Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate YP_426837.1 Rru_A1750 inner-membrane translocator
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000013085.1:YP_426837.1 Length = 452 Score = 427 bits (1098), Expect = e-124 Identities = 211/328 (64%), Positives = 262/328 (79%), Gaps = 2/328 (0%) Query: 93 WIVLALIVGALVWPF--FGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAV 150 +I LA +V A+V+P F +R VD+AT +IY+MLG GLNIVVGLAGLLDLGYV FYAV Sbjct: 113 FIGLAALVLAIVFPITPFSNRYYVDVATTWMIYIMLGWGLNIVVGLAGLLDLGYVAFYAV 172 Query: 151 GAYSYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLF 210 GAYSYALLS FG SFW+CLP+AG+ AA FG +LGFPVLRLRGDYLAIVTLGFGEIIR+ Sbjct: 173 GAYSYALLSQTFGWSFWVCLPLAGVFAAFFGVVLGFPVLRLRGDYLAIVTLGFGEIIRVV 232 Query: 211 LRNLTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVAL 270 L N +T GP+GIS IE+P+FFGL F R A EG +TFH++FG+ Y+ ++VIFL+ + L Sbjct: 233 LLNWYAVTNGPDGISGIERPSFFGLDFARTAPEGGETFHQFFGISYSPDHRVIFLFYLIL 292 Query: 271 LLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSF 330 LA+ R+ R+P+GRAWEALREDEIACR+LG+NPT +KLSAF LGA F GFAGSF Sbjct: 293 ALAVLTNIFTGRIRRLPVGRAWEALREDEIACRSLGINPTNVKLSAFALGAMFGGFAGSF 352 Query: 331 FAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREFSEYRMLM 390 FA RQG ++PESFTF+ESA+ILAIVVLGGMGSQ+GV++AA +++LPE+ REF ++RM Sbjct: 353 FATRQGFISPESFTFMESAVILAIVVLGGMGSQIGVVIAAFFLVVLPEVFREFDQFRMFF 412 Query: 391 FGALMVLMMIWRPQGLLPMQRPHMELRK 418 FGA MV +M+WRP+GLL + P + K Sbjct: 413 FGAAMVAVMVWRPRGLLSYRDPTILFEK 440 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: 625 Number of extensions: 31 Number of successful extensions: 1 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: 452 Length adjustment: 32 Effective length of query: 386 Effective length of database: 420 Effective search space: 162120 Effective search space used: 162120 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: 51 (24.3 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