Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_041097011.1 SUTH_RS03125 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000828635.1:WP_041097011.1 Length = 358 Score = 120 bits (302), Expect = 4e-32 Identities = 105/336 (31%), Positives = 155/336 (46%), Gaps = 59/336 (17%) Query: 37 LLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHT 96 L+ L ALG+NI+VGY G + LG A AVGAY A D A A+ GL Sbjct: 57 LILSLAALGVNILVGYCGQITLGAGASMAVGAY--AAYNFLIRVDGMPALGAILLGGL-- 112 Query: 97 SLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEI-------IRIFLNNLDHP 149 +AA G + GAP+L++RG YLA+ TL I+ F NN Sbjct: 113 -----------VAAAAGIVFGAPSLRVRGLYLAVATLAAQFFWDWAFLRIKWFTNNASS- 160 Query: 150 VNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQD 209 SV V + L FG+ I+S T Y L ++VV ++ L Sbjct: 161 -------------GSVSVADISL------FGWTIDSPTDKYLFCLGVLVVFSLMAKNLVR 201 Query: 210 SRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQ-GFVSPESFS 268 IGR WMAIR+ ++AA +GI KL AF + + + GV+GA++G G P +FS Sbjct: 202 GSIGRQWMAIRDMDVAATVIGIRPMYAKLTAFAVSSFYLGVAGALWGMINLGSWEPAAFS 261 Query: 269 LMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRLDSAILR--Q 326 + S ++ MV++GG+G I G GA + LP L + + + + A++ + Sbjct: 262 IDRSFSLLFMVIIGGMGAISGSFFGAAFIVILPIFLNQMLPLIGGLFGLEVSIALVSHVE 321 Query: 327 LLIALAMIIIMLL-RPRG-------------LWPSP 348 +++ A+I+ L+ P G LWP P Sbjct: 322 IMVFGALIVFFLIVEPHGIARLWATGREKLRLWPFP 357 Lambda K H 0.328 0.144 0.430 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: 349 Number of extensions: 23 Number of successful extensions: 5 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: 358 Length of database: 358 Length adjustment: 29 Effective length of query: 329 Effective length of database: 329 Effective search space: 108241 Effective search space used: 108241 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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