Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Pf6N2E2_1429 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1429 Length = 253 Score = 179 bits (455), Expect = 3e-50 Identities = 99/240 (41%), Positives = 149/240 (62%), Gaps = 8/240 (3%) Query: 1 MLKVSGVHTFYG-AIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMG--- 56 +L++ + Y I A++ V +E+G G++V L+GANGAGKST L RA G Sbjct: 7 ILQIDDIEVLYEQTILAVRSVSLEVGKGQVVVLLGANGAGKSTTLKAASNLVRAERGEVV 66 Query: 57 --RITFEGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPG--SFANE 112 RI ++G+D+T+ + L G+ Q EGR F +++V ENL G++ + + Sbjct: 67 RGRIVYQGRDVTRSAPHTLAASGLVQVLEGRHCFAQLTVEENLLAGALARQVPRRQLLAD 126 Query: 113 LERVLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQI 172 LE V FPRLK R AG SGGEQQM+AIGRALM++P+L+LLDEPS+GLAP +V++I Sbjct: 127 LESVYGHFPRLKLRRKSLAGYTSGGEQQMIAIGRALMAKPQLVLLDEPSMGLAPQIVEEI 186 Query: 173 FQAVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232 F+ V+ +N+ ++ + EQN AL+ AH GYV+ +G+V G+ +L A +++ YL Sbjct: 187 FEIVRQLNQRDGVSFLIAEQNINIALRYAHHGYVLESGRVVSEGSAEQLAARGDLQDFYL 246 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: 160 Number of extensions: 6 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: 253 Length adjustment: 24 Effective length of query: 212 Effective length of database: 229 Effective search space: 48548 Effective search space used: 48548 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