Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate CA265_RS16020 CA265_RS16020 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__Pedo557:CA265_RS16020 Length = 250 Score = 110 bits (275), Expect = 3e-29 Identities = 74/234 (31%), Positives = 122/234 (52%), Gaps = 17/234 (7%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 +++I+D+ K F G L G+ E G +IG +G+GKTT + GL+QPD+G+ Sbjct: 1 MIEIKDIYKSFSGNDVLQGISGKFEEGVTNLIIGGSGSGKTTLLKCMVGLHQPDSGSVLY 60 Query: 65 DGKPYSPSAPHE--VAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKA 122 DG+ ++P + + I FQ LF MTV EN+M ++ T Q Sbjct: 61 DGRDFTPMTYEQRIEVRKEIGMLFQGSALFDSMTVEENIMFPLNMFTDQ----------- 109 Query: 123 AREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAA 182 +R+E+ E+ L+ V + K LS G ++R+ IARA++ +P+ L DEP + Sbjct: 110 SRKEKL---ERVDFCLERVNLAGKNKLFPAELSGGMKKRVGIARAISMNPKYLFCDEPNS 166 Query: 183 GMNATEKLGLRELLVKIQAEGK-TILLIEHDVKLMMGLCNRITVLDYGKPIAEG 235 G++ + + EL+ +I E K T +++ HD+ +MG+ + I L GK EG Sbjct: 167 GLDPKTSIVIDELIQEITEEYKTTTIVVTHDMNSVMGIGDYILFLHEGKKFWEG 220 Lambda K H 0.320 0.138 0.394 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: 142 Number of extensions: 9 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: 255 Length of database: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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