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_232502519.1 LFE_RS09120 ATP-binding cassette domain-containing protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000284315.1:WP_232502519.1 Length = 588 Score = 112 bits (281), Expect = 1e-29 Identities = 73/227 (32%), Positives = 123/227 (54%), Gaps = 17/227 (7%) Query: 4 LKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFL 63 ++VENL ++ +AV +++F V +GEV L+GANGAGKTT R L+GL+ P++GK+ Sbjct: 342 IEVENLDRYFDSFKAVNNLTFHVKKGEVFGLLGANGAGKTTTFRMLAGLLEPTAGKLIVA 401 Query: 64 GQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENL-------EMGAFLKKNREENQANL 116 G++++K+ AQ G + + + ++ LTV +NL + L+K + ++ N Sbjct: 402 GEDVRKVAAQ--ARGKIGYMAQKFSLYSQLTVFQNLIFYSSAYGLSGTLQKEKIQDSLN- 458 Query: 117 KKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIF 176 F LE KN + L G +Q LA+ AL+ P +L LDEP+ G+ P +E + Sbjct: 459 ------FFELEPYKNVSSGILPLGFRQRLALSCALIHEPSILFLDEPTSGVDPNARREFW 512 Query: 177 DIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKEL 223 II + G +VL+ +A DR ++ G ++ G+ E+ Sbjct: 513 HIINALATVGVSVLVTTHFMEEA-EYCDRLLIMAQGALLAMGSPAEI 558 Score = 112 bits (279), Expect = 2e-29 Identities = 64/205 (31%), Positives = 112/205 (54%), Gaps = 2/205 (0%) Query: 14 GMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFLGQEIQKMPAQ 73 G++ A+ +SF + +G + LIG +GAGKTT++R LSGL+ P G I +G + K P Sbjct: 25 GIVTALDKISFSLKKGSITGLIGPDGAGKTTLMRLLSGLLWPDGGDIRIMGNDPSKAPLS 84 Query: 74 KIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSRFPRLEERKNQD 133 V G L +P+ ++ L+V ENL++ A L+ ++ + L L + + Sbjct: 85 --VQGSLGYMPQKFGLYEDLSVQENLDLYANLQGVPKDRRKELYAPLLSMTGLSPFQKRL 142 Query: 134 AATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDIQKQGTTVLLIE 193 A LSGG +Q L + +L+ P +LLLDEP++G+ P+ +E+++I++ + + L + Sbjct: 143 AGQLSGGMKQKLGVACSLVHQPPILLLDEPTVGVDPVSRRELWEILRKLVSESGATLFVS 202 Query: 194 QNANKALAISDRGYVLETGKIVLSG 218 + D +L GK++ SG Sbjct: 203 TSYLDEAERCDEILILYNGKVLGSG 227 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: 312 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 236 Length of database: 588 Length adjustment: 30 Effective length of query: 206 Effective length of database: 558 Effective search space: 114948 Effective search space used: 114948 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: 49 (23.5 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