Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Ac3H11_1939 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1939 Length = 291 Score = 172 bits (436), Expect = 8e-48 Identities = 94/290 (32%), Positives = 172/290 (59%), Gaps = 4/290 (1%) Query: 5 LQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFVA 64 +Q L++G+ G +Y L+ALG+ ++Y + ++FA G++ M+GAF G L+ F+VA Sbjct: 4 VQLLISGVSQGCIYGLIALGFVLIYKATETVSFAQGELMMLGAFCGLALMTVLGFPFWVA 63 Query: 65 LIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLE--YGMVYLVGANTRAFP 122 ++ +++A + GV++E RP+ ++++ IG+ ++L M+ +G +T P Sbjct: 64 VLASVVAMGLFGVLVERAVIRPILGQPAFSIVMLTIGIGYVLRGLVTMIPNIGTDTHTLP 123 Query: 123 QAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLMG 182 + LG + ++ QL+++G + L +LL + + +K+G AM+A S + AA MG Sbjct: 124 VPYKDQSLRLGELVVSAEQLVVIGATGALCVLLFAMFRYSKLGIAMQAASQNQLAAYYMG 183 Query: 183 INVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGAA 242 I V R + L + +A AG+L+A + MG GLK+F AAV+GG G +PGA Sbjct: 184 IPVQRLNGLAWGLAAVVAAVAGLLLA-PITFVHANMGFI-GLKAFPAAVVGGFGSLPGAI 241 Query: 243 LGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNVKEKV 292 +GG VIG++E+ + + F+D Y ++L++L+V+P G+ G+ +++KV Sbjct: 242 VGGLVIGIVESLSGFYLPDGFKDTAAYIVVLIMLMVKPNGLFGEKLRKKV 291 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: 213 Number of extensions: 17 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: 291 Length adjustment: 26 Effective length of query: 266 Effective length of database: 265 Effective search space: 70490 Effective search space used: 70490 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 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