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_043745123.1 AMB_RS18175 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000009985.1:WP_043745123.1 Length = 356 Score = 137 bits (345), Expect = 5e-37 Identities = 97/338 (28%), Positives = 159/338 (47%), Gaps = 43/338 (12%) Query: 88 PSTQRWAVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGF 147 P+++ W + +++ A P S + + I Y + +GLNI+VG G + LG+ F Sbjct: 26 PASRNWCIAGILLAA-ASPLVLSNYLLALLIQIGFYGIAALGLNILVGCTGQISLGHAAF 84 Query: 148 YAVGAYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEII 207 + GA+ A L G A+P+AG+M L G L G P RL+G YLAI T I+ Sbjct: 85 FGFGAFASAWLNNTFGVPVLLAIPLAGVMTTLLGLLFGIPAGRLKGLYLAIATFASQFIL 144 Query: 208 RILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYV 267 TGG +G + P +LFG +E +G FF YV Sbjct: 145 EDFFARANWFTGGSSGAMANP-ISLFG--YEVGGDKG------FF-------------YV 182 Query: 268 VALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFA 327 V + +V++ + N L+R GRA+ A+R+ ++ +G+N T ++ +F I + +AG Sbjct: 183 VLVFVVVMYVLGTN-LLRTRDGRAFVAVRDHYLSAEVMGINLTKYRILSFGISSFYAGVG 241 Query: 328 GSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQE--------- 378 G+ + G V+ E FT + S L ++++GGMGS +G ++ MVLL E Sbjct: 242 GALYGHYLGYVSAEGFTILLSIQFLGMIIIGGMGSVMGTLMGTAFMVLLPEATEAAVSTV 301 Query: 379 ----------MRGFNEYRMLIFGLTMIVMMIWRPQGLL 406 + GL +++ +I+ P GL+ Sbjct: 302 KHFTGDIPALTSALAYIKEATIGLAIVLFLIFEPDGLV 339 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: 446 Number of extensions: 31 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: 356 Length adjustment: 30 Effective length of query: 387 Effective length of database: 326 Effective search space: 126162 Effective search space used: 126162 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