Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AO353_13350 AO353_13350 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__pseudo3_N2E3:AO353_13350 Length = 432 Score = 242 bits (618), Expect = 1e-68 Identities = 145/346 (41%), Positives = 206/346 (59%), Gaps = 52/346 (15%) Query: 14 ALLVLPLILQSFGNAWV-RIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFA 72 AL+V+ ++ F + ++ + L L+YVLL LGLNIVVG AGLLDLGYVAFYA+GAY A Sbjct: 103 ALIVIAIVFPVFADKYLLTVVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLA 162 Query: 73 LMASPHLADNFAAFAAMFPNGLH---TSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLA 129 L G H W V+P++AL+AA G +LG P L++ GDYLA Sbjct: 163 L-------------------GYHYLGLGFWTVLPLSALMAALAGCILGFPVLRMHGDYLA 203 Query: 130 IVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL--------EVFGF 181 IVTLGFGEIIR+ L N ++ T GP G+ + S FG++ + E FG Sbjct: 204 IVTLGFGEIIRLILTNW---LSFTGGPNGM-PVPSPSFFGIEFTRVAKDGGIPFHEFFGT 259 Query: 182 DINSVTLYYYLFLVLVVVSVIICY---RLQDSRIGRAWMAIREDEIAAKAMGINTRNMKL 238 + N + +++ VL +V +++ Y RL +GRAW A+REDEIA +AMG+N +KL Sbjct: 260 EYNPNIKFMFIYAVLFLVVMLVLYIKHRLTRMPVGRAWEALREDEIACRAMGLNHVLVKL 319 Query: 239 LAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLS 298 AF +GAS G++G F ++QGFV+P SF+ ES +I+A+VVLGG+G GV++ A +L+ Sbjct: 320 SAFTLGASTAGLAGVFFASYQGFVNPTSFTFFESALILAIVVLGGMGSTVGVVIAAFVLT 379 Query: 299 ALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 PE+LR A R LL + M+++M+ +PRGL Sbjct: 380 VAPELLR--------------GFAEYRVLLFGILMVLMMIWKPRGL 411 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: 405 Number of extensions: 15 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: 358 Length of database: 432 Length adjustment: 31 Effective length of query: 327 Effective length of database: 401 Effective search space: 131127 Effective search space used: 131127 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: 50 (23.9 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