Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate RR42_RS34795 RR42_RS34795 leucine/isoleucine/valine transporter ATP-binding subunit
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__Cup4G11:RR42_RS34795 Length = 254 Score = 233 bits (593), Expect = 4e-66 Identities = 116/251 (46%), Positives = 170/251 (67%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 +L+IR+++++FGGL A++ V IT E G I +IGPNGAGKTTFFN+I G + P +G L Sbjct: 1 MLEIRNLTRKFGGLSAVHDVSITFETGHINAIIGPNGAGKTTFFNLIAGTHAPTSGQILL 60 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 G+ + ++A+ G+ARTFQ LF TVL+N++VG +RT+ + +F + R Sbjct: 61 KGRNVAGLRADQIARLGVARTFQATHLFDRATVLDNLIVGHRLRTQAGLADVIFNTRRLR 120 Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184 EEE R K+++ LDFVG+ A A ++ +++R+ A ALATD +LL LDEPA G+ Sbjct: 121 EEERLCRAKAEEALDFVGLAHLAHEVAADITQEERKRVAFALALATDAELLLLDEPAGGV 180 Query: 185 NATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKNP 244 N E +GL EL+ K+ GKT+ LIEH + ++M L ++I VL++G+ IAEG PA +Q++P Sbjct: 181 NPEETVGLAELIRKMVRHGKTVCLIEHKMDMIMRLADKIMVLNHGEKIAEGSPAQIQQDP 240 Query: 245 AVIEAYLGAGH 255 VIEAYLGA H Sbjct: 241 QVIEAYLGADH 251 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: 176 Number of extensions: 8 Number of successful extensions: 1 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: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 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