Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate H281DRAFT_06394 H281DRAFT_06394 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__Burk376:H281DRAFT_06394 Length = 233 Score = 181 bits (458), Expect = 1e-50 Identities = 100/235 (42%), Positives = 144/235 (61%), Gaps = 5/235 (2%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 +L V +H FYG L+GV ++I GE V+L+G NGAGKST L I G + G +TF Sbjct: 2 ILDVQQIHGFYGKSHILQGVSLQIAEGETVTLLGRNGAGKSTTLKAIAGVVAPKNGSVTF 61 Query: 61 EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLF 120 G I+ + +++ G+ PE R IF ++V ENL++G+ P +L+ + +F Sbjct: 62 NGATISGLQPHKIASRGVCFVPEHRGIFRLLTVEENLRLGARKDSPW----QLDDIYRIF 117 Query: 121 PRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDIN 180 PRLKER + G +SGGEQQMLA+GRALM+ PRLL+LDEP GLAP++V++I +K I Sbjct: 118 PRLKERRTNGGGQLSGGEQQMLAVGRALMNHPRLLMLDEPVEGLAPVIVEEIVAQLKLI- 176 Query: 181 REQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLEGG 235 RE + + +VEQN +LA R Y++ G + SG A A++ V+ YL G Sbjct: 177 REAGVAILLVEQNLEVCTQLADRHYIIEQGVIVYSGDNASFAADDSVKDRYLGVG 231 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: 165 Number of extensions: 8 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: 233 Length adjustment: 23 Effective length of query: 213 Effective length of database: 210 Effective search space: 44730 Effective search space used: 44730 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