Align protocatechuate 4,5-dioxygenase β subunit (EC 1.13.11.8; EC 1.13.11.57) (characterized)
to candidate PP_2518 PP_2518 gallate dioxygenase
Query= metacyc::MONOMER-3166 (289 letters) >FitnessBrowser__Putida:PP_2518 Length = 420 Score = 248 bits (632), Expect = 2e-70 Identities = 122/289 (42%), Positives = 177/289 (61%), Gaps = 11/289 (3%) Query: 1 MARITASVFTSHVPAIGAAMDMGKTQEAYWAPLFKGYDFSRQWMKDNKPDVIFLVYNDHA 60 MARI + SH P IG A+D K +EA WAP+F+ ++ R W++ +PDV+F ++NDH Sbjct: 1 MARIIGGLAVSHTPTIGFAVDHDKQEEAAWAPIFESFEPIRTWLQQRQPDVLFYIFNDHI 60 Query: 61 TAFSLDCIPTFAIGTAAEFQPADEGWGPRPVPKVVGHPDLASHIAQSVIQQDFDLTIVNK 120 T+F D F +G ++ ADEG PR +P V GH L+ HI QS++ +FD++ Sbjct: 61 TSFFFDHYSAFTLGVDEQYGVADEGGNPRDLPPVGGHAALSRHIGQSLMADEFDMSFFRD 120 Query: 121 MDVDHGLTVPLSLMCGEQDPKTGSWPCPVIPFAVNVVQYPVPTGQRCFNLGRAIRKAVES 180 +DHG P+S + P SWP ++P V V+Q P+PT +RC+ LG+A+R+A+ES Sbjct: 121 KPLDHGFFSPMSALL----PCDESWPVQIVPLQVGVLQLPIPTARRCYKLGQALRRAIES 176 Query: 181 YDQDINVHIWGTGGMSHQLQGARAGLINKEWDNQFLDLLVENPHGLAQMPHIDYVREAGS 240 Y +D+ V I TGG+SHQ+ G R G N EWD QFLDLLV +P L +M +Y G Sbjct: 177 YPEDLKVAIVATGGVSHQVHGERCGFNNPEWDAQFLDLLVNDPQRLTEMTLAEYATLGGM 236 Query: 241 EGIELVMWLIARGAMSDVDGPAPLPKVAHRFYHVPASNTAVGHLILENQ 289 EG E++ WLI RG +S A + + H+ Y++P S T + L+LEN+ Sbjct: 237 EGAEVITWLIMRGTLS-----ANVER-KHQSYYLP-SMTGIATLLLENR 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: 344 Number of extensions: 19 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: 420 Length adjustment: 29 Effective length of query: 260 Effective length of database: 391 Effective search space: 101660 Effective search space used: 101660 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: 49 (23.5 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