Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate WP_011383245.1 AMB_RS04100 2-oxo-hepta-3-ene-1,7-dioic acid hydratase
Query= BRENDA::B0VXM8 (267 letters) >NCBI__GCF_000009985.1:WP_011383245.1 Length = 268 Score = 172 bits (435), Expect = 9e-48 Identities = 99/255 (38%), Positives = 145/255 (56%), Gaps = 8/255 (3%) Query: 14 AELLNEAEREKREVARITEEVPDLSAEEAYKIQEELIKIKTNSGHRIIGPKMGLTSQAKM 73 A L+ AE+ + + +I+ + P++ +AY +Q+ ++ K N G +++G K+GLTS+A Sbjct: 12 AARLHRAEQTRHQCGQISLDHPEMGMADAYAVQKAWVETKINEGRKVVGHKIGLTSRAMQ 71 Query: 74 AQMKVKEPIYGYLFDYMFVPSGGAIHMSELIHPKVEVEIAFILGEDLEGPHVTSTQVLSA 133 ++ EP YG L D M G I M+ I P VEVE+AFIL + LEGP VT TQVLSA Sbjct: 72 QSSQIDEPDYGTLLDDMVFGEGTDIPMARFIVPMVEVELAFILKDRLEGPDVTLTQVLSA 131 Query: 134 TKYVAPALEIIDSRYQ--DFTFTLP----DVIADNASSSRVVIGNTMTPIHSLKTDLDLI 187 T YV PALEIID+R D P D I+DNA+++ +V+G P+ + DL + Sbjct: 132 TDYVIPALEIIDARCHRLDPETKRPRKVFDTISDNAANAGIVMGG--RPVRPMDVDLRWV 189 Query: 188 GAALYINGELKACGAGAAVFNHPANSVAVLANMLARKGERLKAGDIILTGGITEAIQLSA 247 A +Y NG ++ G A V NHPA+ ++ LA A L+ G ++L G T + A Sbjct: 190 AAIMYRNGVIEETGVAAGVLNHPAHGISWLARKFAPHSIALEPGQVVLAGSFTRPVPARA 249 Query: 248 GDTVIGQLDQLGDVS 262 GDT LG ++ Sbjct: 250 GDTFHVDYGPLGAIA 264 Lambda K H 0.316 0.134 0.364 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: 172 Number of extensions: 8 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: 267 Length of database: 268 Length adjustment: 25 Effective length of query: 242 Effective length of database: 243 Effective search space: 58806 Effective search space used: 58806 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