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_012402388.1 BPHY_RS15490 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000020045.1:WP_012402388.1 Length = 594 Score = 195 bits (496), Expect = 2e-54 Identities = 107/252 (42%), Positives = 157/252 (62%), Gaps = 7/252 (2%) Query: 4 PILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIR 63 P+L V +FGGL+AVN V+ +V+ Q++ +IGPNGAGK+T FN +TG Q T G I Sbjct: 345 PLLVVDKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSGAIT 404 Query: 64 LDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAF 123 GE I L +I ++G+ RTFQ+V+L MT +EN+ + H AG++++ A Sbjct: 405 FRGERIDALNSREIVKRGIGRTFQHVKLLPGMTVLENVAIGGH----LRGRAGVWRSVAR 460 Query: 124 RRSEREA--MEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 E M AA + V L E AG+LA G+QR LEIAR + P +L+LDEPA Sbjct: 461 LNGAEEGRLMAEAARQIRRVGLEEHMYDEAGSLALGKQRILEIARALCCDPTLLLLDEPA 520 Query: 182 AGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQI 241 AGL +E L L+ KLR E +++LL+EHDM VM+++D +VV+ G +A+G P+ + Sbjct: 521 AGLRYQEKQQLATLLRKLR-EEGMSLLLVEHDMDFVMNLTDRLVVMEFGTRIAEGLPQDV 579 Query: 242 RDNPDVIKAYLG 253 +++P V++AYLG Sbjct: 580 QNDPAVLEAYLG 591 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: 334 Number of extensions: 18 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: 594 Length adjustment: 30 Effective length of query: 225 Effective length of database: 564 Effective search space: 126900 Effective search space used: 126900 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 Apr 09 2024. 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