Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate N515DRAFT_3950 N515DRAFT_3950 lipopolysaccharide export system ATP-binding protein
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__Dyella79:N515DRAFT_3950 Length = 239 Score = 127 bits (319), Expect = 2e-34 Identities = 78/237 (32%), Positives = 130/237 (54%), Gaps = 9/237 (3%) Query: 1 MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60 ML G+ + + ++ I GE+V L+G NGAGK+T + G A G I Sbjct: 1 MLSAEGLQKRFRTRQVVRDFAFSIREGEVVGLLGPNGAGKTTCFYMVVGLIEADAGTIKL 60 Query: 61 EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQ-----MGSITAKPGSFANELER 115 + DIT +P + +LGI P+ +F R++V +N+ +++AK A ELE Sbjct: 61 DKYDITGLPMHARAKLGIGYLPQEPSVFRRLTVADNIMAVLELRENLSAK--QRAGELES 118 Query: 116 VLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQA 175 +L ++ QR ++SGGE++ + I RAL ++PR +LLDEP G+ P+ V +I + Sbjct: 119 LLDEL-KIAHIADQRGISLSGGERRRVEIARALAAEPRYMLLDEPFAGVDPISVGEIQRI 177 Query: 176 VKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232 V+ + +E+ + V + + N L + R Y++ +G+V GT A +LA+E+VR YL Sbjct: 178 VRHL-KERGIGVLITDHNVRETLGICDRAYILNDGEVLSRGTPAHILADEKVREVYL 233 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: 134 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: 239 Length adjustment: 23 Effective length of query: 213 Effective length of database: 216 Effective search space: 46008 Effective search space used: 46008 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