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_197539624.1 SUTH_RS00445 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000828635.1:WP_197539624.1 Length = 296 Score = 152 bits (385), Expect = 7e-42 Identities = 91/302 (30%), Positives = 161/302 (53%), Gaps = 12/302 (3%) Query: 8 LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67 LQ +V+G +G YALIA+G+ ++Y +NFA G++ MIG +I A+T+ Sbjct: 5 LQLIVSGAAIGCIYALIALGFVLIYKATETVNFAQGDLMMIGGFIGLTAMTVAG------ 58 Query: 68 VPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQ-- 125 L AF +I+ + FG ER+ RPL G ++ IG+ + V + Sbjct: 59 --LPFALAFLLTIVAMALFGMGTERLVLRPLLGQPAFTVVMMTIGLGYLARGLVTMIPYW 116 Query: 126 DSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185 ++ +P ++ G+V+S ++I + T ++ L LF +RLG A +A Sbjct: 117 GTETHTLPVPYKDEVIWLGGEGTGLVVSVEHLVIILATVALVALLYLFFRYTRLGIAMQA 176 Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245 +++ +GI + L + + AA+ VA +LL ++ +GF+ G+KAF AA Sbjct: 177 TSQNQLAAFYMGIPVRRVNMLIWGLSAAICGVAGLLLA-PITFVHANMGFV-GLKAFPAA 234 Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVE 305 V+GG GSIPGA++GGL++G+ E+ + +KD+ A+ +++++L+ +P G+ G + Sbjct: 235 VVGGFGSIPGALVGGLVIGIVESLSGFYLPEGFKDIAAYVVVLIMLVVKPNGLFGDNLTK 294 Query: 306 KV 307 KV Sbjct: 295 KV 296 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: 247 Number of extensions: 12 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: 296 Length adjustment: 27 Effective length of query: 280 Effective length of database: 269 Effective search space: 75320 Effective search space used: 75320 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 Apr 09 2024. 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