Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate N515DRAFT_4159 N515DRAFT_4159 ABC-2 type transport system ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__Dyella79:N515DRAFT_4159 Length = 245 Score = 104 bits (260), Expect = 1e-27 Identities = 70/215 (32%), Positives = 116/215 (53%), Gaps = 8/215 (3%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 +LK++ + H AV +S ++ G+++ L+G NGAGK+T L ++G ++P G+IE Sbjct: 7 LLKLDQVRRHRAGRPAVERLSLTLDRGQILGLLGVNGAGKSTTLAMIAGALKPDEGRIEL 66 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVF-S 121 GQ+ PA + G L +PE +P LTV+E+L+ A L+ R LK+ S Sbjct: 67 DGQDFATHPA--LARGLLGWLPERAPHWPELTVLEHLQAHARLRGLR---AGGLKQACES 121 Query: 122 RFPRLE--ERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDII 179 RLE + A LS G++Q L + AL+ P+LL+LDEP+ L P+ + + +I Sbjct: 122 TIERLELAPLLRRLAGVLSQGQRQRLGLACALLHKPRLLVLDEPANALDPVQVAALRKVI 181 Query: 180 QDIQKQGTTVLLIEQNANKALAISDRGYVLETGKI 214 ++ G V+L + A+ DR +L G++ Sbjct: 182 REEAAAGAAVILSTHLLAETTAVCDRVAILHEGRL 216 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: 112 Number of extensions: 6 Number of successful extensions: 3 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: 245 Length adjustment: 23 Effective length of query: 213 Effective length of database: 222 Effective search space: 47286 Effective search space used: 47286 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 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