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 SMc03119 SMc03119 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >FitnessBrowser__Smeli:SMc03119 Length = 233 Score = 170 bits (431), Expect = 2e-47 Identities = 91/217 (41%), Positives = 136/217 (62%), Gaps = 15/217 (6%) Query: 1 MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60 +L ++ +YG+ LH V + V +GE+VTL+G NG GK+T L + G + G I + Sbjct: 4 LLKVAGLNAWYGESHVLHGVDMTVGEGEMVTLLGRNGVGKTTTLRAIMGIVRERRGEISF 63 Query: 61 EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENL------AMGGFFTDKDDYQVQMD 114 GE+L+ +P + + + VPE R +FS LTV ENL A GG + +D Sbjct: 64 AGEDLMRVPLHRVAHRGLGFVPEERGIFSTLTVYENLLLPPAVAKGG---------MTID 114 Query: 115 KVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFE 174 ++ ELFP L ER +SGGEQQMLAI R L + +++LLDEP+ GLAP+I+Q+I E Sbjct: 115 EIFELFPNLHERRNSAGTKLSGGEQQMLAIARILRTGVRMMLLDEPTEGLAPVIVQRIGE 174 Query: 175 IIEQLRREGVTVFLVEQNANQALKLADRAYVLENGRI 211 ++++L+ G+TV LVEQN A K+ADR Y++++GR+ Sbjct: 175 VLKKLKERGMTVLLVEQNFRFASKVADRFYLMDHGRV 211 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: 151 Number of extensions: 6 Number of successful extensions: 2 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: 233 Length adjustment: 23 Effective length of query: 210 Effective length of database: 210 Effective search space: 44100 Effective search space used: 44100 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