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 WP_041938756.1 FRAAL_RS03130 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000058485.1:WP_041938756.1 Length = 515 Score = 223 bits (568), Expect = 1e-62 Identities = 134/335 (40%), Positives = 190/335 (56%), Gaps = 34/335 (10%) Query: 96 LALVVVAFVWPFFASRGAVD-IATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYT 154 L L+ VA + P S A + I IY +L +GLN+VVG AGLLDLGY+ F+A+GAY Sbjct: 180 LVLLAVAILAPLVVSTAAQQSMVNDIGIYALLALGLNVVVGYAGLLDLGYIAFFAIGAYA 239 Query: 155 YALLAEYAGFGF--------WTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEI 206 A + + PIA ++AAL G +LG P LRLRGDYLAIVTLGFGEI Sbjct: 240 TAYFTSQTAMPWHAPFVLNPFFVFPIALVLAALAGVILGAPTLRLRGDYLAIVTLGFGEI 299 Query: 207 IRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLY 266 I ++ N IT G G +P ++ + GI Y + Y Sbjct: 300 IHLVANNADGITNGARGAFGVPHLSI-----------------DLLGIDYKWGIDPLPYY 342 Query: 267 VVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGF 326 + L +V+ + RL R IGR+W A+REDE+A A G+ +KL AF IGAS +GF Sbjct: 343 YLLLAIVIGVMIAFGRLERSRIGRSWAAIREDEIAAEATGVATLRMKLLAFAIGASVSGF 402 Query: 327 AGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVM-----VLLQEMRG 381 AG FA++Q P+SF+ S ++A+V+ GGMGS+LGV++ AVV+ L +++ Sbjct: 403 AGVLFASKQ-FFNPQSFSLQASFFVVAVVIFGGMGSRLGVVVGAVVLQGLAFYLRDKVQP 461 Query: 382 FNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416 + Y + FG +++MMI+RPQGL+P +R E++ Sbjct: 462 ADRY--IYFGAVIVIMMIFRPQGLVPSRRRRREIE 494 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: 617 Number of extensions: 24 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: 515 Length adjustment: 33 Effective length of query: 384 Effective length of database: 482 Effective search space: 185088 Effective search space used: 185088 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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