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_051378059.1 H566_RS0104985 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000482785.1:WP_051378059.1 Length = 392 Score = 175 bits (444), Expect = 2e-48 Identities = 125/386 (32%), Positives = 199/386 (51%), Gaps = 29/386 (7%) Query: 24 GLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLFRDRIPLKLGRGVGYKVNGSGLKN 83 G+ L T + L +LG+D+Q + A+A R LG + + + L Sbjct: 24 GVALMTAALGL-ILGSDSQPMLLGTLGAMAALGVGARR------LGVAARFGASCAALPG 76 Query: 84 FLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLG 143 L+L + LA + +P I +L+Y + +GLNI +G AG+++ Sbjct: 77 TLALAGLLAFGALATALREDPFPLL-------ILCTLLLYATVCLGLNIQIGYAGVVNFS 129 Query: 144 YVGFYAVGAYTYALLAEYAG-FGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLG 202 + F+ VG+Y A L A L +AG AAL G +L FPVLR RG Y ++VT+ Sbjct: 130 AMAFFGVGSYAAAWLTTNAPTLPHLAVLALAGGAAALVGAMLLFPVLRTRGHYASLVTVA 189 Query: 203 FGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKV 262 F + R + + E GG G+ +P ++FG F TF + G A Sbjct: 190 FAVLFRSFME-VNETFGGAQGM-KLPGLSMFGHDFNDDIELFGLTFTFYAGYA------- 240 Query: 263 ILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGAS 322 VA + L AL + R+ R IG ++A+R DE+A G+N K++AF IG + Sbjct: 241 ----AVAFAIALSALALTWRIERSWIGVNFDAVRSDEIAAACFGINIARWKITAFLIGNA 296 Query: 323 FAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQE-MRG 381 FAG AG+ FA G V P +F F +S ++L+I+VLGG+G+ G++ AA+++++L E ++ Sbjct: 297 FAGVAGALFALMTGFVAPNNFNFGDSLVMLSILVLGGLGNLWGILPAALIVIILPEKLQA 356 Query: 382 FNEYRMLIFGLTMIVMMIWRPQGLLP 407 EYR L++ +I ++++RPQGL P Sbjct: 357 IQEYRFLLYAAAVIAILLFRPQGLFP 382 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: 508 Number of extensions: 43 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: 392 Length adjustment: 31 Effective length of query: 386 Effective length of database: 361 Effective search space: 139346 Effective search space used: 139346 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 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