MMSYN1 0639

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Author Information

Trina Sarkar

Basic Information

  • ID: MMSYN1_0639
  • Name: efflux ABC transporter permease
  • Organism: JCVI-Syn3.0
  • Description: ABC transporters utilize the energy of ATP binding and hydrolysis to transport various substrates across cellular membranes. An effluxer (or exporter) is a specific ABC transporter that is present in both prokaryotes and eukaryotes and pumps toxins and drugs out of the cell using active transport [1]. Additionally, permeases are transmembrane proteins that use a proton gradient to diffuse molecules out of the cell [2].
  • DNA Length: 4146 base pairs.
  • DNA sequence:

ATG AAG ACC AAA AAT AAG AAG AAT AAA TGG CTT GGA CTT ATC TTA AAG AAC TCA CTT AAG AAC TCT TTC AAA TAT AAG TCG CAG TTA TTT GGC CTT GTGTTA TTG GTA ATG ATC ATG TCT CTT ATT ATG TCT CTT ATC AGT GCT ATC AAT TCT CGT GTT CTT GAT AAG TAC GAC GAT TTG ATT ACG AAC TCT AAC CAACAT AAT TTA GTT TTA AAA TTG GAT CCG TAT GAA AAC GTT TCA ACG TCA TTG ATT ACT AGC AAC AAC CAG ATC CAG GCA CAA CAG CAG TTC ATC AAT CGTCTG AAT GAG AAA TTG TAC TCA CGC TAT AAT TTC AAA TTT GAT TGG TCG CGT ACT GAA TCG CGT GAA TTT AAA CAG GTG AAG AGT TTA AAT AAT TTG CAAACT CTG AAG GCC GTA AGC AAG CAG TAC CTG ACG GAT AAT AAG GTT GAC CAA TTA GTA ATC GTT AAG GGG CGT AAT ATT AAT TCT AAT AAG GAA GTT TTAATC GAC CCG ATT TAC GCG AAG AAA CAT AAC ATT AAG ATC AAT GAT ATT ATC CGT TTC CAA AAG GAT GTA TTA GGC GAC CAA TTG CTG GTG AAT TCC CTGGAA AAT AAG ACC ACA ACC AAA CAG CAG TTT GAA GAC ATT AAT AAG ATT ACT AAA CAG GGG TTG ACG GAC AAT AAT GGG ATC TAT CAA ATT AAG TAC GCCAGT TCT TTC GAT TGG TAC CAG GTT GTT GGA TTC GCA AAT AGC GCG GAT TTT ATC TTT CCT ACC ATT AAT GCG TAT TCG CCC ATT CCC AAC CGC CTG AATGAG GGT ATC ATC TAC GTT GAT CCG TTA CGC TTC GGA TTA ATT AAG CAA ACC GAC GGA TTC TAT AAA TAT GAC AGT ACG TCC AGC AAA TTA GTG GTT TCTTCT AAC AAT GAA TGG GAA TCG TTC TAT AGT CTG AAA ACG AAG CAA AAG TTA AGT GAC GAA ATT GTC GAT TGG ATG AAC CAA TAT TTT TCT CAG CTG ATTAAC AAA AAA GCC CAG GAC AAA TGG ATC TAC AAG TTA GAG