Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_083988482.1 BBI00_RS11725 LPS export ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_001684965.1:WP_083988482.1 Length = 353 Score = 146 bits (368), Expect = 6e-40 Identities = 85/235 (36%), Positives = 136/235 (57%), Gaps = 4/235 (1%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 +L+ ENL YG + V+ VS +V +GE+V L+G NGAGKTT + GLV+P+SGKI Sbjct: 2 ILRGENLIKEYGPKKVVKGVSVQVQQGEIVGLLGPNGAGKTTSFYMIVGLVKPTSGKIFL 61 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAF--LKKNREENQANLKKVF 120 QEI + G+ + + VF L+V EN+ MG K ++ E Q ++ Sbjct: 62 DKQEITTDAMYRRAQKGIGYLAQEASVFRKLSVEENI-MGVLQLTKLSKREQQIKCDELI 120 Query: 121 SRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQ 180 F RKN+ LSGGE++ + R L ++P +LLDEP G+ PI +++I I++ Sbjct: 121 EEFSLQHVRKNR-GDLLSGGERRRTEIARCLATSPNFILLDEPFAGVDPIAVEDIQKIVR 179 Query: 181 DIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 + + +L+ + N + LAI+++ Y++ GKI+ G ++LA+ +VR+AYLG Sbjct: 180 SLVDKNIGILITDHNVQQTLAITNKTYIMFEGKILKEGLPEDLANDPQVREAYLG 234 Lambda K H 0.315 0.134 0.358 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: 176 Number of extensions: 3 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: 236 Length of database: 353 Length adjustment: 26 Effective length of query: 210 Effective length of database: 327 Effective search space: 68670 Effective search space used: 68670 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: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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