Align catechol 2,3-dioxygenase (EC 1.13.11.2) (characterized)
to candidate GFF3170 PGA1_c32210 3,4-dihydroxyphenylacetate 2,3-dioxygenase HpaD
Query= BRENDA::Q4J6K0 (313 letters) >FitnessBrowser__Phaeo:GFF3170 Length = 327 Score = 180 bits (457), Expect = 4e-50 Identities = 93/294 (31%), Positives = 159/294 (54%), Gaps = 11/294 (3%) Query: 5 LRLSHVCVRVIDMDKSLFFYRDLLGFHETEKNGDYVYLRGYEEGQHHSLVLKRAESPG-- 62 +RLSHVC+ V D+ S FY ++LG ++ + + +YLR EE HH ++L++++ PG Sbjct: 15 IRLSHVCLNVKDLAASQKFYAEILGLRVSDADENRIYLRAMEERGHHCVILQQSDQPGTV 74 Query: 63 --LSYIAFRVRNVDKMREKLEASGLKTRKFEEKGVDNAIIFSDTGGMPTVFYENMEYVDD 120 + + F ++D+ G T + ++ SD G+P FY M+ ++ Sbjct: 75 EVMGFKTFDEEDLDRADAYFRKKGRPTEWVQRPYQGRTLLTSDNMGIPLEFYHKMDRLEP 134 Query: 121 IRMKFHIHKGVSPIRLAHVNLMVDSNVFENEIKFYQSLGFYETEIFLDKEGKKM-VSWLT 179 I ++ +++GV P+R+ H N S+ + + FY GF TE D++ KK+ +WL Sbjct: 135 IHQQYALYRGVKPLRIDHFNCF--SHDVDASVAFYSDFGFRVTEYTEDEDSKKLWAAWLH 192 Query: 180 KSGDSHNLAISKSSRKTPGFHHFTYYVHDLRDVIRAADIMASAELWDYIERGPGRHGVTQ 239 + G H++A + + P HH ++V + ++I D+MA+ IERGPGRHG++ Sbjct: 193 RKGGVHDMAFTNGTG--PRMHHVAFWVPNPLNIIDLLDLMATTGYVTNIERGPGRHGISN 250 Query: 240 GVYIYLRDPNGGRLEFFTGDYVVLDPDKWKPVVWTYEQFRYRSDYWSRPIPESW 293 ++Y+ DP+G R+E + DY +DPD +P+ W + R W P PESW Sbjct: 251 AFFLYILDPDGHRIEIYCSDYQTVDPD-LEPIKWDLKD-PQRQTLWGAPAPESW 302 Lambda K H 0.321 0.140 0.438 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: 384 Number of extensions: 28 Number of successful extensions: 5 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: 313 Length of database: 327 Length adjustment: 28 Effective length of query: 285 Effective length of database: 299 Effective search space: 85215 Effective search space used: 85215 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 (21.9 bits) S2: 48 (23.1 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