Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_012589117.1 MSIL_RS00330 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000021745.1:WP_012589117.1 Length = 265 Score = 199 bits (507), Expect = 4e-56 Identities = 119/265 (44%), Positives = 162/265 (61%), Gaps = 14/265 (5%) Query: 6 MTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTV 65 M+ PLL ++ LT+R+GGL AV D+ G + A+IGPNGAGKT+LFN I+G Sbjct: 1 MSAAPLLNIKGLTLRYGGLAAVEDLDLIVAEGALDALIGPNGAGKTSLFNLISGLTRQDD 60 Query: 66 GRLTLRHADGKEFLLERMPGYRISQKA--SVARTFQNIRLFGGMSVLENLIVAQHNKLIR 123 G + L A R+ SQ+A +ARTFQN+RLF + +EN++V H + Sbjct: 61 GEIWLGGA--------RIDRLSPSQRARRGLARTFQNLRLFTETTAIENVLVGMH---LH 109 Query: 124 ASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAM 183 G + L + + ER AVD A+ L V L AG+L YG QRRLEIARA+ Sbjct: 110 VGGSLLEILTRFGRFRQAERAAVDAARELLAFVGLSSVEYAPAGSLSYGDQRRLEIARAL 169 Query: 184 CTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLD 243 +P +L LDEPAAG+NP E+ L LL +R + KI +LL+EHDMS+VM + D + VL+ Sbjct: 170 AAKPKLLLLDEPAAGMNPAETAALRLLLEKLRAQ-KISMLLVEHDMSLVMRLCDKITVLN 228 Query: 244 YGRKISDGDPAFVKNDPAVIRAYLG 268 +GRKI++G P V+ +PAVI AYLG Sbjct: 229 FGRKIAEGPPDAVRANPAVIEAYLG 253 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: 204 Number of extensions: 10 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: 265 Length adjustment: 26 Effective length of query: 268 Effective length of database: 239 Effective search space: 64052 Effective search space used: 64052 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