Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate SMc03063 SMc03063 alpha-glucoside ABC transporter permease
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__Smeli:SMc03063 Length = 380 Score = 741 bits (1914), Expect = 0.0 Identities = 380/380 (100%), Positives = 380/380 (100%) Query: 1 MNPSRRSPLTWAVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSRNAVV 60 MNPSRRSPLTWAVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSRNAVV Sbjct: 1 MNPSRRSPLTWAVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSRNAVV 60 Query: 61 RAPSAEDQVERDGKFVISGNLLEGRGEVSAFGFSSREPTKFKPGETAELNDGERLTVQSD 120 RAPSAEDQVERDGKFVISGNLLEGRGEVSAFGFSSREPTKFKPGETAELNDGERLTVQSD Sbjct: 61 RAPSAEDQVERDGKFVISGNLLEGRGEVSAFGFSSREPTKFKPGETAELNDGERLTVQSD 120 Query: 121 GSFEIVSDQRMEGSRGQRIFFTATTPPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVI 180 GSFEIVSDQRMEGSRGQRIFFTATTPPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVI Sbjct: 121 GSFEIVSDQRMEGSRGQRIFFTATTPPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVI 180 Query: 181 PILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTY 240 PILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTY Sbjct: 181 PILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTY 240 Query: 241 MGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPALASF 300 MGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPALASF Sbjct: 241 MGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPALASF 300 Query: 301 AIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIV 360 AIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIV Sbjct: 301 AIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIV 360 Query: 361 FFALQRYLVRGLLAGSVKGG 380 FFALQRYLVRGLLAGSVKGG Sbjct: 361 FFALQRYLVRGLLAGSVKGG 380 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: 627 Number of extensions: 17 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: 380 Length of database: 380 Length adjustment: 30 Effective length of query: 350 Effective length of database: 350 Effective search space: 122500 Effective search space used: 122500 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: 50 (23.9 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