Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate Ga0059261_2636 Ga0059261_2636 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)
Query= BRENDA::A0A076VF18 (308 letters) >FitnessBrowser__Korea:Ga0059261_2636 Length = 284 Score = 120 bits (301), Expect = 4e-32 Identities = 76/209 (36%), Positives = 113/209 (54%), Gaps = 19/209 (9%) Query: 83 MGLQYSGDPAN---PQDKPPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVL 139 +GL Y+ A P + PV +F K + GP D + +P+ ++ K D+EVEL +V+ Sbjct: 76 IGLNYADHAAESNLPIPEEPV--VFNKWVSCIQGPNDPVTIPKDSK--KTDWEVELGIVI 131 Query: 140 GKDAKDVDEKDAMSFVGGYCVVNDVSSR-GLCAKGGQWGMGKSYDTWCPFGPCLVSPSAL 198 G A +V E DA+ V GYCVVNDVS R +G W GK + T+ P GP +V+ + Sbjct: 132 GTAAHNVSEADALDHVAGYCVVNDVSERHWQTERGMTWDKGKGFPTFGPIGPWMVTADEV 191 Query: 199 GADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRK 258 G DP L++ VNGK Q GNT ++ + ++++ LS TL G +I TG+P Sbjct: 192 G-DPQNLSMWLSVNGKKVQDGNTRTMIFTVAQIVSYLSQIMTLLPGDVITTGTP------ 244 Query: 259 APGDAVEQSP---FMKDGDEIRCFVEGCG 284 PG + Q P ++K GD + +E G Sbjct: 245 -PGVGLGQKPEPWYLKAGDVVELGIEKLG 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: 265 Number of extensions: 11 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: 308 Length of database: 284 Length adjustment: 26 Effective length of query: 282 Effective length of database: 258 Effective search space: 72756 Effective search space used: 72756 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