Align protocatechuate 4,5-dioxygenase β subunit (EC 1.13.11.8; EC 1.13.11.57) (characterized)
to candidate Ac3H11_1188 Protocatechuate 4,5-dioxygenase beta chain (EC 1.13.11.8)
Query= metacyc::MONOMER-3166 (289 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1188 Length = 296 Score = 498 bits (1281), Expect = e-146 Identities = 240/295 (81%), Positives = 263/295 (89%), Gaps = 7/295 (2%) Query: 1 MARITASVFTSHVPAIGAAMDMGKTQEAYWAPLFKGYDFSRQWMKDNKPDVIFLVYNDHA 60 MA+ITASVFTSHVPAIGAAMD+GKT E YW P+F GY+F +QW+KD+KPDVIFLVYNDHA Sbjct: 1 MAKITASVFTSHVPAIGAAMDLGKTHEDYWKPVFAGYEFGKQWVKDHKPDVIFLVYNDHA 60 Query: 61 TAFSLDCIPTFAIGTAAEFQPADEGWGPRPVPKVVGHPDLASHIAQSVIQQDFDLTIVNK 120 TAFSLD IPTFAIGTAAE++ ADEG+GPRPVP V+GHPDLA+HIAQSVIQQDFDLTIVNK Sbjct: 61 TAFSLDLIPTFAIGTAAEYEVADEGFGPRPVPMVIGHPDLAAHIAQSVIQQDFDLTIVNK 120 Query: 121 MDVDHGLTVPLSLMCGEQDPKTGSWPCPVIPFAVNVVQYPVPTGQRCFNLGRAIRKAVES 180 M VDHGLTVPLSLM GEQDP G+WPCPVIPFAVNVVQYPVP+G+RC+NLG+AIRKAVES Sbjct: 121 MAVDHGLTVPLSLMFGEQDPVKGAWPCPVIPFAVNVVQYPVPSGRRCYNLGQAIRKAVES 180 Query: 181 YDQDINVHIWGTGGMSHQLQGARAGLINKEWDNQFLDLLVENPHGLAQMPHIDYVREAGS 240 YD+DINVHIWGTGGMSHQLQG RAGLINKE+DN FLD L+ +P A +PHIDYVREAGS Sbjct: 181 YDEDINVHIWGTGGMSHQLQGPRAGLINKEFDNAFLDKLIADPEAAASIPHIDYVREAGS 240 Query: 241 EGIELVMWLIARGAMSDVDGPAPL-------PKVAHRFYHVPASNTAVGHLILEN 288 EGIELVMWLIARGAMSDV A PK+AHRFYHVPASNTAVGHLILEN Sbjct: 241 EGIELVMWLIARGAMSDVARAATADVAGGNPPKLAHRFYHVPASNTAVGHLILEN 295 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: 422 Number of extensions: 7 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: 296 Length adjustment: 26 Effective length of query: 263 Effective length of database: 270 Effective search space: 71010 Effective search space used: 71010 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: 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