Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate YP_428808.1 Rru_A3727 inner-membrane translocator
Query= TCDB::Q8DQH9 (318 letters) >NCBI__GCF_000013085.1:YP_428808.1 Length = 334 Score = 175 bits (444), Expect = 1e-48 Identities = 111/321 (34%), Positives = 176/321 (54%), Gaps = 35/321 (10%) Query: 13 LLLLAGYSLISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAI 72 LL LAG+ L V+ G ++L I++IL + L GF+G FSLG GF+AI Sbjct: 14 LLALAGWGLPMVVSDYGQ------RLLIMGCISVILVASMGLANGFTGVFSLGQVGFVAI 67 Query: 73 GAYAAAIIG-------SKSPTYGAFFGAMLVGA----LLSGAV----ALLVGIPTLRLKG 117 GAY + I+ + P AF + +G LL+GAV A++VG+P +RL G Sbjct: 68 GAYVSGILSLSVADKAAYLPDLPAFLAGVQMGTVPATLLAGAVCAGVAVIVGLPLMRLSG 127 Query: 118 DYLAVATLGVSEIIRIFIINGGSLTNGAAGILGIPNFTTWQMVYFFVVITTIATLNFLRS 177 +++VAT+G I+ I+N S T GA G+P T + ++VIT + S Sbjct: 128 HHVSVATMGFMIIVNSVIVNAESFTRGARTFTGVPTDITLPVALIWMVITLALLGRLIYS 187 Query: 178 PIGRSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFI 237 PIG + SVRED IAA++VG++ K +++AF GA A + GSL ++GS + + F Sbjct: 188 PIGLALRSVREDTIAAQAVGLSVLKTRLLAFTVGAFFAGVGGSLYGHYLGSFSAQTFFFP 247 Query: 238 NSINVLIIVVFGGLGSITGAIVSAIVLGILNMLLQDVA--------------SVRMIIYA 283 ++++I++V GG+GS++GA+V +V+ L+ +L+++ ++ Sbjct: 248 LMVSLIIMLVLGGMGSLSGAVVGVVVVTALSEILRNLERGMDLGFVVVPPLFGASQVVLG 307 Query: 284 LALVLVMIFRPGGLLGTWELS 304 L +LVMI+RP GLL EL+ Sbjct: 308 LLFILVMIYRPRGLLEDRELT 328 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: 268 Number of extensions: 19 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: 334 Length adjustment: 28 Effective length of query: 290 Effective length of database: 306 Effective search space: 88740 Effective search space used: 88740 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