Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 8500739 DvMF_1482 inner-membrane translocator (RefSeq)
Query= TCDB::Q8DQH9 (318 letters) >FitnessBrowser__Miya:8500739 Length = 360 Score = 178 bits (451), Expect = 2e-49 Identities = 100/293 (34%), Positives = 169/293 (57%), Gaps = 20/293 (6%) Query: 22 ISVLVSVGVLNL-----FYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYA 76 ++V V+V +L L + +L + +N+I+ GLNL++G++GQ S GHA F +GAY Sbjct: 40 LAVAVAVALLPLALRSGYQFTVLNVVAVNLIVVTGLNLLMGYAGQISYGHAAFFGMGAYG 99 Query: 77 AAIIGSKSPTYGAF-FGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFI 135 +AI+ S T+G + AM V A A +VG+PTLRLKG+YL +ATLG + I+ + + Sbjct: 100 SAIL---SATHGVDPWLAMGVSACGVAVAAAVVGVPTLRLKGNYLVMATLGFNLIVDVIL 156 Query: 136 INGGSLTNGAAGILGIP-------NFTTWQMVYFFV----VITTIATLNFLRSPIGRSTL 184 + +T G++G +G+P +F T + Y+ ++ I N + SP+GR+ Sbjct: 157 VQWSEVTGGSSGFVGVPPLAVAGISFDTDRSFYWLAWGVALLLLIPARNLVHSPVGRALR 216 Query: 185 SVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSINVLI 244 ++ + E AE+ GV T K+ FV A+ AS+AGSL A ++G V PK + S+ + Sbjct: 217 AIHDSEPGAEACGVPTASYKVQVFVLSAVFASLAGSLHAHYLGIVAPKTFDIFKSVEFVT 276 Query: 245 IVVFGGLGSITGAIVSAIVLGILNMLLQDVASVRMIIYALALVLVMIFRPGGL 297 + + GG+GS+ G + A++L +L +L +I+ L++++IF P G+ Sbjct: 277 MCLIGGMGSLWGGLAGALLLTVLPQMLGVFEEHHDLIFGAILLVMLIFMPRGV 329 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: 231 Number of extensions: 16 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: 360 Length adjustment: 28 Effective length of query: 290 Effective length of database: 332 Effective search space: 96280 Effective search space used: 96280 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