Align Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1) (characterized)
to candidate WP_090446794.1 BLS63_RS16820 benzoate 1,2-dioxygenase small subunit
Query= reanno::WCS417:GFF4630 (163 letters) >NCBI__GCF_900100495.1:WP_090446794.1 Length = 162 Score = 141 bits (355), Expect = 6e-39 Identities = 63/152 (41%), Positives = 95/152 (62%) Query: 12 FFYRKSELCDAQDWDAYVQLFDPQSEFHLPQWDSEHVYTRDPKREMSLIYYANRSGLEDR 71 F YR++ D + WD +++L+ + F +P WD +P+ ++SLI+Y NRSGLEDR Sbjct: 11 FLYREARYLDDKQWDEWLELYASDATFWMPAWDDRDQLVENPQTDISLIWYGNRSGLEDR 70 Query: 72 VFRLRTGKAASATPMPRTLHLINNVRIAEQADGTLEVRLNWHTLFYRLATSEQFYGHATY 131 VFR+RT ++++ P RT H I+N+ + EQADG ++R NWHTL +R + FYG + Y Sbjct: 71 VFRIRTERSSATIPDTRTSHNISNIELLEQADGVCKLRFNWHTLSFRYKVVDHFYGTSFY 130 Query: 132 RLKPDGDSWLITRKHALLLNDTINSVLDFYHL 163 L G + LI K +L ND + V+D YH+ Sbjct: 131 SLDTGGPNPLIKAKKVVLKNDYVRQVIDVYHI 162 Lambda K H 0.323 0.136 0.424 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: 111 Number of extensions: 4 Number of successful extensions: 1 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: 163 Length of database: 162 Length adjustment: 18 Effective length of query: 145 Effective length of database: 144 Effective search space: 20880 Effective search space used: 20880 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 (22.0 bits) S2: 43 (21.2 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