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:
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