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_028584207.1 G494_RS0108595 LPS export ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000429965.1:WP_028584207.1 Length = 243 Score = 138 bits (348), Expect = 9e-38 Identities = 78/237 (32%), Positives = 128/237 (54%), Gaps = 6/237 (2%) Query: 2 SVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIE 61 ++L+ NL Y + V + +V VV L+G NGAGKTT ++ G VRP+SG I Sbjct: 5 ALLETRNLVKEYRSRRVVDQIDLQVKSSSVVGLLGPNGAGKTTTFYSIVGFVRPTSGSIH 64 Query: 62 FLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEM---GAFLKKNREENQANLKK 118 G++I +P K G++ + + VF LTV EN+ + + KN N+ Sbjct: 65 LDGKDITSLPIHKRAERGITYLAQEPSVFKKLTVEENVRIVLEPLGIPKNEIRNRIRELM 124 Query: 119 VFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDI 178 + L E K LSGGE++ + + RAL + P+ +LLDEP G+ P+ + ++ I Sbjct: 125 AELKIEYLAENKGH---ALSGGERRRVEIMRALATRPRFILLDEPFAGVDPLSVADLQQI 181 Query: 179 IQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 I+D++++G VL+ + N + L + D Y++ +GK++ SG ++ S RK YLG Sbjct: 182 IRDLKEKGLGVLISDHNVRETLQVCDFAYIMNSGKVLTSGVATDIIESVVARKMYLG 238 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: 122 Number of extensions: 7 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: 243 Length adjustment: 23 Effective length of query: 213 Effective length of database: 220 Effective search space: 46860 Effective search space used: 46860 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: 46 (22.3 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