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 Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 159 bits (401), Expect = 2e-43 Identities = 99/289 (34%), Positives = 152/289 (52%), Gaps = 33/289 (11%) Query: 4 KVKIEHLTKIFGKRIKTALTMVEQGE---PKNEILKKTGATVGVYDTNFEINEGEIFVIM 60 +V L FG+ A + E+ E P+ + G V + N EI +GE V++ Sbjct: 7 RVTSAKLFPTFGRDCNVAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVV 66 Query: 61 GLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPH 120 G SG GKSTLLRLL L P+ G I + D+ V D L + + ++MVFQ++ L+PH Sbjct: 67 GPSGCGKSTLLRLLAGLETPSRGLIKVGDRRV------DRLPAKARDIAMVFQSYALYPH 120 Query: 121 RTILENTEYGLE----------------------VQNVPKEERR--KRAEKALDNANLLD 156 ++ +N +GL +Q P++E R +R + L Sbjct: 121 LSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDT 180 Query: 157 FKDQYPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQK 216 D+ PKQLSGG +QRV L RA+A +P++ LMDE S LD +R E + +++ LQ + Sbjct: 181 LLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGV 240 Query: 217 TIIFVSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFV 265 T ++V+HD EA+ +GDRIA++ G + Q+ + EI PAN +V F+ Sbjct: 241 TTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRFVAQFI 289 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: 315 Number of extensions: 8 Number of successful extensions: 3 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: 417 Length adjustment: 31 Effective length of query: 376 Effective length of database: 386 Effective search space: 145136 Effective search space used: 145136 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 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