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 Ac3H11_4180 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4180 Length = 367 Score = 176 bits (445), Expect = 1e-48 Identities = 94/229 (41%), Positives = 133/229 (58%), Gaps = 6/229 (2%) Query: 39 GATVGVYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKE 98 G + V + +I GE ++G SGSGK+T L +L PT+G I +D + + Sbjct: 20 GEQLVVRALDLDIQRGEFLSLLGPSGSGKTTTLMMLAGFESPTAGDILLDGKQITRTPPH 79 Query: 99 DLLQVRRKSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFK 158 +++ MVFQN+ LFPH T+ EN Y L V+ VPK E+ +R +KALD L Sbjct: 80 ------KRNFGMVFQNYALFPHLTVGENVAYPLTVRKVPKAEQAERVKKALDMVRLTGMA 133 Query: 159 DQYPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTI 218 D+ P +LSGG QQRV LARAL +P+++LMDE ALD +R MQ EL EL + T Sbjct: 134 DRLPARLSGGQQQRVALARALVFNPQLVLMDEPLGALDKQLREHMQIELKELHRQLGVTF 193 Query: 219 IFVSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFVED 267 ++V+HD EAL + DR+A+ +G I Q+ E + P+N +V FV D Sbjct: 194 VYVTHDQGEALTMSDRVAVFNEGVIQQLADVESLYETPSNRFVAGFVGD 242 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: 7 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: 407 Length of database: 367 Length adjustment: 30 Effective length of query: 377 Effective length of database: 337 Effective search space: 127049 Effective search space used: 127049 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