Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 3606953 Dshi_0381 ABC transporter related (RefSeq)
Query= TCDB::P21630 (233 letters) >FitnessBrowser__Dino:3606953 Length = 274 Score = 186 bits (473), Expect = 3e-52 Identities = 107/242 (44%), Positives = 147/242 (60%), Gaps = 11/242 (4%) Query: 1 MLSFDKVSTYYGK-IQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCG-----SPQAA 54 +L + + Y I L VS+ V KG I L+G NGAGK+T L ++ + Sbjct: 11 LLEVNNIEVIYNHVILVLKGVSLTVPKGGITALLGGNGAGKTTTLKSISNLLHSERGEVT 70 Query: 55 SGSIRYEGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQV--- 111 G+I Y G+ + L S ++++ + V EGR F LTVEENL G + T +D Sbjct: 71 KGTISYRGDRVQDLSPSDMVKRGVIQVMEGRHCFEHLTVEENLLTGAY-TRRDGRGAIAD 129 Query: 112 QMDKVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQ 171 ++ V FPRLKER + +AG SGGEQQM AIGRALMS+P+ +LLDEPS+GLAP ++++ Sbjct: 130 DLELVYTYFPRLKERRKSQAGYTSGGEQQMCAIGRALMSRPETILLDEPSMGLAPQLVEE 189 Query: 172 IFEIIEQL-RREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAY 230 IF I++ L REGV+ L EQN N AL+ A Y+LE+GR+VM A L NP V++ Y Sbjct: 190 IFTIVKNLNEREGVSFLLAEQNTNVALRFAHHGYILESGRVVMEGPAAELRENPDVKEFY 249 Query: 231 LG 232 LG Sbjct: 250 LG 251 Lambda K H 0.318 0.136 0.374 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: 188 Number of extensions: 12 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: 233 Length of database: 274 Length adjustment: 24 Effective length of query: 209 Effective length of database: 250 Effective search space: 52250 Effective search space used: 52250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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