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 H281DRAFT_00988 H281DRAFT_00988 glycine betaine/proline transport system permease protein
Query= TCDB::Q9RQ05 (573 letters) >FitnessBrowser__Burk376:H281DRAFT_00988 Length = 293 Score = 246 bits (629), Expect = 7e-70 Identities = 134/292 (45%), Positives = 189/292 (64%), Gaps = 16/292 (5%) Query: 5 VIGKIPLANWVSSATDWITSTFSSGFDVIQKSGTVLMNGITGALTAVPFWLMIAVVTILA 64 VIGK + +A +++ F GFD + ++ + L A+PF M+ ++ A Sbjct: 5 VIGK-----FAENAVNFLFQHFRGGFDAFSAALGAVIKLLEDGLAAIPFIAMLVLLVAFA 59 Query: 65 ILVSGKKFAFPLFAFIGLCLIANQGLWSDLMSTITLVLLSSLLSIIIGVPLGIWMAKSEL 124 + G F +F + L I GLW+ +ST+ LV+ +++ S++IGVPLGIW A+++ Sbjct: 60 LWRRG--VVFSVFVGVALMAIHYMGLWAQTVSTLALVVAATVFSLVIGVPLGIWGARNKR 117 Query: 125 VAKIVQPILDFMQTMPGFVYLIPAVAFFGIGVVPGVFASVIFALPPTVRMTNLGIRQVST 184 V +++ +LDFMQTMP FVYLIPAV FG+G VP V A+++F++PP VR+T LGIRQV Sbjct: 118 VEMVLRSLLDFMQTMPAFVYLIPAVILFGLGRVPAVIATIVFSMPPVVRLTTLGIRQVRE 177 Query: 185 ELVEAADSFGSTARQKLFKLEFPLAKGTIMAGVNQTIMLALSMVVIASMIGAPGLGRGVL 244 EL+EA SFGST Q L+K++ P A +IMAGVNQTIM+ALSMVV+ASMIGA GLG VL Sbjct: 178 ELLEAGRSFGSTDAQLLWKIQLPNALPSIMAGVNQTIMMALSMVVVASMIGAGGLGEYVL 237 Query: 245 AAVQSADIGKGFVSGISLVILAIIIDRFTQKLNVSPLEKQGNPKLKKWKRWI 296 + +Q DIG GF G+ +V+LAI++DR T+ V K KK KR + Sbjct: 238 SGIQRLDIGIGFEGGLGVVLLAIVLDRLTESFGV---------KAKKAKRTV 280 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: 361 Number of extensions: 12 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: 293 Length adjustment: 31 Effective length of query: 542 Effective length of database: 262 Effective search space: 142004 Effective search space used: 142004 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: 50 (23.9 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