Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_089137089.1 CES79_RS10015 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_002217945.1:WP_089137089.1 Length = 259 Score = 111 bits (278), Expect = 1e-29 Identities = 79/254 (31%), Positives = 135/254 (53%), Gaps = 23/254 (9%) Query: 1 MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60 +L+ +++ +G + A+ DV++ + E+V LIG NGAGK+TL L G +SGSI + Sbjct: 4 LLNVEELVKNFGGLTAVSDVNMHLNDDELVALIGPNGAGKTTLFNLLTGVIGPSSGSITF 63 Query: 61 EGEE----LVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMG-------GFFTD---- 105 G + L G+ + I +A + R+F L+V +N+ + GFF Sbjct: 64 RGTDGTISLNGMKAYKIANLGMARTFQNIRLFKELSVLDNVLIAMTAHYKEGFFQSVFRL 123 Query: 106 ----KDDYQVQMD--KVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDE 159 K + Q++ + ++L++F L+ ++ A + G Q+ L I R L KPK+L LDE Sbjct: 124 PKFYKTESQIRKEAIELLKIFD-LQNDLDKLAKNLPYGIQRRLEIVRGLAMKPKVLFLDE 182 Query: 160 PSLGLAPIIIQQIFEIIEQLRRE-GVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGA 218 P+ G+ P + +I Q++R+ +TV L+E + + + LA R YVL++G ++ T Sbjct: 183 PAAGMNPEETADLTRLIRQVQRDFHITVLLIEHDMSLVMNLASRIYVLDHGSLLAEGTPT 242 Query: 219 ALLTNPKVRDAYLG 232 + N V AYLG Sbjct: 243 EIQQNKAVIKAYLG 256 Lambda K H 0.318 0.136 0.374 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: 129 Number of extensions: 5 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: 233 Length of database: 259 Length adjustment: 24 Effective length of query: 209 Effective length of database: 235 Effective search space: 49115 Effective search space used: 49115 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: 41 (21.7 bits) S2: 46 (22.3 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