Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF3784 Psest_3853 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__psRCH2:GFF3784 Length = 266 Score = 134 bits (336), Expect = 3e-36 Identities = 88/264 (33%), Positives = 139/264 (52%), Gaps = 16/264 (6%) Query: 9 TPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRL 68 T +L+ L FGG VAVN+V + ++ A+IGPNGAGKTT+FN +T F P+ G + Sbjct: 19 TVMLSARGLRKEFGGFVAVNNVDLDVRHAQVHALIGPNGAGKTTVFNLLTKFLQPSAGSI 78 Query: 69 TLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFS 128 L D + R +++ + + R+FQ +F ++VL+N+ VA L R G + Sbjct: 79 RLLDHD-----ITRTDPAKVA-RMGLVRSFQISAVFPHLTVLDNVRVA----LQRPGGLA 128 Query: 129 IAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPV 188 L + S R A+ L ++ V L + A +L YG +R LEIA + EP Sbjct: 129 TQFWLPMRSLNRLNERALQL----IESVGLADKRHELAADLSYGRKRVLEIATTLALEPK 184 Query: 189 MLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKI 248 +L LDEP AG+ + +A+++ + + VL++EH++ VV + V VL G + Sbjct: 185 VLLLDEPMAGMGHEDVHVVAEIIREVATQR--AVLMVEHNLKVVADLCHQVTVLQRGEIL 242 Query: 249 SDGDPAFVKNDPAVIRAYLGEEED 272 + GD V D V AY+G ++D Sbjct: 243 TSGDYRTVSQDERVRVAYMGTDDD 266 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: 192 Number of extensions: 18 Number of successful extensions: 4 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: 266 Length adjustment: 26 Effective length of query: 268 Effective length of database: 240 Effective search space: 64320 Effective search space used: 64320 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