Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_028488570.1 Q394_RS0106530 fumarylacetoacetate hydrolase family protein
Query= BRENDA::A0A076VF18 (308 letters) >NCBI__GCF_000621325.1:WP_028488570.1 Length = 294 Score = 115 bits (287), Expect = 2e-30 Identities = 82/233 (35%), Positives = 120/233 (51%), Gaps = 19/233 (8%) Query: 67 TLLSPLAPTDVPAIRGMGLQY---SGDPANPQDK----PPVACLFFKASQALAGPGDDIV 119 TLL+P+ P + +GL Y + + AN + P +F K ++ G D V Sbjct: 68 TLLAPI-PRPRKNVMCLGLNYLEHAEETANQIGRTGKAPQYPIVFTKCPTSVIG--QDAV 124 Query: 120 LPRLARD-EKNDYEVELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSSRGLCAKGGQWGM 178 +P + D+E EL VVLGK K + +A+ V GY V+ND+S+R + Q+ + Sbjct: 125 VPFDPDTCSQLDWEAELGVVLGKGGKKIAAANALDHVFGYTVINDLSARDIQLSHKQYFL 184 Query: 179 GKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHG 238 GKS D CP GP +V+ + ADP L I VNG Q NT +++ + +I LS G Sbjct: 185 GKSLDGGCPMGPWIVTADDI-ADPQNLAIACRVNGVTKQASNTRNMIFNVASIIEWLSRG 243 Query: 239 TTLQAGSLILTGSPIALGRKAPGDAVEQSP-FMKDGDEIRCFVEGCGTLINSV 290 TL+AG +I TG+P +G V + P F+ GD + C VE G L NS+ Sbjct: 244 MTLEAGDVIATGTPSGVG------FVREPPEFLLPGDVVECEVESVGVLRNSI 290 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: 240 Number of extensions: 15 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: 294 Length adjustment: 27 Effective length of query: 281 Effective length of database: 267 Effective search space: 75027 Effective search space used: 75027 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 Apr 09 2024. 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