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 Dsui_2059 Dsui_2059 ABC-type branched-chain amino acid transport system, permease component
Query= TCDB::P21628 (417 letters) >FitnessBrowser__PS:Dsui_2059 Length = 287 Score = 159 bits (402), Expect = 1e-43 Identities = 100/290 (34%), Positives = 158/290 (54%), Gaps = 36/290 (12%) Query: 122 IYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFG 181 ++ +L + + + + GLL L F VGAY ALL + + F + L G+ L Sbjct: 20 VHALLALSIWLTLS-CGLLSLANAAFMGVGAYVSALLTLHLEWSFGSVLLAGGIAPTLVA 78 Query: 182 FLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRA 241 ++G PVLRL G YLA+ TL FGE++RI + N+ EITGGP G+ IP T Sbjct: 79 LIIGAPVLRLSGVYLAMATLAFGEVVRITVLNL-EITGGPEGLNGIPLAT---------- 127 Query: 242 PEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVA 301 EG + +AL+L +A++ + RL R +GRA+EA++EDEVA Sbjct: 128 -EG---------------------WHIALILA-VAVYGLARLRRSKVGRAFEAIKEDEVA 164 Query: 302 CRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMG 361 R +G+N KL AF++GA AG AG+ A ++P + F + IL + VLGG Sbjct: 165 ARLMGINVDRYKLLAFSLGAFIAGVAGALNAHFTFFISPREYGFENAVDILTMAVLGGTS 224 Query: 362 SQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQR 410 S +G +L + ++ LL E +R ++R L+ G +++++++ P+GL +R Sbjct: 225 SLIGPMLGSSILTLLPELLRSLQDFRSLVNGAVLVLVVLFLPKGLWESRR 274 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: 302 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 287 Length adjustment: 29 Effective length of query: 388 Effective length of database: 258 Effective search space: 100104 Effective search space used: 100104 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: 49 (23.5 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