Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate HSERO_RS14710 HSERO_RS14710 amino acid ABC transporter ATPase
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__HerbieS:HSERO_RS14710 Length = 243 Score = 224 bits (570), Expect = 2e-63 Identities = 117/235 (49%), Positives = 163/235 (69%), Gaps = 2/235 (0%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 +L+V + YG IEA+KG+ + + GEI +L+GANGAGKST L+ I G +A+ GR+ Sbjct: 10 ILQVEDLAVAYGHIEAVKGISLSLNEGEITALVGANGAGKSTSLLAISGLVKAQRGRVLL 69 Query: 61 EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKP-GSFANELERVLTL 119 GQD+ QM + +V G+ Q EGR ++V ENL +G+ T K A +LE V +L Sbjct: 70 HGQDLLQMSPHRIVESGVVQVAEGRATLTTLTVEENLGLGAYTRKDKDGVARDLEWVYSL 129 Query: 120 FPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDI 179 FP LK R + AG +SGGEQQMLAIGRALM++P++LLLDEPS+GLAPL++++IF+ V++I Sbjct: 130 FPVLKNRAAGLAGNLSGGEQQMLAIGRALMAKPKVLLLDEPSMGLAPLIIQEIFRIVQEI 189 Query: 180 NREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLEG 234 N+ MTV +VEQN AL++A RGYV+ GK+ + +GA LL N +V AYL G Sbjct: 190 NK-TGMTVLLVEQNVRQALRIAQRGYVLETGKIVLEDSGANLLGNPKVVEAYLGG 243 Lambda K H 0.320 0.136 0.377 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: 159 Number of extensions: 5 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: 236 Length of database: 243 Length adjustment: 23 Effective length of query: 213 Effective length of database: 220 Effective search space: 46860 Effective search space used: 46860 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: 46 (22.3 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