Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF3209 PGA1_c32620 high-affinity branched-chain amino acid transport ATP-binding protein
Query= TCDB::Q55164 (267 letters) >FitnessBrowser__Phaeo:GFF3209 Length = 269 Score = 159 bits (401), Expect = 8e-44 Identities = 86/247 (34%), Positives = 145/247 (58%), Gaps = 1/247 (0%) Query: 22 QGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFNGDS 81 + ++ FGG+ A+ ++EG I +IGPNGAGK+++ N++S F P +GEVLF G Sbjct: 21 KNITLRFGGVVAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGEVLFRGKP 80 Query: 82 IGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQKEER 141 Q+ P+++A +G RTFQ + ++VL+N++ + + I + + EE Sbjct: 81 RPQMRPYEVARQGIARTFQNIALFDGMSVLDNVMTGRLNFMKTNIFQQAIWRGKAEAEET 140 Query: 142 ANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVNPTL 201 NRE +++ + + A + L G +K +E+ARAL + PKL+LLDEP AG+N Sbjct: 141 ENREAVERIIDFLEIQAIRKTPVARLPYGLKKRVELARALAAEPKLLLLDEPMAGMNVEE 200 Query: 202 IGQICEHIVNWNRQ-GITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDPRVL 260 + I++ N + G T +IEH+M V+M L V V+ G+ + DGTP++++++ V+ Sbjct: 201 KEDMSRFILDVNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGKKIGDGTPDEVRNNQDVI 260 Query: 261 EAYLGDS 267 +AYLG S Sbjct: 261 DAYLGVS 267 Lambda K H 0.319 0.136 0.389 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: 179 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: 267 Length of database: 269 Length adjustment: 25 Effective length of query: 242 Effective length of database: 244 Effective search space: 59048 Effective search space used: 59048 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 (21.7 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