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 AO356_28380 AO356_28380 ABC transporter permease
Query= TCDB::P21628 (417 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28380 Length = 355 Score = 131 bits (330), Expect = 3e-35 Identities = 103/334 (30%), Positives = 156/334 (46%), Gaps = 42/334 (12%) Query: 92 RWAVLALVVVAFVWPFFASRGAVDIATLI--LIYVMLGIGLNIVVGLAGLLDLGYVGFYA 149 R + AL++ AFV + A LI L+ + G+GLN++ G AG L LG F A Sbjct: 26 RHGLAALLLFAFVVVPWLGNDYWFSAILIPFLVLSLAGLGLNLLTGYAGQLSLGSAAFMA 85 Query: 150 VGAY-TYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIR 208 VGA+ TY L AG ++ + G+ AAL L G P LR++G YL + TL + Sbjct: 86 VGAFATYNLEIRVAGLPLLVSIALGGLTAALVAVLFGLPSLRIKGFYLLVSTLAAQFFVT 145 Query: 209 ILLRNMTEITGGP-NGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYV 267 L + + +G+ S P+ +FG+ + AP G Y+ Sbjct: 146 WALTRFSWFSNNSASGVISAPRLDVFGVNLD--APAGR--------------------YL 183 Query: 268 VALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFA 327 + L +V+ ++ L+R +GR W A+R+ + A +G+ KL AF I F G A Sbjct: 184 LTLSVVVALFWLGKNLVRSELGRNWMAVRDMDTAAAVIGIALAKTKLLAFAISGFFLGVA 243 Query: 328 GSFFA-ARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVL----------- 375 G+ +A A G V P F S IL I+++GG+GS LG L A +VL Sbjct: 244 GALWAFAYLGTVEPHGFDLNRSFQILFIIIIGGLGSLLGNFLGAAFIVLFPVLLSNLVSL 303 Query: 376 ----LQEMRGFNEYRMLIFGLTMIVMMIWRPQGL 405 L + + +IFG +I+ +I P+GL Sbjct: 304 LPGGLVDAGQVENLQKMIFGALIILFLIKEPEGL 337 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: 354 Number of extensions: 25 Number of successful extensions: 5 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: 355 Length adjustment: 30 Effective length of query: 387 Effective length of database: 325 Effective search space: 125775 Effective search space used: 125775 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