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 GFF3209 PGA1_c32620 high-affinity branched-chain amino acid transport ATP-binding protein
Query= TCDB::P21629 (255 letters) >FitnessBrowser__Phaeo:GFF3209 Length = 269 Score = 193 bits (490), Expect = 3e-54 Identities = 92/252 (36%), Positives = 155/252 (61%), Gaps = 6/252 (2%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 ++E+ +T+RFGG++A+ ++ + E ++ ++IGPNGAGK+++ N ++GFY P G + Sbjct: 17 VMEMKNITLRFGGVVAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGEVLF 76 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLF---KTP 121 G+ + +++AR+G+ RTFQN+ LF M+ ++N++ + + TN K Sbjct: 77 RGKPRPQMRPYEVARQGIARTFQNIALFDGMSVLDNVMTGRLNFMKTNIFQQAIWRGKAE 136 Query: 122 AFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 A REA+E +LE + L YG ++R+E+AR + P++L+LDEP Sbjct: 137 AEETENREAVERIIDFLE---IQAIRKTPVARLPYGLKKRVELARALAAEPKLLLLDEPM 193 Query: 182 AGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQI 241 AG+N +E +D+ I + E T+ LIEHDM +VM +SD +VV++ G + DGTP+++ Sbjct: 194 AGMNVEEKEDMSRFILDVNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGKKIGDGTPDEV 253 Query: 242 RDNPDVIKAYLG 253 R+N DVI AYLG Sbjct: 254 RNNQDVIDAYLG 265 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: 181 Number of extensions: 6 Number of successful extensions: 1 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: 269 Length adjustment: 25 Effective length of query: 230 Effective length of database: 244 Effective search space: 56120 Effective search space used: 56120 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: 47 (22.7 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