Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate RR42_RS31850 RR42_RS31850 2-keto-4-pentenoate hydratase
Query= metacyc::MONOMER-15110 (260 letters) >FitnessBrowser__Cup4G11:RR42_RS31850 Length = 260 Score = 169 bits (428), Expect = 5e-47 Identities = 97/254 (38%), Positives = 141/254 (55%), Gaps = 1/254 (0%) Query: 1 MDKTVIKDLARFLVDAEVEKKEVLKLTNEHPDLTVEDGYAIQEQLVQMKLEQGYRIVGPK 60 M +I L L A + V L+ +TV D Y IQ+Q V +L G RI G K Sbjct: 1 MKPDLIASLGEELHQALTARVPVAPLSGRGDPITVRDAYRIQQQFVAHRLAHGDRITGKK 60 Query: 61 MGLTSQAKMKQMNVNEPIYGYIFDYM-VVNGQELSMSELIHPKVEAEIAFILGKDIEGPG 119 +G+TS + ++V++P +G + M +GQ + + LI P+ E EIAF L +D+ GPG Sbjct: 61 IGVTSLPVQQMLDVHQPDFGMLLASMRYPDGQPIPAATLIQPRAEGEIAFFLKRDLRGPG 120 Query: 120 ITGAQVLAATEYVVPALEIIDSRYQNFQFTLPDVIADNASSSRVFLGSTIKRPDNMELDL 179 +T A VLAATE V EI+DSR +++ + D +ADNAS LG P ++L Sbjct: 121 VTRADVLAATEAVSACFEIVDSRILDWRIRIEDTVADNASCGAYVLGEERVSPAGLDLAG 180 Query: 180 LGVTLSINGQIKDLGAGAAVVGHPANSVAMLANMLARKGLKLKAGQIILSGGITGAVMLN 239 +TL NG + G G+A +GHPA +VA LAN L G+ L AG+ ILSG + + + Sbjct: 181 CAMTLEKNGVVVATGQGSAALGHPAEAVAWLANTLGALGIGLLAGETILSGSLAALIPVV 240 Query: 240 VGDSVTGKFDGLGT 253 GD + + DG+G+ Sbjct: 241 AGDRLHLRIDGIGS 254 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: 169 Number of extensions: 6 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: 260 Length of database: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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 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