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_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= TCDB::Q9RQ06 (407 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 190 bits (482), Expect = 7e-53 Identities = 94/232 (40%), Positives = 148/232 (63%), Gaps = 6/232 (2%) Query: 34 ILKKTGATVGVYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVA 93 ++K+ G TV V +T+ I GE+ ++G SG GK+T+LR++ L PT G I+I + + Sbjct: 50 LMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIKGRRIN 109 Query: 94 TLNKEDLLQVRRKSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNAN 153 + ++++ M+FQN+ LFPH+TI EN +GL+ +NV +EE R++ +AL+ Sbjct: 110 DT------PIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVR 163 Query: 154 LLDFKDQYPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAK 213 L + +Y QLSGG QQR+ LARA+ +P++LLMDE SALD +R EM+ E+ +Q + Sbjct: 164 LPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQ 223 Query: 214 FQKTIIFVSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFV 265 T +FV+HD EAL + ++I +MKDG+ Q GT E++ P N +V F+ Sbjct: 224 LNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFL 275 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: 335 Number of extensions: 11 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: 406 Length adjustment: 31 Effective length of query: 376 Effective length of database: 375 Effective search space: 141000 Effective search space used: 141000 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 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