Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate H281DRAFT_05891 H281DRAFT_05891 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= reanno::Phaeo:GFF1304 (288 letters) >FitnessBrowser__Burk376:H281DRAFT_05891 Length = 318 Score = 109 bits (272), Expect = 9e-29 Identities = 85/292 (29%), Positives = 135/292 (46%), Gaps = 23/292 (7%) Query: 7 RSAARIMMAPAVILLLGWMLVPLTMTLYFSFKKY------LPLRGGDLGWVGFDNYARFL 60 R+ A + + P ++LLL + PL L SF + +P R +VG DNY L Sbjct: 30 RTIAWLFILPTILLLLAINIFPLIWALRLSFTNFKSNMPSVPAR-----FVGIDNYVDIL 84 Query: 61 SSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSA 120 + W ++Q T V + + V+LG LALL+N+ G L++ P + P V Sbjct: 85 TDEDIWYAMQVTARFVFWSVGLEVLLGFGLALLINRQFRGHSFWTTLILLPMMLSPAVVG 144 Query: 121 LVWKNMFMDPVNGLFAHLWKAF-GAEPVSW--LSEASLQ--SIILIVSWQWLPFATLILL 175 W + P GLF + F G P S+ + + SL +I+++ +W W P+ LI L Sbjct: 145 NFW-TFLLQPQTGLFNDIVGFFTGIAPGSFQMIGDVSLAPWTIVMVDTWMWTPYVMLICL 203 Query: 176 TAIQSLDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQ 235 ++S+ EAAE+D A P +F ITLP + + VL + I +F + + T Sbjct: 204 AGLRSIPDYIYEAAEVDRATPWRQFWSITLPMTLPFLMLAVLFRGIENFKMFDMVNLLTS 263 Query: 236 GSFG--TKTLTYLIYQRVLESQNVGLGSAGGVYAII----LANIVAIFLMRI 281 G G T+T++ + + E G SA + + ANI L R+ Sbjct: 264 GGPGSVTETVSITLKRAAFEKWQTGYSSALAIILFVTVFGAANIYVKALNRV 315 Lambda K H 0.328 0.140 0.430 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: 259 Number of extensions: 16 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: 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