Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate PP_4864 PP_4864 High-affinity branched-chain amino acid transport ATP-binding protein BraF
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__Putida:PP_4864 Length = 291 Score = 205 bits (521), Expect = 1e-57 Identities = 117/280 (41%), Positives = 168/280 (60%), Gaps = 31/280 (11%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 +L + ++ +FGG++AL+ V + + R QI+ LIGPNGAGKTT FN +TG Y+ G EL Sbjct: 6 ILSVDNLMMQFGGIKALSDVSLKVRRNQIFALIGPNGAGKTTVFNCLTGFYKASGGRIEL 65 Query: 65 D------------GKPY------SPS------------APHEVAKAGIARTFQNIRLFGE 94 + G+ + SP+ H V +AG+ARTFQNIRLF E Sbjct: 66 NVRGSHTNVIQLLGERFQAADFVSPARFANRMYYKMFGGTHLVNRAGLARTFQNIRLFKE 125 Query: 95 MTVLENVMVGCHVRTKQNVFGAVFRHKAAREEEAAIREKSQKLLDFVGIGQFAKRTARHL 154 M+V+EN++V H+ +N+ V KA R+ E+ + + L+ V + A R A L Sbjct: 126 MSVVENLLVAQHMWVNRNLLAGVLNTKAYRKAESDALDHAFYWLEVVDLVDCANRLAGEL 185 Query: 155 SYGDQRRLEIARALATDPQLLALDEPAAGMNATEKLGLRELLVKIQAEGK-TILLIEHDV 213 SYG QRRLEIARA+ T P+++ LDEPAAG+N E L ++ ++ E T++LIEHD+ Sbjct: 186 SYGQQRRLEIARAMCTRPKIICLDEPAAGLNPQETEALSRMIRVLRDEHDITVVLIEHDM 245 Query: 214 KLMMGLCNRITVLDYGKPIAEGVPADVQKNPAVIEAYLGA 253 ++M + + I VLD+G IAEG P D++ NP VI AYLGA Sbjct: 246 GMVMSISDHIVVLDHGNVIAEGAPQDIRHNPTVIAAYLGA 285 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: 192 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: 255 Length of database: 291 Length adjustment: 25 Effective length of query: 230 Effective length of database: 266 Effective search space: 61180 Effective search space used: 61180 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: 47 (22.7 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