Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_050656959.1 C1M55_RS12530 fumarylacetoacetate hydrolase family protein
Query= uniprot:A0A2E7P912 (281 letters) >NCBI__GCF_002893965.1:WP_050656959.1 Length = 257 Score = 143 bits (360), Expect = 4e-39 Identities = 77/185 (41%), Positives = 113/185 (61%), Gaps = 4/185 (2%) Query: 72 KFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVVI 131 K ICIG NYADH AE PA+PV+F K +++VGP + +P S + +E EL VVI Sbjct: 59 KVICIGKNYADHIAEMGGEAPADPVIFLKPNTSIVGPGAPIVLPPTSNEVHFEGELAVVI 118 Query: 132 GKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLVTRDEV 191 G+ + A+S V GY + NDVS R++Q G W + KG DTF P+GPW+ T + Sbjct: 119 GQPCKDVPAAKALSVVLGYTIANDVSARDHQ-RHDGQWTRAKGHDTFCPLGPWIETSLDA 177 Query: 192 ADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGVGMGV 251 +D + + EV+G+ Q+ +T+ ++ + I+ ++S M+L PGDVI TGTP GVG V Sbjct: 178 SD---VDIRTEVNGQVKQDSSTAFLLHDIPKIIEWISAVMTLLPGDVILTGTPAGVGPIV 234 Query: 252 KPEAV 256 ++V Sbjct: 235 DGDSV 239 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: 229 Number of extensions: 7 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: 257 Length adjustment: 25 Effective length of query: 256 Effective length of database: 232 Effective search space: 59392 Effective search space used: 59392 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 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