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 GFF3356 HP15_3298 glycine betaine/L-proline ABC transporter, ATPase subunit
Query= TCDB::Q9RQ06 (407 letters) >FitnessBrowser__Marino:GFF3356 Length = 352 Score = 280 bits (717), Expect = 4e-80 Identities = 140/280 (50%), Positives = 199/280 (71%) Query: 3 VKVKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMGL 62 +K+ I +L KIFG AL V +G K ++L++ +G+ D N +I++GEI VIMGL Sbjct: 5 IKISIRNLYKIFGPTPDVALEYVRKGMGKADLLEQQRHVLGLRDINVDIHDGEITVIMGL 64 Query: 63 SGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHRT 122 SGSGKSTL+R LNRLI+PT+G+I +D +D+ + ++E L ++RR+ MSMVFQ F L PH+T Sbjct: 65 SGSGKSTLIRHLNRLIDPTAGEIRVDGEDIMSYSEEQLRKLRRERMSMVFQKFALLPHKT 124 Query: 123 ILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALAND 182 +LEN +++ + A K L L + QYP QLSGGMQQRVG+ARAL +D Sbjct: 125 VLENAGMAKDIRGYTTSDFEADARKWLARVGLEGNEYQYPHQLSGGMQQRVGIARALVSD 184 Query: 183 PEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDGK 242 I+LMDEAFSALDPLIR +MQD LLELQ + QKTI+F++HDL+EAL++ D + I+KDG+ Sbjct: 185 APIMLMDEAFSALDPLIRSDMQDLLLELQEELQKTIVFITHDLDEALKLADHLVILKDGE 244 Query: 243 IMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMIP 282 ++Q G +EIL NP + Y+ F+ D++RA+V+ ++M P Sbjct: 245 VVQQGDPQEILLNPGDPYIVDFISDINRARVLRVRSVMSP 284 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: 387 Number of extensions: 20 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 407 Length of database: 352 Length adjustment: 30 Effective length of query: 377 Effective length of database: 322 Effective search space: 121394 Effective search space used: 121394 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 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