Align FAA hydrolase family protein (characterized, see rationale)
to candidate H281DRAFT_05440 H281DRAFT_05440 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Burk376:H281DRAFT_05440 Length = 283 Score = 146 bits (368), Expect = 6e-40 Identities = 76/206 (36%), Positives = 115/206 (55%), Gaps = 2/206 (0%) Query: 67 VGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVE 126 + N + C+GLNYA+H E+N +PV+F + ++ VG + P S++ D+E E Sbjct: 70 IPNPDQIFCVGLNYAEHVKETNRETTEQPVIFMRLPASQVGHGQPMLRPPESQQFDYEGE 129 Query: 127 LGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLV 186 + V+IG+GG I E DA +H+AGY ND S R++Q W GK G GPW+V Sbjct: 130 IAVIIGRGGRRIAEADAWNHIAGYACYNDGSVRDWQ-RHTTQWGPGKNFYRTGAFGPWMV 188 Query: 187 TRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPG 246 T DE+ + + ++G+ Q T +I G+A ++YLS F L PGDVI TGTP G Sbjct: 189 TSDEIEPNALMMLVTRLNGQEVQRATTQMLIHGIAKQIAYLSTFTPLAPGDVIVTGTPGG 248 Query: 247 VGMGVKPEAVYLRAGQTMRLGIDGLG 272 VG P +++ G + + +D +G Sbjct: 249 VGAKRNP-PLFMEPGDRVEVEVDRIG 273 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: 255 Number of extensions: 12 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: 283 Length adjustment: 26 Effective length of query: 255 Effective length of database: 257 Effective search space: 65535 Effective search space used: 65535 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