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_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= TCDB::Q9RQ06 (407 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 369 bits (946), Expect = e-106 Identities = 194/405 (47%), Positives = 278/405 (68%), Gaps = 9/405 (2%) Query: 2 PVKVKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMG 61 PVK+++++L KIFG + K A+ +++QG K I +KT TVGV D +FEI +GEIFVIMG Sbjct: 4 PVKIEVKNLYKIFGPQPKKAMALLKQGLDKEAIFEKTETTVGVQDASFEIFKGEIFVIMG 63 Query: 62 LSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHR 121 LSGSGKST++R+LNRLIEPTSG++ ID +D+ +N + L++VRR +SMVFQ+F L PH Sbjct: 64 LSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAKLSMVFQSFALMPHM 123 Query: 122 TILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALAN 181 T+L+N +GLE+ V K+ R +RA +AL+ L + + P +LSGGMQQRVGLAR LA Sbjct: 124 TVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPDELSGGMQQRVGLARGLAV 183 Query: 182 DPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDG 241 DP+ILLMDEAFSALDPLIR EMQDELL+LQAK ++TI+F+SHDL+EA+RIGDRIAIM+ G Sbjct: 184 DPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLDEAMRIGDRIAIMEGG 243 Query: 242 KIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMIPALTTNIDVDG--PSVALKK 299 +++Q+GT EEIL NPA+DYV+ F VD ++TA +I T DG P L++ Sbjct: 244 RVVQVGTPEEILQNPADDYVRAFFRGVDPTNILTAGDIATQTQVTIPITDGKNPRAGLQR 303 Query: 300 MKTEEVSSLMAVDRKRQFRGVVTSEQAIAARKNN---QSLKDVMTTDVGTVTKEMLVRDI 356 + + +D ++ F+GVV+++ +N+ + + +V K+ ++DI Sbjct: 304 LVKNDRDYAYVLDSEKTFKGVVSTDSLRDMLENDNVPHLIPNAYLEEVVAAHKDDSLQDI 363 Query: 357 LPIIYDAPTPLAVVDDQGYLKGILIRGIVLEAL----ADIPDEVE 397 LP + P PL ++DD G G + + + L+ L +D P ++E Sbjct: 364 LPKVAAHPWPLPILDDDGRYLGAISKNLFLKTLHRNQSDEPADME 408 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: 482 Number of extensions: 17 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: 415 Length adjustment: 31 Effective length of query: 376 Effective length of database: 384 Effective search space: 144384 Effective search space used: 144384 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