Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_012536544.1 AFE_RS06880 fumarylacetoacetate hydrolase family protein
Query= uniprot:A0A2E7P912 (281 letters) >NCBI__GCF_000021485.1:WP_012536544.1 Length = 227 Score = 95.5 bits (236), Expect = 9e-25 Identities = 65/192 (33%), Positives = 98/192 (51%), Gaps = 7/192 (3%) Query: 70 IGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGV 129 + + C+G NYADHA E EP F K SA++ N + P G+ EVEL V Sbjct: 23 VRRIFCVGQNYADHAREMGSAPDTEPFFFMKPASAILRNNSVLPYPPGTTDLQPEVELVV 82 Query: 130 VIGKGGSYIDE-KDAMSHVAGYCVVNDVSEREYQ---IERGGTWDKGKGCDTFGPIGPWL 185 + KGG +I K +V GY V D++ R+ Q E+G W+ K D P Sbjct: 83 ALHKGGKHIPTGKVDDDYVFGYAVGLDMTRRDLQRAAREKGQPWEMAKAFDHSAPC--TA 140 Query: 186 VTRDEVADPQKLG-MWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTP 244 +T + + G + L+V+G+ Q+ + M++ + IV +LS + L PGD++ TGTP Sbjct: 141 ITPEFYSGTIARGKVELKVNGQIRQSADVGDMLWKIPQIVHFLSNQVELFPGDLLFTGTP 200 Query: 245 PGVGMGVKPEAV 256 GVG VK + + Sbjct: 201 AGVGPVVKGDVI 212 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: 177 Number of extensions: 11 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: 227 Length adjustment: 24 Effective length of query: 257 Effective length of database: 203 Effective search space: 52171 Effective search space used: 52171 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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