Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_073036563.1 BUB04_RS02235 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_900129305.1:WP_073036563.1 Length = 295 Score = 182 bits (462), Expect = 8e-51 Identities = 96/291 (32%), Positives = 171/291 (58%), Gaps = 7/291 (2%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMN 60 M +++ +NG+++GS+Y L ALG T+++G++K+INFAHG + M+ + Y+ + + Sbjct: 1 MLFLIEDAINGILMGSIYGLTALGLTVIFGVLKVINFAHGSLLMVSMYAAYWTVALTGWH 60 Query: 61 FFVALIVAMLATAILGVVIEFLAYRPLRHSTR-----IAVLITAIGVSFLLEYGMVYLVG 115 ++AL++ A + G ++ + +P+ + + I V+I GV ++L+ + L G Sbjct: 61 PYLALVIVAPAMFVFGYYLQDIVIKPIFKAEQDVREPITVIIVTTGVWYILDNLTLLLFG 120 Query: 116 ANTRAFPQ-AIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVD 174 R ++ ++G + ++ +L +++ L + QKT++G+A+RA S+D Sbjct: 121 PQYRTLQDNPLRGRMLEIGQMLISVPKLWGFAAAVLTASGLYLFFQKTRLGRAVRATSLD 180 Query: 175 SDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGG 234 AA LMGIN + + F +G+A AG A V + +YN P +GV +K F+ VLGG Sbjct: 181 RQAASLMGINQYKVYNIAFGIGTATAGIAAVTLVPFYNVF-PTVGVLFDIKGFIIVVLGG 239 Query: 235 IGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILG 285 +G I GA LGG +IGL+E+ F + + +AIVYG+ LL+L V+P+G+ G Sbjct: 240 LGSIGGALLGGIIIGLIESVGPQFMTATWTEAIVYGLFLLVLFVKPSGLFG 290 Lambda K H 0.330 0.146 0.407 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: 208 Number of extensions: 10 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: 292 Length of database: 295 Length adjustment: 26 Effective length of query: 266 Effective length of database: 269 Effective search space: 71554 Effective search space used: 71554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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