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 WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease
Query= TCDB::Q9X9R5 (276 letters) >NCBI__GCF_003217355.1:WP_110804034.1 Length = 382 Score = 105 bits (263), Expect = 1e-27 Identities = 74/239 (30%), Positives = 118/239 (49%), Gaps = 19/239 (7%) Query: 47 PPLWFGGNLFKNLEAAWEQAGLGTAMLNSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSG 106 PP GN + + A G+G A LN++ V TV +L + A +A A +RF Sbjct: 153 PPRLTTGNYARVITAE----GIGRAFLNTMTVTIPATVIPILIAAFAAYALAWMRFPGRA 208 Query: 107 LLLLLTIGTMMIPPQLAVVPLYLWMSDLGWSNQLHTVILPSLVTAFGT----FFMRQYLV 162 LL+ +G +++P QLA++PL + +G + + L T FG + +R Y+V Sbjct: 209 LLVATIVGLLVVPLQLALIPLLKLHNQIGLNQSYLGIWLAH--TGFGLPLAIYLLRNYMV 266 Query: 163 QALPTELIEAARVDGASSLRIVWHVVFPAARPAMAVLGLLTFVFAWNDFLWPIIALNQQN 222 LP E+IE+ARVDGA+ +I +V P + PA+A + F++ WND L + L Sbjct: 267 -GLPREIIESARVDGATEFQIFRRIVLPLSFPALASFAIFQFLWVWNDLLVATVFLGNAT 325 Query: 223 PTVQVGPELARHRVL-----PDQAVIMAGALLGTLPLLVAFLLFGKQIVGGIMQGAIKG 276 T + L R L D ++ A A + L+ F K +V G++ G++KG Sbjct: 326 DTQVMTGAL---RALLGSRGGDWEILAASAFVSIAVPLIVFFALQKYLVRGLLAGSVKG 381 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: 313 Number of extensions: 15 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: 276 Length of database: 382 Length adjustment: 28 Effective length of query: 248 Effective length of database: 354 Effective search space: 87792 Effective search space used: 87792 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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