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 BPHYT_RS15595 BPHYT_RS15595 ABC transporter
Query= TCDB::P21629 (255 letters) >FitnessBrowser__BFirm:BPHYT_RS15595 Length = 257 Score = 231 bits (589), Expect = 1e-65 Identities = 114/248 (45%), Positives = 167/248 (67%), Gaps = 1/248 (0%) Query: 6 LEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLD 65 L V G+ RFGGL A++ V L+++ Q+ +IGPNGAGKTT FN +TG Y P G +LD Sbjct: 7 LSVKGVNKRFGGLQALSEVGLEIKSGQIYGLIGPNGAGKTTFFNVITGLYTPDSGEFKLD 66 Query: 66 GEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRR 125 GE +++A+ G+ RTFQN+RLF MTA+EN++V +H + +F+TPA R+ Sbjct: 67 GENYTPTAVYQVAKAGIARTFQNIRLFGGMTALENVMVGRHVRTKHGLIGAVFQTPAERK 126 Query: 126 SEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLN 185 ERE E A LE V + ++A+ ++ L+YG QRRLEIAR + T P++L LDEPAAG+N Sbjct: 127 EEREIKERAIELLEYVGIAQYADYTSRNLSYGHQRRLEIARALATDPKLLALDEPAAGMN 186 Query: 186 PKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDNP 245 E +L L+ K+R++ T+LLIEHD+KLVM + + + V++ G +A G P+ ++ +P Sbjct: 187 ATEKVELTKLLDKIRAD-GKTILLIEHDVKLVMGLCNQMTVLDYGKVIAQGLPQDVQKDP 245 Query: 246 DVIKAYLG 253 VI+AYLG Sbjct: 246 KVIEAYLG 253 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: 190 Number of extensions: 7 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 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: 47 (22.7 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