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 GFF3114 HP15_3057 leucine/isoleucine/valine transporter permease subunit
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Marino:GFF3114 Length = 423 Score = 507 bits (1305), Expect = e-148 Identities = 252/419 (60%), Positives = 324/419 (77%), Gaps = 5/419 (1%) Query: 2 SQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLFR 61 + + + ALF A + +++SYPI+G L GI + + GADA T+ + AA+ +F++Q+FR Sbjct: 3 ANNFRHALFCAFITLIISYPIIGFNLEAQGINVTLTGADASTIVMVLFAAVIVFLFQMFR 62 Query: 62 DRIPLKLGRGVGYKVNGSGLKNFLS--LPSTQRWAVLALVVVAFVWPFFASRGAVDIATL 119 ++I L + + + + S + + W + +VV+A WPFF SRGAVD+ATL Sbjct: 63 EQIMGGL-KSIPHPLPQSNKEPMAENRRAKIESWVLTGIVVLALFWPFFVSRGAVDLATL 121 Query: 120 ILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAAL 179 +LIY+ML +GLN+VVGLAGLLDLGYV FYAVGAYT+ALL++Y G FW ALPI ++AAL Sbjct: 122 VLIYIMLALGLNVVVGLAGLLDLGYVAFYAVGAYTFALLSQYTGISFWLALPIGALLAAL 181 Query: 180 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFER 239 FG +LGFPVLRLRGDYLAIVTLGFGEIIRILL N T +TGGPNGIG IP PTLFG+ F R Sbjct: 182 FGLVLGFPVLRLRGDYLAIVTLGFGEIIRILLNNWTTLTGGPNGIGGIPDPTLFGMEFGR 241 Query: 240 RA-PEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRED 298 R EG +FHE FGIAY+ +KVI LY++AL+L + VI R MRMP+GRAWEALRED Sbjct: 242 RVKEEGNTSFHETFGIAYSGEHKVIFLYLIALVLAVFTALVIRRFMRMPVGRAWEALRED 301 Query: 299 EVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLG 358 E+A R+LGL+ T VKLSAFTIGA FAGFAG+ FA++QG ++PESF F+ESA+ILAIVVLG Sbjct: 302 EIAARSLGLSRTAVKLSAFTIGAFFAGFAGTVFASKQGFISPESFVFLESAIILAIVVLG 361 Query: 359 GMGSQLGVILAAVVMVLLQEM-RGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416 GMGSQ+GV+LAA+ + +L E+ R F+EYRMLIFG M++MM+WRPQGL+PM+R H+ELK Sbjct: 362 GMGSQIGVVLAAIAVTILPELAREFSEYRMLIFGAAMVLMMVWRPQGLMPMRRIHIELK 420 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: 589 Number of extensions: 30 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: 423 Length adjustment: 32 Effective length of query: 385 Effective length of database: 391 Effective search space: 150535 Effective search space used: 150535 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