Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 5210884 Shew_3310 ABC transporter-related protein (RefSeq)
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__PV4:5210884 Length = 243 Score = 138 bits (348), Expect = 9e-38 Identities = 82/249 (32%), Positives = 140/249 (56%), Gaps = 15/249 (6%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 +L+ + L K + V DV+L + G++VGL+GPNGAGKTT F ++ G+ + +G + + Sbjct: 5 ILKAENLAKSYKSRAVVQDVSLTVKTGQIVGLLGPNGAGKTTTFYMVVGLVQSDKGRIFI 64 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122 D L + A G+G Q +F+ L+V DN++ S L Sbjct: 65 DDDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNIMAVLQTR-------SDLNNDG-- 115 Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182 E+EL+ LL+ F + ++ LS G++RR+EI RALA PK + LDEP AG+ Sbjct: 116 -REEELE----HLLEEFHITHIRDSHGMALSGGERRRVEIARALAANPKFILLDEPFAGV 170 Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242 +P ++ ++I ++K+ + +++ +H++ ++V E+ Y++ +G LIA+GTP EI N Sbjct: 171 DPISVIDIKKIIEQLKNR-GLGVLITDHNVRETLDVCEKAYIVSHGNLIAEGTPAEILDN 229 Query: 243 KRVIEAYLG 251 ++V YLG Sbjct: 230 QQVRAVYLG 238 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: 148 Number of extensions: 9 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: 243 Length adjustment: 24 Effective length of query: 230 Effective length of database: 219 Effective search space: 50370 Effective search space used: 50370 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