Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate AO356_25565 AO356_25565 2-oxo-hepta-3-ene-1,7-dioate hydratase
Query= metacyc::MONOMER-15110 (260 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25565 Length = 267 Score = 193 bits (491), Expect = 3e-54 Identities = 110/261 (42%), Positives = 156/261 (59%), Gaps = 7/261 (2%) Query: 1 MDKTVIKDLARFLVDAEVEKKEVLKLTNEHPDLTVEDGYAIQEQLVQMKLEQGYRIVGPK 60 +D+T I+ A L AE +++V + + +HPD+T+ED YAIQ V K++ G ++VG K Sbjct: 2 LDQTFIQQAAARLDRAERSREQVRQFSLDHPDITIEDAYAIQRAWVAQKIQDGRKLVGHK 61 Query: 61 MGLTSQAKMKQMNVNEPIYGYIFDYMVVN-GQELSMSELIHPKVEAEIAFILGKDIEGPG 119 +GLTS+A N+ EP YG + D M + G ++ I P+VE E+AFILGK ++GP Sbjct: 62 IGLTSRAMQVSSNITEPDYGALLDDMFFDEGTDIPFERFIVPRVEVELAFILGKPLKGPN 121 Query: 120 ITGAQVLAATEYVVPALEIIDSRYQNFQFTLP------DVIADNASSSRVFLGSTIKRPD 173 +T VL ATE+V+PALEIID+R Q D I+DNA+++ V +G RP Sbjct: 122 VTVFDVLDATEWVIPALEIIDARIQQIDPQTKATRKVFDTISDNAANAGVVMGGRAVRPT 181 Query: 174 NMELDLLGVTLSINGQIKDLGAGAAVVGHPANSVAMLANMLARKGLKLKAGQIILSGGIT 233 ++L + L NG I++ G AAV+ HPA VA LAN LA + L+ GQIIL G T Sbjct: 182 EIDLRKVPAVLYRNGVIEESGVSAAVLNHPAKGVAWLANKLAAYDVTLQPGQIILGGSFT 241 Query: 234 GAVMLNVGDSVTGKFDGLGTI 254 V N GD+ +D LG+I Sbjct: 242 RPVAANPGDTFHVDYDMLGSI 262 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: 174 Number of extensions: 7 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: 267 Length adjustment: 25 Effective length of query: 235 Effective length of database: 242 Effective search space: 56870 Effective search space used: 56870 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