Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_078716394.1 B5D49_RS04215 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_900167125.1:WP_078716394.1 Length = 251 Score = 207 bits (527), Expect = 2e-58 Identities = 122/258 (47%), Positives = 163/258 (63%), Gaps = 10/258 (3%) Query: 12 LTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLR 71 L ++ +++ FGG+ A++ VSF GEI +IGPNGAGKTT+FN ITG Y P+ GR++ Sbjct: 4 LKLDDVSIHFGGVQALSKVSFELGGGEILGLIGPNGAGKTTIFNVITGVYRPSSGRVSY- 62 Query: 72 HADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAG 131 DG+ LL + P + KA +ARTFQNIRLF M+ +EN +VAQH R +G + Sbjct: 63 --DGRS-LLGKRPHQIL--KAGIARTFQNIRLFTAMTAVENCMVAQH---CRTAGSVLGA 114 Query: 132 LLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLC 191 + P+ R E + A L + + + AD A NLPYG QR LEIARA+ + P + Sbjct: 115 VFRTPAQRREESRTHERAMEALRFMGMEDKADEAARNLPYGRQRHLEIARALASHPQTIL 174 Query: 192 LDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDG 251 LDEPAAGLNP ES EL ++ I + I VLL+EHDM VVM + VVV+DYG+ I+ G Sbjct: 175 LDEPAAGLNPVESAELMRVIERIAAQ-GINVLLVEHDMKVVMGVCHRVVVMDYGQLIAKG 233 Query: 252 DPAFVKNDPAVIRAYLGE 269 P V+ DP VI AYLG+ Sbjct: 234 RPEEVQRDPKVIEAYLGQ 251 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: 179 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: 251 Length adjustment: 25 Effective length of query: 269 Effective length of database: 226 Effective search space: 60794 Effective search space used: 60794 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