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_073040675.1 BUB04_RS14305 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_900129305.1:WP_073040675.1 Length = 315 Score = 169 bits (428), Expect = 1e-46 Identities = 107/315 (33%), Positives = 166/315 (52%), Gaps = 24/315 (7%) Query: 93 WAVLALV-VVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVG 151 WA A V+A ++ + T+I I+ +L +GLN+++G AG + LG+ FY +G Sbjct: 8 WATAAFAGVIAVASVTVSNAYHQQLLTIIGIHTLLALGLNMLMGYAGQISLGHAAFYGLG 67 Query: 152 AYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILL 211 AY +L + G+ W A P+ A +++G P L+L G YLA+ TLG G I ++ Sbjct: 68 AYGTGILTTHYGWSPWAAFPVVLTAAGWLAYVIGRPTLKLSGYYLAMGTLGLGIIAHVIF 127 Query: 212 RNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALL 271 R +TGG +G+ IP P G T GM IL++V Sbjct: 128 REWDSMTGGASGMVGIP-PLQVGGTVLSLGRSGM-----------------ILVWVT--- 166 Query: 272 LVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFF 331 VL A F+ +RL+ IGRA AL + + A A G++ +K F+ A A AG + Sbjct: 167 -VLTAFFLCSRLVDSRIGRALRALGDSQGAAAACGIDTGRLKAVIFSFSAVLAALAGFLY 225 Query: 332 AARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQE-MRGFNEYRMLIF 390 A G ++P SF F+ S ++ +VV+GGM S G + A V+ +L E + F++Y M ++ Sbjct: 226 AHLVGFISPSSFDFLMSIRMVTMVVIGGMASIWGSLFGASVITMLPEWLHVFSDYEMTVY 285 Query: 391 GLTMIVMMIWRPQGL 405 GL ++V+MI+ PQGL Sbjct: 286 GLVLMVVMIFLPQGL 300 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: 386 Number of extensions: 30 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: 315 Length adjustment: 29 Effective length of query: 388 Effective length of database: 286 Effective search space: 110968 Effective search space used: 110968 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