Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate SM_b21112 SM_b21112 bifunctional 2-hydroxyhepta-2,4-diene-1, 7-dioatesomerase/5-carboxymethyl-2-oxo-hex-3-ene-1, 7-dioatedecarboxylase
Query= BRENDA::A0A076VF18 (308 letters) >FitnessBrowser__Smeli:SM_b21112 Length = 281 Score = 147 bits (371), Expect = 3e-40 Identities = 108/287 (37%), Positives = 150/287 (52%), Gaps = 25/287 (8%) Query: 22 YGEPQQDGDLGLLYSNG--ERITARVV-AAPWTSSPASTSSPRVLTVQTLLSPLA-PTDV 77 YGEP Q+ GLL S+G ++ V A P+ L V+TL + P Sbjct: 6 YGEPGQEKP-GLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGNPRLG 64 Query: 78 PAIRG------MGLQYSGDPANP-QDKPPVACLFFKASQALAGPGDDIVLPRLARDEKND 130 P + G +GL YS A PP +F KA+ A+ GP DD+VLPR EK D Sbjct: 65 PCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPR--GSEKTD 122 Query: 131 YEVELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSSRGL-CAKGGQWGMGKSYDTWCPFG 189 +EVEL +V+GK AK V E +A+ +V GYC V+DVS R + GQW GKS DT+ P G Sbjct: 123 WEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGPTG 182 Query: 190 PCLVSPSALGADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILT 249 P LV+ + ADP L + VNG+ Q G+T +V L++ LS +L+ G +I T Sbjct: 183 PWLVTKDEV-ADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIIST 241 Query: 250 GSP--IALGRKAPGDAVEQSPFMKDGDEIRCFVEGCGTLINSVRDEA 294 G+P + +G K P ++K GD + +EG G+ VR +A Sbjct: 242 GTPPGVGMGMKPP-------RYLKAGDVVELGIEGLGSQKQRVRADA 281 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: 273 Number of extensions: 14 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: 281 Length adjustment: 26 Effective length of query: 282 Effective length of database: 255 Effective search space: 71910 Effective search space used: 71910 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