Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate Ga0059261_2473 Ga0059261_2473 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)
Query= reanno::psRCH2:GFF3447 (327 letters) >FitnessBrowser__Korea:Ga0059261_2473 Length = 334 Score = 377 bits (968), Expect = e-109 Identities = 200/336 (59%), Positives = 235/336 (69%), Gaps = 18/336 (5%) Query: 1 MKLATLNQGRDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGLE 60 MKLA+L GRDG LVVVS DLA IA TLQAALDDW+ +LE + L LE Sbjct: 1 MKLASLKHGRDGKLVVVSNDLAWCADAAHIAPTLQAALDDWD----RLEGDLRNLATDLE 56 Query: 61 EGAFA---FDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGA 117 F + +PLPRAY WADGSAYVNHV LVR+ARGAEMPESFWHDPLMYQGG+ Sbjct: 57 HETIPMLRFHERQAAAPLPRAYQWADGSAYVNHVALVRQARGAEMPESFWHDPLMYQGGS 116 Query: 118 DAFIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLI 177 D F+ PI LADE+WG DLE E+ V+T DVP+G + +A + I+L+ L NDVSLRNLI Sbjct: 117 DGFLGARDPIPLADESWGCDLEAEVVVVTGDVPLGVSREDALAAIRLVGLTNDVSLRNLI 176 Query: 178 PGELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDM 237 PGELAKGFGF+QSKP+S+FSPV VTPD LG+ W+DGK+HR L+ +NG+ FG+ +AG DM Sbjct: 177 PGELAKGFGFFQSKPASAFSPVFVTPDSLGDWWKDGKLHRKLMVDLNGKPFGRAEAGEDM 236 Query: 238 TFNFPTLVAHAARTRPLGAGTIIGSGTVSNYDRSAGS-----------SCLAEKRMLEVV 286 TF+F TLVAHAA+TR LGAGTIIGSGTVSN D + G SCLAE R +E + Sbjct: 237 TFDFGTLVAHAAKTRALGAGTIIGSGTVSNRDANGGPGKPIAEGGVGYSCLAEVRTVETI 296 Query: 287 EHGEAKTPFLKFGDRVRIEMFDAAGQSIFGAIDQQV 322 G TPFLK GD VRI D IFG I+Q V Sbjct: 297 NGGAPVTPFLKAGDTVRIWAEDDKHHPIFGVIEQTV 332 Lambda K H 0.318 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: 404 Number of extensions: 8 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: 327 Length of database: 334 Length adjustment: 28 Effective length of query: 299 Effective length of database: 306 Effective search space: 91494 Effective search space used: 91494 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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