GAT CCA AAC TAT CGT TTC AAC TCC CGC ACG TCT GTT ATT AAA AAG ACT ATC AGT GCA TACAAT ATT TAT TCA TTC ATT GTC TTA CTT GCA GTC ATC TCC GTG GTG CTG TAT ACC ACA TTT TTG ATT ACT AAA AAG CAA ATT TTG AAT TCT CGC GGT CAGATT GGT ACT ATG CGT GCC ATC GGC TAT AAG AAG CGT CAG ATG GTG CTG AAT TAT GTC ATG ATG CCG TTT TTC ACC TCT ATC GTA GGG GGA ATT TTA GGCTAC ATT CTT TCA TGT CTT ATC AGC ATT ATC ATT ATC AAC CGT TTT TCC AAT TAC TTT TCA TTG GAC TAT GGG GTA TTT TCT TTC GAC TGG ATT GGG TTATTG AAC AAC TTA ATC TTT ATG TGG TTG ATT ATT TCC TCC ATC TCG TTT CTT ATT GGA TAC CTG ATT ATG AAG AAG GGA GCC ATT AAT CTG CTG GAA AATCGC AAT GCG AAA AAA ATT TCC AAA TTA GGC TCA CTT ATT AAG AGT TTA TCG AAT AAG CGT AAA TTT AAC CAC CGC TTG CGC GCA GCG CTG TTG GTG AACTCG GGT TCC AAA TTA ACT GGT GTA GGA TTC GTT GTT CTG ATC GCA ACT ATC TTG TTT ACG ATT TCA TTT GTC AGT CCC AAT CTT TTA AAG AAC AAT AAAATT TAC GCC TAC AAC GGG GTT AAA TAC AAT CAA ATC GTG GAA TAC TCA CAA CCA ACG TAT AAT AAC CCC TTT TCA TTC ATC CGT GTT TTT AAT CCT GACAAA AAG TCC GAT GAT AAA TAC AAT ATC ATT AAG AAT AAT AAC CGT TAC TTG GCC ACG AGC CTG CCG ACG AAA AAC AAC CAA TAT GAC CTG CAG ACA ATTATT AAT GAC TAT CTG AAT CAG ACG TAC AAC AAT GCT TAC TAC AGC CTG GCA ATC GAT TTA CAG GAC AAA CAG GAG GTG CAA GCA ATC AAT TTG GCT CTGAGC AAC ATG AAA CTT TTA CAA GCG CAA GAC ATT GCA CTG ACC AAA CAA TAT TTC AAA TAT ATT TCG AGT TTG TCA ATT ACA CCC TCT TCA ATC CAT CACATC TTG TTA AAA AAC TGG CCA GAC TAT GAT AAC CTG ATT AAT AAG TTA AAG GAG ATT AAG GAA AAT GAG TTC GAA ACT TTG TTA AAT CAG TTT AAG TACCTT CAG CAA TTC TAT GCG ACC TAC ACA AAC TCC ATC GGA CTT GCA ATC AAT CGT AGT TAC ATC AAC TCC TTC GAC TTA AAA GAT AAA AAA GAC CTT CGCATC CAA AAA TTT AAT AAT AAT TCC TCC GAC CAA AAC AAC TTG AAG ACA AAG GCG TAC GAC GAT ATC TTA AAT TCC GAT CTT TTG GCT TTG TCT AAA TCCTCA TTC TCG GCA AAG GAC TTT AAG AAT AAG ATC ATT GAC CAA TTC AAG TTA ACT AAC TCG GAT AGC TCT TTA GGT ATG TAT CAC ATT CTT GAT AAC AAGTGG AAT AAG TCA AAC AGC ATT TCG GAC CAG TTC CTT GAC ATT TCT GCT TTC GAC TTT ATC AAT AAG AAA TAT AAG CTG GAC GAC TTG AAG GAC TTG GTCATT AAG CTT TCA