Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate H281DRAFT_02528 H281DRAFT_02528 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)
Query= BRENDA::A0A076VF18 (308 letters) >FitnessBrowser__Burk376:H281DRAFT_02528 Length = 278 Score = 137 bits (346), Expect = 2e-37 Identities = 80/189 (42%), Positives = 107/189 (56%), Gaps = 9/189 (4%) Query: 98 PPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGG 157 P LF KA + GP DDIVLPR EK D+EVEL V+GK A V E DA+S+V G Sbjct: 92 PEEPILFNKAPSCIVGPDDDIVLPR--GSEKTDWEVELAFVIGKRAHYVSEADALSYVFG 149 Query: 158 YCVVNDVSSRGL-CAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKLA 216 YCV NDVS R +GGQW GK ++ P GP LV+ + DP KL + VNG+ Sbjct: 150 YCVCNDVSERAFQLERGGQWVKGKCAPSFGPIGPYLVTAEEI-PDPQKLPLWLEVNGERV 208 Query: 217 QKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSPFMKDGDEI 276 Q +T+D++ I +++ +S L G LI TG+P +G ++ ++K GD + Sbjct: 209 QNSDTSDMIFSIRTIVSYVSQFVVLMPGDLITTGTPPGVGL-----GMKPERYLKRGDTV 263 Query: 277 RCFVEGCGT 285 R VEG GT Sbjct: 264 RLSVEGLGT 272 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: 246 Number of extensions: 16 Number of successful extensions: 5 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: 308 Length of database: 278 Length adjustment: 26 Effective length of query: 282 Effective length of database: 252 Effective search space: 71064 Effective search space used: 71064 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: 48 (23.1 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