Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate H281DRAFT_05513 H281DRAFT_05513 branched-chain amino acid transport system permease protein
Query= SwissProt::P22729 (425 letters) >FitnessBrowser__Burk376:H281DRAFT_05513 Length = 597 Score = 143 bits (361), Expect = 1e-38 Identities = 98/317 (30%), Positives = 159/317 (50%), Gaps = 25/317 (7%) Query: 88 KQKLFLVALLVLAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYA 147 K FL A+L+ + W + G + IA I +G+N++VGLSG + LG FYA Sbjct: 15 KAPYFLCAILLAGLPWIWSGGFG-IHIAQSFCYTAIAVIGVNLLVGLSGQMSLGQAAFYA 73 Query: 148 IGAYTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRI 207 IGAY L + G + +AAA G ++G LR RG YLA+ TL G +V I Sbjct: 74 IGAYASVLTSLKLGWPIAASVLFGVAVAAAVGTVVGVFALRTRGLYLAMTTLAVGFVVSI 133 Query: 208 LLLNNTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLV 267 L +TGG G+S +P+ ++F T W +LY+V Sbjct: 134 LAQRWVGLTGGTMGLSGVPQ-----VDFGDTIHGEIW------------------YLYVV 170 Query: 268 ALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAG 327 L+V+ + + + + +GR A R+ E S+G+ ++ F +SAA AG +G Sbjct: 171 GGTLLVVQI-LNDYVFDSRIGRCLLATRDSEAFAASVGIKVPIVRSAIFAVSAALAGLSG 229 Query: 328 TLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSM 387 LFA + GFV ++F+ S +L V+GG+G++ + +L+ EL+ + Y + Sbjct: 230 GLFAHQSGFVGSDAFSVTLSLSLLIAAVIGGLGARIGPLAGTAILMTIVELVAGLDRYGL 289 Query: 388 LMLGGLMVLMMIWRPQG 404 ++ GG+M+L+++ PQG Sbjct: 290 MVYGGIMLLVLLVFPQG 306 Lambda K H 0.330 0.145 0.436 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: 432 Number of extensions: 8 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: 425 Length of database: 597 Length adjustment: 34 Effective length of query: 391 Effective length of database: 563 Effective search space: 220133 Effective search space used: 220133 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 52 (24.6 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