Align D-mannose and D-mannitol transporter (characterized)
to candidate BPHYT_RS21780 BPHYT_RS21780 MFS transporter
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__BFirm:BPHYT_RS21780 Length = 460 Score = 213 bits (543), Expect = 8e-60 Identities = 129/401 (32%), Positives = 208/401 (51%), Gaps = 18/401 (4%) Query: 6 RSLIIIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGW 65 R +I+ ++ L I+Y+DR ++VA P I+ + GL+T ++G++FS+F YAA IGGW Sbjct: 11 RHIILAVMCLMYFISYIDRVNIAVAGPLIRHEMGLTTVQLGLVFSAFAYPYAAMQIIGGW 70 Query: 66 AADRYGAKTTLLLAMVLWSLFSGLTVLTVGFAS----LVLIRILFGMGEGPLSVTTSKMV 121 AD+YG K L + ++W G+ L GFA LV++R G+GEG T ++ Sbjct: 71 LADKYGPKLVLTVLSLIW----GVATLATGFAGSVTMLVVMRFALGIGEGGAFPTATRAF 126 Query: 122 NNWYTPKRRARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFK 181 W R A G + S LGGAI+ P+V + T GW+ +FI++ + L W ++ Sbjct: 127 TYWMPVAERGFAQGITHSFARLGGAITPPLVLAVVATGGWRDAFILLGIASLAWTVLYLF 186 Query: 182 FVKERPE------GEGAEDILRAEGQGELAAQPVFPLRFYLKQPTVLFTSLAFFSYNYTL 235 PE E +I G + A P R +++ + + F Y + L Sbjct: 187 VFTNSPEQNRRITPEETAEIGYRAGDCDRAKHAATPWRKLVRR--MWLVTFVDFCYGWLL 244 Query: 236 FFFLTWFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKV 295 + +LTW PSYL + G ++K +++ T +P + G +G LGG +SD ++K TGR+ F+R Sbjct: 245 WVYLTWLPSYLRESRGFDLKQLALFTALPLLAGVIGDTLGGVVSDKLYKITGRLRFARCT 304 Query: 296 VLVTCLLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVS 355 VLV + V + T AV ++ + FFL +T + W + D + G Sbjct: 305 VLVVGMGGSLVFLLPMVSATNPLTAVWFLSASFFFLEITNPVLWTLPLD-IAGKYAGTAG 363 Query: 356 GFMHFLANTSGIVGPTLTGFLVQFTGSFTSAF-LLAGLLTV 395 G M+ +G+V P + G+L++ TGS+ F + AGLL V Sbjct: 364 GMMNTGFGVAGMVSPVVFGYLIEKTGSYNVPFNISAGLLAV 404 Lambda K H 0.329 0.142 0.439 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: 600 Number of extensions: 35 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: 430 Length of database: 460 Length adjustment: 32 Effective length of query: 398 Effective length of database: 428 Effective search space: 170344 Effective search space used: 170344 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: 51 (24.3 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