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_043745123.1 AMB_RS18175 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQH9 (318 letters) >NCBI__GCF_000009985.1:WP_043745123.1 Length = 356 Score = 150 bits (378), Expect = 6e-41 Identities = 95/303 (31%), Positives = 159/303 (52%), Gaps = 32/303 (10%) Query: 30 VLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYAAAIIGSKSPTYGA 89 VL+ + + +L QIG I A+GLN++VG +GQ SLGHA F GA+A+A + + T+G Sbjct: 45 VLSNYLLALLIQIGFYGIAALGLNILVGCTGQISLGHAAFFGFGAFASAWLNN---TFGV 101 Query: 90 -FFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFIINGGSLTNGAAGI 148 A+ + +++ + LL GIP RLKG YLA+AT I+ F T G++G Sbjct: 102 PVLLAIPLAGVMTTLLGLLFGIPAGRLKGLYLAIATFASQFILEDFFARANWFTGGSSGA 161 Query: 149 LGIP----------NFTTWQMVYFFVVITTIATLNFLRSPIGRSTLSVREDEIAAESVGV 198 + P + + +V FVV+ + N LR+ GR+ ++VR+ ++AE +G+ Sbjct: 162 MANPISLFGYEVGGDKGFFYVVLVFVVVMYVLGTNLLRTRDGRAFVAVRDHYLSAEVMGI 221 Query: 199 NTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSINVLIIVVFGGLGSITGAI 258 N TK +I++F + A + G+L ++G V + +T + SI L +++ GG+GS+ G + Sbjct: 222 NLTKYRILSFGISSFYAGVGGALYGHYLGYVSAEGFTILLSIQFLGMIIIGGMGSVMGTL 281 Query: 259 VSAIVL------------------GILNMLLQDVASVRMIIYALALVLVMIFRPGGLLGT 300 + + G + L +A ++ LA+VL +IF P GL+ Sbjct: 282 MGTAFMVLLPEATEAAVSTVKHFTGDIPALTSALAYIKEATIGLAIVLFLIFEPDGLVHR 341 Query: 301 WEL 303 W L Sbjct: 342 WRL 344 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: 265 Number of extensions: 18 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: 356 Length adjustment: 28 Effective length of query: 290 Effective length of database: 328 Effective search space: 95120 Effective search space used: 95120 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 Sep 17 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