Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_011159528.1 TX73_RS20375 FAA hydrolase family protein
Query= BRENDA::A0A076VF18 (308 letters) >NCBI__GCF_000195775.1:WP_011159528.1 Length = 233 Score = 85.9 bits (211), Expect = 8e-22 Identities = 64/206 (31%), Positives = 99/206 (48%), Gaps = 22/206 (10%) Query: 85 LQYSGDPANPQDKPPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAK 144 L++ + N + +PP F K + + G I P L +D +EVEL V L Sbjct: 38 LEHVREMGNDERQPPF--FFAKHADMVTPDGATIPYPPLTKDLH--HEVELVVALKSGRL 93 Query: 145 DVDEKDAMSFVGGYCVVNDVSSRGLCA----KGGQWGMGKSYDTWCPFGPCLVSPSALGA 200 ++ + A+ V GY V D++ R L K W +GKS+D P G + P++ Sbjct: 94 NIPVERALDHVWGYAVGIDLTRRDLQIASRKKEQPWEIGKSFDASAPCGA--LRPASEIG 151 Query: 201 DPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAP 260 P I VNG Q G+ ++++ +PE+IA+LS L AG +I+TG+P + +P Sbjct: 152 HPATGKIWLSVNGTERQTGDLSEMIWNVPEIIAKLSAQVELAAGDIIMTGTPAGVAALSP 211 Query: 261 GDAVEQSPFMKDGDEIRCFVEGCGTL 286 GDA I C ++G GTL Sbjct: 212 GDA------------IACGIDGIGTL 225 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: 193 Number of extensions: 9 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: 233 Length adjustment: 25 Effective length of query: 283 Effective length of database: 208 Effective search space: 58864 Effective search space used: 58864 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