Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate HSERO_RS20055 HSERO_RS20055 metal-dependent hydrolase
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__HerbieS:HSERO_RS20055 Length = 597 Score = 199 bits (505), Expect = 2e-55 Identities = 116/260 (44%), Positives = 159/260 (61%), Gaps = 10/260 (3%) Query: 10 PLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLT 69 PLL V+ + RFGGLVAVNDVSF GEI +IGPNGAGK+T FN +TG + GR+ Sbjct: 344 PLLEVDQINKRFGGLVAVNDVSFKVKAGEIVGLIGPNGAGKSTTFNLVTGLLHASGGRVG 403 Query: 70 LRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSI 129 D + +P I+ + +ARTFQ++RL GM+VLEN+ + H + GF Sbjct: 404 FNGRD-----IAGLPARAIA-RLGIARTFQHVRLLPGMTVLENVALGAHMR--SQQGFLK 455 Query: 130 AGLLGLPSYTRTEREA-VDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPV 188 + + R E +A +D A L RV L +AGNL G QR LEIARA+C +P+ Sbjct: 456 NTVNAMLHLERAEEQALLDEAARALHRVGLQHLMHEQAGNLALGQQRILEIARALCCDPL 515 Query: 189 MLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKI 248 +L LDEPAAGL E L+ +L +R + + +LL+EHDM VM ++DH+VV+++G KI Sbjct: 516 LLLLDEPAAGLRHLEKQALSKVLQELRAD-GMSILLVEHDMEFVMELTDHIVVMEFGAKI 574 Query: 249 SDGDPAFVKNDPAVIRAYLG 268 ++G P + PAVI AYLG Sbjct: 575 AEGTPQEIARHPAVIEAYLG 594 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: 424 Number of extensions: 27 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: 597 Length adjustment: 31 Effective length of query: 263 Effective length of database: 566 Effective search space: 148858 Effective search space used: 148858 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 Sep 17 2021. 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