Align FAA hydrolase family protein (characterized, see rationale)
to candidate GFF3340 PGA1_c33930 fumarylacetoacetate hydrolase family protein
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Phaeo:GFF3340 Length = 229 Score = 93.2 bits (230), Expect = 5e-24 Identities = 70/226 (30%), Positives = 106/226 (46%), Gaps = 15/226 (6%) Query: 50 DLESLPAVEGSPRIGACVGNIGKFICIGLNYADHAAESNLPIPAE-PVVFNKWTSAVVGP 108 DL +PA+ R + IG+ C+G NYA HAAE + + E P F K V Sbjct: 7 DLPPVPAIPVEGRDESWP--IGRIFCVGRNYAAHAAEMGVEVDREQPFYFTKSACHAVLS 64 Query: 109 NDDVKIPRGSKKTDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQI---ER 165 +V P+G++ E+EL V I A + + GY D++ R+ Q+ ++ Sbjct: 65 GAEVPYPQGTENFHHEMELVVAISAPLQDATVAQARAAIWGYGCALDMTRRDLQLRERQK 124 Query: 166 GGTWDKGKGCDTFGPIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVS 225 W GK + P D A P +WL V+ + Q+ + + +I+ V I+ Sbjct: 125 QRPWSLGKDLENGSVFAPLRAAEDWGA-PGDQRIWLRVNDEIRQDASLAELIWSVEDILC 183 Query: 226 YLSRFMSLQPGDVISTGTPPGVGMGVKPEAVYLRAGQTMRLGIDGL 271 +LS + L+PGD++ TGTP GVG V AG + GIDGL Sbjct: 184 HLSLYYHLRPGDLVMTGTPAGVGPVV--------AGDDIEGGIDGL 221 Lambda K H 0.316 0.138 0.419 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: 181 Number of extensions: 11 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: 281 Length of database: 229 Length adjustment: 24 Effective length of query: 257 Effective length of database: 205 Effective search space: 52685 Effective search space used: 52685 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: 42 (22.0 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