Align HMG aldolase monomer (EC 4.1.3.17) (characterized)
to candidate PP_4462 PP_4462 putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Query= metacyc::MONOMER-3184 (227 letters) >FitnessBrowser__Putida:PP_4462 Length = 221 Score = 90.5 bits (223), Expect = 2e-23 Identities = 57/186 (30%), Positives = 94/186 (50%), Gaps = 12/186 (6%) Query: 38 GLLKPYMRPIYAGKQVSGTAVTVLLQPGDNWMMHVAAEQIQPGDIVVAAVTAECSDGYFG 97 G + ++ + K+V GTAVT+ L D+ ++H ++PG IVV + +G Sbjct: 36 GFMDGEIQALGNSKRVVGTAVTLALPAQDSTLLHYTLGLLKPGHIVVIDRLGDRKHACWG 95 Query: 98 DLLATSFQARGARALIIDAGVRDVKTLQEMDFPVWSKAISSKGT-IKATLGSVNIPIVCA 156 + + GA A +ID D +QE DFP+WS+ +S T I G +N+P+ C Sbjct: 96 GGVTQAAVTAGASAAVIDGMCTDPHEIQEHDFPIWSRGVSPITTRIYGLGGKLNMPVSCG 155 Query: 157 GMLVTPGDVIVADDDGVVCVPAARAVEVLAAAQKRES---------FEGEKRAKL--ASG 205 G+ V PGD+++ D++GV+ + A EV+ A ++ EGEK L A+ Sbjct: 156 GVAVCPGDIVICDENGVLVLSPAELDEVVQTALAKQDRGVENCRRIREGEKLGDLSGATA 215 Query: 206 VLGLDM 211 ++ DM Sbjct: 216 IVEADM 221 Lambda K H 0.319 0.135 0.388 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: 108 Number of extensions: 9 Number of successful extensions: 2 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: 227 Length of database: 221 Length adjustment: 22 Effective length of query: 205 Effective length of database: 199 Effective search space: 40795 Effective search space used: 40795 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