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 AO353_12265 AO353_12265 hypothetical protein
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12265 Length = 274 Score = 295 bits (756), Expect = 8e-85 Identities = 145/263 (55%), Positives = 202/263 (76%) Query: 4 KVKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMGLS 63 K++++++ KIFG R AL M+ Q + K+++L +TG +GV D + I GEIFVIMGLS Sbjct: 6 KIEVKNVFKIFGDRSADALDMIRQNKSKDQVLAETGCVIGVNDLSLSIATGEIFVIMGLS 65 Query: 64 GSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHRTI 123 GSGKSTL+R +NRLI+PTSG I +D D+ + E L + RR +SMVFQ+FGL PH+ + Sbjct: 66 GSGKSTLVRHINRLIDPTSGVILVDGVDILQYDMEALREFRRHKISMVFQSFGLLPHKNV 125 Query: 124 LENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALANDP 183 L+N YGL+V+ K+ +RA+ ++ L ++++YP QLSGGM+QRVGLARALA D Sbjct: 126 LDNVAYGLKVRGESKQVCAERAQHWINTVGLQGYENKYPHQLSGGMRQRVGLARALAADT 185 Query: 184 EILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDGKI 243 +I+LMDEAFSALDPLIR EMQD+LLELQ KTI+F++HDL+EA+RIG+RIAI+KDG++ Sbjct: 186 DIILMDEAFSALDPLIRAEMQDQLLELQQTLHKTIVFITHDLDEAVRIGNRIAILKDGQL 245 Query: 244 MQIGTGEEILTNPANDYVKTFVE 266 +Q+GT +EIL +PA++YV FV+ Sbjct: 246 IQVGTPKEILHSPADEYVDRFVQ 268 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: 305 Number of extensions: 7 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: 274 Length adjustment: 28 Effective length of query: 379 Effective length of database: 246 Effective search space: 93234 Effective search space used: 93234 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: 49 (23.5 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