Align BusAB aka OPUABC, 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 16768 b2678 glycine betaine transporter subunit (NCBI)
Query= TCDB::Q9RQ05 (573 letters) >FitnessBrowser__Keio:16768 Length = 354 Score = 248 bits (634), Expect = 2e-70 Identities = 131/266 (49%), Positives = 174/266 (65%), Gaps = 2/266 (0%) Query: 9 IPLANWVSSATDWITSTFSSGFDVIQKSGTVLMNGITGALTAVPFWLMIAVVTILAILVS 68 IPL +WV+ DW+ + F F ++ ++NG L +P + I V ++A +S Sbjct: 62 IPLDSWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQIS 121 Query: 69 GKKFAFPLFAFIGLCLIANQGLWSDLMSTITLVLLSSLLSIIIGVPLGIWMAKSELVAKI 128 G + + L I G WS M T+ LVL + L I+IG+PLGIW+A+S AKI Sbjct: 122 G--VGMGVATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKI 179 Query: 129 VQPILDFMQTMPGFVYLIPAVAFFGIGVVPGVFASVIFALPPTVRMTNLGIRQVSTELVE 188 ++P+LD MQT P FVYL+P V FGIG VPGV ++IFALPP +R+T LGI QV +L+E Sbjct: 180 IRPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIE 239 Query: 189 AADSFGSTARQKLFKLEFPLAKGTIMAGVNQTIMLALSMVVIASMIGAPGLGRGVLAAVQ 248 A+ SFG++ RQ LFK++ PLA TIMAGVNQT+MLALSMVVIASMI GLG+ VL + Sbjct: 240 ASRSFGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIG 299 Query: 249 SADIGKGFVSGISLVILAIIIDRFTQ 274 D+G V G+ +VILAII+DR TQ Sbjct: 300 RLDMGLATVGGVGIVILAIILDRLTQ 325 Lambda K H 0.319 0.134 0.396 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: 550 Number of extensions: 26 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 573 Length of database: 354 Length adjustment: 33 Effective length of query: 540 Effective length of database: 321 Effective search space: 173340 Effective search space used: 173340 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 (21.8 bits) S2: 51 (24.3 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