Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate N515DRAFT_3950 N515DRAFT_3950 lipopolysaccharide export system ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__Dyella79:N515DRAFT_3950 Length = 239 Score = 147 bits (370), Expect = 3e-40 Identities = 88/251 (35%), Positives = 137/251 (54%), Gaps = 15/251 (5%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 +L + L K F V D + EGE+VGL+GPNGAGKTT F ++ G+ E GT+ L Sbjct: 1 MLSAEGLQKRFRTRQVVRDFAFSIREGEVVGLLGPNGAGKTTCFYMVVGLIEADAGTIKL 60 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122 D + + G + A LG+G Q +F+ LTV DN++ LR Sbjct: 61 DKYDITGLPMHARAKLGIGYLPQEPSVFRRLTVADNIMAVLE-----------LRENLSA 109 Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182 K L+ LKI + A+ +LS G++RR+EI RALA EP+ + LDEP AG+ Sbjct: 110 KQRAGELESLLDELKIAHI---ADQRGISLSGGERRRVEIARALAAEPRYMLLDEPFAGV 166 Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242 +P E+ ++R +K E I +++ +H++ + + +R Y+L G ++++GTP I + Sbjct: 167 DPISVGEIQRIVRHLK-ERGIGVLITDHNVRETLGICDRAYILNDGEVLSRGTPAHILAD 225 Query: 243 KRVIEAYLGGE 253 ++V E YLG E Sbjct: 226 EKVREVYLGRE 236 Lambda K H 0.319 0.139 0.385 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: 156 Number of extensions: 7 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: 254 Length of database: 239 Length adjustment: 24 Effective length of query: 230 Effective length of database: 215 Effective search space: 49450 Effective search space used: 49450 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 (21.7 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