Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Dsui_1113 Dsui_1113 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__PS:Dsui_1113 Length = 278 Score = 192 bits (489), Expect = 4e-54 Identities = 106/239 (44%), Positives = 146/239 (61%), Gaps = 8/239 (3%) Query: 2 LKVSGVHTFYG-AIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRIT- 59 L ++ + Y I LKGV + + G+IV+L+GANGAGKST L I A G +T Sbjct: 16 LSINNIEVIYDHVILVLKGVSLTVPKGKIVALLGANGAGKSTTLKAISNLLHAERGDVTK 75 Query: 60 ----FEGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITA--KPGSFANEL 113 F+G + Q+ ELV+ G+ Q EGR F +S+ ENL G+ T L Sbjct: 76 GSVEFKGTRVDQLTPNELVKRGVIQVMEGRHCFAHLSIEENLLTGAYTRGNSRAELKQNL 135 Query: 114 ERVLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIF 173 E V FPRLK R + +AG SGGEQQM AIGRALM++P ++LLDEPS+GLAP +V++IF Sbjct: 136 EMVYHYFPRLKTRRTSQAGYTSGGEQQMCAIGRALMAKPEMILLDEPSMGLAPQIVEEIF 195 Query: 174 QAVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232 + VKD+N + ++ + EQN AL+ A GY++ NG+V M G EL +NE+V+ YL Sbjct: 196 EIVKDLNSRENVSFLLAEQNTMVALRYADLGYILENGRVVMEGDAKELASNEDVKEFYL 254 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: 168 Number of extensions: 10 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: 278 Length adjustment: 24 Effective length of query: 212 Effective length of database: 254 Effective search space: 53848 Effective search space used: 53848 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