Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 8500739 DvMF_1482 inner-membrane translocator (RefSeq)
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Miya:8500739 Length = 360 Score = 168 bits (426), Expect = 2e-46 Identities = 99/317 (31%), Positives = 170/317 (53%), Gaps = 24/317 (7%) Query: 96 LALVVVAFVWPFFASRG-AVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYT 154 LA+ V + P G + ++ + +++ GLN+++G AG + G+ F+ +GAY Sbjct: 40 LAVAVAVALLPLALRSGYQFTVLNVVAVNLIVVTGLNLLMGYAGQISYGHAAFFGMGAYG 99 Query: 155 YALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNM 214 A+L+ G W A+ ++ A+ ++G P LRL+G+YL + TLGF I+ ++L Sbjct: 100 SAILSATHGVDPWLAMGVSACGVAVAAAVVGVPTLRLKGNYLVMATLGFNLIVDVILVQW 159 Query: 215 TEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVL 274 +E+TGG +G +P + G++F+ T F+ +A+ VALLL++ Sbjct: 160 SEVTGGSSGFVGVPPLAVAGISFD--------TDRSFYWLAWG----------VALLLLI 201 Query: 275 LALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAAR 334 A L+ P+GRA A+ + E A G+ K+ F + A FA AGS A Sbjct: 202 PA----RNLVHSPVGRALRAIHDSEPGAEACGVPTASYKVQVFVLSAVFASLAGSLHAHY 257 Query: 335 QGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQEMRG-FNEYRMLIFGLT 393 G+V P++F +S + + ++GGMGS G + A+++ +L +M G F E+ LIFG Sbjct: 258 LGIVAPKTFDIFKSVEFVTMCLIGGMGSLWGGLAGALLLTVLPQMLGVFEEHHDLIFGAI 317 Query: 394 MIVMMIWRPQGLLPMQR 410 ++VM+I+ P+G+ P R Sbjct: 318 LLVMLIFMPRGVSPWLR 334 Lambda K H 0.330 0.146 0.439 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: 345 Number of extensions: 21 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: 417 Length of database: 360 Length adjustment: 30 Effective length of query: 387 Effective length of database: 330 Effective search space: 127710 Effective search space used: 127710 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 50 (23.9 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