Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF3281 PS417_16795 ABC transporter
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__WCS417:GFF3281 Length = 257 Score = 179 bits (453), Expect = 8e-50 Identities = 113/263 (42%), Positives = 154/263 (58%), Gaps = 19/263 (7%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L V +++ F G+ A+N +SF GEI A+IGPNGAGK++L N + G Y Sbjct: 5 ILQVRDISLSFKGIKAINALSFEVARGEICALIGPNGAGKSSLLNVLNGVY--------- 55 Query: 71 RHADGKEFLLERMPGYRI----SQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASG 126 D E + E +RI + + + RTFQN LF MSVL+N++ ++ +R+S Sbjct: 56 -RFDAGEIVFEDQHFHRIDPLGAARRGIGRTFQNNALFKKMSVLDNILTGL-SRHMRSSV 113 Query: 127 FSIAGLLGLPSYTRTEREAVDL-AKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCT 185 A LGLP R E EA L A+ L+ + L D GNL YG Q+R+E+ RA+ Sbjct: 114 IEQA--LGLPR-ARREAEAFRLRAQGILEFLELQAHRDVLVGNLSYGLQKRVELGRALIA 170 Query: 186 EPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYG 245 P +L LDEP AG+N E E+A + + + V+LIEHDM VVM +SDHVVVLDYG Sbjct: 171 GPSLLLLDEPMAGMNAEEKQEMARFVADVNRDLGTTVVLIEHDMGVVMGLSDHVVVLDYG 230 Query: 246 RKISDGDPAFVKNDPAVIRAYLG 268 RK+ DG PA V+ +P VI AYLG Sbjct: 231 RKVGDGTPADVQANPEVIAAYLG 253 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: 182 Number of extensions: 6 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: 257 Length adjustment: 25 Effective length of query: 269 Effective length of database: 232 Effective search space: 62408 Effective search space used: 62408 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