Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012335137.1 M446_RS26260 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000019365.1:WP_012335137.1 Length = 475 Score = 261 bits (668), Expect = 2e-74 Identities = 152/323 (47%), Positives = 202/323 (62%), Gaps = 27/323 (8%) Query: 29 WVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAA 88 W+ +A L L YV+L GLNIVVG AGLLDLGYVAFYAVGAY +AL+++ Sbjct: 147 WIDLAILVLTYVMLGWGLNIVVGLAGLLDLGYVAFYAVGAYTYALLSTT----------- 195 Query: 89 MFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDH 148 S WI +P+A LLAA +G +LG P L+LRGDYLAIVTL FGEIIR+ L N Sbjct: 196 -----FGFSFWICLPLAGLLAACWGMLLGFPVLRLRGDYLAIVTLAFGEIIRLVLINW-- 248 Query: 149 PVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDI-------NSVTLYYYLFLVLVVVSV 201 + + G G+ I V FGL + F + + V YYL L L +++ Sbjct: 249 -TDFSGGAAGISSIPRVTFFGLPFSADEDGFAATLGIAFSPMHRVVFLYYLILALALLTN 307 Query: 202 IICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGF 261 + R++ +GRAW A+REDEIA +++GINT N KL AF +GA FGG +G+ F QGF Sbjct: 308 GVTLRMRRLPLGRAWEALREDEIACRSLGINTTNTKLTAFALGAMFGGFAGSFFAVRQGF 367 Query: 262 VSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRLDS 321 VSPESF+ +ES +I+A+VVLGG+G GV + AV + A PE+LR + G L+A+ D Sbjct: 368 VSPESFNFLESAIILAIVVLGGMGSQIGVAIAAVAMVAGPELLRNL-GFLKAVFGEGFDP 426 Query: 322 AILRQLLIALAMIIIMLLRPRGL 344 + R LL LAM+++M+ RPRGL Sbjct: 427 SEYRLLLFGLAMVLMMIWRPRGL 449 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: 462 Number of extensions: 21 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: 475 Length adjustment: 31 Effective length of query: 327 Effective length of database: 444 Effective search space: 145188 Effective search space used: 145188 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 24 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