Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_050462656.1 AKL27_RS09910 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= TCDB::P21628 (417 letters) >NCBI__GCF_001189915.1:WP_050462656.1 Length = 408 Score = 497 bits (1280), Expect = e-145 Identities = 258/418 (61%), Positives = 318/418 (76%), Gaps = 15/418 (3%) Query: 1 MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWT-IAAAALAMFVWQL 59 M +LK A+ +A+L +++ P+LGLKL+ G ++ + Q WT + A LA+F++QL Sbjct: 1 MPITLKNAVAAAILTAILTTPLLGLKLQLEGYRVVL-----QAHWTPVLIAVLAVFLFQL 55 Query: 60 FRDRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATL 119 F+ + + L P+ QR+A++ L+ VA VWPFF SRG VD+ TL Sbjct: 56 FKPALSRTTAN-----IRLPALPKLQ--PTQQRYALMVLLAVALVWPFFGSRGNVDVVTL 108 Query: 120 ILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAAL 179 LIYV+LG+GLNIVVG AGLLDLGYVGFYAVG YTYALL +Y G FW LP+A M+AL Sbjct: 109 ALIYVVLGLGLNIVVGFAGLLDLGYVGFYAVGGYTYALLNQYFGLSFWECLPLAAGMSAL 168 Query: 180 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFER 239 FGFLLGFPVLRLRGDYLAIVTLGFGEIIR+LL N+T +TGGP+G+ IPKPT+FG+ R Sbjct: 169 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRLLLNNLTSLTGGPDGVSGIPKPTVFGIEMAR 228 Query: 240 RAP-EGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRED 298 A EG TFH+ G+ Y + VI LY + LLLVL FV +RL+RMP+GRAWEALR+D Sbjct: 229 TASVEGGTTFHDMLGLTYQGGHMVIFLYFLGLLLVLFTYFVTSRLIRMPMGRAWEALRDD 288 Query: 299 EVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLG 358 E+ACR+LG+NPT +KLSAFT+GA+FAG AGSFFAARQGLV PESFTFIESA+ILAIVVLG Sbjct: 289 EIACRSLGINPTKIKLSAFTLGAAFAGLAGSFFAARQGLVNPESFTFIESALILAIVVLG 348 Query: 359 GMGSQLGVILAAVVMVLLQEM-RGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLEL 415 GMGSQLGVILAA+++ +L E+ R F EYRMLIFGL M++MMIWRPQGLLP RPH+EL Sbjct: 349 GMGSQLGVILAAILLTILPEVARSFAEYRMLIFGLVMVLMMIWRPQGLLPATRPHVEL 406 Lambda K H 0.330 0.146 0.439 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: 618 Number of extensions: 35 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: 417 Length of database: 408 Length adjustment: 31 Effective length of query: 386 Effective length of database: 377 Effective search space: 145522 Effective search space used: 145522 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 50 (23.9 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