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 BWI76_RS22070 BWI76_RS22070 proline/betaine ABC transporter permease ProW
Query= TCDB::Q9RQ05 (573 letters) >FitnessBrowser__Koxy:BWI76_RS22070 Length = 354 Score = 239 bits (610), Expect = 1e-67 Identities = 134/289 (46%), Positives = 179/289 (61%), Gaps = 9/289 (3%) Query: 9 IPLANWVSSATDWITSTFSSGFDVIQKSGTVLMNGITGALTAVPFWLMIAVVTILAILVS 68 IPL +WV+ DW+ F F I+ +++ L +P + I + +++A +S Sbjct: 62 IPLDSWVTHGIDWVVMHFRPLFQGIRVPVDYILSAFQQLLLGMPAPVAIIIFSLIAWQIS 121 Query: 69 GKKFAFPLFAFIGLCLIANQGLWSDLMSTITLVLLSSLLSIIIGVPLGIWMAKSELVAKI 128 I L I G WS M T+ LVL + L ++IG+PLGIW+A+S AKI Sbjct: 122 S--VGMGAATLISLIAIGAIGAWSQAMVTLALVLTALLFCMLIGLPLGIWLARSPRAAKI 179 Query: 129 VQPILDFMQTMPGFVYLIPAVAFFGIGVVPGVFASVIFALPPTVRMTNLGIRQVSTELVE 188 ++P+LD MQT P FVYL+P V FGIG VPGV ++IFALPP VR+T LGI QV +L+E Sbjct: 180 IRPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIVRLTILGINQVPADLIE 239 Query: 189 AADSFGSTARQKLFKLEFPLAKGTIMAGVNQTIMLALSMVVIASMIGAPGLGRGVLAAVQ 248 A+ SFG++ RQ LFK++ PLA TIMAGVNQT+MLALSMVVIASMI GLG+ VL + Sbjct: 240 ASRSFGASPRQLLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIG 299 Query: 249 SADIGKGFVSGISLVILAIIIDRFTQKLNVSPLEKQGNPKLKKWKRWIA 297 D+G V G+ +VILAII+DR TQ + +GN +RW A Sbjct: 300 RLDMGLATVGGVGIVILAIILDRLTQAVG-RDSRSRGN------RRWYA 341 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: 519 Number of extensions: 21 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: 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