Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate Ac3H11_4985 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:D8IUY5 (404 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4985 Length = 345 Score = 153 bits (387), Expect = 6e-42 Identities = 115/379 (30%), Positives = 187/379 (49%), Gaps = 72/379 (18%) Query: 16 RISLLLLLALMIVFPFVAQQFGNSWVRIMDVALLYIMLALGLNVVVGFAGLLDLGYIAFY 75 ++ L + AL+++FPF+A + W+ + + + + A GLN++ G+ GL+ LG AF Sbjct: 23 KVWLAVGAALLVLFPFMASDY---WLYLACLVSINVASATGLNILTGYTGLVSLGQAAFM 79 Query: 76 AIGAYSAGLLASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNGIHLSLWLIVPISAFL 135 +GAY+ AV+E+ V T P V N L F+ Sbjct: 80 GLGAYTV---------AVLETKVGT-PFVLNLLA----------------------GGFV 107 Query: 136 AALFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGINLIDPIKVF 195 A L G ++G P+L+++G YLAI T+ I N T G G+++ Sbjct: 108 AMLGGIVVGIPSLRVKGLYLAIATIAASFIAHFIFANWK----FTGGTGGLSV------- 156 Query: 196 GVSLAGEPGSGSMVKVFGMSMPSVNAYYFLFLLLCIGVIFFSVRLQDSRLGRAWVAIRED 255 K+FGM++ + Y+L + + I ++ + L +R+GRA++AIR+ Sbjct: 157 -----------PPAKLFGMALDTSFRLYWLIVPVTILMLLGAANLFRTRVGRAFIAIRDR 205 Query: 256 EIAAKAMGINTRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSLTESIAVLAMVVLG 315 +I+A+ +GI KLL+F + + + GVAG ++ F V+PESF L SI LA +++G Sbjct: 206 DISAEVLGIPLLRYKLLSFGLSSFYAGVAGGLWAYFFRVVTPESFPLLMSIFFLAAIIVG 265 Query: 316 GIGHIPGVVLGGVILAALPEVLRHVVE-------------PVQMAIFGKVWIDAEVLRQL 362 G+G I G +LG V + +PE+L+ VV+ PV+ IFG + I V Sbjct: 266 GMGSILGGILGAVFMTMVPELLKLVVDLMPGGSELTVLLSPVRTVIFGLLIIGFLVFEP- 324 Query: 363 LYGLAMVVIMLTRPAGLWP 381 +GLA V + R LWP Sbjct: 325 -HGLAEVWRRVRRFFHLWP 342 Lambda K H 0.327 0.143 0.430 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: 372 Number of extensions: 22 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: 404 Length of database: 345 Length adjustment: 30 Effective length of query: 374 Effective length of database: 315 Effective search space: 117810 Effective search space used: 117810 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 (21.7 bits) S2: 50 (23.9 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