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_011385948.1 AMB_RS18170 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000009985.1:WP_011385948.1 Length = 297 Score = 143 bits (361), Expect = 4e-39 Identities = 95/306 (31%), Positives = 161/306 (52%), Gaps = 21/306 (6%) Query: 8 LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67 LQ LVNGL VG+ Y ++A+ + ++Y ++NFA GE +IG++ + +T S Sbjct: 7 LQLLVNGLIVGTLYGVVAMCFVLIYKSTQVVNFAQGEFLLIGAWTCWWLVT--------S 58 Query: 68 VPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQDS 127 + L AF + + FG +++ + RPL G + ++ IG+SIF Q + Sbjct: 59 MALPFYVAFPMTFLFMMVFGIALQMIVLRPLIGEPVISVIMVTIGLSIFFQAVMKSIFGV 118 Query: 128 KEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRACA 187 + P + P V + G+ + ++ VV+ ++M F SR+G A RA A Sbjct: 119 WAQPFPEIFPVKSV----DILGLSVQPAYLMSLVVSIVIMGLFAWFFKYSRMGLAMRATA 174 Query: 188 EDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAVL 247 + ++ LGI+ + A + I A ++A+A V++GM GV + + F GIK F A ++ Sbjct: 175 FNQQVAQSLGISVKAVFATAWAISAMVSALAGVVVGMVNGV-SSALSFF-GIKVFPAVIV 232 Query: 248 GGIGSIPGAMLGGLLLGVAEAFGADVFGDQY------KDVVAFGLLILVLLFRPTGILGR 301 GG+ SI GA+LGGL++GV E A+ QY V F +L+++L+ +P G+ G Sbjct: 233 GGLDSIIGAVLGGLIIGVLENL-AEYADGQYLHLGNLYTVAPFYVLVIILMIKPYGLFGT 291 Query: 302 PEVEKV 307 +E+V Sbjct: 292 KTIERV 297 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: 265 Number of extensions: 20 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: 297 Length adjustment: 27 Effective length of query: 280 Effective length of database: 270 Effective search space: 75600 Effective search space used: 75600 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 17 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