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_029134108.1 A3GO_RS0115075 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000428045.1:WP_029134108.1 Length = 233 Score = 191 bits (484), Expect = 1e-53 Identities = 96/233 (41%), Positives = 154/233 (66%), Gaps = 4/233 (1%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 +L L YG QA+ + FE++ E+V++IGANGAGK+T L+ L+GL++ + + Sbjct: 4 LLSTHKLKAFYGDFQALFGIDFEIHTHEIVAIIGANGAGKSTFLKALTGLLQVDKESVFY 63 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSR 122 G+ + +IV+ G++ VPEGR +FP L+V ENL+MG F + E + LK++++ Sbjct: 64 KGENLGGCRPHEIVSNGIAMVPEGRRLFPSLSVAENLKMGQFTGR---EGRWTLKQIYAL 120 Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDI 182 FP LEE+++ A +LSGG+QQM+++GRALMS P+LL+ DE S+GLAPI I+EI+ + I Sbjct: 121 FPILEEKQDMPATSLSGGQQQMVSIGRALMSNPELLICDEISLGLAPIVIKEIYAALGKI 180 Query: 183 QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 ++G T +++EQ+ A +S R Y L+ G++ L G E+ + +E+ AY G Sbjct: 181 TQEGLTAIIVEQDVGTAKRVSQRLYCLQEGRVSLQGNSDEV-THDEIAHAYFG 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: 166 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: 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