Align Anthranilate 1,2-dioxygenase ferredoxin subunit (characterized)
to candidate HSERO_RS18275 HSERO_RS18275 CDP-6-deoxy-L-threo-D-glycero-4-hexulose-3- dehydrase reductase
Query= SwissProt::Q84BZ1 (108 letters) >FitnessBrowser__HerbieS:HSERO_RS18275 Length = 360 Score = 149 bits (376), Expect = 3e-41 Identities = 64/103 (62%), Positives = 86/103 (83%) Query: 6 LAEWHPLGAIDEFTEDEPAARVAGQKPIAVFRIGDELFAMHDLCSHGHARLSEGYVEDGC 65 ++EW +G D+F E E AA AG + +AVFR+G+E+FA+ DLC+HG+A+LS+GYVEDGC Sbjct: 1 MSEWFDVGHADDFAEGEVAAARAGGQAVAVFRLGEEIFALKDLCTHGNAKLSDGYVEDGC 60 Query: 66 VECPLHQGLIDIRTGAPKCAPITEPVRVYPIRIVDGQVEVNVG 108 VECPLHQGL DIR+GAP+CAP+TE VR +P+R+V G+VE+ VG Sbjct: 61 VECPLHQGLFDIRSGAPRCAPVTEAVRSFPVRVVAGRVEIGVG 103 Lambda K H 0.321 0.140 0.441 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: 132 Number of extensions: 5 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: 108 Length of database: 360 Length adjustment: 20 Effective length of query: 88 Effective length of database: 340 Effective search space: 29920 Effective search space used: 29920 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: 44 (21.6 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