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_011649777.1 RL_RS27135 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000009265.1:WP_011649777.1 Length = 249 Score = 180 bits (456), Expect = 3e-50 Identities = 106/251 (42%), Positives = 147/251 (58%), Gaps = 11/251 (4%) Query: 6 LEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLD 65 LE L RFGG A N V+L VE ++IGPNGAGKTT+ N LTG +PT G + +D Sbjct: 5 LETRNLVKRFGGFTATNDVSLTVESGARHALIGPNGAGKTTLINLLTGVLKPTSGQVIVD 64 Query: 66 GEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR- 124 GE+I L H+ R+G+ RTFQ +LF T +E++L+A + F A+R Sbjct: 65 GEDITSLSSHRRVRRGIARTFQINQLFSGFTPLESVLLAINERDG-------FGRSAWRP 117 Query: 125 -RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183 + +A + A LE L+ G +AYG+QR LEIA +RPR+L+LDEPAAG Sbjct: 118 LAAHLDATDEAVDLLERFGLSGVMGEKTGRIAYGKQRLLEIALAFASRPRVLLLDEPAAG 177 Query: 184 LNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRD 243 + +E ++ A++ L +E VTV+LIEHDM LV S +D I V+ G + +GT +I Sbjct: 178 VAEEERSEVLAIVRSLPAE--VTVVLIEHDMDLVFSFADRISVLVAGVVMVEGTVGEIAA 235 Query: 244 NPDVIKAYLGE 254 +P V YLGE Sbjct: 236 DPRVKAVYLGE 246 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: 167 Number of extensions: 5 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 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