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 BWI76_RS07275 BWI76_RS07275 ABC transporter
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Koxy:BWI76_RS07275 Length = 368 Score = 242 bits (617), Expect = 2e-68 Identities = 158/366 (43%), Positives = 205/366 (56%), Gaps = 54/366 (14%) Query: 85 LSLPSTQR--WAVLALVVVAF-VWPFFASRGA----VDIATLILIYVMLGIGLNIVVGLA 137 L P+ R W+ + L+V A V P AS+ V + L+YVML +GLNIVVG Sbjct: 6 LDTPAVSRRFWSGMTLLVCALLVAPMVASQLGGNYWVRVIDFALLYVMLALGLNIVVGYT 65 Query: 138 GLLDLGYVGFYAVGAYTYALLAE------YAGFGFW----------TALPIAGMMAALFG 181 GLLD+G++ FYAVGAY ALLA + W +P+A ++AA G Sbjct: 66 GLLDMGFIAFYAVGAYLAALLASPHLLDVFPILNSWFPDGLHTSWLVIIPLAALVAAGCG 125 Query: 182 FLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNM---TEITGGPNGIGSIPKPTLFGLTFE 238 +LG P L+LRGDYLAIVTLGFGEIIRIL+RN+ IT G GI + LFGL F Sbjct: 126 IVLGAPTLKLRGDYLAIVTLGFGEIIRILMRNLDRPVNITNGAKGISGVDSLNLFGLKFS 185 Query: 239 RRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRED 298 + +FG + L Y + +L+++ +FV RL IGRAW A+RED Sbjct: 186 G--------VYHWFGFKVPALW---LWYYLLMLVIVAIIFVCLRLQHSRIGRAWHAIRED 234 Query: 299 EVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLG 358 E RA+G+N KL AF IGASF G AG+ F A QG V+PESFT ES +LA+VVLG Sbjct: 235 EDVARAMGINLRNYKLLAFAIGASFGGVAGALFGAFQGFVSPESFTLQESIAVLAMVVLG 294 Query: 359 GMGSQLGVILAAVVMVLLQEMRG----------FNE-------YRMLIFGLTMIVMMIWR 401 GMG GVIL AV++ L E+ F E R L +GL ++++M+ R Sbjct: 295 GMGHIPGVILGAVLLTALPELLRSQAAPVQQALFGEVLIDPEVLRQLFYGLALVLVMLLR 354 Query: 402 PQGLLP 407 PQG+ P Sbjct: 355 PQGIWP 360 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: 462 Number of extensions: 27 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: 368 Length adjustment: 31 Effective length of query: 386 Effective length of database: 337 Effective search space: 130082 Effective search space used: 130082 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