Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF3203 PGA1_c32560 high-affinity branched-chain amino acid transport ATP-binding protein
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__Phaeo:GFF3203 Length = 278 Score = 189 bits (480), Expect = 5e-53 Identities = 104/240 (43%), Positives = 147/240 (61%), Gaps = 8/240 (3%) Query: 1 MLKVSGVHTFYG-AIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRIT 59 +L+V+ + Y I LKGV +++ G I +L+G NGAGK+T L + + G +T Sbjct: 15 LLEVNNIEVIYNHVILVLKGVSLKVPKGGITALLGGNGAGKTTTLKAVSNLLHSERGEVT 74 Query: 60 -----FEGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGS--FANE 112 + G+ I ELV+ G+ Q EGR F ++V ENL G+ T G+ + Sbjct: 75 KGSISYRGERIQDRDPAELVKKGVIQVMEGRHCFEHLTVEENLLTGAYTRSDGNANIQRD 134 Query: 113 LERVLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQI 172 LE V + FPRLKER +AG SGGEQQM+A+GRALMS+P +LLDEPS+GLAP +V+QI Sbjct: 135 LEMVYSYFPRLKERRRSQAGYTSGGEQQMVAMGRALMSRPETILLDEPSMGLAPQLVEQI 194 Query: 173 FQAVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232 F+ VK IN + +T + EQN AL+ +H GY++ +G+V M G AEL N +V+ YL Sbjct: 195 FEIVKSINENEGVTFLLAEQNTNVALRYSHYGYILESGRVVMDGPAAELRENPDVKEFYL 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: 167 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: 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