Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_013075385.1 BTUS_RS06870 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000092905.1:WP_013075385.1 Length = 452 Score = 265 bits (677), Expect = 2e-75 Identities = 148/354 (41%), Positives = 213/354 (60%), Gaps = 25/354 (7%) Query: 5 KTNWIIGAVALLVLPLILQSFGNAWVRIADLAL---LYVLLALGLNIVVGYAGLLDLGYV 61 K WI AV L + + S G A+ ++A +Y+ +A+GLNIVVG+AGLLDLG+V Sbjct: 61 KVQWIWAAVVLGAILPLAASTGPAYESYMEVATQMGIYIAMAVGLNIVVGFAGLLDLGFV 120 Query: 62 AFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTL 121 AF+++GAY +A+ S + P GL W+ +P+ +A FG +LG P L Sbjct: 121 AFFSLGAYTYAIFFSDQANQFLSGHHFPLPGGL---FWLFLPLGMFIAGLFGVLLGLPVL 177 Query: 122 KLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGF 181 +++GDYLAIVTLGFGEIIRI NNLD PVN+TNG G+ + ++FG+ F F Sbjct: 178 RVKGDYLAIVTLGFGEIIRIIFNNLDKPVNITNGAIGISSVRPPELFGV-------TFTF 230 Query: 182 DINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAF 241 + YYYL LVL+ +RL+ SRIGRAW A+REDEIAA+AMG+ KL AF Sbjct: 231 PHH----YYYLVLVLLAGVFYAVHRLEHSRIGRAWKAVREDEIAAQAMGVPLVRTKLTAF 286 Query: 242 GMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVL----- 296 GASF G+ G +F A Q F+ P SF+++ES+ I+ MV+LGG+G +PG ++GA L Sbjct: 287 AAGASFSGLMGVVFAAKQAFIDPTSFTMLESITILVMVILGGMGSLPGAVVGACLVTVLN 346 Query: 297 LSALPEV---LRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPS 347 L LP++ L +A L + +++ L + +I+ + RP+G+ P+ Sbjct: 347 LQLLPQLTNWLNQLAAQGMISFPPALSPSKMQRFLFGMLLILFTVFRPKGVLPA 400 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: 439 Number of extensions: 12 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: 452 Length adjustment: 31 Effective length of query: 327 Effective length of database: 421 Effective search space: 137667 Effective search space used: 137667 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