Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF3453 PS417_17675 ABC transporter
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__WCS417:GFF3453 Length = 249 Score = 157 bits (397), Expect = 2e-43 Identities = 100/259 (38%), Positives = 148/259 (57%), Gaps = 15/259 (5%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 LL + L + +G AVN V+ G I IIGPNGAGKT+LF+C+TG T G + Sbjct: 4 LLETKDLELAYGAFHAVNGVNLKVEAGTIHTIIGPNGAGKTSLFHCLTGERQATAGAI-- 61 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 H DGK + + G R+ +AR+FQ LF +SV ENL +A A G A Sbjct: 62 -HFDGKNLMRKPAHG-RVG--LGMARSFQLTSLFQNLSVRENLRLA-------AQGRDGA 110 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 L ++RE +++A L+R++L AD AG L +G QR LE+ ++C++P +L Sbjct: 111 RALNFWRRVDSKREHLEMADQVLERLQLTARADTLAGELSHGQQRVLEVGMSICSKPKLL 170 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEP +G+ + + L++ + +H VLLIEH+MS+VM+IS + V+ +G+ + + Sbjct: 171 MLDEPTSGMGIDDIPIMTQLISDLGRDHT--VLLIEHNMSIVMSISQRITVMSHGQILVE 228 Query: 251 GDPAFVKNDPAVIRAYLGE 269 G P FV+ D V AYLGE Sbjct: 229 GTPEFVRADERVRTAYLGE 247 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: 193 Number of extensions: 7 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: 249 Length adjustment: 25 Effective length of query: 269 Effective length of database: 224 Effective search space: 60256 Effective search space used: 60256 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