Align Anthranilate 1,2-dioxygenase small subunit; EC 1.14.12.1 (characterized)
to candidate RR42_RS26420 RR42_RS26420 dioxygenase
Query= SwissProt::Q84BZ2 (161 letters) >FitnessBrowser__Cup4G11:RR42_RS26420 Length = 171 Score = 102 bits (255), Expect = 2e-27 Identities = 47/150 (31%), Positives = 82/150 (54%), Gaps = 1/150 (0%) Query: 13 EIYMLQNRYIGHLDNDRLERWPEMFTEDCTYEIVPKENADLGLPVGIVHCTNQRMLRDRV 72 EI + Y LD +E WPE FTEDC Y + +EN +LGLPVG+V+ + M+ DR Sbjct: 22 EIDAFHSEYCAVLDAGMVETWPEFFTEDCIYRVTARENVELGLPVGLVYAEGRGMMHDRA 81 Query: 73 VSLRHANIYEEHTYRHMTSGLAIVAQRD-GEIDTESNYVVVQTRSNGESNVYQAGKYYDT 131 V++ ++ H+ + + + + GEI +++++++QT G + ++ AG Y+D Sbjct: 82 VAIARTQMFAPRYMLHLVTNTRVTDESEYGEIQAQASFLLLQTLVEGPTTIHMAGTYHDR 141 Query: 132 VVRTPDGLRYKAKRVIYDTSRVQTLLATPI 161 R L ++V+YDT+ + L P+ Sbjct: 142 FARIEGKLLLAERQVVYDTTIIANDLVYPV 171 Lambda K H 0.319 0.135 0.401 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: 81 Number of extensions: 2 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: 161 Length of database: 171 Length adjustment: 18 Effective length of query: 143 Effective length of database: 153 Effective search space: 21879 Effective search space used: 21879 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: 43 (21.2 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