Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate AZOBR_RS32280 AZOBR_RS32280 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQH9 (318 letters) >FitnessBrowser__azobra:AZOBR_RS32280 Length = 323 Score = 163 bits (412), Expect = 6e-45 Identities = 96/305 (31%), Positives = 166/305 (54%), Gaps = 29/305 (9%) Query: 12 LLLLLAGYSLISVLVS------VGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLG 65 LL LLAG +L+ V+ + ++ LFY +LA LNL+VG+ G+FSLG Sbjct: 8 LLALLAGAALLPFAVTDQYILHLAIMALFYA----------VLASSLNLVVGYVGEFSLG 57 Query: 66 HAGFMAIGAYAAAIIGSKSPTYGAFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATL 125 H F+ GAY AA++ +++ + + + L+S +G TLRL+G Y + TL Sbjct: 58 HTAFLGTGAYTAALLSTQAGM--PMWMTIPLAGLVSAVFGFAIGAITLRLQGPYFVIVTL 115 Query: 126 GVSEIIRIFIINGGSLTNGAAGILGIP-----NFTTWQMVYFFVVITTIATL------NF 174 +E++RI N ++TNG G+ G+ N FF+++ IA + F Sbjct: 116 SFAEVLRIVANNWIAVTNGPMGLAGVGQTLFGNVAVTDKAGFFLIVLGIAAVALYLSYRF 175 Query: 175 LRSPIGRSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDY 234 + S GR+ ++VRE+ A+S+GV+ + AFV GA A +AG A +I V P+ + Sbjct: 176 VYSNAGRAAVAVRENRYVAQSIGVDPFGTAMQAFVLGAFLAGLAGGFYAHYISFVGPEVF 235 Query: 235 TFINSINVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDVASVRMIIYALALVLVMIFRP 294 F ++I+V+ GG G++ G + A+++ +L L++V +R+ ++ L ++ +++F P Sbjct: 236 RFAFMATMIIMVLLGGKGTLIGPLAGAVIVTVLEEYLREVQELRLTLFGLIVMAIVLFLP 295 Query: 295 GGLLG 299 GL+G Sbjct: 296 NGLMG 300 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: 209 Number of extensions: 10 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: 318 Length of database: 323 Length adjustment: 28 Effective length of query: 290 Effective length of database: 295 Effective search space: 85550 Effective search space used: 85550 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 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