TTA TGG TTT TCC GTG ATG TTC TAC AAG CGT GAT GAC CAA GCC TTA ATT CAG GCT GCC TAT TCG CGC GCG CCG TAT TTC GTT AAA CAGAAC TTA AAG ATC TCA TAT AAT AGT AAT AAG GAT TAC ACC TTA GGC TTC AAC TTG ACC ACT TTT AAC AAG AAC TAC GAA CAA CTT GGT ACT TTA CTG AACGTC AAA ACT CTT GAC AAC AAA CAC ACT TTC AAA ATC TAC GGC ATC CTG AAC AAC CAC GAT TAC ATC GAC TTG TAT GAT CAG AAC AAG ACC GAT TTA ATTAAA AAG CTG TTC GAC TCA GAA CAG AAT TCT ATC ATT ATT AAT CAG ACC ATC GCT AAA CGC CTT AAT CTT AAG CCC AAC GAT AAA ATC TCC TTA AAC GTCTTG CAA AAT GAG TTA CAA CAC ATC AAA AAC AAC AAG ACG ACC ATC TTT AAA ACC TCG GAC TGG TCA ATG AAG CAG GAC ACG AGC TAT GAT TCC TTT ATTCAA CGT TCG GAC ATT TCG ACG AAT AAT CTT AAG GTA AAG ACT AAC AAT TCT GTT CTT GAA CTT AAC AAC GGG TTC AGT GAC GTG AAT TCA TAC TAT CAAAGT TAT TTA AAC AAT GAA TTG AAG CTT GGT ACG AAA ATC CAA AAC AAA ACG TTT AAA ATC GTT GGT ATC CAT GAT GGA TAC AAC GAA AAC ATG GCC TGGATT AAA GAA TCC GAC GCG CAG GAA ATT CTG AAT TAC AAG CAG AAT AAG AGC ATT TGG TGG AAA GAT ATT TTC GCT CCC CAG TGG AAC AAG ACG TTT AGCTCT ATC CAG GCA AAA CAA GTT CTT AAT GAT ACG TTG GAC TTG AAT AAT AAG TCC CTG ACC GAC TAT AGT TAT GAG CAA TTC GTA AAT GAG TTT ATC AATAAT AAG AAC CAC AAA AAC CAT AAG ATC GCC AAA AAG GTG TTA CAG ATC TTC GAC AAT CAG TTC CCG ATC TTT AAC TAT AAA TAT TCA AAA TCC AAT GACATC GGG AAT TTA GAT ACG ATC GTA AGT ACG TAC AGC AAA ATT GCA GAT TAT AAC CCT GTT TCG CTT AAT GGT CAA CAT CTG GAG AAC AAA ACG TCA TACGAC GGT ATC GGG CAG GGT GTG ATC CAA ACG ATC ACA CCG ATC CAA ATC ACC AAA CAG ATC CTG GAC CAA ATT TCG AAC CTG GTT ATG TTG GCC CTT GTGTTA GCA ATC ATC ACC ATT CTT ATG ATC GCA TTT GTA ATT ATC TTA TTA ACC ACA AGC TTA ATC ATT TCG GAC AAC ACT CGT TTT ATC GCT ACA CTG AAGGTC CTT GGC TAC TCT AAC AAG TAT ATC ACT GAG AAT ATT CTT GGA ATG TAC TTC ATC GTG ATT GCC AAT ATG TTA GTT ATC GGC TTC GTT TCT GGG TGGTTC ATC TTC GAT TCT ACG ATC AAA TCG TTA TAC TCG ATC ATT GTA CTG CCT ATC ATC TTC CCG ATT TGG CTT CCA TTT GCC GTT ATC TTG GCG GTG AGCGGT ATT TAT TTG ATC ACC TTA ATT GTA GGT TTT AAC TCG ATT TAT AAG ACC GAT GCC ACT CTT ACC TTA AAG GAT AAC GAT GTG


