Align CBP protein aka CebF, 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 15431 b1311 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= TCDB::Q9X9R6 (306 letters) >FitnessBrowser__Keio:15431 Length = 293 Score = 121 bits (303), Expect = 2e-32 Identities = 86/292 (29%), Positives = 141/292 (48%), Gaps = 27/292 (9%) Query: 19 PYAFV--APFFLLFGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYENLLSSDFFWN 76 P+A + AP LL G P++ S + L+ T+ G+ NY +LS FW+ Sbjct: 12 PFALLLLAPSLLLLGGLVAWPMVSNIEISFLRLPLNPNIESTFVGVSNYVRILSDPGFWH 71 Query: 77 ALKNTLTIGIISTVPQLLAALALAHLLNYKLRGSTAWRVVMLTPYATSVAAATLVFTLLY 136 +L T+ + + LA+A N + R R +++ Y T + +LVF Y Sbjct: 72 SLWMTVWYTALVVAGSTVLGLAVAMFFNREFRLRKTARSLVILSYVTP--SISLVFAWKY 129 Query: 137 SWDGGMVNWILDFFGVDPVN-------WRESDWGSQFAVSSIVIWRWTGYNALIYLAAMQ 189 ++ G I+++ GVD ++ W ++ S V IWR+ Y + +LA +Q Sbjct: 130 MFNNGY--GIVNYLGVDLLHLYEQAPLWFDNPGSSFVLVVLFAIWRYFPYAFISFLAILQ 187 Query: 190 AIPADLYESAALDGANRWQQFRHVTVPQLRPTILFTVVVSTIGATQLFGEPLLFGGVSGS 249 I LYE+A +DGAN WQ+FR VT+P + P + V + TI +F + L Sbjct: 188 TIDKSLYEAAEMDGANAWQRFRIVTLPAIMPVLATVVTLRTIWMFYMFADVYLL------ 241 Query: 250 KGGSEHQYQTLGLYMYDQGWIIGNLGKASAIAWSMFLILLIVAAVNLLLTRR 301 + LG+Y+Y + +LGKA+AI+ +F+I+ V +LLTR+ Sbjct: 242 ----TTKVDILGVYLYKTAFAFNDLGKAAAISVVLFIIIFAV----ILLTRK 285 Lambda K H 0.324 0.137 0.441 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: 275 Number of extensions: 20 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: 306 Length of database: 293 Length adjustment: 27 Effective length of query: 279 Effective length of database: 266 Effective search space: 74214 Effective search space used: 74214 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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