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 AZOBR_RS25635 AZOBR_RS25635 high-affinity branched-chain amino acid ABC transporter (permease protein) (fragment)
Query= TCDB::P21628 (417 letters) >FitnessBrowser__azobra:AZOBR_RS25635 Length = 328 Score = 201 bits (512), Expect = 2e-56 Identities = 115/314 (36%), Positives = 174/314 (55%), Gaps = 23/314 (7%) Query: 94 AVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAY 153 A+L V + V F IA L LI+++L +++V G+AGLL LG+ FY VGAY Sbjct: 8 ALLVFVGLPAVLAGFDRGYFYQIANLALIFILLSASMHLVTGVAGLLHLGHAAFYGVGAY 67 Query: 154 TYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRN 213 T ALL+ G GF LP++G++AAL FL+ P +RL Y A+ TL G+++ +++ N Sbjct: 68 TAALLSTKFGLGFTVTLPLSGLVAALIAFLVALPTMRLVSIYFAVATLAIGQMLYLVMLN 127 Query: 214 MTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLV 273 E T GPNGI LFG + R + Y +V Sbjct: 128 WVEFTKGPNGIIVTKGLELFGFSLSGR----------------------LATYYTVATVV 165 Query: 274 LLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAA 333 L + I RL G A ++RED+ A+G++ +K+ AFT+ A FAG AGS +A Sbjct: 166 ALCVLAIGRLSHSYYGNALRSIREDDQCADAMGVSTARLKMEAFTLSAFFAGVAGSLWAH 225 Query: 334 RQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGL 392 G ++P F F ES +ILA+VV+GG+GS G ++ A++++LL E +R F ++R ++ GL Sbjct: 226 MTGYISPGDFKFSESILILAMVVVGGLGSLPGAVIGALLLILLPEGLRAFGDFRNIMVGL 285 Query: 393 TMIVMMIWRPQGLL 406 M + ++ P+GLL Sbjct: 286 VMFLSILLLPKGLL 299 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: 387 Number of extensions: 29 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: 328 Length adjustment: 30 Effective length of query: 387 Effective length of database: 298 Effective search space: 115326 Effective search space used: 115326 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: 49 (23.5 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