Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_013403237.1 CALHY_RS06835 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000166355.1:WP_013403237.1 Length = 256 Score = 202 bits (515), Expect = 5e-57 Identities = 113/263 (42%), Positives = 162/263 (61%), Gaps = 9/263 (3%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L ++++T+ FGG+VA+N+V+ G I +IGPNGAGKTT+FN I+G Y P GR+ Sbjct: 1 MLRIKNVTVNFGGIVALNNVNIDIEKGAIIGLIGPNGAGKTTVFNVISGIYNPNTGRIEF 60 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 + D + Y++S ++RTFQNIRLF +SV++N+ ++ H + S Sbjct: 61 SNYD-----ITYKKTYQVSA-LGISRTFQNIRLFKELSVIDNVKISFHKNI---SYNLFD 111 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 + + + E + A+ L L E A NLPYG QR+LEI RA+ T P +L Sbjct: 112 AIFRTSKFLKEEEQNHKKAEELLKIFGLYEKRFELAKNLPYGEQRKLEIVRALATSPKLL 171 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEPAAG+NP+E+ EL L+ +I++ + +LLIEHDMSVVM I + + VLDYG I+ Sbjct: 172 LLDEPAAGMNPQETQELKKLIKFIKERFDLTILLIEHDMSVVMDICEKIYVLDYGEVIAV 231 Query: 251 GDPAFVKNDPAVIRAYLGEEEDE 273 G P VKN+P VI AYLGE + E Sbjct: 232 GTPVEVKNNPRVIEAYLGEGDLE 254 Lambda K H 0.319 0.137 0.397 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: 188 Number of extensions: 6 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: 294 Length of database: 256 Length adjustment: 25 Effective length of query: 269 Effective length of database: 231 Effective search space: 62139 Effective search space used: 62139 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 (21.8 bits) S2: 47 (22.7 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