Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_013529094.1 MESCI_RS06155 ATP-binding cassette domain-containing protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000185905.1:WP_013529094.1 Length = 518 Score = 350 bits (899), Expect = e-101 Identities = 173/276 (62%), Positives = 217/276 (78%), Gaps = 5/276 (1%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L V+HL+M+FGGLVA+ D+SF+A GEITA+IGPNGAGKTT+FNCITGFY P+ G +TL Sbjct: 17 ILQVDHLSMKFGGLVAIGDLSFAAKRGEITALIGPNGAGKTTVFNCITGFYKPSEGMITL 76 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 DG FLLER+P + I +A VARTFQNIRLF GM++LENL+VAQHNKL++ASG+++ Sbjct: 77 NRNDGSTFLLERLPNHEIPARAKVARTFQNIRLFSGMTLLENLLVAQHNKLMKASGYTVL 136 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 GL G Y + E+V+LAK+WL++ L++ AD AG+LPYGAQRRLEIARAMCT P +L Sbjct: 137 GLFGFSGYRKASAESVELAKHWLEKADLVDRADDPAGDLPYGAQRRLEIARAMCTGPELL 196 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 CLDEPAAGLNP+ES L +LL I++ +LLIEHDMSVVM ISDHVVVL+YGRKISD Sbjct: 197 CLDEPAAGLNPKESAALNELLIDIKNTSGASILLIEHDMSVVMQISDHVVVLEYGRKISD 256 Query: 251 GDPAFVKNDPAVIRAYLGEEEDEELPPEIKADLPEV 286 G P V+ DP VI AYLG +++ E++A L EV Sbjct: 257 GSPQSVRTDPRVIAAYLGVDDE-----EVEAVLTEV 287 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: 390 Number of extensions: 14 Number of successful extensions: 1 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: 518 Length adjustment: 30 Effective length of query: 264 Effective length of database: 488 Effective search space: 128832 Effective search space used: 128832 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: 50 (23.9 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