Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_013707421.1 DESAC_RS12405 DUF2437 domain-containing protein
Query= BRENDA::A0A076VF18 (308 letters) >NCBI__GCF_000195295.1:WP_013707421.1 Length = 252 Score = 123 bits (309), Expect = 4e-33 Identities = 84/220 (38%), Positives = 114/220 (51%), Gaps = 18/220 (8%) Query: 72 LAPTDVPAIRGMGLQYSGDPANPQDKPPVACLFF-KASQALAGPGDDIVLPRLARDEKND 130 LAP + I +GL Y A + P L F K S A+ GP IV P + + D Sbjct: 48 LAPCEPSKIIALGLNYRDHAAEMRMALPTEPLIFLKPSTAVIGPSTPIVYP--PQSCRVD 105 Query: 131 YEVELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSSRGLCAKGGQWGMGKSYDTWCPFGP 190 YE EL VV+G+ V E A +++ GY VNDV++R L K GQ+ KS+DT+CP GP Sbjct: 106 YEAELGVVIGRPVSKVSEAKAKNYILGYTCVNDVTARDLQKKDGQFTRSKSFDTFCPLGP 165 Query: 191 CLVSPSALGADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTG 250 + + ADP L + +NG+ Q T +LV + LI+ +SH TL G +I TG Sbjct: 166 WIETDI---ADPDNLVVEAILNGERRQHSTTQNLVFGVAALISFISHIMTLLPGDVIATG 222 Query: 251 SPIALGRKAPGDAVEQSPFMKDGDEIRCFVEGCGTLINSV 290 +P +G PGD + EIR VEG G+L N V Sbjct: 223 TPSGVGPMQPGDHI----------EIR--VEGVGSLHNHV 250 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: 218 Number of extensions: 15 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: 252 Length adjustment: 25 Effective length of query: 283 Effective length of database: 227 Effective search space: 64241 Effective search space used: 64241 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