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 YP_004144287.1 Mesci_5138 glycine betaine/L-proline ABC transporter ATPase
Query= TCDB::Q9RQ06 (407 letters) >NCBI__GCF_000185905.1:YP_004144287.1 Length = 361 Score = 273 bits (699), Expect = 5e-78 Identities = 139/281 (49%), Positives = 191/281 (67%), Gaps = 5/281 (1%) Query: 2 PVKVKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATV--GVYDTNFEINEGEIFVI 59 PVK+ ++ K+FG A + + + K + T A + V + EI +GEIF+I Sbjct: 20 PVKLACRNVWKLFGSN---AANFIRERDGKASMADVTAAGLVGAVRAVDLEIRQGEIFII 76 Query: 60 MGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFP 119 MGLSGSGKSTL+R ++RL+EPT GK+ + D+ ++ L+++RR M MVFQNF L P Sbjct: 77 MGLSGSGKSTLVRCMSRLVEPTHGKVEFEGNDLLKISDAALIELRRHRMGMVFQNFALLP 136 Query: 120 HRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARAL 179 H +LEN + L +Q + R RA + ++ L + YP++LSGG QQRVG+AR+L Sbjct: 137 HLNVLENIAFPLSIQGQDRATREARAREVIELVGLRGREHFYPRELSGGQQQRVGIARSL 196 Query: 180 ANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMK 239 A PEI +DE FSALDPLIRREMQDEL+ LQ KTI+F++HD +EA+R+ DRIAIMK Sbjct: 197 ATKPEIWFLDEPFSALDPLIRREMQDELMRLQMMLHKTIVFITHDFDEAIRLADRIAIMK 256 Query: 240 DGKIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIM 280 DG+++QIGT EE++ NPA DYV F DVDRAKVI+A ++M Sbjct: 257 DGEVIQIGTPEELVVNPATDYVAEFTRDVDRAKVISARSLM 297 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: 337 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 407 Length of database: 361 Length adjustment: 30 Effective length of query: 377 Effective length of database: 331 Effective search space: 124787 Effective search space used: 124787 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