Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate Pf6N2E2_1648 Maltose/maltodextrin ABC transporter, permease protein MalG
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1648 Length = 280 Score = 119 bits (299), Expect = 8e-32 Identities = 74/228 (32%), Positives = 123/228 (53%), Gaps = 6/228 (2%) Query: 153 NYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLV 212 NYA VL A R+ NSL VA+ + +L++ AAYAL + F GR V+L +V+G+ + Sbjct: 58 NYAAVLGQASFLRAIGNSLVVALCVVALALLLSLTAAYALGRVKFRGRGVVLMMVLGVSM 117 Query: 213 VPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIME 272 P L L ++ +G + T + L++T F LP +++L +M LP E+ E Sbjct: 118 FPQVAVLSGLFEVIRALGLY-----NTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEE 172 Query: 273 SARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLV-LTGR 331 +A +DGAS + +++LPL +PAL + + F+ WN+ L A+ F + V + Sbjct: 173 AAIMDGASPWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDSQRTVPVAIA 232 Query: 332 LVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379 L++ W +L A++ + V +I+ QR +V GL AG++KG Sbjct: 233 LISGGSPHELPWGLLMAASVLVTVPLVILVLIFQRRIVSGLTAGALKG 280 Lambda K H 0.324 0.139 0.418 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: 220 Number of extensions: 8 Number of successful extensions: 3 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: 380 Length of database: 280 Length adjustment: 28 Effective length of query: 352 Effective length of database: 252 Effective search space: 88704 Effective search space used: 88704 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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