Align 2-pyrone-4,6-dicarboxylate lactonase (EC 3.1.1.57) (characterized)
to candidate AO356_23965 AO356_23965 hypothetical protein
Query= BRENDA::D1MW98 (305 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23965 Length = 276 Score = 132 bits (333), Expect = 7e-36 Identities = 98/284 (34%), Positives = 138/284 (48%), Gaps = 25/284 (8%) Query: 25 PAGAVDAHCHVFGPGNEFPFAPERKYTP-CDASKAQLYALRDHLGFARNVVVQATCHGAD 83 P +D H HVF E A R+YTP DA+ AQ G + V+VQ + G D Sbjct: 8 PMTGIDCHAHVFS--RELELAAVRRYTPDYDATLAQYLGHLHAHGLSHGVLVQPSFLGTD 65 Query: 84 NRAMVDACKSSGGKARGVATVKRSISDAELQELHDAGVRGVRFNFV-KRLVDFTPKDELM 142 NR ++ A + + + RGV V+R +S AEL ++ GV GVR N + K L DF +D Sbjct: 66 NRYLLAALRQAPEQLRGVVVVERDVSRAELDDMARLGVVGVRLNLMGKALPDF--RDAAW 123 Query: 143 E-IAGRIAKLGWHVVIYFEAVDLPELWDFFTALPTTVVVDHMGRPDVTKGVDSEEFALFL 201 + G IA+L WHV ++ VDLP L VVVDH GRPD G+D FA L Sbjct: 124 HGLLGHIAELDWHVELHANLVDLPGLMAQLLPWGIKVVVDHFGRPDACSGLDQPGFAQ-L 182 Query: 202 KFMREHKNVWSKVSCPERLSVSGPKALHGEQNAYQDVVPFARRVVEEF-----PERVLWG 256 + + VW KVS RL + + L FAR + PER++WG Sbjct: 183 MALGQGGQVWMKVSGIYRLGATASRNLE-----------FARASLALLERSFGPERLVWG 231 Query: 257 TDWPHPNLKDHMPDDGLLVDFIPHIAPTAQLQQKLLVDNPMRLY 300 +DWPH + H+ + ++ + + +A L L+V P L+ Sbjct: 232 SDWPHTQHEAHVGFETVMAQ-LRALECSASLIHALMVQAPQALF 274 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: 292 Number of extensions: 20 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: 276 Length adjustment: 26 Effective length of query: 279 Effective length of database: 250 Effective search space: 69750 Effective search space used: 69750 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