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_007728726.1 C1M55_RS16600 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_002893965.1:WP_007728726.1 Length = 448 Score = 157 bits (397), Expect = 4e-43 Identities = 97/286 (33%), Positives = 157/286 (54%), Gaps = 4/286 (1%) Query: 4 MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFV 63 +++ V+GL G V A+ +G +++YG L NFAHG++ +GA + + SF + Sbjct: 157 LIRTTVDGLRFGLVIAIAGVGLSLIYGTTGLTNFAHGEMVTLGAVAAWVINTSFGVPLIP 216 Query: 64 ALIVAMLATAILGVVIEFLAYRPLRHSTR--IAVLITAIGVSFLLEYGMVYLVGANTRAF 121 A I+A+ +G++ + ++PLR IA L+ +IG++ L Y ++ F Sbjct: 217 ATILAIFVGIGIGLLTNGIVWKPLRKRKTGLIAQLVVSIGLAISLRYLILIFFSDRAEPF 276 Query: 122 PQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLM 181 V + GPI+LT+ +++ +SL++++ + +++QKT++GKAMRAVS + D A Sbjct: 277 DDYQGQVEKNWGPIALTDANAIVMIVSLVVLVGVALLLQKTRIGKAMRAVSDNRDLAASS 336 Query: 182 GINVNRTISFTFALGSALAGAAGVL--IALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIP 239 GINV R I F + LG LA GVL I+ ++ MG L F LGG+G Sbjct: 337 GINVERVIMFVWGLGGGLAALGGVLFGISELGGRVQWEMGFKLLLLMFAGITLGGLGTAY 396 Query: 240 GAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILG 285 GA LG ++GLL +T D + +L++IL+VRP GILG Sbjct: 397 GALLGCVIVGLLVQLSTLIINPDLKYIGGLLVLIVILVVRPQGILG 442 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: 255 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: 448 Length adjustment: 29 Effective length of query: 263 Effective length of database: 419 Effective search space: 110197 Effective search space used: 110197 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: 49 (23.5 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