Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_041096232.1 SUTH_RS00450 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQH9 (318 letters) >NCBI__GCF_000828635.1:WP_041096232.1 Length = 358 Score = 172 bits (435), Expect = 1e-47 Identities = 108/323 (33%), Positives = 173/323 (53%), Gaps = 31/323 (9%) Query: 22 ISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYAAAIIG 81 +++L + +L+ + + + IGI I+ +GL L+ GF+GQ SLGHAGF+A+GAY A + Sbjct: 30 LALLAAPWLLSEYTLSQITFIGIYAIVCLGLMLLAGFTGQVSLGHAGFLAMGAYTEAYLQ 89 Query: 82 SKSPTYGAFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFIINGGSL 141 F ++ + AL++G +++G+P LR+KG YL++ATL I+ ++ + Sbjct: 90 GLG---WPFLISLPMSALVAGITGIMIGLPALRVKGMYLSIATLAFGFILEEVVVRAEHI 146 Query: 142 TNGAAG-------ILGIPNFTTWQMVYFFV----VITTIATLNFLRSPIGRSTLSVREDE 190 T G AG I GI NF Y+ V V+ + LN LRSP GR+ +++R+ E Sbjct: 147 TGGNAGRQLGNLTIAGI-NFDDGTHFYYLVTGIAVLCILGALNLLRSPTGRAFVAIRDSE 205 Query: 191 IAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSINVLIIVVFGG 250 ++A+S+G+N K AF A A IAG+L A I + P + F+ SI +L++VV GG Sbjct: 206 VSAQSMGINLAHYKTTAFALSAALAGIAGALYAHKIRFITPDQFGFLQSIELLMMVVIGG 265 Query: 251 LGSITGAIVSAIVLGILNML-----------LQDVASVRMIIYALALVLVMIFRPGGLLG 299 LGSI GAI ++ L L ++ I+ L+ +++F P GL G Sbjct: 266 LGSIQGAIFGPAFWFLVQQLIVTGKDWLPPALGQQTGLQPTIFGFILIAIVLFEPLGLYG 325 Query: 300 TW-----ELSLSRFFKKSKKEEQ 317 W L + F++K + Q Sbjct: 326 RWLKFRTFLEIFPFYRKGMFKRQ 348 Lambda K H 0.327 0.143 0.403 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: 232 Number of extensions: 17 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: 318 Length of database: 358 Length adjustment: 28 Effective length of query: 290 Effective length of database: 330 Effective search space: 95700 Effective search space used: 95700 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 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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