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_108402619.1 B9Z44_RS12860 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_003063475.1:WP_108402619.1 Length = 291 Score = 161 bits (407), Expect = 2e-44 Identities = 102/302 (33%), Positives = 164/302 (54%), Gaps = 15/302 (4%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66 +LQ +GL GS YAL A+G+T+++ G INFA GE M+ +++ M+G Sbjct: 4 FLQLFFSGLATGSIYALAALGFTLLWQASGTINFAQGEFVMLPAFM---------MLGFL 54 Query: 67 SVPLMMLAAFAASIIVTS-AFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQ 125 + ++ +FAAS +V+ G+ +R PL + +++ IG+SI ++NAV Sbjct: 55 AAGFPLVLSFAASCVVSVFVLGWLFKRGVVDPLFKFGMMPIVVATIGLSIAMRNAVRAGY 114 Query: 126 DSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185 ++ P L P ++ GV IS I FV ++ F++++ GRA +A Sbjct: 115 SAEPHPFPNLFPDEVY----NIAGVTISATDIGTFVFAIALVLVTQAFLAKTVTGRAMQA 170 Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245 A++ + ++LGIN +I TF I A LAA AA+L+ Y + +G G KAF AA Sbjct: 171 VAQNTESASVLGINVPRMIFYTFAINALLAAAAAILVTPTY-LAKFDMGASLGNKAFFAA 229 Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVE 305 ++GG + GA+LGG+++GV E A YKD VA + ++V+LF+P G+LG+ Sbjct: 230 IIGGFNNSRGALLGGVIVGVCENLAAAYISPAYKDAVALVIFMVVILFKPQGLLGKKVER 289 Query: 306 KV 307 KV Sbjct: 290 KV 291 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: 238 Number of extensions: 9 Number of successful extensions: 5 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: 291 Length adjustment: 27 Effective length of query: 280 Effective length of database: 264 Effective search space: 73920 Effective search space used: 73920 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