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_012045884.1 BBTA_RS28020 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000015165.1:WP_012045884.1 Length = 290 Score = 168 bits (426), Expect = 1e-46 Identities = 102/293 (34%), Positives = 170/293 (58%), Gaps = 13/293 (4%) Query: 8 LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67 ++ L+NGL +G+ YALIA+G T++YG++ ++NFAHG + + ++ ++ + A GLD Sbjct: 8 VEALLNGLMLGAIYALIALGLTLIYGVLHIVNFAHGALLTVAMFMVWL---VCARYGLD- 63 Query: 68 VPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQDS 127 P + + A + A GY ++R P G L+ +G+SI ++NA++ + S Sbjct: 64 -PYLAILVVAPLMF---ALGYGLQRFIIGPASHGKDNGILLVTLGLSIIIENALLAAFQS 119 Query: 128 KEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRACA 187 + I T ++ F + +++S+ +++ F VT L L + ++ +G+A RA A Sbjct: 120 DTRTITT----DYSFRVVELGPLLLSFPRVVGFGVTIATTILLWLVLHQTDIGKAIRAVA 175 Query: 188 EDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAVL 247 ++ +L+GI+ ++ A+TF IG A AVAA LL M ++P G + AFT VL Sbjct: 176 KEKLGASLVGISVPHVYAMTFAIGCACLAVAAGLL-MPSFYVSPKTGAAFVLVAFTIVVL 234 Query: 248 GGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILG 300 GG+GSIPGA++GGLL+GV EA + GD + F + I+ LL RPTG+ G Sbjct: 235 GGMGSIPGALIGGLLIGVVEAASSLFLGDSLGQIGIFLIFIVTLLVRPTGLFG 287 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: 303 Number of extensions: 20 Number of successful extensions: 4 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: 290 Length adjustment: 27 Effective length of query: 280 Effective length of database: 263 Effective search space: 73640 Effective search space used: 73640 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