Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate AO356_28650 AO356_28650 2-keto-4-pentenoate hydratase
Query= metacyc::MONOMER-15110 (260 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28650 Length = 254 Score = 100 bits (250), Expect = 2e-26 Identities = 61/207 (29%), Positives = 109/207 (52%), Gaps = 4/207 (1%) Query: 38 GYAIQEQLVQMKLEQGYRIVGPKMGLTSQAKMKQMNVNEPIYGYIFDYMVVN-GQELSMS 96 GY +Q + ++ + G R+ G K+ +A + ++EP+ G + D MVV G+ +S++ Sbjct: 34 GYTLQREALRRRQAGGERLTGWKVAFAGRAAQDRFGIDEPVLGALTDAMVVEPGRGVSLA 93 Query: 97 ELIHPKVEAEIAFILGKDIEGPGITGAQVLAATEYVVPALEIIDSRYQNFQFTLPDVIAD 156 LI PK+E E+AF+LG+ + + +LAA + PA EI D R+Q ++F + +AD Sbjct: 94 RLIQPKLEIELAFVLGRTLVPGFYSDEDILAAVSEIAPAFEIADCRWQGWRFGVGAFLAD 153 Query: 157 NASSSRVFLGSTIK-RPDNMELDLLGVTLSINGQIKDLGAGAAVVGHPANSVAMLANMLA 215 NA++ LG ++ P+ +L L L+ +G G A P ++ L L Sbjct: 154 NAAAGLYCLGPRVRFHPE--QLAHLNYRLACDGVPCGEGNAQAREDTPQANLCWLVRRLL 211 Query: 216 RKGLKLKAGQIILSGGITGAVMLNVGD 242 G ++AGQ++LSG + + + + Sbjct: 212 ADGQCVEAGQVVLSGALLAPLEIKASE 238 Lambda K H 0.317 0.137 0.374 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: 138 Number of extensions: 10 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: 260 Length of database: 254 Length adjustment: 24 Effective length of query: 236 Effective length of database: 230 Effective search space: 54280 Effective search space used: 54280 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 (21.6 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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