Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_012964619.1 FERP_RS00400 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000025505.1:WP_012964619.1 Length = 246 Score = 166 bits (419), Expect = 5e-46 Identities = 91/252 (36%), Positives = 152/252 (60%), Gaps = 13/252 (5%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 ++ V LT RFGG++A N ++ +V++ +V+ +IGPNG+GKTTV N +TGF +P G + Sbjct: 1 MIRVENLTKRFGGVVAANNISFEVKKGEVLGIIGPNGSGKTTVVNLITGFIKPDSGKVFF 60 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 G++I P H+IA GVVRTFQNVR F + A +NL++ + +F F+ Sbjct: 61 AGKDITSKPPHEIANLGVVRTFQNVRPFYNLPAYKNLIIPLYSPRAKSF-------EEFK 113 Query: 125 RSEREAMEYAAHWLEEVNL---TEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 +R+ A LEEV + + A L +G +RLE+AR + +P +L+ DE Sbjct: 114 HGDRD--HIALDLLEEVGFERDSPIPYKPASALPHGYIKRLELARALALKPEVLICDELF 171 Query: 182 AGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQI 241 +GL+ E L ++ KL +E+ +T++++EH +K + ++D +VV+ G +A+G PE+I Sbjct: 172 SGLSQAEIASLLPILEKL-NENGLTLIMVEHRLKELFELADKVVVLEYGEKIAEGKPEEI 230 Query: 242 RDNPDVIKAYLG 253 ++ V +A+LG Sbjct: 231 VEDEKVKEAFLG 242 Lambda K H 0.320 0.137 0.391 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: 161 Number of extensions: 7 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: 255 Length of database: 246 Length adjustment: 24 Effective length of query: 231 Effective length of database: 222 Effective search space: 51282 Effective search space used: 51282 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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