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_034411543.1 H566_RS0113090 hypothetical protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000482785.1:WP_034411543.1 Length = 612 Score = 187 bits (475), Expect = 4e-52 Identities = 99/249 (39%), Positives = 157/249 (63%), Gaps = 3/249 (1%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 +++ +T RFGGL+A N ++L+V+ ++V++IGPNGAGK+T+FN ++G PT G IR Sbjct: 364 LVDAREVTRRFGGLVANNAMDLQVKAGEIVALIGPNGAGKSTMFNQISGVDAPTSGEIRF 423 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 G + GL IA G+ R+FQ+VR+ M+ +EN+ + H + A ++ R Sbjct: 424 RGRRVDGLGARAIAALGMSRSFQHVRMLPAMSVLENVAIGAHLRGSRGVFACAWRLD--R 481 Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 E + AA + V L E + AG+L+ GQQR +EIAR + + P +L+LDEPAAGL Sbjct: 482 ADEARLIAEAARQIRRVGLEERMHAPAGSLSLGQQRVMEIARALCSDPCLLLLDEPAAGL 541 Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244 +E L L+ +LR+E + VL++EHDM VM ++D +VV+ G +A+G P+ ++ + Sbjct: 542 RHQEKAALGELLRRLRAE-GMAVLIVEHDMDFVMGLADRVVVMEFGRKIAEGLPQDVQQD 600 Query: 245 PDVIKAYLG 253 P V++AYLG Sbjct: 601 PKVLEAYLG 609 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: 335 Number of extensions: 16 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: 612 Length adjustment: 31 Effective length of query: 224 Effective length of database: 581 Effective search space: 130144 Effective search space used: 130144 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: 50 (23.9 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