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_043743999.1 AMB_RS09135 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000009985.1:WP_043743999.1 Length = 304 Score = 323 bits (827), Expect = 4e-93 Identities = 161/302 (53%), Positives = 224/302 (74%) Query: 6 HYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGL 65 ++LQQL+NGLT+G+ Y L+A+GYTMVYG++GMINFAHG +YM+G++I+ I + + Sbjct: 3 YFLQQLINGLTLGAIYGLVALGYTMVYGVLGMINFAHGTIYMVGAFISLITFLVATTVLG 62 Query: 66 DSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQ 125 SVPL ++ A++ +T+ +G++ ERVAYRPLR RL PLISAIG+SI LQN V +Q Sbjct: 63 TSVPLALVLTLVAAMALTALWGWTAERVAYRPLRSAPRLAPLISAIGVSIMLQNFVAQAQ 122 Query: 126 DSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185 ++ K +P + G +S V +S+MQ++I +T +M T I+R+ LGRA RA Sbjct: 123 GARAKPLPPVFRGGITLMDSGDFVVSLSWMQMVIMALTLALMAVFTWVITRTALGRAQRA 182 Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245 C +D+KM +LLGI+ + +I+ TFVIGA LA VA +++ + YGVI+ IGFLAGIKAFTAA Sbjct: 183 CEQDMKMASLLGIDVDRVISTTFVIGAGLAGVAGMMVTLYYGVIDFYIGFLAGIKAFTAA 242 Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVE 305 VLGGIGS+PGAMLGGLL+G+ EAF + F +YKDV F +L+ VL+FRPTG+LGRP+VE Sbjct: 243 VLGGIGSLPGAMLGGLLIGLIEAFWSAYFSIEYKDVATFSILVAVLVFRPTGLLGRPDVE 302 Query: 306 KV 307 K+ Sbjct: 303 KI 304 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: 324 Number of extensions: 5 Number of successful extensions: 1 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: 304 Length adjustment: 27 Effective length of query: 280 Effective length of database: 277 Effective search space: 77560 Effective search space used: 77560 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 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