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 Dsui_0628 Dsui_0628 ABC-type branched-chain amino acid transport system, permease component
Query= TCDB::P21628 (417 letters) >FitnessBrowser__PS:Dsui_0628 Length = 358 Score = 251 bits (641), Expect = 2e-71 Identities = 157/353 (44%), Positives = 203/353 (57%), Gaps = 41/353 (11%) Query: 93 WAVLALV-VVAFVWPFFASRGA----VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGF 147 WA A + +V V PF G + I ++Y+ML +GLNIVVG AGLLDLGY+ F Sbjct: 14 WAGYAAIGIVLAVLPFLVGAGLGNAWLRILNFAMLYIMLALGLNIVVGFAGLLDLGYIAF 73 Query: 148 YAVGAYTYALLAEYAGFGF----WTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGF 203 YAVGAY YALLA FG W LP+ ++A G LLG P LRLRGDYLAIVTLGF Sbjct: 74 YAVGAYLYALLAS-PHFGLHWPVWAILPLGAVVAGGAGALLGAPTLRLRGDYLAIVTLGF 132 Query: 204 GEIIRILLRNMT---EITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNY 260 GEIIRI + N+ IT GP GI SI + G+T + G+ + + Sbjct: 133 GEIIRIFMNNLNAPVNITNGPQGISSIDPFHVGGVTLAKPL--------SVLGVTVPSLH 184 Query: 261 KVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIG 320 L+ LLL L+ +FV RL IGRAW A+REDE+A +A G+N +KL AF++G Sbjct: 185 AYYYLF---LLLALVIIFVTIRLEDSRIGRAWVAIREDEIAAKACGINVRNIKLLAFSMG 241 Query: 321 ASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQE-- 378 A+F G AG FA+ QG V+PESF +ES M+L +VVLGGMG GVIL +++ +L E Sbjct: 242 ATFGGVAGGLFASFQGFVSPESFGLMESIMVLCMVVLGGMGHIPGVILGGILLTILPEAF 301 Query: 379 ---------------MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416 + RML+FGL +I +M++RP GL P EL+ Sbjct: 302 RHAAVPLQKYAFGKVVVDPESLRMLLFGLALIAVMLYRPAGLWPSATRKRELQ 354 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: 486 Number of extensions: 27 Number of successful extensions: 5 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: 358 Length adjustment: 30 Effective length of query: 387 Effective length of database: 328 Effective search space: 126936 Effective search space used: 126936 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