Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_012333613.1 M446_RS18405 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQH9 (318 letters) >NCBI__GCF_000019365.1:WP_012333613.1 Length = 295 Score = 160 bits (404), Expect = 5e-44 Identities = 96/295 (32%), Positives = 163/295 (55%), Gaps = 27/295 (9%) Query: 31 LNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYAAAIIGSKSPTYGAF 90 + + + IL GI ++LA+GLNL G +G + GH GF IGAY AA++ S + Sbjct: 1 MEAYIIAILIISGIYVLLALGLNLQYGLTGITNFGHVGFFCIGAYTAALLSQVSVPWPFA 60 Query: 91 FGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFIINGGSLTNGAAGILG 150 F L GA L+ A +G+ +L+L+ DY A+ +LG SE++RI + + LT G GI G Sbjct: 61 F---LAGAALAALAAWPLGLISLKLRDDYFAIVSLGFSEVVRIVVTSEKWLTKGVQGITG 117 Query: 151 IPNFTTW---------QMVYFFVVITTIATLN---FLRSPIGRSTLSVREDEIAAESVGV 198 IP + ++ V + +A L+ +RSP GR ++R++E A +++G Sbjct: 118 IPKLFAFLGTGTAQALAVLLLLVAVNMLAGLSKSRIVRSPFGRMIEAIRDNEEAVKALGK 177 Query: 199 NTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSINVLIIVVFGGLGSITGAI 258 + + KI + GA A IAG A +IG +VP+ + + + + + ++ GG+G I+GA+ Sbjct: 178 DPSTFKIQVLMLGAALAGIAGGFYAHYIGYIVPEQFIPLITFYIWMAIIIGGVGPISGAL 237 Query: 259 VSAIVL-----------GILNMLLQ-DVASVRMIIYALALVLVMIFRPGGLLGTW 301 V ++L G + + + ++AS+R+ + LALVL ++RP GL+G + Sbjct: 238 VGTLILMFFLEGSRFLRGFIPFVSEVEMASIRLGVIGLALVLFTLYRPQGLMGDY 292 Lambda K H 0.327 0.143 0.403 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: 207 Number of extensions: 11 Number of successful extensions: 5 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: 318 Length of database: 295 Length adjustment: 27 Effective length of query: 291 Effective length of database: 268 Effective search space: 77988 Effective search space used: 77988 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 (21.6 bits) S2: 48 (23.1 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