Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate 8502215 DvMF_2925 5-carboxymethyl-2-hydroxymuconate Delta-isomerase (RefSeq)
Query= BRENDA::A0A076VF18 (308 letters) >FitnessBrowser__Miya:8502215 Length = 260 Score = 113 bits (282), Expect = 5e-30 Identities = 68/193 (35%), Positives = 102/193 (52%), Gaps = 17/193 (8%) Query: 98 PPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGG 157 P F KA A+ G G I++P+ + DYE EL +V+G+ +++ + V G Sbjct: 70 PDEPVFFLKAPTAVIGSGQPILVPQGVG--RVDYEGELAIVVGRQCRNISPDAVPAHVFG 127 Query: 158 YCVVNDVSSRGLCAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKLAQ 217 Y NDV++R + G +G K YDT+CP GP + + D L + T VNG++ Q Sbjct: 128 YTCANDVTARDQQRRDGLFGRCKGYDTFCPVGPWIETDLP---DTASLAVRTLVNGEVRQ 184 Query: 218 KGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSPFMKDGDEIR 277 +GNTAD++ E+++ +S TL G LILTG+P+ +G P GDE+R Sbjct: 185 QGNTADMLFTPNEMVSAISRVMTLLPGDLILTGTPVGVGPIVP------------GDEVR 232 Query: 278 CFVEGCGTLINSV 290 +E G LIN V Sbjct: 233 VEIEQVGLLINPV 245 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: 255 Number of extensions: 12 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: 260 Length adjustment: 26 Effective length of query: 282 Effective length of database: 234 Effective search space: 65988 Effective search space used: 65988 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 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