Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate BWI76_RS03870 BWI76_RS03870 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
Query= BRENDA::A0A076VF18 (308 letters) >FitnessBrowser__Koxy:BWI76_RS03870 Length = 254 Score = 122 bits (306), Expect = 9e-33 Identities = 85/215 (39%), Positives = 108/215 (50%), Gaps = 17/215 (7%) Query: 83 MGLQYSGDPANPQDKPPVACL-FFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGK 141 +GL Y+ + PP L F KA G + V P E YE EL VV+GK Sbjct: 49 LGLNYADHASELAFTPPTEPLVFIKAPNTFIGHRQESVRPDNV--EYMHYEAELVVVIGK 106 Query: 142 DAKDVDEKDAMSFVGGYCVVNDVSSRGLCAKGGQWGMG-KSYDTWCPFGPCLVSPSALGA 200 A+ V E DAM++V GY V ND + R + + KS DT P GP +V A+ Sbjct: 107 TARKVAEADAMAYVAGYTVCNDYAIRDYLENYYRPNLRVKSRDTLTPIGPWIVGKEAI-P 165 Query: 201 DPHKLTITTHVNGKLAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAP 260 DPH L + T VNG+L Q+G TADL+ IP LIA LS TLQ G +I TG+P L P Sbjct: 166 DPHNLALCTWVNGELRQQGTTADLIFSIPFLIAYLSEFMTLQPGDMIATGTPKGLSDVVP 225 Query: 261 GDAVEQSPFMKDGDEIRCFVEGCGTLINSVRDEAA 295 GDE+ VEG G L+N + + A Sbjct: 226 ------------GDEVIVEVEGVGRLVNHIISQQA 248 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: 201 Number of extensions: 12 Number of successful extensions: 3 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: 254 Length adjustment: 26 Effective length of query: 282 Effective length of database: 228 Effective search space: 64296 Effective search space used: 64296 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 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