Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_092054671.1 BQ4888_RS05425 FAA hydrolase family protein
Query= BRENDA::A0A076VF18 (308 letters) >NCBI__GCF_900111775.1:WP_092054671.1 Length = 218 Score = 111 bits (278), Expect = 1e-29 Identities = 65/169 (38%), Positives = 98/169 (57%), Gaps = 8/169 (4%) Query: 98 PPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGG 157 P LF K + ++ G + +V+P ++D + +EVEL V++GK K++ K+A++ V G Sbjct: 37 PEKPVLFIKPASSIIGRHEAVVIPAFSQDCQ--HEVELAVLIGKWGKNISAKEALNHVAG 94 Query: 158 YCVVNDVSSRG----LCAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNG 213 Y V D++ R L KG W + K +DT CP + P+A DPH L IT VN Sbjct: 95 YGVALDMTLRDVQNELKQKGLPWEIAKGFDTACPLSDFV--PAAEVGDPHNLRITLKVNE 152 Query: 214 KLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGD 262 +L Q GNTA ++ +IPE+I +S TL+ G +ILTG+P +G GD Sbjct: 153 QLRQDGNTAQMMRRIPEIIQAVSEIFTLEEGDVILTGTPSGVGAVKSGD 201 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: 154 Number of extensions: 10 Number of successful extensions: 4 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: 218 Length adjustment: 24 Effective length of query: 284 Effective length of database: 194 Effective search space: 55096 Effective search space used: 55096 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 24 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