Align protocatechuate 4,5-dioxygenase β subunit (EC 1.13.11.8; EC 1.13.11.57) (characterized)
to candidate H281DRAFT_01373 H281DRAFT_01373 protocatechuate 4,5-dioxygenase beta subunit (EC 1.13.11.8)
Query= metacyc::MONOMER-3166 (289 letters) >FitnessBrowser__Burk376:H281DRAFT_01373 Length = 281 Score = 298 bits (762), Expect = 1e-85 Identities = 140/289 (48%), Positives = 191/289 (66%), Gaps = 11/289 (3%) Query: 1 MARITASVFTSHVPAIGAAMDMGKTQEAYWAPLFKGYDFSRQWMKDNKPDVIFLVYNDHA 60 MARI + TSHVP IG A D GK + WAPLFKGY+ W+ + KPD + + YNDHA Sbjct: 1 MARIIGGIGTSHVPTIGMAYDKGKQNDPAWAPLFKGYEPVANWLAERKPDAMVMFYNDHA 60 Query: 61 TAFSLDCIPTFAIGTAAEFQPADEGWGPRPVPKVVGHPDLASHIAQSVIQQDFDLTIVNK 120 +F DC PTFA+G + + ADEG G RP+P + GHPDLA HIA+ ++ +FDLTI Sbjct: 61 NSFFFDCYPTFALGVSGNHEFADEGAGKRPLPDIAGHPDLAIHIAEQLVNDEFDLTIFQD 120 Query: 121 MDVDHGLTVPLSLMCGEQDPKTGSWPCPVIPFAVNVVQYPVPTGQRCFNLGRAIRKAVES 180 +DHG PLSLM P G WP ++P VNV+QYP+PT RC+ LG+A+R+A+ES Sbjct: 121 RPLDHGCNSPLSLML----PHAGGWPLALVPVQVNVLQYPLPTANRCYRLGQALRRAIES 176 Query: 181 YDQDINVHIWGTGGMSHQLQGARAGLINKEWDNQFLDLLVENPHGLAQMPHIDYVREAGS 240 +++D++V + GTGG+SHQ+ G R+G N EWD +FLDL+V P LA M H+DYVR G+ Sbjct: 177 FEEDLDVVVVGTGGLSHQVHGERSGFNNTEWDMEFLDLIVHEPQRLAAMKHVDYVRLGGA 236 Query: 241 EGIELVMWLIARGAMSDVDGPAPLPKVAHRFYHVPASNTAVGHLILENQ 289 E +E +MWL RGA+ P + HR Y++ A++TA+ I E++ Sbjct: 237 ESVETIMWLAMRGAL------GPKIRELHRNYYL-ATSTAMAVTIYEDE 278 Lambda K H 0.321 0.137 0.439 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: 295 Number of extensions: 14 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: 289 Length of database: 281 Length adjustment: 26 Effective length of query: 263 Effective length of database: 255 Effective search space: 67065 Effective search space used: 67065 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: 47 (22.7 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