Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate Ac3H11_1487 5-carboxymethyl-2-oxo-hex-3- ene-1,7-dioate decarboxylase (EC 4.1.1.68) / 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (EC 5.3.3.-)
Query= BRENDA::A0A076VF18 (308 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1487 Length = 255 Score = 95.5 bits (236), Expect = 1e-24 Identities = 82/233 (35%), Positives = 114/233 (48%), Gaps = 28/233 (12%) Query: 72 LAPTDVPAIRGMGLQY-------SGD-PANPQDKPPVACLFFKASQALAGPGDDIVLPRL 123 L P +V I +GL Y SG+ +D+P V F K AL G P Sbjct: 38 LPPFEVGTIIALGLNYADHLKELSGELTVTTKDEPLV---FLKGPGALIGHNGQTRRP-- 92 Query: 124 ARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSSRGLCAKGGQWGMG-KSY 182 A YE EL VV+GK A+ V + DA+ V GY V ND + R + + K+ Sbjct: 93 ADAAFMHYECELAVVIGKTARGVKKADALQHVAGYTVCNDYAIRDYLENWYRPNLRVKNR 152 Query: 183 DTWCPFGPCLVSPSALGADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQ 242 DT GP V + + DPH L + T VNG++ Q+G+T ++V I ELI LS TL+ Sbjct: 153 DTCTVLGPWFVDAADV-PDPHDLQLRTLVNGQVVQQGHTGNMVNDIAELIEYLSGFMTLR 211 Query: 243 AGSLILTGSPIALGRKAPGDAVEQSPFMKDGDEIRCFVEGCGTLINS-VRDEA 294 AG +ILTG+P E + GD++ ++G G L+N+ V DEA Sbjct: 212 AGDVILTGTP------------EGVVNVSVGDQVVTEIDGIGRLVNTIVGDEA 252 Lambda K H 0.316 0.135 0.411 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: 210 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 308 Length of database: 255 Length adjustment: 26 Effective length of query: 282 Effective length of database: 229 Effective search space: 64578 Effective search space used: 64578 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