Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_045583514.1 AL072_RS26405 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_001305595.1:WP_045583514.1 Length = 301 Score = 349 bits (895), Expect = e-101 Identities = 169/303 (55%), Positives = 235/303 (77%), Gaps = 5/303 (1%) Query: 6 HYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGL 65 +++QQL+NGL++G+ Y LIAIGYTMVYGIIGMINFAHGE+YMIG+++A I + +G+ Sbjct: 3 YFIQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGALGI 62 Query: 66 DSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQ 125 VPL +L AS++ TS +G+++ER+AYRPLR RL PLISAIGMSIFLQN + + Q Sbjct: 63 TWVPLALLIMLVASMLFTSVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYIQILQ 122 Query: 126 DSKEKAIPTLLPGNFVFGESSMNGVV-ISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184 ++ K + +LPGN M+G V +SY+++ V+T ++M G T+ I+R+ LGRA R Sbjct: 123 GARSKPLQPILPGNLTL----MDGAVSVSYVRLATIVITLVLMVGFTILINRTSLGRAQR 178 Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTA 244 AC +D KM LLG+N + +I+LTFV+GAALAAVA +++ + YGVI+ IGFLAG+K+FTA Sbjct: 179 ACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKSFTA 238 Query: 245 AVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEV 304 AVLGG+GS+PGAMLGG+++G+ EAF + G ++KDV F +L+LVL+FRPTG+LGRPE+ Sbjct: 239 AVLGGVGSLPGAMLGGVVIGLIEAFWSGYVGSEWKDVATFSILVLVLIFRPTGLLGRPEI 298 Query: 305 EKV 307 EKV Sbjct: 299 EKV 301 Lambda K H 0.328 0.145 0.413 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: 367 Number of extensions: 13 Number of successful extensions: 2 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: 307 Length of database: 301 Length adjustment: 27 Effective length of query: 280 Effective length of database: 274 Effective search space: 76720 Effective search space used: 76720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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