Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_038020839.1 HA49_RS04975 fumarylacetoacetate hydrolase family protein
Query= uniprot:A0A2E7P912 (281 letters) >NCBI__GCF_000757425.2:WP_038020839.1 Length = 219 Score = 129 bits (323), Expect = 7e-35 Identities = 68/181 (37%), Positives = 104/181 (57%), Gaps = 3/181 (1%) Query: 71 GKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVV 130 GK +C+G NYA H +E P EPVVF K +A+ + + G + EVEL V+ Sbjct: 17 GKVVCVGSNYAKHISEMGSITPEEPVVFIKPETALCDLRQPLSLLSGLGEIHHEVELAVL 76 Query: 131 IGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQI---ERGGTWDKGKGCDTFGPIGPWLVT 187 IG E+ + +AGY V D++ R Q ++G W+K KG D P+ ++ Sbjct: 77 IGSTLQQASEEQVLPAIAGYGVALDLTLRTVQAGLKKKGQPWEKSKGFDNSCPVSGFIPA 136 Query: 188 RDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGV 247 + DPQ + LE++G+ Q+GNTS M++ + +++Y+SRF +L+PGD+I TGTP GV Sbjct: 137 AEFNGDPQNTPLKLEINGEVRQSGNTSDMMYKIVPLIAYMSRFFTLRPGDIILTGTPEGV 196 Query: 248 G 248 G Sbjct: 197 G 197 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: 181 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: 219 Length adjustment: 24 Effective length of query: 257 Effective length of database: 195 Effective search space: 50115 Effective search space used: 50115 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 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