Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate PfGW456L13_3525 ABC transporter, ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3525 Length = 243 Score = 79.0 bits (193), Expect = 1e-19 Identities = 78/241 (32%), Positives = 106/241 (43%), Gaps = 29/241 (12%) Query: 12 LTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLR 71 L V L +G A+ VSFS G A++GPNGAGK+TL +T Y G + Sbjct: 4 LEVSDLGFAYGSREALRKVSFSLEPGRFAALLGPNGAGKSTLIALLTRLYDLQHGEI--- 60 Query: 72 HADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAG 131 G P R + FQ L +SV +NL H A Sbjct: 61 RVGGCSLRSAARPALR-----QLGVVFQQSTLDLDLSVEQNL--RYH-----------AA 102 Query: 132 LLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLC 191 L GL R V+LA+ L R + G+ +RR+EIARA+ EP +L Sbjct: 103 LHGLSRRQTDLRVDVELARQALTDRRRERVRELNGGH-----RRRVEIARALLHEPRLLL 157 Query: 192 LDEPAAGLNPRESGEL-ADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDE +AGL+P L + + RDEH I VL H + V SD +++L GR ++ Sbjct: 158 LDEASAGLDPASRLALNQHIRSLCRDEH-ISVLWTTHLLDEVQP-SDDLLILHQGRLVAS 215 Query: 251 G 251 G Sbjct: 216 G 216 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: 161 Number of extensions: 9 Number of successful extensions: 2 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: 243 Length adjustment: 25 Effective length of query: 269 Effective length of database: 218 Effective search space: 58642 Effective search space used: 58642 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