Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate H281DRAFT_03231 H281DRAFT_03231 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= TCDB::O30832 (290 letters) >FitnessBrowser__Burk376:H281DRAFT_03231 Length = 321 Score = 117 bits (292), Expect = 4e-31 Identities = 87/287 (30%), Positives = 146/287 (50%), Gaps = 9/287 (3%) Query: 4 QHSKTAARLMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMESFTGWDNYYYFLTDP 63 + + AA L ++PA +++ +++I P+ T+ SF ++ + +F G NY Sbjct: 42 RRQRRAAFLFLAPACVMVAIYVIWPILSTIRLSFFNWDGMTE--PTFVGLANYTELFHTQ 99 Query: 64 AFSAALTNTILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVW 123 F AL N ++ ++ LL +G + +AL L+Q G IV+ L APF + V L++ Sbjct: 100 TFYTALKNNLIWLLLFLLAPPMG-LAVALYLNQAVAGIRIVKSLFFAPFVLSGVVVGLIF 158 Query: 124 KNMFMNPVNGMFAHIARGLGLPPFDFLSQAPLASIIGIVAWQWLPFATLILLTALQSLDR 183 + F +P G+ A I G G+P A L I+ W + ++ LT L SL+ Sbjct: 159 -SWFYDPTFGLLAVIL-GHGVPVLGDPRYATLG-IVFAALWPQTAYCMILYLTGLTSLNA 215 Query: 184 EQMEAAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTAST 243 EQ+EAA M+GA H+ +P L + +++ I L F I V T GGP +ST Sbjct: 216 EQIEAARMEGARGWSMLWHVILPQLRPTTFMAIVVTIIGALRSFDLISVMTGGGPFESST 275 Query: 244 NITYLVYAQSLLNYDVGGGSAGGIVAVVLANIVAIFLMRMIGKNLDA 290 + Y +Y Q++ Y +G +A VAVVL I+ ++++ + + L A Sbjct: 276 VLAYYMYDQAIKYYRIGYSAA---VAVVLFGIMLVYIVYHLRRMLRA 319 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: 226 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: 321 Length adjustment: 27 Effective length of query: 263 Effective length of database: 294 Effective search space: 77322 Effective search space used: 77322 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