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 AZOBR_RS23480 AZOBR_RS23480 glycine/betaine ABC transporter ATP-binding protein
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__azobra:AZOBR_RS23480 Length = 398 Score = 362 bits (928), Expect = e-104 Identities = 188/394 (47%), Positives = 271/394 (68%), Gaps = 5/394 (1%) Query: 1 MPVKVKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIM 60 M K+ + +T+IFG+ + AL +++ G K EI K+TG TVGV D +FE+ GEIFVIM Sbjct: 1 MTAKIAVNGVTRIFGRHPRQALDLLKAGLSKEEIFKRTGQTVGVLDASFEVEAGEIFVIM 60 Query: 61 GLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPH 120 GLSGSGKSTL+R+LNRLI+PT+G+I ID +D+ L++ +L ++RR+ + MVFQ+F L PH Sbjct: 61 GLSGSGKSTLVRMLNRLIDPTAGEIRIDGRDITKLSRAELTELRRRDLGMVFQSFALLPH 120 Query: 121 RTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALA 180 + EN +GLE+ + RR +A++ALD L + + +P++LSGGMQQRVGLARALA Sbjct: 121 LRVWENAAFGLEIAGESLKARRDKAQQALDAVGLGAYAESFPRELSGGMQQRVGLARALA 180 Query: 181 NDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKD 240 N+P +LLMDEAFSALDPLIR EMQDELL LQA+ Q+TI+F+SHDL+EA+RIGDR+AIM+ Sbjct: 181 NEPSVLLMDEAFSALDPLIRTEMQDELLRLQAERQRTIVFISHDLDEAIRIGDRLAIMEG 240 Query: 241 GKIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMIPALTTNI--DVDGPSVALK 298 G+I+Q+G +EIL PANDYV++F ++D K++TA +I T I +GP A++ Sbjct: 241 GQIIQVGRPDEILKQPANDYVRSFFRNIDVTKILTAGDIARRDQVTLIRHTGEGPRAAVR 300 Query: 299 KMKTEEVSSLMAVDRKRQFRGVVTSE---QAIAARKNNQSLKDVMTTDVGTVTKEMLVRD 355 +++ + D +R+F GVV+ E AI + +L + + + + ++ + + Sbjct: 301 QLRERDREFGYVQDGRRRFHGVVSVETLVTAIERHNGSATLDEALLPGIEPLPVDLPMDE 360 Query: 356 ILPIIYDAPTPLAVVDDQGYLKGILIRGIVLEAL 389 +LP I AP PL VVD QG G + + LE L Sbjct: 361 VLPRIASAPCPLPVVDGQGAYVGAISKTAYLETL 394 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: 417 Number of extensions: 19 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: 398 Length adjustment: 31 Effective length of query: 376 Effective length of database: 367 Effective search space: 137992 Effective search space used: 137992 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