Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_013525179.1 MESCI_RS31065 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000185905.1:WP_013525179.1 Length = 254 Score = 228 bits (582), Expect = 8e-65 Identities = 128/261 (49%), Positives = 169/261 (64%), Gaps = 9/261 (3%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 LL V L + FGGL ++D+SFS G I ++IGPNGAGKT+LFNC+TGFY P G ++L Sbjct: 3 LLEVRDLRLSFGGLKVLHDISFSVEKGAINSLIGPNGAGKTSLFNCLTGFYKPKGGSISL 62 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 G+ + +P +RI+ +ARTFQNIRLF MSVLEN + QH R+ ++ Sbjct: 63 ---SGRP--ITGLPPHRITA-LGLARTFQNIRLFKEMSVLENAMSGQH---CRSRHGIVS 113 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 +L LP+ R E + WL V + + A AG L YG QRRLE+ARA+ + P ++ Sbjct: 114 AILHLPAQRREEEAIRAIGMRWLGFVGIEQHAHRRAGGLSYGDQRRLELARALASAPELI 173 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEPAAGLN RE +L L+ IRDE + VLLIEHDM +VM +S+ +VV DYG+KI+D Sbjct: 174 LLDEPAAGLNEREKLDLIHLIRRIRDETGVTVLLIEHDMGLVMQVSEKIVVFDYGQKIAD 233 Query: 251 GDPAFVKNDPAVIRAYLGEEE 271 G P V+ DP VI AYLG E+ Sbjct: 234 GAPEAVRADPRVIEAYLGTED 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: 210 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: 254 Length adjustment: 25 Effective length of query: 269 Effective length of database: 229 Effective search space: 61601 Effective search space used: 61601 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