Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate PP_2021 PP_2021 L-alpha-hydroxyglutaric acid gamma-lactonase
Query= uniprot:Q9HWH7 (388 letters) >FitnessBrowser__Putida:PP_2021 Length = 376 Score = 334 bits (857), Expect = 2e-96 Identities = 188/380 (49%), Positives = 249/380 (65%), Gaps = 16/380 (4%) Query: 10 LALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSV-KGPLRVAHTSNPS 68 L A L + A AA+L LVG+YT+G+S+GI Y FD G + PL+V + +PS Sbjct: 8 LLTASLMSLTISAHAATL---LVGSYTDGASQGIYRYHFDDKAGQIGPTPLQVVKSVSPS 64 Query: 69 YLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLS 128 +L + DQR LF VNE +G A+S+ G ++ ++QV T D PT++SLS Sbjct: 65 WLVLSADQRQLFAVNETPQG-------HASSFSISS-KGEIKPLNQVVTQGDEPTHASLS 116 Query: 129 HDGRYLFVANYSVQPE--GSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHSVV 185 D RYLFVANY+V P+ GS+ V+PV DG+L PVVQ H+AS V+P RQ HVHS+V Sbjct: 117 RDQRYLFVANYAVNPDPGGSLVVIPVAKDGTLKPVVQQARHKASGVNPERQAGAHVHSLV 176 Query: 186 SSPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFA 245 SPDGQ+L+A DLGADKVF+YRY A+ PL AA PA V PPGSGPRHL+F A GR A Sbjct: 177 LSPDGQHLYASDLGADKVFIYRYDGASADHPLTAAIPASVALPPGSGPRHLLFDAKGRHA 236 Query: 246 YLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDD 305 YLTLE++ +V++F + +G L + Q L AG LHLSADGRFL V NRG Sbjct: 237 YLTLEMNAEVVMFDVQ-DGNLVERQRLPLTERQEAAAKAAGGLHLSADGRFLYVSNRGTA 295 Query: 306 NQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSG 365 N++V F+V GQL F++RR EG PREFA P F+LVANQ S+Q+ V RDP+SG Sbjct: 296 NEIVAFSVGKQDGQLTFLQRRPAEGDHPREFALDPSDNFLLVANQKSNQIVVIRRDPRSG 355 Query: 366 QVGKTLQSVEVGSPSDLRFV 385 ++ +T+Q+++ +PSDL+F+ Sbjct: 356 KLLETVQTLKQDAPSDLKFI 375 Lambda K H 0.318 0.135 0.395 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: 557 Number of extensions: 32 Number of successful extensions: 10 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: 388 Length of database: 376 Length adjustment: 30 Effective length of query: 358 Effective length of database: 346 Effective search space: 123868 Effective search space used: 123868 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: 50 (23.9 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