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 GFF523 PS417_02665 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >FitnessBrowser__WCS417:GFF523 Length = 425 Score = 417 bits (1072), Expect = e-121 Identities = 222/416 (53%), Positives = 290/416 (69%), Gaps = 16/416 (3%) Query: 1 MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLF 60 + +S+ + + L+ ++V PI+G+ L LE A+ +A + F LF Sbjct: 9 IKKSVVDTVLAGLISLVVFGPIVGVVLDGYSFNLE----PARVALLVAIVMVGRFAMSLF 64 Query: 61 RDRIPLKLGRGV----GYKVNGSGLKNFL-SLPSTQRWAVLALVVVAFVWPFFASRGAVD 115 L+ +GV G++ GSG+ S RW + AL+V+A V+P FA++ + Sbjct: 65 -----LQTPKGVKILQGFESTGSGVHVLAPDYKSRLRWIIPALIVIAIVFPIFANKYLLT 119 Query: 116 IATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGM 175 + L LIYV+LG+GLNIVVGLAGLLDLGYV FYA+GAY AL +Y G GFWT LP+A + Sbjct: 120 VVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWTVLPLAAI 179 Query: 176 MAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGL 235 AAL G +LGFPVLR+ GDYLAIVTLGFGEIIR++L N TGGPNG+ +P PT GL Sbjct: 180 AAALAGCILGFPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGM-PVPSPTFLGL 238 Query: 236 TFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEAL 295 F +RA +G FHEFFGI YN N K + +Y+V L+VL L++ +RL RMP+GRAWEAL Sbjct: 239 EFGKRAKDGGIPFHEFFGIDYNPNIKFLFIYIVLFLVVLAVLYIKHRLTRMPVGRAWEAL 298 Query: 296 REDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIV 355 REDE+ACR++GLN +VKLSAFTIGAS AG AG FFA+ QG V P SFTF ESA+ILAIV Sbjct: 299 REDEIACRSMGLNHVLVKLSAFTIGASTAGLAGVFFASYQGFVNPSSFTFFESALILAIV 358 Query: 356 VLGGMGSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQR 410 VLGGMGS +GV++AA V+ + E +R F+EYR+L+FG+ M+VMMIWRP+GL+ + R Sbjct: 359 VLGGMGSTVGVVIAAFVLTVAPELLRSFSEYRVLLFGVLMVVMMIWRPRGLIRISR 414 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: 39 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: 425 Length adjustment: 32 Effective length of query: 385 Effective length of database: 393 Effective search space: 151305 Effective search space used: 151305 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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