Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF3209 PGA1_c32620 high-affinity branched-chain amino acid transport ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Phaeo:GFF3209 Length = 269 Score = 201 bits (510), Expect = 2e-56 Identities = 116/269 (43%), Positives = 168/269 (62%), Gaps = 23/269 (8%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 ++ ++++T+RFGG+VA+ D+SF GEI AIIGPNGAGK+++ N I+GFY P G + Sbjct: 17 VMEMKNITLRFGGVVAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGEVLF 76 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 R GK +M Y ++++ +ARTFQNI LF GMSVL+N++ + N ++ + F A Sbjct: 77 R---GKP--RPQMRPYEVARQG-IARTFQNIALFDGMSVLDNVMTGRLN-FMKTNIFQQA 129 Query: 131 GLLGLPSYTRTE-REAVDLAKYWLDRVRLLEFADWEA------GNLPYGAQRRLEIARAM 183 G TE REAV+ R+++F + +A LPYG ++R+E+ARA+ Sbjct: 130 IWRGKAEAEETENREAVE---------RIIDFLEIQAIRKTPVARLPYGLKKRVELARAL 180 Query: 184 CTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLD 243 EP +L LDEP AG+N E +++ + + DE + LIEHDM VVM +SD VVV+D Sbjct: 181 AAEPKLLLLDEPMAGMNVEEKEDMSRFILDVNDEFGTTIALIEHDMGVVMDLSDRVVVMD 240 Query: 244 YGRKISDGDPAFVKNDPAVIRAYLGEEED 272 YG+KI DG P V+N+ VI AYLG D Sbjct: 241 YGKKIGDGTPDEVRNNQDVIDAYLGVSHD 269 Lambda K H 0.319 0.137 0.397 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: 227 Number of extensions: 8 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: 294 Length of database: 269 Length adjustment: 26 Effective length of query: 268 Effective length of database: 243 Effective search space: 65124 Effective search space used: 65124 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