Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate H281DRAFT_05891 H281DRAFT_05891 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= reanno::Dino:3607126 (288 letters) >FitnessBrowser__Burk376:H281DRAFT_05891 Length = 318 Score = 160 bits (405), Expect = 3e-44 Identities = 98/291 (33%), Positives = 154/291 (52%), Gaps = 13/291 (4%) Query: 1 MSGQVPRKTVFAFIGPAVIGLALVGIAPLLYALWTSL-HFYNLTKLRRVEFIGLENYWTV 59 ++G R + FI P ++ L + I PL++AL S +F + F+G++NY + Sbjct: 24 LTGLSDRTIAWLFILPTILLLLAINIFPLIWALRLSFTNFKSNMPSVPARFVGIDNYVDI 83 Query: 60 LTDEVFWQAMGRTFFLLGTALPLQIALGLGIALVLHQP--GLTLVKTLARLSLVLPMATT 117 LTDE W AM T + ++ L++ LG G+AL++++ G + TL ++LPM + Sbjct: 84 LTDEDIWYAMQVTARFVFWSVGLEVLLGFGLALLINRQFRGHSFWTTL----ILLPMMLS 139 Query: 118 YAVVGLLGQVMFNQKFGVVNQLLG------GADINWIGDPENAFAMIIFWDVWQWTPFVA 171 AVVG + + G+ N ++G IGD A I+ D W WTP+V Sbjct: 140 PAVVGNFWTFLLQPQTGLFNDIVGFFTGIAPGSFQMIGDVSLAPWTIVMVDTWMWTPYVM 199 Query: 172 LVLLAGLTMVPGEVEEAARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVF 231 L+ LAGL +P + EAA ++ + W + LP LP L+ ++ R + K+FDMV Sbjct: 200 LICLAGLRSIPDYIYEAAEVDRATPWRQFWSITLPMTLPFLMLAVLFRGIENFKMFDMVN 259 Query: 232 TLTRGGPGSSTEFISLMIQRVGFRGFDQGLASAQAIILLIITIVLAQIYIR 282 LT GGPGS TE +S+ ++R F + G +SA AIIL + A IY++ Sbjct: 260 LLTSGGPGSVTETVSITLKRAAFEKWQTGYSSALAIILFVTVFGAANIYVK 310 Lambda K H 0.329 0.144 0.440 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: 304 Number of extensions: 14 Number of successful extensions: 3 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: 288 Length of database: 318 Length adjustment: 27 Effective length of query: 261 Effective length of database: 291 Effective search space: 75951 Effective search space used: 75951 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