Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate WP_011384270.1 AMB_RS09430 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >NCBI__GCF_000009985.1:WP_011384270.1 Length = 262 Score = 105 bits (263), Expect = 8e-28 Identities = 65/203 (32%), Positives = 111/203 (54%), Gaps = 18/203 (8%) Query: 26 VKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRESLV 85 ++++ EV+ + ++LVG+SG+GK+T ++I L+P G++Y E K+ +S Sbjct: 31 LQDLDLEVRHGDFIALVGQSGAGKSTLLRVIAGLVPAVLGQVYVEPP------KEPDS-- 82 Query: 86 EFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRVGIDPK 145 R++ VFQD P R L LE ++ E +L VG+ Sbjct: 83 ---RQIGMVFQDA-----RLLPWRRVLANVEYGLEGLVKSRHERRRRALAALDLVGLT-- 132 Query: 146 DVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELREEQG 205 + ++PH +SGGQ+QR+ +AR +RP L++ DEP +D ++R G+ L + + G Sbjct: 133 EFADRWPHHLSGGQRQRVGLARALAVRPALLLMDEPFGALDPATRHGLQDQLLSIWQATG 192 Query: 206 TSIIFITHDLGLAYYVSDNIFVM 228 TSIIF+THD+ A Y++D + V+ Sbjct: 193 TSIIFVTHDIDEATYLADRVIVL 215 Lambda K H 0.319 0.139 0.397 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: 179 Number of extensions: 9 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: 268 Length of database: 262 Length adjustment: 25 Effective length of query: 243 Effective length of database: 237 Effective search space: 57591 Effective search space used: 57591 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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