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_045580995.1 AL072_RS06645 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQH9 (318 letters) >NCBI__GCF_001305595.1:WP_045580995.1 Length = 315 Score = 190 bits (482), Expect = 4e-53 Identities = 117/300 (39%), Positives = 170/300 (56%), Gaps = 18/300 (6%) Query: 12 LLLLLAGYSLISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMA 71 L++L A +++ + N FY+ I G N ++ VGLNL++G++GQ SLGHAGF Sbjct: 12 LMVLAAAIAVLPAFLP----NNFYLDIAILAGFNAVVCVGLNLLIGYAGQISLGHAGFFG 67 Query: 72 IGAYAAAIIGSKSPTYG-AFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEI 130 IGAYA+ ++ TYG A+L GA + G +A V P LRLKG YLA+ATLG+ I Sbjct: 68 IGAYASGVLVG---TYGWPPVLALLAGAAVVGLLAFAVAKPILRLKGHYLAMATLGIGII 124 Query: 131 IRIFIINGGSLTNGAAG-------ILGIPNF--TTWQMVYFFVVITTI-ATLNFLRSPIG 180 + I + LT G G I GI + W V +++ + +LN + SP+G Sbjct: 125 VSIVLRTESGLTGGPDGMMVEPFRIFGIELYGEKVWYWVVGVLLVGVVWLSLNLIDSPMG 184 Query: 181 RSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSI 240 R+ +V E+AAE VGV+T + K++ FV A+ AS+AGSL A + G + P F SI Sbjct: 185 RALRAVHGSEVAAEVVGVDTARFKVLVFVLSAVFASVAGSLFAHYAGLITPAKADFFKSI 244 Query: 241 NVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDVASVRMIIYALALVLVMIFRPGGLLGT 300 ++ +VVFGG+ S GA+V A+VL +L L + I+ L+ M+F P GLL T Sbjct: 245 ELVTMVVFGGMASTFGAVVGAVVLTLLPQALTMFQDYQQIVLGGILMATMVFMPKGLLPT 304 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: 235 Number of extensions: 11 Number of successful extensions: 3 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: 315 Length adjustment: 27 Effective length of query: 291 Effective length of database: 288 Effective search space: 83808 Effective search space used: 83808 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