Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate 3608584 Dshi_1978 inner-membrane translocator (RefSeq)
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__Dino:3608584 Length = 317 Score = 140 bits (352), Expect = 7e-38 Identities = 99/316 (31%), Positives = 154/316 (48%), Gaps = 41/316 (12%) Query: 114 VDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALL------SHY--FGLS 165 V AT+ I + LGLN+ G GL + G V F+ G Y+ +L +H FGL Sbjct: 9 VFFATIASILAIAVLGLNLHWGNTGLFNGGVVAFFGAGGYATLILGGTPQAAHLGGFGLP 68 Query: 166 FWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGIS 225 + + L ++A +L+G +RLR DYLAI T G +RN + GG +G+ Sbjct: 69 YGLALLGGLVIAGLLAWLVGLLTIRLRHDYLAIATFGVAVAFENLVRNAQRLAGGASGLR 128 Query: 226 NIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLR 285 FER A+ + GL YN+ F +++A L+A + RL+R Sbjct: 129 G----------FERPLADTIPP-----GLAYNA---AFFAFVLAALIA--TYLGLERLIR 168 Query: 286 MPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTF 345 P GR A+REDE A RALG +P I+L+AF +G+ G AG+ +A ++P+ Sbjct: 169 GPFGRLLRAIREDETAARALGKSPDRIRLTAFVIGSVILGLAGALYATFYAFISPQDVLP 228 Query: 346 IESAIILAIVVLGGMGSQLGVILAAIVM-------------ILLPEMMREFSEYRMLMFG 392 I + I A++++GG G+ G I A ++ E+ + ++ G Sbjct: 229 ILTFQIWAMLIVGGAGNNRGAIAGAFLIWGAWTASGWALSRFAPIEVQLYTGSIQFVLIG 288 Query: 393 ALMVLMMIWRPQGLLP 408 ++V M++WRPQGL P Sbjct: 289 CVIVGMLLWRPQGLFP 304 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: 453 Number of extensions: 32 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: 418 Length of database: 317 Length adjustment: 29 Effective length of query: 389 Effective length of database: 288 Effective search space: 112032 Effective search space used: 112032 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 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