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_028997558.1 H537_RS0108420 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQH9 (318 letters) >NCBI__GCF_000430725.1:WP_028997558.1 Length = 284 Score = 176 bits (447), Expect = 5e-49 Identities = 95/263 (36%), Positives = 150/263 (57%), Gaps = 3/263 (1%) Query: 35 YVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYAAAIIGSKSPTYGAFFGAM 94 Y ++ +G N +LA+ + L + G ++ + FM IGAY A+++ + T F A+ Sbjct: 11 YSNLVLTLGTNALLALSIYLTLS-CGLLAMANGAFMGIGAYTASLLSMNTAT--PFPLAL 67 Query: 95 LVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFIINGGSLTNGAAGILGIPNF 154 L G VA L+G PTLRL G YLA+ATLG E++RI I+N T GA G+ GIP Sbjct: 68 LAGMAAPAVVAFLIGKPTLRLSGVYLAMATLGFGEVVRILILNTEDWTGGALGLNGIPQL 127 Query: 155 TTWQMVYFFVVITTIATLNFLRSPIGRSTLSVREDEIAAESVGVNTTKIKIIAFVFGAIT 214 T W V F VV R+ IGR+ +++EDE AA +G++ K++AFV GA Sbjct: 128 TQWWHVLFAVVAALFVLWQLRRTRIGRAFEAIKEDETAAALMGIDIAAHKMLAFVLGAAL 187 Query: 215 ASIAGSLQAGFIGSVVPKDYTFINSINVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDV 274 A +AG+L A + P +Y F + +L + + GG+ +TG ++ A++L +L +L+ + Sbjct: 188 AGLAGALNAHLTFFIGPNEYGFDRGVEILTMAILGGINGLTGPVLGAVILTLLPEVLRGL 247 Query: 275 ASVRMIIYALALVLVMIFRPGGL 297 R+++ L LV++ +F P GL Sbjct: 248 RDFRLVVNGLILVVITLFLPRGL 270 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: 197 Number of extensions: 8 Number of successful extensions: 1 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: 284 Length adjustment: 27 Effective length of query: 291 Effective length of database: 257 Effective search space: 74787 Effective search space used: 74787 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: 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