Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate GFF3551 PS417_18185 5-carboxymethyl-2-hydroxymuconate isomerase
Query= BRENDA::A0A076VF18 (308 letters) >FitnessBrowser__WCS417:GFF3551 Length = 283 Score = 98.6 bits (244), Expect = 2e-25 Identities = 64/200 (32%), Positives = 105/200 (52%), Gaps = 10/200 (5%) Query: 95 QDKPPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSF 154 +D P +F + + + I+ P+++ K D+E EL VV+GK A+ V+ DA+ + Sbjct: 92 RDMPTYPMIFTRFADSQVAHLQPIIRPKVSH--KLDFEGELAVVIGKTARHVNAADALDY 149 Query: 155 VGGYCVVNDVSSRGLCAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGK 214 V GY ND S R Q+ GK++ FGP +V+ + DP +L +TT +NG+ Sbjct: 150 VAGYACYNDGSVRDWQKHTLQFVPGKNFPQTGGFGPWMVTHDEIN-DPQELELTTRLNGE 208 Query: 215 LAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSP-FMKDG 273 + Q T+D++ + +LI S T L G +I++G+ +G A + P +MK G Sbjct: 209 VMQHTRTSDMIFDVRQLIEYCSTFTELAPGDVIVSGTTGGVG------AFREPPVWMKPG 262 Query: 274 DEIRCFVEGCGTLINSVRDE 293 D + + G G L NS+ DE Sbjct: 263 DTVEVEITGIGRLRNSIADE 282 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: 236 Number of extensions: 13 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: 283 Length adjustment: 26 Effective length of query: 282 Effective length of database: 257 Effective search space: 72474 Effective search space used: 72474 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