Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 8500412 DvMF_1162 ABC transporter related (RefSeq)
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__Miya:8500412 Length = 241 Score = 204 bits (519), Expect = 1e-57 Identities = 111/241 (46%), Positives = 164/241 (68%), Gaps = 8/241 (3%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICG-----SPRARM 55 +L + ++ YG IEAL G+ + GEIV+LIGANGAGKST L +I +P+ Sbjct: 2 LLSIENLYVKYGNIEALHGLSFHVNEGEIVTLIGANGAGKSTTLKSIMRLPPPEAPKVSG 61 Query: 56 GRITFEGQDITQMPTYELV-RLGIAQSPEGRRIFPRMSVLENLQMGSITAKPG-SFANEL 113 G I F+G+ + + +++V +L +A PEGR IF ++V+ENL + + K + + +L Sbjct: 62 GDILFKGKSLLNVEPHDVVSKLHVALVPEGRHIFGNLTVMENLMLATYARKNDPAISRDL 121 Query: 114 ERVLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIF 173 ER+ LFPRL ER +QR+ T+SGGEQQMLA+GRALM+ +LLLDEPS+GLAPL++ ++F Sbjct: 122 ERIFDLFPRLAERRTQRSDTLSGGEQQMLAVGRALMTSCEVLLLDEPSMGLAPLLMYEMF 181 Query: 174 QAVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLE 233 + +K++NRE +T+ +VEQNA AL++A RGYV+ G++ G LL + EV+ AYL Sbjct: 182 RTLKELNRE-GLTIIVVEQNARLALQVASRGYVLDTGEIVAQGPSESLLNDPEVKKAYLG 240 Query: 234 G 234 G Sbjct: 241 G 241 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: 157 Number of extensions: 6 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: 236 Length of database: 241 Length adjustment: 23 Effective length of query: 213 Effective length of database: 218 Effective search space: 46434 Effective search space used: 46434 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