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_029133957.1 A3GO_RS0114210 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000428045.1:WP_029133957.1 Length = 449 Score = 409 bits (1051), Expect = e-119 Identities = 226/423 (53%), Positives = 293/423 (69%), Gaps = 19/423 (4%) Query: 5 LKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWT-IAAAALAMFVWQL---F 60 LK + +AL+ + ++ +LGL RTV G T W +A A +++F +L F Sbjct: 18 LKESAIAALVALGLTIVMLGL--RTVDT---TTGLGITTRWPLVAVAVISVFAGRLLFAF 72 Query: 61 R-----DRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVD 115 R + P+ R + +K F ++ +A +V + PF A R +D Sbjct: 73 RREWKASKGPVSRDRKEEEDRAATIIKRFSTIGGP---VFIAFALVLPLMPF-ADRYVID 128 Query: 116 IATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGM 175 IAT +LIYVMLG GLNIVVGLAGLLDLGYV FYAVGAY+YAL A Y FW LP+AG+ Sbjct: 129 IATYVLIYVMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALFAFYFDLSFWVCLPLAGL 188 Query: 176 MAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGL 235 AA FG LLGFPVLRLRGDYLAIVTLGFGEIIRI+L N + T GP+GI IP+P+ FGL Sbjct: 189 CAASFGVLLGFPVLRLRGDYLAIVTLGFGEIIRIILLNWYKFTNGPDGISGIPRPSFFGL 248 Query: 236 TFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEAL 295 F+R A EG QTFH+FF + Y++ +++I LY + L+L L+ F R+ +MP+GRAWEAL Sbjct: 249 EFKRTAVEGTQTFHQFFDLDYSSMHRLIFLYYLILILALITNFFTLRIRKMPVGRAWEAL 308 Query: 296 REDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIV 355 REDE+ACR+LG+NPT KL+AF +GA FAGFAGSFFA RQ ++PESFTFIESA+ILAIV Sbjct: 309 REDEIACRSLGINPTNTKLTAFALGAMFAGFAGSFFATRQAFISPESFTFIESAVILAIV 368 Query: 356 VLGGMGSQLGVILAAVVMVLLQEM-RGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLE 414 VLGGMGSQ+GV +AAV+++ E+ RG EYRML FG M+ +M+W+P+GLL + P ++ Sbjct: 369 VLGGMGSQVGVAIAAVLLIGGTELFRGLEEYRMLAFGGLMVAIMVWKPRGLLAHREPTIK 428 Query: 415 LKP 417 L P Sbjct: 429 LHP 431 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: 591 Number of extensions: 29 Number of successful extensions: 3 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: 449 Length adjustment: 32 Effective length of query: 385 Effective length of database: 417 Effective search space: 160545 Effective search space used: 160545 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: 51 (24.3 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