Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate YP_002823302.1 NGR_b10960 2-keto-4-pentenoate hydratase
Query= BRENDA::A0A076VF18 (308 letters) >NCBI__GCF_000018545.1:YP_002823302.1 Length = 279 Score = 137 bits (344), Expect = 4e-37 Identities = 83/207 (40%), Positives = 118/207 (57%), Gaps = 14/207 (6%) Query: 83 MGLQYSGDPANPQ-DKPPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGK 141 +GL Y+ A D PP +F KA+ A+ GP D++++PR D+EVEL VV+GK Sbjct: 74 IGLNYADHAAESGLDVPPEPVVFMKATSAIVGPNDNVIIPR--GSVATDWEVELGVVIGK 131 Query: 142 DAKDVDEKDAMSFVGGYCVVNDVSSRGLCAK-GGQWGMGKSYDTWCPFGPCLVSPSALGA 200 AK V + +A+ V GYCV+NDVS R K GQW GKS D++ P GP LV+ + A Sbjct: 132 KAKYVSQAEALEHVAGYCVINDVSERDFQTKRSGQWTKGKSCDSFGPTGPWLVTRDEI-A 190 Query: 201 DPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSP--IALGRK 258 DP KL + VNG+ Q G+T +V + L++ LS TL G +I TG+P + +G K Sbjct: 191 DPQKLGMWLKVNGETKQDGSTGTMVYGVAYLVSYLSQFMTLHPGDIISTGTPPGVGMGFK 250 Query: 259 APGDAVEQSPFMKDGDEIRCFVEGCGT 285 P ++K GD I ++G G+ Sbjct: 251 PP-------QYLKAGDVIELGIDGLGS 270 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: 254 Number of extensions: 13 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: 279 Length adjustment: 26 Effective length of query: 282 Effective length of database: 253 Effective search space: 71346 Effective search space used: 71346 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 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