Align CBP protein aka CebG, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate SM_b20969 SM_b20969 sugar uptake ABC transporter permease
Query= TCDB::Q9X9R5 (276 letters) >FitnessBrowser__Smeli:SM_b20969 Length = 270 Score = 166 bits (421), Expect = 4e-46 Identities = 96/267 (35%), Positives = 148/267 (55%), Gaps = 3/267 (1%) Query: 12 VTYVVLTVFALVSLAPLVWTAIAASRTNHRLAETPPPLWFGGNLFKNLEAAWEQAGLGTA 71 V Y L + + + +AP WT + A ++ L PP LW ++N AAW + GT Sbjct: 5 VLYATLILLSALFIAPFYWTFMTAVKSTAELYRFPPVLWPSEWHWENFAAAWSKQPFGTY 64 Query: 72 MLNSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQLAVVPLYLWM 131 + NS+IV T+ +L S+L F FA+ RF L +L + TMMIP + ++PLY+ Sbjct: 65 LSNSLIVVVLSTIGQLLSSSLVAFGFARFRFPGRDALFVLLLATMMIPWDVKMIPLYMEF 124 Query: 132 SDLGWSNQLHTVILPS-LVTAFGTFFMRQYLVQALPTELIEAARVDGASSLRIVWHVVFP 190 + LGW N L +I+P+ AF F +RQY++ +P E+ EAAR+DGA+S I W + P Sbjct: 125 NMLGWINTLKPLIVPAYFADAFFVFLLRQYIM-TIPMEIDEAARMDGANSFDIYWRIHLP 183 Query: 191 AARPAMAVLGLLTFVFAWNDFLWPIIALNQQNP-TVQVGPELARHRVLPDQAVIMAGALL 249 PA+ ++G F+ AWND+L P+I LN Q+ T+ +G + + D I A ++ Sbjct: 184 LMLPALVLVGTFHFMNAWNDYLGPLIFLNDQSKYTLTLGLSMFKGLHEIDVTSIAAITVI 243 Query: 250 GTLPLLVAFLLFGKQIVGGIMQGAIKG 276 LP L F L + I+ G + ++KG Sbjct: 244 LCLPPLALFFLAQRYIMDGAVGSSVKG 270 Lambda K H 0.327 0.140 0.434 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: 231 Number of extensions: 11 Number of successful extensions: 1 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: 276 Length of database: 270 Length adjustment: 25 Effective length of query: 251 Effective length of database: 245 Effective search space: 61495 Effective search space used: 61495 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 (21.7 bits) S2: 47 (22.7 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