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_090443350.1 BLS63_RS09635 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_900100495.1:WP_090443350.1 Length = 233 Score = 125 bits (313), Expect = 1e-33 Identities = 77/249 (30%), Positives = 137/249 (55%), Gaps = 17/249 (6%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 +L + ++ +G + A++GV+++V++ ++V++IG NGAGK+T+ L G + G IR Sbjct: 1 MLNFNNVSTFYGKIQALHGVSMEVQKGEIVTLIGANGAGKSTLLMTLCGSPRAASGSIRY 60 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 G+E+ GL +I RK + + R+F +T ENL+ + G F Sbjct: 61 QGDELVGLDTPEIMRKSIAVVPEGRRVFARLTVEENLV-----------MGGFFTAKGEF 109 Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 R + + + L+E LT+ AGT++ G+Q+ L I R +M++P++L+LDEP+ GL Sbjct: 110 REQLDKVLQLFPRLQE-RLTQ----RAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGL 164 Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244 P + +I +LR + VT+ L+E + + ++D V+ G + G+ EQ+ + Sbjct: 165 APIIIQQIFDIIEQLRKD-GVTIFLVEQNANQALKLADRGYVLENGRIVMQGSGEQLLSD 223 Query: 245 PDVIKAYLG 253 P V AYLG Sbjct: 224 PKVRDAYLG 232 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: 147 Number of extensions: 12 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: 233 Length adjustment: 24 Effective length of query: 231 Effective length of database: 209 Effective search space: 48279 Effective search space used: 48279 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