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_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2058 Length = 360 Score = 187 bits (474), Expect = 6e-52 Identities = 121/345 (35%), Positives = 178/345 (51%), Gaps = 39/345 (11%) Query: 38 TGATVGVYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNK 97 + A + V +FE+ G + I+G SG GK+T LR++ L PTSG+IFI +DV TL Sbjct: 21 SSAALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTSGEIFIGGKDVTTLGP 80 Query: 98 EDLLQVRRKSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDF 157 ++++SM+FQ++ LFPH ++EN YGL + PKE+ R +A +AL L+ F Sbjct: 81 A------QRNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEALRGVGLVGF 134 Query: 158 KDQYPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKT 217 D+ P +LSGG QQRV LARAL +PE+LL DE S LD +RREM++E+ LQ + T Sbjct: 135 DDRLPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIRALQQRLSLT 194 Query: 218 IIFVSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAE 277 + +V+HD EA+ + D+I +M G I Q G+ + P +++V F+ E Sbjct: 195 VAYVTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFM----------GE 244 Query: 278 NIMIPALTTNIDVDG----------PSVALKKMKTEEVSSLMAVDRKRQFRGVVTSEQAI 327 ++ PA+ D DG P VA+K + A RQ G++ + A Sbjct: 245 AMLFPAVA---DADGTVALGPLVLRPRVAVKSGPVKVAVRPEAWRITRQGEGLLPARLA- 300 Query: 328 AARKNNQSLKDVMTTDVGTVTKEMLVRDILPIIYDAPTPLAVVDD 372 K V T E + I + D LAV DD Sbjct: 301 ---------KSAYLGAVHEYTFETALGSIFVVSSDLDDVLAVGDD 336 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: 310 Number of extensions: 19 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: 407 Length of database: 360 Length adjustment: 30 Effective length of query: 377 Effective length of database: 330 Effective search space: 124410 Effective search space used: 124410 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