CAA CGC TTA GCG GAA CTT CAA TCT GAA AAC AAA CTT CTT GAG GCG CAG CGT TTA GAA CAG CGT ACA AAG TAC GAC CTT GAG TCA CTT GAG GAG TTT GGC TTT TGT AGT GGG ATT GAA AAT TAC AGC TCA CAC CTG GAT TTC CGT AGC AAA GGG CAG CGC CCT TAT GTC TTG CTT GAT TAT TTC AAC AAT GAC TTT ATC ACT ATC ATC GAC GAA TCT CAT ATC ACT TTG CCA CAG ATC CGT GGT ATG TAT AAT ACA GAC CGC TCT CGT AAA CTG ACC TTG GTC GAG TAT GGT TTC CGC CTG CCA AGT GCA TTA GAC AAC CGC CCA TTG AAT TTT GAT GAA TTC AAC TCA CTT ATT AAG CAA GTC ATC TAT ACA AGT GCC ACC CCA GGA GAT TAT GAG CTG GAC CTG GTA AAT CAT CAA GTA GTC CAG CAG ATT ATC CGT CCG ACA GGT TTA TTG GAT CCG CAG ATT GAG ATT CGT AAG ACT ACA AAC CAA ATT GAT GAT ATT ATC AAT GAA ATC CAC CTG CGT AAA TTA CAA AAT GAG CGT GTT TTT ATT ACC ACT TTA ACA ATC CGC ATG TCA GAG GAT TTA ACC GCG TTC TTG CAG GAG AAA AAC ATT AAA GTC GCA TAC TTA CAT TCG GAG TTA AAA ACA TTA GAG CGC TCC GAG ATC TTA AAT GAC CTG CGC AAA GGG GTA TAC GAC GTA GTT GTA GGC GTT AAT CTT CTG CGC GAA GGT TTA GAC CTT CCA GAG GTC AGC CTG GTT TGC ATC CTT GAT GCC GAC AAG CAG GGC TTC CTT CGC AAT TAT CGC TCA TTG ATC CAA ACG ATC GGG CGC GTC GCC CGT AAC GTC AAC GGC AAA GCA ATC ATG TAC GCG GAC ACT GTC TCA CAA GCA ATG GAC GAA GCC ATC AAA GAA ACC AAC CGT CGT CGT AAA ATT CAG GAA GAG TTC AAT AAA AAG CAC AAC ATT ACG CCG AAA ACG ATC TCC AAA GCG ATC TCA GAG TCA ATC CTT AGC GAG CAG ACC AAG AAG ACC CTG GCG AAG GCT AAG AAG ATT AAG GAC AAG AAA CAA AAA CTG CAA ACA ATT CAG CAA ACG ATT GAT ACC TTA CGT CAA GAA ATG CTG CAG GCA GCC AAA GAA CTG GAT TTC GAA CGC GCG GCG ATC CTT CGT GAC ACT ATC ATC GAA TTG GAA AAT GAA AAA AAT ACA AAC TAA

  • Amino Acid length: 665 amino acids.
  • Amino Acid sequence:

MFIANNKYKLVTKYKPSGDQNQAIEKLNKGIIENKKHQVLLGATGTGKTFTIANIIAKHNKQALVIAHNKTLAMQLYYELKEMFPENRVEYFVSNFDFFQPEAYIPSKDLYIDKDSRQNMELDMMRLSACNALLTRNDTIVVASVAALFALQNPLEYSSAFIELKVGQKIKRNELLTWLVRSGYTRNDIENQLGSFSAKGDVVKIVPGWVNNIMFRISLFDDEIESIHTLNTITNSILDNITTVTIHPAQSYITPQDKLKTICNNIRNELVQRLAELQSENKLLEAQRLEQRTKYDLESLEEFGFCSGIENYSSHLDFRSKGQRPYVLLDYFNNDFITIIDESHITLPQIRGMYNTDRSRKLTLVEYGFRLPSALDNRPLNFDEFNSLIKQVIYTSATPGDYELDLVNHQVVQQIIRPTGLLDPQIEIRKTTNQIDDIINEIHLRKLQNERVFITTLTIRMSEDLTAFLQEKNIKVAYLHSELKTLERSEILNDLRKGVYDVVVGVNLLREGLDLPEVSLVCILDADKQGFLRNYRSLIQTIGRVARNVNGKAIMYADTVSQAMDEAIKETNRRRKIQEEFNKKHNITPKTISKAISESILSEQTKKTLAKAKKIKDKKQKLQTIQQTIDTLRQEMLQAAKELDFERAAILRDTIIELENEKNTN

Function and Homologs

  • Product: UvrABC system protein B
  • Module: ATP
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Mycoplasma capricolum, A0A084EHF5_MYCCA, 3344/99.7%/0.0/99.5%, [1]
    • Mycoplasma leachii, E4PSL2_MYCLG, 3342/99.8%/0.0/99.5%, [2]
    • Mycoplasma capricolum, Q2SR91_MYCCT, 3337/99.5%/0.0/99.2%, [3]
  • Equivalent E. coli / JCVI functional protein: EG11062.

Expression

  • Expression Level: medium
  • Expression Level Hypothesis: The gene has expression level medium because it's important for the DNA lesions to be repaired, but not too important because a gene can still be expressed even without perfect DNA base pairing.
  • Expression Level References and Description: M. genitalium model data
  • Expression Time: early
  • Expression Level Hypothesis: I think the expression time is "early" because the uvrb gene needs to repair any malformed DNA before it is transcribed to RNA. As a result, we'd want this gene to be expressed early in the lifecycle.
  • Expression Time References and Description: Gene description

Gene Context

  • Other Components: MMSYN1_0824_rperez4
  • Possible Dependencies: DNA
  • Process: DNA repair
    • Inputs: mutated DNA
    • Outputs: fixed DNA
    • Reference: Wikipedia

Construct

  • Synthesis Score: The synthesis score of your construct: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details: For example, had to use a rare codon to fix folding energy;
  • GenBank File: A link to the GenBank file. file