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 YP_428496.1 Rru_A3415 inner-membrane translocator
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000013085.1:YP_428496.1 Length = 295 Score = 155 bits (391), Expect = 2e-42 Identities = 102/305 (33%), Positives = 159/305 (52%), Gaps = 37/305 (12%) Query: 116 IATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGM 175 + + LIY ++ +GLN+ G GL++ G VGF+A+GAYT ALL AG+ ALP A Sbjct: 8 VTVIALIYSLMTLGLNLQYGFTGLINFGVVGFFAIGAYTSALLV-VAGWPILLALPCAVA 66 Query: 176 MAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPK-PTLFG 234 +AL + + LRLR +Y AIV LGF E IR+++ + +TGG G+ IP G Sbjct: 67 ASALVSWPVALLSLRLRIEYFAIVMLGFAETIRLVVTSEGWLTGGVQGVTGIPSLAAALG 126 Query: 235 LTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEA 294 L+ E +L +VAL V+ +++ RL+ P GR A Sbjct: 127 LSME----------------------STLLTALVALGAVIGVVWLSRRLVASPFGRIIRA 164 Query: 295 LREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAI 354 +R+DE A +ALG P K++ F +G++ AG AG+ +A ++P+ F + + I Sbjct: 165 IRDDEDAVQALGKAPGRFKVAVFVLGSASAGLAGALYAHYITYISPDQFMSLLTFYIWVA 224 Query: 355 VVLGGMGSQLGVILAAVVMVLLQEMRGF-------------NEYRMLIFGLTMIVMMIWR 401 ++LGG+G G +L V++ L E F R+ + GL ++V+M +R Sbjct: 225 MILGGVGRVGGAVLGTAVLIGLMEGSRFLRDILPGVAEVEMASIRLGVIGLALMVLMRFR 284 Query: 402 PQGLL 406 P+GLL Sbjct: 285 PEGLL 289 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: 377 Number of extensions: 23 Number of successful extensions: 4 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: 295 Length adjustment: 29 Effective length of query: 388 Effective length of database: 266 Effective search space: 103208 Effective search space used: 103208 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 Sep 24 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