  • Amino Acid length: 1381 amino acids.
  • Amino Acid sequence:

MKTKNKKNKWLGLILKNSLKNSFKYKSQLFGLVLLVMIMSLIMSLISAINSRVLDKYDDLITNSNQHNLVLKLDPYENVSTSLITSNNQIQAQQQFINRLNEKLYSRYNFKFDWSRTESREFKQVKSLNNLQTLKAVSKQYLTDNKVDQLVIVKGRNINSNKEVLIDPIYAKKHNIKINDIIRFQKDVLGDQLLVNSLENKTTTKQQFEDINKITKQGLTDNNGIYQIKYASSFDWYQVVGFANSADFIFPTINAYSPIPNRLNEGIIYVDPLRFGLIKQTDGFYKYDSTSSKLVVSSNNEWESFYSLKTKQKLSDEIVDWMNQYFSQLINKKAQDKWIYKLEDPNYRFNSRTSVIKKTISAYNIYSFIVLLAVISVVLYTTFLITKKQILNSRGQIGTMRAIGYKKRQMVLNYVMMPFFTSIVGGILGYILSCLISIIIINRFSNYFSLDYGVFSFDWIGLLNNLIFMWLIISSISFLIGYLIMKKGAINLLENRNAKKISKLGSLIKSLSNKRKFNHRLRAALLVNSGSKLTGVGFVVLIATILFTISFVSPNLLKNNKIYAYNGVKYNQIVEYSQPTYNNPFSFIRVFNPDKKSDDKYNIIKNNNRYLATSLPTKNNQYDLQTIINDYLNQTYNNAYYSLAIDLQDKQEVQAINLALSNMKLLQAQDIALTKQYFKYISSLSITPSSIHHILLKNWPDYDNLINKLKEIKENEFETLLNQFKYLQQFYATYTNSIGLAINRSYINSFDLKDKKDLRIQKFNNNSSDQNNLKTKAYDDILNSDLLALSKSSFSAKDFKNKIIDQFKLTNSDSSLGMYHILDNKWNKSNSISDQFLDISAFDFINKKYKLDDLKDLVIKLSLWFSVMFYKRDDQALIQAAYSRAPYFVKQNLKISYNSNKDYTLGFNLTTFNKNYEQLGTLLNVKTLDNKHTFKIYGILNNHDYIDLYDQNKTDLIKKLFDSEQNSIIINQTIAKRLNLKPNDKISLNVLQNELQHIKNNKTTIFKTSDWSMKQDTSYDSFIQRSDISTNNLKVKTNNSVLELNNGFSDVNSYYQSYLNNELKLGTKIQNKTFKIVGIHDGYNENMAWIKESDAQEILNYKQNKSIWWKDIFAPQWNKTFSSIQAKQVLNDTLDLNNKSLTDYSYEQFVNEFINNKNHKNHKIAKKVLQIFDNQFPIFNYKYSKSNDIGNLDTIVSTYSKIADYNPVSLNGQHLENKTSYDGIGQGVIQTITPIQITKQILDQISNLVMLALVLAIITILMIAFVIILLTTSLIISDNTRFIATLKVLGYSNKYITENILGMYFIVIANMLVIGFVSGWFIFDSTIKSLYSIIVLPIIFPIWLPFAVILAVSGIYLITLIVGFNSIYKTDATLTLKDNDV

Function and Homologs

  • Product: Efflux ABC transporter permease
  • Module: ATP-binding cassette (ABC) transporter
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • ABC transporter permease [Mycoplasma mycoides], 2732 / 100% / 0.0 / 100%, WP_023905968.1
    • efflux ABC transporter, permease protein [Mycoplasma mycoides subsp. capri str. GM12], 2731 / 100% / 0.0 / 100% ACU78569.1
  • Equivalent E. coli / JCVI functional protein: EG12386

Expression

  • Expression Level: low
    • Expression Level Hypothesis: I hypothesize that the protein's expression level is low because it uses active transport to remove excess waste and can thus be reused.
    • Expression Level References and Description: To determine the protein expression le9vel, I looked at the expression level for the close relative MMSYN1_0531, another efflux ABC transporter permease. It also had pertinent information regarding the expression level hypothesis which I then later corroborated with Boundless Microbiology. The gene sheet was linked in the M.Genitalium dataset, found at File:MgenitaliumSimProteinCounts.xlsx.
  • Expression Time: late
    • Expression Level Hypothesis: Since this protein is responsible for removing waste, I hypothesize that it is expressed later in a cell life cycle, after the cell has accumulated waste.
    • Expression Time References and Description: Again, I looked at the expression time for the close relative MMSYN1_0531 which was linked in the "M.Genitalium" dataset.

Gene Context

  • Other Components in the functional module: ybbA. According to the e.coli gene specification sheet, ybbA is the ATP binding component and ybbB is the membrane component.
  • Possible Dependencies: ATP
  • Process: Metabolite uptake transport
    • Inputs: ATP, molecule/substrate being transported
    • Outputs: ADP, phosphate, same molecule/substrate that has now been transported to other side of the membrane

Construct

We will handle this - not part of your assignment

  • Synthesis Score: The synthesis score: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file
  • https://en.wikipedia.org/wiki/ATP-binding_cassette_transporter
  • https://en.wikipedia.org/wiki/Permease
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