Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_078715624.1 B5D49_RS00115 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_900167125.1:WP_078715624.1 Length = 219 Score = 80.1 bits (196), Expect = 4e-20 Identities = 66/216 (30%), Positives = 102/216 (47%), Gaps = 44/216 (20%) Query: 6 MTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTV 65 M+T+PLL +E +G + DV+ + G++ + GPNGAGKTTL + G P+ Sbjct: 1 MSTSPLLRLEKAAKFYGAKLVFRDVTCAVEPGQVMLVAGPNGAGKTTLLKVMAGLSRPSA 60 Query: 66 GRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRAS 125 G + L +P R + TF L+ G++ L+NL Sbjct: 61 GTVRL-----------DVPPERTAYLGHA--TF----LYPGLTALQNL------------ 91 Query: 126 GFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCT 185 GF A + GL R+ ++ +++ L+RV L+ A+ AG+ G +RL +AR Sbjct: 92 GF-WARMYGL---RRSRKQLMEM----LERVGLVRVAEERAGSFSRGMSQRLNLARVFLV 143 Query: 186 EPVMLCLDEPAAGLN-------PRESGELADLLTYI 214 +P +L LDEP GL+ RE G LA+ T I Sbjct: 144 DPALLFLDEPGTGLDVTSLALLRREIGRLAEAGTSI 179 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: 142 Number of extensions: 6 Number of successful extensions: 2 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: 219 Length adjustment: 24 Effective length of query: 270 Effective length of database: 195 Effective search space: 52650 Effective search space used: 52650 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