Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__WCS417:GFF2365 Length = 325 Score = 215 bits (548), Expect = 1e-60 Identities = 108/303 (35%), Positives = 184/303 (60%) Query: 23 DQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVA 82 D++G+ +VF +L + A F T+ N + S++G++A GM + + + DLSV Sbjct: 23 DRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVG 82 Query: 83 SVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIV 142 S++A AG+ +A+V L V+AG+ G + G+VNGF++A L I + TL + I Sbjct: 83 SILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIA 142 Query: 143 RGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLA 202 RG+ +I++DG + +++ ALG + PI + +IF ++L TT+GR A Sbjct: 143 RGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYA 202 Query: 203 IGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISAC 262 +GGNE++AR +G+ V + ++V+SGL++ +AG++L++R TS P + YEL I+A Sbjct: 203 VGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAV 262 Query: 263 VLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQ 322 V+GG SL GG G I + G L++G + N +NLL +S + Q V +GLI++ AV+ D +++ Sbjct: 263 VIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRK 322 Query: 323 KAK 325 K + Sbjct: 323 KKR 325 Lambda K H 0.327 0.141 0.414 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 361 Number of extensions: 27 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 328 Length of database: 325 Length adjustment: 28 Effective length of query: 300 Effective length of database: 297 Effective search space: 89100 Effective search space used: 89100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory