Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate RR42_RS00385 RR42_RS00385 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
Query= BRENDA::A0A076VF18 (308 letters) >FitnessBrowser__Cup4G11:RR42_RS00385 Length = 280 Score = 146 bits (368), Expect = 6e-40 Identities = 90/214 (42%), Positives = 121/214 (56%), Gaps = 14/214 (6%) Query: 75 TDVPAIRGMGLQYSGDPANP-QDKPPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEV 133 T + I +GL Y+ A P +F KA+ +L GP D ++LPR EK D+EV Sbjct: 67 TGIGKIVAIGLNYADHAAEAGMALPAEPIVFLKANSSLNGPNDPVMLPR--GSEKTDWEV 124 Query: 134 ELCVVLGKDAKDVDEKDAMSFVGGYCVVNDVSSRGL-CAKGGQWGMGKSYDTWCPFGPCL 192 EL VV+GK A+DV DA+S V GYCVVNDVS R +GG W GK DT+CP GP L Sbjct: 125 ELGVVIGKVARDVSLADALSHVAGYCVVNDVSEREFQIERGGTWDKGKGCDTFCPVGPWL 184 Query: 193 VSPSALGADPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSP 252 V+ + DP L + VNG+ QKG+TA +V + L++ +S TL G LI TG+P Sbjct: 185 VTRDEV-PDPQALGLWLDVNGQRVQKGSTATMVFDVATLVSYVSRFMTLHPGDLICTGTP 243 Query: 253 --IALGRKAPGDAVEQSPFMKDGDEIRCFVEGCG 284 + +G K P F+K GD +R ++G G Sbjct: 244 PGVGMGFKPP-------RFLKAGDTMRLGIDGLG 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: 286 Number of extensions: 16 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: 280 Length adjustment: 26 Effective length of query: 282 Effective length of database: 254 Effective search space: 71628 Effective search space used: 71628 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