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_073039916.1 BUB04_RS12270 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQH9 (318 letters) >NCBI__GCF_900129305.1:WP_073039916.1 Length = 296 Score = 181 bits (459), Expect = 2e-50 Identities = 105/287 (36%), Positives = 174/287 (60%), Gaps = 15/287 (5%) Query: 31 LNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYAAAIIGSKSPTYGAF 90 +N + V + + I I+A GLN++VG++GQ SLGHA F IGAYA+A++ +K+ F Sbjct: 1 MNAYVVTVATLVAIQSIVACGLNVVVGYAGQISLGHAAFFGIGAYASALLTTKAGL--TF 58 Query: 91 FGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFIINGGSLTNGAAGILG 150 + A+ + ++G V LL+GIP+LR++ D+LA+ T+G++ I+ + GA GI G Sbjct: 59 WTALPLVIAITGLVGLLLGIPSLRVRDDFLAITTIGINFIVEAVFLYV-PFFGGALGIGG 117 Query: 151 IPNFTTWQ-----MVYFFVVITTIATLN-----FLRSPIGRSTLSVREDEIAAESVGVNT 200 IP T + + Y ++ + +A + F RS G + ++REDE AA S+G++ Sbjct: 118 IPRVTFFHVKMKGLPYLYLCLAFLALVLLVCRWFTRSWAGLACFALREDETAAASMGISP 177 Query: 201 TKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSINVLIIVVFGGLGSITGAIVS 260 + K++AFV G A + G+L A F+ + D++F S+ +L +VV GG+G++ G + Sbjct: 178 VRFKLLAFVLGTAMAGLGGALYAHFMRFISAGDFSFPVSVMLLSMVVLGGMGTLWGPTLG 237 Query: 261 AIVLGILNMLLQDVASVRMIIYALALVLVMIFRPGGLLGTWELSLSR 307 A++L L L + + +R +IY L L+L++ F+PGGLLG E SL R Sbjct: 238 AVILVSLPELFRPLLEIRFLIYTLLLLLMIRFQPGGLLG--EASLVR 282 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: 219 Number of extensions: 12 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: 296 Length adjustment: 27 Effective length of query: 291 Effective length of database: 269 Effective search space: 78279 Effective search space used: 78279 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