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 AO356_09255 AO356_09255 glycine/betaine ABC transporter
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_09255 Length = 372 Score = 297 bits (761), Expect = 3e-85 Identities = 164/357 (45%), Positives = 233/357 (65%), Gaps = 18/357 (5%) Query: 3 VKVKIEHLTKIFGKRIKTAL-TMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMG 61 V V +++ KIFG+ A+ +V+QG K IL+ VGV + + ++ GEIF IMG Sbjct: 11 VLVDCQNVWKIFGESAPAAMQAVVQQGLTKTRILQDYSCVVGVSNVSLQVRRGEIFCIMG 70 Query: 62 LSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHR 121 LSGSGKSTL+RLLN+LI P+SGK+ + +D++TL+ L +VR + + MVFQ+ L P+R Sbjct: 71 LSGSGKSTLIRLLNKLITPSSGKVLVKGKDLSTLSAAQLREVRARHIGMVFQSVALLPNR 130 Query: 122 TILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALAN 181 T+LENT +GLEVQ + K ER K AE+AL L ++ +YP +LSGGMQQRVGLARA+ Sbjct: 131 TVLENTAFGLEVQGIGKAERYKVAERALAKVGLSEWSQRYPSELSGGMQQRVGLARAITA 190 Query: 182 DPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDG 241 DPE++LMDE FSALDPLIRR++QDE +L + K+ +F++HDL+EA+RIGDRIAIMKDG Sbjct: 191 DPEVILMDEPFSALDPLIRRQLQDEFRQLTKELGKSAVFITHDLDEAIRIGDRIAIMKDG 250 Query: 242 KIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMIPALTTNIDVDGPSVA--LKK 299 I+Q+GT EEI+ PA+DYV FV + R ++ A ++M P G +A +K Sbjct: 251 VIIQVGTAEEIVLKPADDYVAEFVAGISRLHLVKAHSVMTPVAPFKAANPGCDIARLIKT 310 Query: 300 MKTEEVSSLMAVDRKRQFRGVVTSEQAIAARKNNQSLKDVMTTDVGTVTKEMLVRDI 356 +++ L+ + V SE+ A +N DV+ VG +T L+R + Sbjct: 311 RLDADINELIGL--------TVKSERDALAVVDN----DVV---VGIITPRDLLRGV 352 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: 376 Number of extensions: 13 Number of successful extensions: 1 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: 372 Length adjustment: 30 Effective length of query: 377 Effective length of database: 342 Effective search space: 128934 Effective search space used: 128934 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