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 PP_2774 PP_2774 glycine betaine ABC transporter, ATPase/permease fusion protein
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__Putida:PP_2774 Length = 698 Score = 219 bits (557), Expect = 3e-61 Identities = 108/231 (46%), Positives = 161/231 (69%) Query: 37 KTGATVGVYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLN 96 ++ +T V N + GE+ +MG SGSGKSTLLR +NRLIEP+SG++ ID + +++L Sbjct: 48 RSDSTNAVEQVNLAVRRGEVLCLMGTSGSGKSTLLRHVNRLIEPSSGEVLIDGEVLSSLT 107 Query: 97 KEDLLQVRRKSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLD 156 + L Q+R + + MVFQ+FGL PHR++L+N LE++ P+ RR A + L L Sbjct: 108 QPTLRQLRSQRIGMVFQHFGLLPHRSVLDNVALPLELRGEPESTRRTAALRQLQAVGLKA 167 Query: 157 FKDQYPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQK 216 + +++P +LSGGMQQRVGLARAL +P+ILLMDE FSALDP IRR++Q L+L + Sbjct: 168 WSERFPHELSGGMQQRVGLARALVTNPDILLMDEPFSALDPTIRRDLQGRFLQLVRERGI 227 Query: 217 TIIFVSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFVED 267 T + V+HD EALR+ DRIA+++ G+++Q+GT E+L +PA++ V F ++ Sbjct: 228 TTLLVTHDPGEALRLADRIAVLRGGRLIQVGTPGELLEHPADEGVAVFFDE 278 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: 522 Number of extensions: 24 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: 698 Length adjustment: 35 Effective length of query: 372 Effective length of database: 663 Effective search space: 246636 Effective search space used: 246636 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: 52 (24.6 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