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_018125396.1 B149_RS0111940 LPS export ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000375485.1:WP_018125396.1 Length = 241 Score = 141 bits (356), Expect = 1e-38 Identities = 81/236 (34%), Positives = 127/236 (53%), Gaps = 8/236 (3%) Query: 4 LKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFL 63 L +LS YG + V + + EVV L+G NGAGKTT L+G+V+P SG + Sbjct: 5 LSASDLSKRYGRKEVVHSIRLSLGREEVVGLLGPNGAGKTTTFYMLAGIVKPYSGDVYLN 64 Query: 64 GQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENL----EMGAFLKKNREENQANLKKV 119 G+ I +P + G+S +P+ +F LTV +NL E + + E L + Sbjct: 65 GRNITDLPLHERARLGVSYLPQESSIFRKLTVRQNLQIILEQTDMTPRQQRERADELMDM 124 Query: 120 FSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDII 179 FS + + +Q + LSGGE++ L + RAL+ +P +LLDEP G+ PI + +I +II Sbjct: 125 FS----ITKLADQASMYLSGGERRRLEIARALIMSPDFILLDEPFAGIDPIAVIDIQEII 180 Query: 180 QDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 ++ G +L+ + N + L I DR Y++ G I+L GT ++ S R+ YLG Sbjct: 181 SVLKSMGIGILISDHNVRETLNICDRAYLVYEGTIILDGTPADIVQSSRARQIYLG 236 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: 128 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: 241 Length adjustment: 23 Effective length of query: 213 Effective length of database: 218 Effective search space: 46434 Effective search space used: 46434 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