Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 15431 b1311 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= TCDB::O30832 (290 letters) >FitnessBrowser__Keio:15431 Length = 293 Score = 107 bits (268), Expect = 2e-28 Identities = 83/289 (28%), Positives = 142/289 (49%), Gaps = 23/289 (7%) Query: 10 ARLMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMES-FTGWDNYYYFLTDPAFSAA 68 A L+++P+++LL + P+ + SFLR L P +ES F G NY L+DP F + Sbjct: 14 ALLLLAPSLLLLGGLVAWPMVSNIEISFLRLPL-NPNIESTFVGVSNYVRILSDPGFWHS 72 Query: 69 LTNTILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSAL-VWKNMF 127 L T+ V+ + V G+ +A+ ++ F + R LVI + V P++S + WK MF Sbjct: 73 LWMTVWYTALVVAGSTVLGLAVAMFFNREFRLRKTARSLVILSY-VTPSISLVFAWKYMF 131 Query: 128 MNPVNGMFAHIARGLGLPPFDFLSQAPL---------ASIIGIVAWQWLPFATLILLTAL 178 N I LG+ QAPL ++ W++ P+A + L L Sbjct: 132 NNGYG-----IVNYLGVDLLHLYEQAPLWFDNPGSSFVLVVLFAIWRYFPYAFISFLAIL 186 Query: 179 QSLDREQMEAAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGP 238 Q++D+ EAAEMDGA+A RF +T+P + + VV ++TI++ +FA++ + T Sbjct: 187 QTIDKSLYEAAEMDGANAWQRFRIVTLPAIMPVLATVVTLRTIWMFYMFADVYLLT---- 242 Query: 239 GTASTNITYLVYAQSLLNYDVGGGSAGGIVAVVLANIVAIFLMRMIGKN 287 T + +Y + D+G +A +V ++ V + + + N Sbjct: 243 -TKVDILGVYLYKTAFAFNDLGKAAAISVVLFIIIFAVILLTRKRVNLN 290 Lambda K H 0.329 0.142 0.429 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: 15 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: 290 Length of database: 293 Length adjustment: 26 Effective length of query: 264 Effective length of database: 267 Effective search space: 70488 Effective search space used: 70488 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