Align FAA hydrolase family protein (characterized, see rationale)
to candidate Ga0059261_1678 Ga0059261_1678 Fumarylacetoacetate (FAA) hydrolase family
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Korea:Ga0059261_1678 Length = 325 Score = 110 bits (276), Expect = 3e-29 Identities = 80/239 (33%), Positives = 115/239 (48%), Gaps = 16/239 (6%) Query: 42 SLDKIRKLDLESLPAVEGSPRIGACVGNIGKFICIGLNYADHAAESNLPIPAE----PVV 97 S+ +L L A+E S R+ A + YA A +PA P Sbjct: 84 SIRDFANFELHCLQALEASMRMRAASQPDPEAA-----YAGFKASGAYDLPASWYQRPYY 138 Query: 98 FNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVS 157 F G + ++ PR S D+E+E VIG G+ I E DA +H+ GY + ND S Sbjct: 139 FKGNRMTCSGHDSVIQWPRFSGTMDYELEFAAVIGTRGADIAEADADAHIFGYMIYNDFS 198 Query: 158 EREYQIE----RGGTWDKGKGCDTFGPIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNT 213 R+ Q+ R G KGK DT +GPW+VTRDE+ D L M ++G+ N+ Sbjct: 199 ARDEQVRDQQFRMGP-SKGKDFDTGNAMGPWIVTRDELPDVSNLAMTSRINGEVQGRSNS 257 Query: 214 STMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLG 272 S M F A ++++SR +L PGDV +GT G G G + YL G + L ++G+G Sbjct: 258 SGMQFSFAQCIAFVSRDETLYPGDVFGSGT-AGNGCGFE-TGRYLEPGDVIELEVEGIG 314 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: 281 Number of extensions: 19 Number of successful extensions: 2 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: 325 Length adjustment: 27 Effective length of query: 254 Effective length of database: 298 Effective search space: 75692 Effective search space used: 75692 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: 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