Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate PP_0616 PP_0616 Branched-chain amino acid ABC transporter, ATP binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__Putida:PP_0616 Length = 250 Score = 171 bits (434), Expect = 1e-47 Identities = 106/258 (41%), Positives = 152/258 (58%), Gaps = 12/258 (4%) Query: 1 MSREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGG 60 MS +L+ +L + +G AV GV L V+ + +IGPNGAGKT++F+CLTG Q T G Sbjct: 1 MSDYLLETRHLELAYGPFKAVAGVDLKVRAGTIHTIIGPNGAGKTSLFHCLTGERQATAG 60 Query: 61 TILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENL-LIAQHRHLNTNFFAGLFK 119 IL +G+ I P H G+ R+FQ LF++++ ENL L AQ R GL Sbjct: 61 KILFNGQDIIRKPSHGRVALGMARSFQLTSLFQNLSVRENLRLAAQGRD-------GLGA 113 Query: 120 TPAFRKSEREAMEY--AEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILML 177 +R E + + A+ L+++ L+ A AG L++GQQR LE+ + +P +LML Sbjct: 114 LNFWRSVEHKRSHWNTADQVLERLKLSARAETLAGELSHGQQRVLEVGMSICAKPTLLML 173 Query: 178 DEPAAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGT 237 DEP +G+ + + LI L +H TVLLIEH+M +VMSIS I V++ G L +GT Sbjct: 174 DEPTSGMGIDDIPVMTDLISDLGRDH--TVLLIEHNMSIVMSISQRITVMSHGQILVEGT 231 Query: 238 PEQIRDNPEVIKAYLGEA 255 PEQ+R++ V AYLGEA Sbjct: 232 PEQVRNDERVRTAYLGEA 249 Lambda K H 0.321 0.138 0.398 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: 170 Number of extensions: 7 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: 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