Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Synpcc7942_2177 Synpcc7942_2177 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__SynE:Synpcc7942_2177 Length = 296 Score = 154 bits (388), Expect = 3e-42 Identities = 91/288 (31%), Positives = 162/288 (56%), Gaps = 5/288 (1%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMN 60 ++ + Q +NGL GS+ AL A G T++YGI++L NFA G+ +GA+ + NS ++ Sbjct: 12 LSQLAQLAINGLATGSLLALAATGLTLIYGILRLTNFAQGEFLTLGAYFT-LVANSLGLS 70 Query: 61 FFVALIVAMLATAILGVVIEFLAYRPLRHS--TRIAVLITAIGVSFLLEYGMVYLVGANT 118 ++A+ + +AT L ++ E + + PLR ++I IG+S L ++ + GA Sbjct: 71 LWLAIPLGAIATIALCLLGEAVLWEPLRRQRVNTTTLIILTIGLSLFLRNLVILIWGAGN 130 Query: 119 RAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAA 178 +A+ A+Q G N L+++G + L +LL ++Q+T +GK MRA++ D D A Sbjct: 131 QAYRLAVQPALTLWGLRITLNSLLVVIGAAAAL-VLLHWVLQRTSIGKGMRAIADDPDLA 189 Query: 179 QLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGII 238 ++ G+ V I +T+ + L AG L L ++ P MG L F +A+LGGIG Sbjct: 190 RVSGVPVETVIRWTWVIAGGLTAIAGGLYGLI-TAVRPTMGWNLILPLFASAILGGIGSP 248 Query: 239 PGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGK 286 GA GG ++G + +T + ++++ A+ + IL+ +L++RP G+ + Sbjct: 249 YGAIAGGLILGFAQELSTYWLPAEYKLAVAFVILIGVLVIRPQGLFAR 296 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: 185 Number of extensions: 11 Number of successful extensions: 5 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: 296 Length adjustment: 26 Effective length of query: 266 Effective length of database: 270 Effective search space: 71820 Effective search space used: 71820 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