Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate BPHYT_RS22775 BPHYT_RS22775 sugar ABC transporter permease
Query= TCDB::O30832 (290 letters) >FitnessBrowser__BFirm:BPHYT_RS22775 Length = 325 Score = 115 bits (289), Expect = 1e-30 Identities = 88/289 (30%), Positives = 146/289 (50%), Gaps = 13/289 (4%) Query: 4 QHSKTAARLMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGME--SFTGWDNYYYFLT 61 + + AA L ++PA +++ ++++ P+ T+ SF ++ GM SF G NY Sbjct: 46 RRQRRAAFLFLAPACVMVAIYVVWPILSTIRLSFFNWD----GMSEPSFVGLANYVELFH 101 Query: 62 DPAFSAALTNTILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSAL 121 F AL N ++ ++ LL +G + +AL L+Q G IV+ L APF + V L Sbjct: 102 AQTFYTALKNNLIWLLLFLLAPPMG-LAVALYLNQAVAGIRIVKSLFFAPFVLSGVVVGL 160 Query: 122 VWKNMFMNPVNGMFAHIARGLGLPPFDFLSQAPLASIIGIVAWQWLPFATLILLTALQSL 181 ++ + F +P G+ A I G G+P A I+ W + ++ LT L SL Sbjct: 161 IF-SWFYDPTFGLLAVIL-GHGVPVLGDPRYATFG-IVFAALWPQTAYCMILYLTGLTSL 217 Query: 182 DREQMEAAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTA 241 + EQ+EAA M+GA H+ +P L + +++ I L F I V T GGP + Sbjct: 218 NAEQIEAARMEGARGWSMLWHVILPQLRPTTFMAIVVTIIGALRSFDLISVMTGGGPFES 277 Query: 242 STNITYLVYAQSLLNYDVGGGSAGGIVAVVLANIVAIFLMRMIGKNLDA 290 ST + Y +Y Q++ Y +G +A VAVVL I+ ++++ + + L A Sbjct: 278 STVLAYYMYDQAIKYYRIGYSAA---VAVVLFAIMLVYIVYHLRRMLRA 323 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: 234 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: 290 Length of database: 325 Length adjustment: 27 Effective length of query: 263 Effective length of database: 298 Effective search space: 78374 Effective search space used: 78374 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