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 BWI76_RS22065 BWI76_RS22065 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__Koxy:BWI76_RS22065 Length = 400 Score = 353 bits (906), Expect = e-102 Identities = 183/392 (46%), Positives = 274/392 (69%), Gaps = 3/392 (0%) Query: 1 MPVKVKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIM 60 M +K++I++L KIFG+ + A +++G K +IL+KTG ++GV + + I EGEIFVIM Sbjct: 1 MAIKLEIKNLYKIFGEHPQRAFKYIDKGLSKEQILEKTGLSLGVKNASLTIEEGEIFVIM 60 Query: 61 GLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPH 120 GLSGSGKST++RLLNRLIEPT G++ ID D+A ++ +L +VRRK ++MVFQ+F L PH Sbjct: 61 GLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPH 120 Query: 121 RTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALA 180 T+L+N +G+E+ VP +ER+++A +AL L ++ YP +LSGGM+QRVGLARALA Sbjct: 121 MTVLDNAGFGMELAGVPTQERQEKALEALRQVGLENYAHAYPDELSGGMRQRVGLARALA 180 Query: 181 NDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKD 240 +P+ILLMDEAFSALDPLIR EMQDEL +LQA+ Q+T++F+SHDL+EA+RIGDRIAIM++ Sbjct: 181 INPDILLMDEAFSALDPLIRTEMQDELTKLQARHQRTVVFISHDLDEAMRIGDRIAIMQN 240 Query: 241 GKIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMIPA---LTTNIDVDGPSVAL 297 G+++Q+GT +EIL NPANDYV+TF VD ++V +A++I + L GP AL Sbjct: 241 GEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRSPVGLIRKTPGFGPRSAL 300 Query: 298 KKMKTEEVSSLMAVDRKRQFRGVVTSEQAIAARKNNQSLKDVMTTDVGTVTKEMLVRDIL 357 K ++ E+ ++R +F G+++ + AA Q + + V + + ++L Sbjct: 301 KLLQDEDREYGYVIERGNKFVGIISIDSLKAALSEGQGIDAALIDSPQAVDAQTPLSELL 360 Query: 358 PIIYDAPTPLAVVDDQGYLKGILIRGIVLEAL 389 + AP + V+D+ GI+ + ++L+AL Sbjct: 361 SHVGHAPCAVPVIDEGQQYVGIISKRMLLQAL 392 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: 419 Number of extensions: 14 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: 400 Length adjustment: 31 Effective length of query: 376 Effective length of database: 369 Effective search space: 138744 Effective search space used: 138744 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