Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Dsui_2057 Dsui_2057 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__PS:Dsui_2057 Length = 237 Score = 232 bits (592), Expect = 4e-66 Identities = 122/236 (51%), Positives = 171/236 (72%), Gaps = 4/236 (1%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 +L+V + YG IEA+KG+D + GEI +L+GANGAGKST L+ + G + G+I F Sbjct: 4 LLRVHDLAVAYGHIEAVKGLDFHLNEGEITALVGANGAGKSTTLLALSGLIKPTRGKIEF 63 Query: 61 EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITA--KPGSFANELERVLT 118 +G+DI+++P +++V G+ Q EGR I ++V ENLQ+G+ T K G A+ +E V Sbjct: 64 QGEDISRLPAHQIVERGLVQVAEGRAILTTLTVEENLQLGAYTRQDKEGIPAS-MEEVYQ 122 Query: 119 LFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKD 178 LFPRLKER Q AG +SGGEQQMLAIGRALM++P+LLLLDEPS+GLAP+VV++IF+ + + Sbjct: 123 LFPRLKERSQQFAGNLSGGEQQMLAIGRALMAKPKLLLLDEPSMGLAPIVVQEIFRILVE 182 Query: 179 INREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLEG 234 INR + +T+ +VEQN ALK+A GYV+ GK+ ++ +GA LLAN +V AYL G Sbjct: 183 INR-RGLTILLVEQNVRQALKIAKHGYVIETGKIVLADSGANLLANPKVEEAYLGG 237 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: 181 Number of extensions: 9 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: 237 Length adjustment: 23 Effective length of query: 213 Effective length of database: 214 Effective search space: 45582 Effective search space used: 45582 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