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 BPHYT_RS04430 BPHYT_RS04430 amino acid ABC transporter ATPase
Query= TCDB::P21630 (233 letters) >FitnessBrowser__BFirm:BPHYT_RS04430 Length = 244 Score = 215 bits (547), Expect = 7e-61 Identities = 112/241 (46%), Positives = 158/241 (65%), Gaps = 9/241 (3%) Query: 1 MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60 MLS + YGK++ LH +S++V K +VTLIG+NGAGK+T + + G + ++G I Sbjct: 1 MLSIRNLHAGYGKVKVLHGISIDVPKASVVTLIGSNGAGKTTTMRAISGMIRPSAGEITM 60 Query: 61 ----EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGF-----FTDKDDYQV 111 + + + L S I R +A PEGRRVF+ ++V +NL +G F + D + Sbjct: 61 GVGTDAKRIDALDSHRIARLGLAHSPEGRRVFATMSVTDNLILGAFPRLTSARPRGDVKA 120 Query: 112 QMDKVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQ 171 +++ +E+FPRLKER Q AGT+SGGEQQMLA+ RA+M P L+LLDEPS+GLAPI++++ Sbjct: 121 DLERAIEMFPRLKERRHQLAGTLSGGEQQMLAMARAIMMNPDLVLLDEPSMGLAPILVEE 180 Query: 172 IFEIIEQLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYL 231 +F II L+ +GVT+ LVEQ A AL +AD YVLENGRI H L +P V+ AYL Sbjct: 181 VFRIIGNLKSQGVTMLLVEQFAAAALNVADYGYVLENGRIAAHGPATELRNDPSVKAAYL 240 Query: 232 G 232 G Sbjct: 241 G 241 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: 157 Number of extensions: 8 Number of successful extensions: 3 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: 244 Length adjustment: 23 Effective length of query: 210 Effective length of database: 221 Effective search space: 46410 Effective search space used: 46410 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