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 GFF3453 PS417_17675 ABC transporter
Query= TCDB::P21629 (255 letters) >FitnessBrowser__WCS417:GFF3453 Length = 249 Score = 185 bits (470), Expect = 7e-52 Identities = 112/254 (44%), Positives = 154/254 (60%), Gaps = 12/254 (4%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 +LE L + +G AVNGVNLKVE + ++IGPNGAGKT++F+CLTG Q T G I Sbjct: 4 LLETKDLELAYGAFHAVNGVNLKVEAGTIHTIIGPNGAGKTSLFHCLTGERQATAGAIHF 63 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENL-LVAQHRHLNTNFLAGLFKTPAF 123 DG+ + P H G+ R+FQ LF+ ++ ENL L AQ R G + Sbjct: 64 DGKNLMRKPAHGRVGLGMARSFQLTSLFQNLSVRENLRLAAQGRD-------GARALNFW 116 Query: 124 RR--SEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 RR S+RE +E A LE + LT A+ AG L++GQQR LE+ + ++P++LMLDEP Sbjct: 117 RRVDSKREHLEMADQVLERLQLTARADTLAGELSHGQQRVLEVGMSICSKPKLLMLDEPT 176 Query: 182 AGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQI 241 +G+ + + LI+ L +H TVLLIEH+M +VMSIS I V++ G L +GTPE + Sbjct: 177 SGMGIDDIPIMTQLISDLGRDH--TVLLIEHNMSIVMSISQRITVMSHGQILVEGTPEFV 234 Query: 242 RDNPDVIKAYLGEA 255 R + V AYLGEA Sbjct: 235 RADERVRTAYLGEA 248 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: 175 Number of extensions: 10 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: 249 Length adjustment: 24 Effective length of query: 231 Effective length of database: 225 Effective search space: 51975 Effective search space used: 51975 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 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