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_076582356.1 BB347_RS07330 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_001971705.1:WP_076582356.1 Length = 383 Score = 112 bits (280), Expect = 1e-29 Identities = 77/249 (30%), Positives = 136/249 (54%), Gaps = 28/249 (11%) Query: 1 MSVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKI 60 M+ + ++ L YG AV DVS E+++GE++ L+G +G+GK+T LR L+GL P+ G I Sbjct: 1 MTDITLQGLEKRYGETTAVEDVSVEIDDGELLCLLGPSGSGKSTTLRMLAGLETPTEGAI 60 Query: 61 EFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLK-----KNREENQAN 115 G+++ PA S V + +FP TV+EN+ G ++ + RE QA Sbjct: 61 RLDGEDVTDQPAYD---RNTSTVFQDWALFPHKTVLENVAFGLKMRDVSKDERRERAQAM 117 Query: 116 LKKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGL-------A 168 L++V ++ ++D TLSGG++Q +A+ R+L P +LLLDEP L Sbjct: 118 LERV-----QMGGYDDEDPTTLSGGQKQRVALARSLAVNPDVLLLDEPLSNLDKRLREDM 172 Query: 169 PIFIQEIFDIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEE 228 I ++EI D +++ T + + + ++A ++DR ++ G+++ G E+ + + Sbjct: 173 QIELREIHDDLEE------TFVHVTHDQDEAFTLADRIGIMNEGELIQVGDPDEVYENPK 226 Query: 229 VR--KAYLG 235 R +A+LG Sbjct: 227 NRFIEAFLG 235 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: 178 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: 383 Length adjustment: 27 Effective length of query: 209 Effective length of database: 356 Effective search space: 74404 Effective search space used: 74404 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: 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