Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_012045993.1 BBTA_RS28615 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000015165.1:WP_012045993.1 Length = 332 Score = 155 bits (391), Expect = 2e-42 Identities = 100/325 (30%), Positives = 164/325 (50%), Gaps = 23/325 (7%) Query: 94 IVLALIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAY 153 + + +I G ++ P +R + I + + + +GLN+ +G AG + L F +GAY Sbjct: 12 LAIIVIAGLIIIPMNFNRYGLYILSQWAVMTIAAMGLNLTLGYAGQVSLAQGAFVGIGAY 71 Query: 154 SYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRN 213 A+L+ + G L + ++ G+LLG+P LR++ YLA VTL F ++ L RN Sbjct: 72 GAAILTTH-GWPLISALGLVIVICFIVGWLLGYPALRVQHHYLAFVTLAFSTLMFLVFRN 130 Query: 214 LTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLA 273 + +T G GISNI +P FG + F YL L Sbjct: 131 ESWLTNGIYGISNIPRPEIFGFPTRKPLP---------------------FYYLCLGSLG 169 Query: 274 LAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAA 333 L L + L+R P GRA+ ALRE+ I ++LG++ L AF +G+A G AG +A Sbjct: 170 LVTL-AMWWLIRSPWGRAFMALRENPIRAQSLGIDTRRYTLMAFAIGSALGGIAGVLYAP 228 Query: 334 RQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREFSEYRMLMFGA 393 V P F S +L +V++GG G LG L A++ +LLPE +R Y ++++ A Sbjct: 229 LTQYVDPVPFNLQLSLDLLMMVIVGGSGFMLGPFLGAMIAVLLPEWLRFAEGYYLMLYAA 288 Query: 394 LMVLMMIWRPQGLLPMQRPHMELRK 418 ++ ++I+ P G+L + ++ R+ Sbjct: 289 AVIALLIYSPSGILGILDRYLSSRR 313 Lambda K H 0.331 0.145 0.439 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: 403 Number of extensions: 29 Number of successful extensions: 3 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: 418 Length of database: 332 Length adjustment: 30 Effective length of query: 388 Effective length of database: 302 Effective search space: 117176 Effective search space used: 117176 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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