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_050462657.1 AKL27_RS09915 high-affinity branched-chain amino acid ABC transporter permease LivH
Query= TCDB::P21627 (307 letters) >NCBI__GCF_001189915.1:WP_050462657.1 Length = 309 Score = 376 bits (965), Expect = e-109 Identities = 189/301 (62%), Positives = 237/301 (78%), Gaps = 3/301 (0%) Query: 9 QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDSV 68 QQLVNGL++G+ YALIAIGYTMVYGIIGMINFAHGE+YMIGSYI + +T + + + Sbjct: 10 QQLVNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIGSYIGLVTLTAIGIQAGYPL 69 Query: 69 PLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQDSK 128 PL++ AA S++VT +G+++ERVAYRPLRGG RL+PLISAIGMSIFLQN V + Q S+ Sbjct: 70 PLILGAALIVSVVVTGLYGWTVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQGSR 129 Query: 129 EKAIPTLLPG--NFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRAC 186 + ++P L+ G F G S V I Y +++I VT ++M LTLFI RSR+GRACRAC Sbjct: 130 DMSVPVLISGAIEFQMGSSDFT-VTIPYSRLIIVGVTLMLMVALTLFIGRSRMGRACRAC 188 Query: 187 AEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAV 246 AED+ M NLLGI++N +I+ TFV+GA LAAV VL+ + G +NP IGF+AGIKAFTAAV Sbjct: 189 AEDMGMANLLGIDTNRVISFTFVLGAMLAAVGGVLIALTIGKLNPFIGFIAGIKAFTAAV 248 Query: 247 LGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVEK 306 LGGIGSIPGAMLGGLLLG+AE F A +YKDVV+F LL+L+LLFRPTG+LG+P+VEK Sbjct: 249 LGGIGSIPGAMLGGLLLGLAETFAAGYLPAEYKDVVSFALLVLILLFRPTGLLGKPDVEK 308 Query: 307 V 307 V Sbjct: 309 V 309 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: 388 Number of extensions: 11 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: 309 Length adjustment: 27 Effective length of query: 280 Effective length of database: 282 Effective search space: 78960 Effective search space used: 78960 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