Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 17516 b3455 leucine/isoleucine/valine transporter subunit (NCBI)
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__Keio:17516 Length = 255 Score = 134 bits (336), Expect = 2e-36 Identities = 83/249 (33%), Positives = 142/249 (57%), Gaps = 16/249 (6%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 +L V L + +G + AV +V+ E+ E+VSLIG NGAGKTT+ L+G +P+ G I Sbjct: 5 LLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILL 64 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMEN--------LEMGAF--LKKNREEN 112 Q ++ +P Q+I G+ + + +F +TV+EN L+ G F L K Sbjct: 65 RDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFR 124 Query: 113 QANLKKVFSRFPRLE-----ERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGL 167 +A + + LE E N+ A+ L+ G+Q+ L + R +++ P++L+LDEP+ GL Sbjct: 125 RAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGL 184 Query: 168 APIFIQEIFDIIQDIQK-QGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASS 226 P +E+ ++I +++ TT+LLIE + + ISDR YV+ G + +GT +++ ++ Sbjct: 185 NPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIRNN 244 Query: 227 EEVRKAYLG 235 +V +AYLG Sbjct: 245 PDVIRAYLG 253 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: 155 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: 255 Length adjustment: 24 Effective length of query: 212 Effective length of database: 231 Effective search space: 48972 Effective search space used: 48972 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