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_085770056.1 B1812_RS01695 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= TCDB::Q9RQ06 (407 letters) >NCBI__GCF_002117405.1:WP_085770056.1 Length = 436 Score = 147 bits (371), Expect = 6e-40 Identities = 92/226 (40%), Positives = 136/226 (60%), Gaps = 18/226 (7%) Query: 51 INEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSM 110 + EGEI ++G SG GKSTLLR+++ L + G++ + VA ++M Sbjct: 38 LKEGEIVGLLGRSGCGKSTLLRIVSGLNRASGGEVRYRGEKVAG---------PVDGVAM 88 Query: 111 VFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQ 170 VFQ+F LFP T+L N E GL + P+EE RKRA +A+D L F++ YPK++SGGM+ Sbjct: 89 VFQSFALFPWLTVLANVELGLRAKGAPREEARKRALQAIDIIGLDGFENAYPKEISGGMR 148 Query: 171 QRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQ---KTIIFVSHDLNE 227 QRVG ARAL P +LLMDE FSALD L ++ +LL+L + + K+I+ V+H++ E Sbjct: 149 QRVGFARALVVAPSLLLMDEPFSALDVLTAETLRTDLLDLWVEGRMPIKSILMVTHNIEE 208 Query: 228 ALRIGDRIAIMKD--GKI-MQIGTGEEILTNPANDYVKTFVEDVDR 270 A+ + DRI ++ G+I +IG + +P N F + VDR Sbjct: 209 AVLMCDRIVVLSSNPGRIAAEIGVS---MQHPRNRLDPEFRQLVDR 251 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: 366 Number of extensions: 19 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: 436 Length adjustment: 32 Effective length of query: 375 Effective length of database: 404 Effective search space: 151500 Effective search space used: 151500 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