Align anthranilate 1,2-dioxygenase (deaminating, decarboxylating) large subunit [EC: 1.14.12.1] (characterized)
to candidate Ac3H11_2755 Large subunit naph/bph dioxygenase
Query= reanno::WCS417:GFF4629 (463 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2755 Length = 466 Score = 140 bits (352), Expect = 1e-37 Identities = 73/215 (33%), Positives = 115/215 (53%), Gaps = 5/215 (2%) Query: 33 MFTEPQLFDLEMELIFEKNWIYACHESELANNHDFVTMRAGRQPMIITRDGEGQLNALIN 92 + ++ +L+ LEME IF K W++ HE+E+ N+ DFV G +++TRD EGQ++ ++N Sbjct: 30 VLSDAELYQLEMEKIFAKTWVFLAHETEIPNSGDFVQRDMGSDSVLVTRDREGQVHVVLN 89 Query: 93 ACQHRGTTLTRVGKGNQSTFTCPFHAWCYKSDGRLVKVKAPGEYPDG--FDKATRGLKKA 150 C HRG ++ + GN C +H W +K +G + E G K L KA Sbjct: 90 VCTHRGMKVSTLDVGNTQAHMCIYHGWAFKPNGDFIGAPVDKECMHGKMMSKEQLSLTKA 149 Query: 151 RIESYKGFVFISLDVAGTDSLEDFLGDAKVFFDMMVAQSATGELEVLPGKSAYTYDGNWK 210 R+ Y G +F + ++ G S ++FLGDAK ++D M ++ +G +EVL + NWK Sbjct: 150 RVAVYGGMIFATWNLDG-PSFDEFLGDAKFYYDTMWCRTTSG-MEVLGPPQRFIIKANWK 207 Query: 211 LQNENG-LDGYHVSTVHYNYVATVQHRQQVNTENG 244 E G DGYH T+H + ++ N E G Sbjct: 208 TAAEQGACDGYHTLTLHRWLGEIGPYAKKPNAEGG 242 Lambda K H 0.319 0.136 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: 563 Number of extensions: 24 Number of successful extensions: 4 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: 463 Length of database: 466 Length adjustment: 33 Effective length of query: 430 Effective length of database: 433 Effective search space: 186190 Effective search space used: 186190 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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