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_011649171.1 RL_RS34940 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000009265.1:WP_011649171.1 Length = 290 Score = 175 bits (443), Expect = 1e-48 Identities = 98/291 (33%), Positives = 168/291 (57%), Gaps = 13/291 (4%) Query: 8 LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67 L+Q VNG+ GS YA++A+G TM++G++ INFAHGE YM+G++ A+ AI D Sbjct: 6 LEQSVNGIVTGSVYAIVAVGMTMIFGVLRAINFAHGEYYMLGTFGAWFAI--------DY 57 Query: 68 VPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQDS 127 + L + ++ T A Y + ++ R + G +++ +G+++ LQN ++L Sbjct: 58 LGLSYEVSIVVGVLATIAVAYVVGQLVMRRMVGAPAESGVLATLGIALILQNTIILVFGG 117 Query: 128 KEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRACA 187 K G ++ S + G ++ +ILI VV LV GL L +S +RLG A RA + Sbjct: 118 GYK----FFAGGYIEPVSIL-GFSLAEQRILILVVCLLVFIGLELMVSYTRLGMAMRAVS 172 Query: 188 EDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAVL 247 ++++ +++GI+ ++ TF++GAALAA++ VL + G+G L K ++ Sbjct: 173 QNVECCSVVGIDVPQVVLRTFMLGAALAALSGVLTAPVNVSVYGGMGELITFKTLPIIIM 232 Query: 248 GGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGI 298 GG+G++ G + ++LGVAE+ A G Q++D V F LIL+L++RP G+ Sbjct: 233 GGLGNVRGTFVAAMILGVAESLVATYVGLQFRDTVGFATLILMLMWRPHGL 283 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: 282 Number of extensions: 19 Number of successful extensions: 2 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