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_041097906.1 SUTH_RS06105 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000828635.1:WP_041097906.1 Length = 593 Score = 200 bits (509), Expect = 5e-56 Identities = 109/251 (43%), Positives = 158/251 (62%), Gaps = 3/251 (1%) Query: 3 RPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLI 62 R +L V +T RFGGL+A N +NL V +V+++IGPNGAGK+T+FNC++G + G I Sbjct: 342 REVLLVRNVTKRFGGLVANNAMNLTVRAGEVMALIGPNGAGKSTLFNCISGVSPASEGEI 401 Query: 63 RLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPA 122 + I L +IA+ G+ RTFQ+VRL ++MT +EN + H NF+ ++ Sbjct: 402 HFMDQRIDALASREIAKLGISRTFQHVRLNQDMTVLENAAIGAHLRGRKNFVQSAWRLD- 460 Query: 123 FRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182 R ER + AAH L+ L E +AG+L G+QR +EIAR + + P +L+LDEPAA Sbjct: 461 -REEERRLLWEAAHQLQRCGLGEHLFDAAGSLPLGKQRIVEIARALCSDPTLLLLDEPAA 519 Query: 183 GLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIR 242 GL E L L+ KLR E + +LL+EHDM VM ++D +VV+ G LA+G P++I+ Sbjct: 520 GLRHLEKRALAELLDKLRGE-GMAILLVEHDMDFVMGLADRVVVMEFGEHLAEGLPQEIQ 578 Query: 243 DNPDVIKAYLG 253 NP V++AYLG Sbjct: 579 ANPKVLEAYLG 589 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: 333 Number of extensions: 15 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: 593 Length adjustment: 30 Effective length of query: 225 Effective length of database: 563 Effective search space: 126675 Effective search space used: 126675 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