Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate BPHYT_RS27970 BPHYT_RS27970 sugar ABC transporter permease
Query= uniprot:Q6MNM1 (272 letters) >FitnessBrowser__BFirm:BPHYT_RS27970 Length = 317 Score = 129 bits (325), Expect = 6e-35 Identities = 65/204 (31%), Positives = 115/204 (56%), Gaps = 1/204 (0%) Query: 68 NSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLPFYIILSK 127 NSLV+ +T L V L + +AYA +R++ + +LF +L T+M P + +P Y++ Sbjct: 114 NSLVIGFGSTFLAVFLGTLAAYAFSRFKVPLADDLLFFILSTRMMPPIAVAIPIYLMYRA 173 Query: 128 LRLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMIFYKIILPVS 187 L L DS G+ ++Y++ + +W +K + D IPRE EEAAL+DG ++ F K++LP + Sbjct: 174 LGLSDSCVGMIVLYTAVNVSLAVWLLKGFMDEIPREYEEAALVDGYTRLQAFVKVVLPQA 233 Query: 188 SPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSFQASLATQWGLYAAGALIVS 247 + TA+F + +W+EY A+ +L T+P + W AA + Sbjct: 234 ITGIAATAIFCLIFAWNEYAFAS-LLTSGDAQTMPPFIPFIIGEGGQDWPAVAAATTLFV 292 Query: 248 VPVLILFISISRYLVSGLTMGSVK 271 +P+LI + + ++L+ G+T G+V+ Sbjct: 293 LPILIFTVVLRKHLLRGITFGAVR 316 Lambda K H 0.329 0.139 0.421 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: 232 Number of extensions: 11 Number of successful extensions: 2 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: 272 Length of database: 317 Length adjustment: 26 Effective length of query: 246 Effective length of database: 291 Effective search space: 71586 Effective search space used: 71586 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 (21.8 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