Align Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized)
to candidate BPHYT_RS33285 BPHYT_RS33285 sugar ABC transporter permease
Query= TCDB::Q9KZ08 (303 letters) >FitnessBrowser__BFirm:BPHYT_RS33285 Length = 269 Score = 140 bits (353), Expect = 3e-38 Identities = 84/259 (32%), Positives = 136/259 (52%), Gaps = 3/259 (1%) Query: 42 VLTLASLVALFPVAWLVYLSLGPDKNDYLHPGRIWSK-MTFDNYAFVLQDTNFFDWLKSS 100 VLT+ L AL P+ W++ +SL ++ + + IW +TFDNY + D +++ +S Sbjct: 11 VLTVYILFALIPLYWMLSISLRTNE-ETMSAFAIWPHHVTFDNYKVIFTDPSWYWGYINS 69 Query: 101 LIVSLGTTVIGVLVAATTGYAVSRMRFPGYRKLMWVLLVTQMFPIAVLIVPMYQILSKLQ 160 +I L TV+ VLVA YA SR RF G + + + LL +M P AV ++P +Q+ S + Sbjct: 70 IIYVLMNTVMSVLVALPAAYAFSRYRFLGDKHMFFWLLTNRMTPPAVFLLPFFQLYSSVG 129 Query: 161 LIDNYFGLILVYCSTAVPYCAWLLKGYFDTIPFEIDEAGRVDGLTPFGTFFRLILPLARP 220 L+D Y + L + VP W+L+G+ +P EIDE +DG T F ++ LPL + Sbjct: 130 LMDTYIAVALAHMLFNVPLAVWILEGFMSGVPREIDETAYIDGYTFPAFFIKIFLPLIKS 189 Query: 221 GLAVAGFYSFITAFGEVAFASTFMLSDTKYTFAVGLQSFVSEHDAQRNLMAATAVLVAIP 280 G+ V F+ F+ ++ E+ A T + K AV + VS +++A VL +P Sbjct: 190 GVGVTAFFCFMFSWVELLLARTLTTVNAKPIAAV-MTRTVSAAGMDWGVLSAAGVLTIVP 248 Query: 281 VSAFFYLVQKNLVTGLTAG 299 + Y V+ + G G Sbjct: 249 GALVIYFVRNYIAKGFAMG 267 Lambda K H 0.326 0.139 0.422 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: 257 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 303 Length of database: 269 Length adjustment: 26 Effective length of query: 277 Effective length of database: 243 Effective search space: 67311 Effective search space used: 67311 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 (21.6 bits) S2: 47 (22.7 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