MMSYN1 0531

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Author Information

Feddi Roth

Basic Information

  • ID: MMSYN1 0531
  • Name: efflux ABC transporter permease
  • Organism: JCVI-Syn3.0
  • Description: This gene is involved in efflux, which is the mechanism through which cells remove substances such as toxins or waste [1]. Efflux uses pumps out these compounds through active transport [2]. ABC transporters, or ATP-binding cassette transporters, are transmembrane proteins that use ATP to move substances across cell membranes [3]. Permeases are transmembrane proteins that use a proton gradient to diffuse molecules out of the cell [4].
  • DNA Length: 3,384 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 1,482 amino acids.
  • Amino Acid sequence:

MRHIIKSYLKTFFKKNYVSTFGILLFIITLATVIIGMLATPLQLNNRINYLAKHNTSYNSILDTRSMNYDPKFTYNYFYLNKEINNKDTNYTKLSELYIKAINSELEQNFTNTSTDKKENNLYIYDSNNLEDRVKIDFIGNLINSDLFRYRNGALIKTESYIFNKDYNNDQNNLNSFSNISNQVLNRIISDFHQSMSDGISLDNNAKYDYVVSEFYKAYSRFNSFLTINEINLIDKPILTFKFTEILNKLNDNKIDEITKFLVKQLQDLKNKIKNHQKERIYLPSFLVFSDKFSKVLANEKFLYDDRIYIVDQLLDNVENFVLQTKKTFKIQQSSVGQLLPFLTLQLTSDNQIFKNTNKDFNQIQFDKNHKNSEFAKKWDVNINYQQKVNPTQIVISSSYAKARNLKINDEFIIPSSNISDIYLSLINKKDAYYLGSINSKIVGIGSTFDDIVSKNSATDYFQDKTSYVVGYTSKEFINSIRNSRWNFSNKFDTSYQVNFRVKNLNNSTSKDLNKHFIIKFDNWSDESYSVFDKSSSLITEWYSLRTSQAISSIKVQVIIYIVIGIFVLLLSFVFINFALKKEMNETRRQIGIFKSFGYKVVELSWIFALKTWLTMFFGLIIGYILSIPIQIYSSSNFVNSVTFTFNSIYISPLLIIFLIIIIPFIFLMGSYWASIIYIKEPVLSLMNNLKKSKRTKSGAITNLLSKHNIGFNYRMRLSFIKNAKGKFAVVQILFGFASLTYTLLFVAQAILFQSINQSLATIKQDVITKSMWNVNKKIDNTSTNDKLSYTNKNDPKTRQTLSYHDLNKKNINTYLNNDLKQTDIRYRVELFLKLLNNTFNSLSNEKKVSMILPLDYAKKTLTPFLQPGKTDKNDYEVLTKDNQYYLSYISRFNLYNQNQKWQSALNDFKNNKEIKLTLNDLSQKQHSSDLFYDLNHPKKDELQNTIIGLQSTRNNSNNTLFLSSFAKIFSYKLVQAYSLFQVVNHYKQFNNDINKAWMHLQKDNDLLSFNPDDQKYWTIANNPLLEKIINKNLKNKPNKDKKELFDTTSNFSIDSLLNSTNLSNASQSILLASMIMQDLNNKLENNPIVSFNQMFYDSSTDLLSAVIRVSNSDILNPGSYALNLYRLKDHNFGDVNQFLNFKGVSIKGFQDLSKLPEKHNNLPTFNVIVPYYYAKSKNLDINSKIVVETRTTFVKKFVLNVVGINKSETLSISKTPDIFLDYDLFANEMFSEDLYKNNNPLIFNQLWSKNKILEGTINFTKLDDSFKTIKYYGNNLAIDIRKDAPIFLSMYSNIFNEFNNFISKYQELDQQNDIYNTPNPAITTLSRLNSKLFNFNLVKQTISKITTITNQVMLLFILLVSLLLTIILVVVMNIVVDESKKTILTLRAIGYENSEVNWIVMGSYIIGAIISFIIAYLLSNLIWWSFLYYVSYKWHIYIFLAFDFKTLFVTFSVIAFVLFIGWLFSDKQVKKTAITQVTQAE

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.
    • ftsX-like permease [Mycoplasma feriruminatoris], 2395/100%/0.0/84%, WP_008362873
    • ABC transporter permease [Mycoplasma capricolum], 2361/100%/0.0/83%, WP_046784015
    • ABC transporter permease [Mycoplasma leachii], 2336/100%/0.0/82%, WP_013447695
  • Equivalent E. coli / JCVI functional protein: EG13263. The most similar E. Coli gene found so far is microcin J25 efflux ABC transporter permease/ATPase [Escherichia coli str. K-12 substr. MG1655] 20.0/16%/0.7/23% NP_416715. This protein was not available on any of the given databases but a similar one, ybbP, with slightly more information was found on EcoSyc and when compared with MMSYN1 0531, a similar but slightly lower alignment was found 18.1/13%/3.7/25% and it is this gene for which I wrote the equivalent homolog page linked above. When intitially researching for an equivalent E. Coli gene, no results were found using Blast, EcoCyc, and the other databases provided. However when researching for a gene with a similar function in E. Coli, I found the genes above. While both proteins are not a great match when their amino acids were aligned with MMSYN1 0531 using BLAST, they seem to have similar functions to those of MMSYN1 0531.

Expression

  • Expression Level: low
    • Expression Level Hypothesis: I hypothesize that the expression level for this protein would be low because since this protein uses active transport to remove waste or toxins from the cell, it can be reused and some cell waste can also be broken down within the cell by the lysosome, so only a few are necessary to remove excess waste from the cell.
    • Expression Level References and Description: I gathered expression data using the homolog E. Coli protein from the "quantitative proteome" of E. coli reported by Schmidt et al in 2015 at File:EcoliProteomicExpressionData.xlsx and information about similar proteins found in the whole cell model Mycoplasma genitalium created by a group at Stanford using File:MgenitaliumSimProteinCounts.xlsx. The E.Coli homolog EG13263 was reported to have a low expression level. Additionally, similar proteins with low expression levels from the mycoplasma genitalium cell model spreadsheet spreadsheet are multidrug ABC transporter, ATP-binding/permease protein and toxin ABC transporter, ATP-binding/permease protein, and multidrug ABC transporter, ATP-binding/permease protein indicaing that it is likely that the expression level for this protein is low.
  • Expression Time: late
    • Expression Time Hypothesis: A trans-membrane efflux protein will only be necessary when the cell begins to produce waste which will be later in its life cycle thus I would infer that this gene would be expressed earlier rather than later.
    • Expression Time References and Description: The expression time was inferred (see hypothesis above) but no resources were found and thus I am unsure about my choice of expression time.

Gene Context

  • Other Components: ybbA,according to information from the E.coli homolog, ybbA is the putative ATP-binding component while ybbP is the putative membrane component[5]
  • Possible Dependencies: ATP
  • Process: metabolite uptake transport
    • Inputs: ATP, molecule being transported
    • Outputs: ADP, phosphate, molecule being transported (now on the other side of the membrane)

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
  • https://en.wikipedia.org/wiki/Efflux_(microbiology)
  • https://en.wikipedia.org/wiki/Efflux_(microbiology)
  • https://en.wikipedia.org/wiki/ATP-binding_cassette_transporter
  • https://en.wikipedia.org/wiki/Permease
  • https://ecocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=ABC-61-CPLX
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