Align FAA hydrolase family protein (characterized, see rationale)
to candidate 206303 DVU0875 fumarylacetoacetate hydrolase family protein
Query= uniprot:A0A2E7P912 (281 letters) >MicrobesOnline__882:206303 Length = 259 Score = 143 bits (360), Expect = 4e-39 Identities = 77/201 (38%), Positives = 117/201 (58%), Gaps = 11/201 (5%) Query: 72 KFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVVI 131 K +C+GLNY HA E + +P EPV F K +A++G + + +P + D+E EL +V+ Sbjct: 50 KVVCVGLNYRGHAGELGMDVPDEPVFFLKAPTAIIGTGEPIVLPPAVGRVDYEGELALVV 109 Query: 132 GKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLVTRDEV 191 GK I + A H+ G+ NDV+ R+ Q +R G + + KG DTF P+GPW+ T E Sbjct: 110 GKQCRNITPEQAREHIFGFTCANDVTARDIQ-KRDGLFGRCKGYDTFCPVGPWIETALE- 167 Query: 192 ADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGVGMGV 251 DP L + V+G+ Q GNT+ M+ ++S +SR M+L PGD++ TGTP G+G Sbjct: 168 -DPGNLTLRTVVNGEVRQQGNTADMLVHPFELLSSISRVMTLLPGDLVLTGTPEGIGP-- 224 Query: 252 KPEAVYLRAGQTMRLGIDGLG 272 + AG +R+ ID +G Sbjct: 225 ------IHAGDEVRVEIDEVG 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: 217 Number of extensions: 14 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: 259 Length adjustment: 25 Effective length of query: 256 Effective length of database: 234 Effective search space: 59904 Effective search space used: 59904 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 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