Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_011939016.1 GURA_RS10785 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000016745.1:WP_011939016.1 Length = 250 Score = 226 bits (577), Expect = 3e-64 Identities = 128/260 (49%), Positives = 171/260 (65%), Gaps = 10/260 (3%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L+V +T RFGG+ A+ DVSFS IT IIGPNGAGKTTLFN +TG YTPT G + L Sbjct: 1 MLSVRQITQRFGGITALEDVSFSIGKDLITGIIGPNGAGKTTLFNIVTGIYTPTSGSVLL 60 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 D + R+P + + V RTFQNI LFG M+VLEN++V H+K +SGF +A Sbjct: 61 GDKD-----ISRLPSEKRAYLGMV-RTFQNIELFGKMTVLENVMVGLHSK--SSSGF-LA 111 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 +P + R ER D A WL+ + + A EA NLP+G R LEIARA+ EP +L Sbjct: 112 CAFKMPWHLREERRIRDNAMRWLEFTGIADLAQQEAANLPFGKGRLLEIARALALEPKIL 171 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 +DEPAAGLN +E+ EL+ L+ IR E + V+L+EHDM +VM I D +VVL+ GRK+++ Sbjct: 172 LMDEPAAGLNSKETHELSLLIRKIR-EMGVTVVLVEHDMELVMDICDSIVVLNLGRKLAE 230 Query: 251 GDPAFVKNDPAVIRAYLGEE 270 G P ++ +P V+ AYLGEE Sbjct: 231 GTPREIQENPEVVAAYLGEE 250 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: 183 Number of extensions: 9 Number of successful extensions: 4 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: 250 Length adjustment: 25 Effective length of query: 269 Effective length of database: 225 Effective search space: 60525 Effective search space used: 60525 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 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