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 GFF1277 Psest_1310 ABC-type branched-chain amino acid transport system, permease component
Query= TCDB::P21628 (417 letters) >FitnessBrowser__psRCH2:GFF1277 Length = 418 Score = 646 bits (1667), Expect = 0.0 Identities = 326/417 (78%), Positives = 365/417 (87%), Gaps = 1/417 (0%) Query: 1 MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLF 60 MS +L+ A FSALLVI V+ P+ GLKL TVGI++EV GA+ T W IAA A+AMFVWQLF Sbjct: 1 MSGNLRTAFFSALLVIAVAVPVFGLKLTTVGIRVEVHGAEIGTFWIIAACAVAMFVWQLF 60 Query: 61 RDRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLI 120 R + +G NFL+LPSTQRW +LALV+VA VWPF+ SRGAVDIATLI Sbjct: 61 RTHLAAGWAASPSLPTVPAGAGNFLTLPSTQRWIILALVLVALVWPFYGSRGAVDIATLI 120 Query: 121 LIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALF 180 LIYVMLG+GLNIVVGLAGLLDLGYVGFYAVGAYTYALL+ Y G GFWTALPIAG MAALF Sbjct: 121 LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYTYALLSHYYGVGFWTALPIAGAMAALF 180 Query: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERR 240 GFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMT +TGGPNGI I KPTLFGL+F+RR Sbjct: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTSVTGGPNGISGIDKPTLFGLSFDRR 240 Query: 241 APEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEV 300 A EGMQTFHE+FG+AYN+ KVI LY++ALLLVLL LFVINRL+RMPIGRAWEALREDE+ Sbjct: 241 AAEGMQTFHEYFGVAYNSVNKVIFLYLIALLLVLLTLFVINRLLRMPIGRAWEALREDEI 300 Query: 301 ACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGM 360 ACRALG+NPT++KLSAFT+GA+FAGFAGSFFAARQGLV+PESFTFIESA+ILAIVVLGGM Sbjct: 301 ACRALGMNPTVIKLSAFTLGATFAGFAGSFFAARQGLVSPESFTFIESAIILAIVVLGGM 360 Query: 361 GSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416 GSQLGVILAA+VM+LL E MR F+EYRML+FG M++MMIWRPQGLLPMQRPHLELK Sbjct: 361 GSQLGVILAAIVMILLPELMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHLELK 417 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: 664 Number of extensions: 29 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: 418 Length adjustment: 32 Effective length of query: 385 Effective length of database: 386 Effective search space: 148610 Effective search space used: 148610 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 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