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_023434296.1 N177_RS20205 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000496075.1:WP_023434296.1 Length = 312 Score = 325 bits (833), Expect = 8e-94 Identities = 171/310 (55%), Positives = 229/310 (73%), Gaps = 8/310 (2%) Query: 6 HYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGL 65 +++QQL+NGLT+GS Y LIAIGYTMVYGIIGMINFAHG+++M+GS+IA IAI + Sbjct: 3 YFVQQLINGLTLGSIYGLIAIGYTMVYGIIGMINFAHGDIFMVGSFIALIAIIAFGLTAG 62 Query: 66 DSVPLMMLAAFAASII---VTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVM 122 S+ +++LA +I +TS +G+++ER+AYRPLRG RL PLI+AIGMSI LQN V Sbjct: 63 SSLAVLILALILVLLIAMALTSVYGWTVERLAYRPLRGSFRLAPLITAIGMSIVLQNFVQ 122 Query: 123 LSQDSKEKAIPTLLPGNFVFGE-----SSMNGVVISYMQILIFVVTFLVMFGLTLFISRS 177 ++Q ++ K + L G F E ++ V +S+ QILI V T ++M TL I+++ Sbjct: 123 IAQGARVKPLQPLFSGGFTLMELEGPTGAVFRVNLSFAQILIIVTTVVLMTVFTLIIAKT 182 Query: 178 RLGRACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLA 237 LGR+ RAC +D KM LLG+N + I+LTFV+GAALAAVA ++ + YGVI+ IGF+A Sbjct: 183 SLGRSQRACEQDRKMAALLGVNVDRTISLTFVMGAALAAVAGLMYLLYYGVIDFYIGFIA 242 Query: 238 GIKAFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTG 297 G+KAFTAAVLGGIGS+PGAMLGGLL+G+ E F + F +YKDV AF +L +VL+F P+G Sbjct: 243 GVKAFTAAVLGGIGSLPGAMLGGLLIGLIETFWSAYFSIEYKDVAAFSILAIVLIFLPSG 302 Query: 298 ILGRPEVEKV 307 ILGRPEVEKV Sbjct: 303 ILGRPEVEKV 312 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: 358 Number of extensions: 16 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: 307 Length of database: 312 Length adjustment: 27 Effective length of query: 280 Effective length of database: 285 Effective search space: 79800 Effective search space used: 79800 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