Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_012966165.1 FERP_RS08405 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000025505.1:WP_012966165.1 Length = 233 Score = 211 bits (536), Expect = 1e-59 Identities = 102/233 (43%), Positives = 160/233 (68%), Gaps = 1/233 (0%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 +L+ +L YG +Q + V+ +VN+G + +++GANG GKTT L+T+ G+++P G + F Sbjct: 1 MLETRDLESGYGEMQVLWGVNLKVNKGSITTILGANGVGKTTTLKTIFGIIKPWKGTVTF 60 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSR 122 +++ + V G++ VPEGRH+FP +TV ENL +GA+ K+ E + NL V+ Sbjct: 61 KREDVTLKKPHEKVEMGIAYVPEGRHLFPLMTVEENLRLGAYTKRAEERFEENLSFVYDL 120 Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDI 182 FP L+ER+ Q A TLSGGEQQML + RALMS+P+L+L+DEPS GLAP + ++F++I+ + Sbjct: 121 FPILKERRKQRAGTLSGGEQQMLTIARALMSSPELILMDEPSQGLAPKVVMDLFEVIRKL 180 Query: 183 QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 ++ G T+LL+EQN +L I+D Y++ G+I G E+ S E++RKAY+G Sbjct: 181 KEGGLTILLVEQNVYASLEIADYVYLMSEGRIFAEGRRDEI-SEEDIRKAYVG 232 Lambda K H 0.315 0.134 0.358 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: 175 Number of extensions: 4 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: 236 Length of database: 233 Length adjustment: 23 Effective length of query: 213 Effective length of database: 210 Effective search space: 44730 Effective search space used: 44730 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 46 (22.3 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