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 CA265_RS04345 CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD
Query= TCDB::P21630 (233 letters) >FitnessBrowser__Pedo557:CA265_RS04345 Length = 216 Score = 107 bits (266), Expect = 2e-28 Identities = 72/217 (33%), Positives = 116/217 (53%), Gaps = 6/217 (2%) Query: 1 MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60 ML + YG +Q L V+ EV+KGEIV++IG +GAGKSTLL L + GS++ Sbjct: 1 MLKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQL 60 Query: 61 EG---EELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFF--TDKDDYQVQMDK 115 +G +L G ST ++I V + + + EN+ + F T+K + + + Sbjct: 61 KGTVINKLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAKTNKKQAETRAFE 120 Query: 116 VLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEI 175 +L+LF LK+R + + +SGGEQQ +AI RAL++ P ++L DEPS L + ++ Sbjct: 121 LLDLFG-LKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGLHQL 179 Query: 176 IEQLRREGVTVFLVEQNANQALKLADRAYVLENGRIV 212 LR F++ + K +DR +++G IV Sbjct: 180 FVSLRDNFHQTFVIVTHNEHLAKTSDRVVSMKDGLIV 216 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: 104 Number of extensions: 4 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: 216 Length adjustment: 22 Effective length of query: 211 Effective length of database: 194 Effective search space: 40934 Effective search space used: 40934 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