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 WP_011373501.1 SUDEN_RS09795 phosphate ABC transporter ATP-binding protein PstB
Query= TCDB::Q9RQ06 (407 letters) >NCBI__GCF_000012965.1:WP_011373501.1 Length = 261 Score = 121 bits (304), Expect = 2e-32 Identities = 80/220 (36%), Positives = 133/220 (60%), Gaps = 15/220 (6%) Query: 56 IFVIMGLSGSGKSTLLRLLNRLIE-----PTSGKIFIDDQDVATLNKEDLLQVRRKSMSM 110 I ++G SG GK+TLLR NR+ + SG+I D+++ T +KEDL+++R + + M Sbjct: 42 ITALIGPSGCGKTTLLRSFNRMHDLYPNNKYSGEITFKDRNILT-SKEDLIKLRIQ-IGM 99 Query: 111 VFQNFGLFPHRTILENTEYGLEVQNVP-KEERRKRAEKALDNANLL-DFKDQYPKQ---L 165 +FQ FP +I +N YGL++Q + + E R EKAL +A + + KD+ L Sbjct: 100 IFQKPTAFP-MSIFDNVAYGLKLQGIKNRTELSGRVEKALKDAAIWNEVKDRLKHDANGL 158 Query: 166 SGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDL 225 SGG QQR+ +ARA+A +PE+LL DE SALDP+ +++ ++EL+ + +II V+H++ Sbjct: 159 SGGQQQRLCIARAVAVEPEVLLFDEPTSALDPISTGGIEELIVELRERV--SIIIVTHNM 216 Query: 226 NEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFV 265 +A R+ D M G+++++G EEI P + ++ Sbjct: 217 QQAARVSDYTGFMYLGELIELGKTEEIFVTPKEKLTEEYI 256 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: 257 Number of extensions: 15 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: 261 Length adjustment: 28 Effective length of query: 379 Effective length of database: 233 Effective search space: 88307 Effective search space used: 88307 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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