Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate SMc02357 SMc02357 high-affinity branched-chain amino acid ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Smeli:SMc02357 Length = 244 Score = 151 bits (381), Expect = 2e-41 Identities = 101/258 (39%), Positives = 140/258 (54%), Gaps = 24/258 (9%) Query: 12 LTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLR 71 L V +++ F GL A++ VS S GE+ +IGPNG+GKTTL N ITG G + Sbjct: 6 LAVNDVSVEFTGLRALDHVSLSVAAGEVVGLIGPNGSGKTTLINAITGQVKLATGTI--- 62 Query: 72 HADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAG 131 A G L P R A V+R+FQ +R+F M+V+EN+ A K Sbjct: 63 -AAGDTTLSGLSP--REIALAGVSRSFQIVRIFNSMTVMENVEAAALAK----------- 108 Query: 132 LLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLC 191 G ER AK L + L AD +L YG +RR+EIARA+ EP L Sbjct: 109 --GASRTVSAER-----AKGLLAELGLTAKADELGESLSYGDKRRVEIARALAAEPRFLL 161 Query: 192 LDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDG 251 LDEPAAG+N E+ L L + ++ +G+L+I+HDM ++M + + VL GR I++G Sbjct: 162 LDEPAAGMNDAETETLLHTLAELPEKRGLGLLIIDHDMGLIMRLCHRLHVLASGRTIAEG 221 Query: 252 DPAFVKNDPAVIRAYLGE 269 D A V++ PAVI AYLG+ Sbjct: 222 DAAHVRSHPAVIEAYLGK 239 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: 184 Number of extensions: 12 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: 244 Length adjustment: 25 Effective length of query: 269 Effective length of database: 219 Effective search space: 58911 Effective search space used: 58911 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