Align BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized)
to candidate WP_013403450.1 CALHY_RS07950 methionine ABC transporter ATP-binding protein
Query= TCDB::Q9RQ06 (407 letters) >NCBI__GCF_000166355.1:WP_013403450.1 Length = 343 Score = 167 bits (423), Expect = 4e-46 Identities = 88/223 (39%), Positives = 141/223 (63%), Gaps = 1/223 (0%) Query: 46 DTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRR 105 + N I +G+IF I+G SG+GKSTL+R +N L +PT G I ID ++ L+ +L ++R+ Sbjct: 23 NVNLNIEKGDIFGIIGPSGAGKSTLIRCINMLEKPTHGSIEIDGVEMTKLSPTELKEMRK 82 Query: 106 KSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQL 165 K + ++FQ+F L RT+ N + LE+ + K+ R ++ L+ L + D YP QL Sbjct: 83 K-VGIIFQHFNLLSSRTVKGNVAFPLEIAGLDKKTIDNRVKELLELVGLTNKTDSYPSQL 141 Query: 166 SGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDL 225 SGG +QRVG+ARALAN+P++LL DEA SALDP + + L E+ +F TI+ V+H++ Sbjct: 142 SGGQKQRVGIARALANNPKVLLCDEATSALDPETTLSILNLLKEINREFGITIVVVTHEM 201 Query: 226 NEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFVEDV 268 N +I +++A+M+ G+I++ G EI NP + F+ + Sbjct: 202 NVVKQICNKVAVMEKGQIVEQGLLTEIFANPKTKIAQNFLRSL 244 Lambda K H 0.316 0.135 0.364 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: 302 Number of extensions: 7 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: 407 Length of database: 343 Length adjustment: 30 Effective length of query: 377 Effective length of database: 313 Effective search space: 118001 Effective search space used: 118001 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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