Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate WP_038207166.1 Q392_RS12075 FAA hydrolase family protein
Query= reanno::psRCH2:GFF3447 (327 letters) >NCBI__GCF_000745855.1:WP_038207166.1 Length = 337 Score = 380 bits (977), Expect = e-110 Identities = 191/334 (57%), Positives = 241/334 (72%), Gaps = 13/334 (3%) Query: 1 MKLATLNQG--RDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDG 58 MKLATL + RDG LVVVSRDL + +A LQ ALDDW+ P L+ +Y+RLNDG Sbjct: 1 MKLATLRRPGRRDGELVVVSRDLKRCASAAAVAPHLQRALDDWDVIAPSLQQLYERLNDG 60 Query: 59 LEEGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGAD 118 A D AC SPLPRAY W DGSAY+NHVELVRKARGA++P SF+ DPLMYQGG+D Sbjct: 61 AIADAMDLDPAACESPLPRAYQWLDGSAYLNHVELVRKARGAQVPASFYEDPLMYQGGSD 120 Query: 119 AFIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIP 178 +FI P I +ADE WGID E E+ V+T DVP+GATP +A + ++L+ML NDVSLR+++ Sbjct: 121 SFIGPRGNI-VADEPWGIDFEAEVTVVTGDVPLGATPEQAHAAVRLVMLANDVSLRHVLR 179 Query: 179 GELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMT 238 E+AK GF QSKP+++F+PVAVTPDELG W +VH P++ H+NG+LFG+P AG MT Sbjct: 180 TEIAKELGFVQSKPATAFTPVAVTPDELGPAWEGARVHLPMMVHLNGKLFGKPHAGEGMT 239 Query: 239 FNFPTLVAHAARTRPLGAGTIIGSGTVSNYDRS----------AGSSCLAEKRMLEVVEH 288 F+F L+AHAARTR + AG+I GSGTVSN S G C+AE RM E +E Sbjct: 240 FDFSRLIAHAARTRDIEAGSIFGSGTVSNKQGSLWGSSVENGGVGYCCIAEVRMYETIER 299 Query: 289 GEAKTPFLKFGDRVRIEMFDAAGQSIFGAIDQQV 322 G+A+T F++ GD VRIEMFDA G+S+FGAI+ +V Sbjct: 300 GQAQTEFMRHGDTVRIEMFDAGGRSVFGAIENRV 333 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: 367 Number of extensions: 14 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: 327 Length of database: 337 Length adjustment: 28 Effective length of query: 299 Effective length of database: 309 Effective search space: 92391 Effective search space used: 92391 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 24 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