Align 2-pyrone-4,6-dicarboxylate lactonase (EC 3.1.1.57) (characterized)
to candidate 3607183 Dshi_0604 amidohydrolase 2 (RefSeq)
Query= BRENDA::D1MW98 (305 letters) >FitnessBrowser__Dino:3607183 Length = 286 Score = 194 bits (493), Expect = 2e-54 Identities = 109/285 (38%), Positives = 151/285 (52%), Gaps = 11/285 (3%) Query: 16 NPSKPQFKLPAGAVDAHCHVFGPGNEFPFAPERKYTPCDASKAQLYALRDHLGFARNVVV 75 +PS P+ LP GA D H HV P + PF R YTP A+ AQ AL LG R V+V Sbjct: 11 DPSPPKRPLPPGATDCHSHVIVPEADHPFVANRSYTPPPATLAQYKALHARLGIERAVIV 70 Query: 76 QATCHGADNRAMVDACKSSGGKARGVATVKRSISDAELQELHDAGVRGVRFNFVKRLVDF 135 Q + +G DN ++A G RG+A V +S +LQ ++ AG+RG R N + Sbjct: 71 QPSVYGTDNSVTLEAIAGYGPGCRGIAVVDADVSMRDLQAMNAAGIRGARINML--FSGG 128 Query: 136 TPKDELMEIAGRIAKLGWHVVIYFEAVDLPELWDFFTALPTTVVVDHMGRPDVTKGVDSE 195 D+L +A RIA L WH + + L +L LP VV+DHMG G+D Sbjct: 129 IGLDDLEPLARRIADLDWHFQLLIDGPTLADLEARLANLPVPVVIDHMGHMQTHDGLDQP 188 Query: 196 EFALFLKFMREHKNVWSKVSCPERLSVSGPKALHGEQNAYQDVVPFARRVVEEFPERVLW 255 F L+ + N W K+S R+S P+ ++DVVPFA+ ++ + E ++W Sbjct: 189 GFRA-LRRLVVRGNTWVKLSGNYRMSSQRPR--------FEDVVPFAQALISDNSEHMVW 239 Query: 256 GTDWPHPNLKDHMPDDGLLVDFIPHIAPTAQLQQKLLVDNPMRLY 300 GTDWPHP + D MPDDG LVD + + +Q++LVDNP LY Sbjct: 240 GTDWPHPAMLDFMPDDGSLVDALDAYVTSQDQKQRILVDNPATLY 284 Lambda K H 0.321 0.138 0.443 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: 325 Number of extensions: 18 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: 305 Length of database: 286 Length adjustment: 26 Effective length of query: 279 Effective length of database: 260 Effective search space: 72540 Effective search space used: 72540 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 (21.9 bits) S2: 48 (23.1 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