Align protocatechuate 3,4-dioxygenase (subunit 1/2) (EC 1.13.11.3) (characterized)
to candidate SM_b20577 SM_b20577 protocatechuate 3,4-dioxygenase subunit beta
Query= BRENDA::A0A193DXP2 (246 letters) >FitnessBrowser__Smeli:SM_b20577 Length = 253 Score = 408 bits (1049), Expect = e-119 Identities = 190/244 (77%), Positives = 209/244 (85%) Query: 3 NQPPETGPFFARNRDIHPLAYAPGYKTSILRSPQRALISLEGTKSEITGPVFGHGMLNPL 62 N PETG FFAR+R HP A+APGYKTS+LRSPQ+AL+SL+GT SEITGPVFGH ML L Sbjct: 10 NGKPETGAFFARDRAWHPPAFAPGYKTSVLRSPQKALLSLDGTISEITGPVFGHSMLGEL 69 Query: 63 DNDLILNYARPGEMPVGPRILVHGRVLDERGRGVDGALVEFWQANAGGRYRHKKESYLAA 122 DNDLI N+A PGE +G RI+VHGRVLDERG V G LVEFWQANAGGRYRHKKESYLA Sbjct: 70 DNDLIHNFASPGESAIGERIIVHGRVLDERGHPVHGVLVEFWQANAGGRYRHKKESYLAP 129 Query: 123 IDPNFGGVGRTITDENGYYWFKTIQPGAYPWPNGVNDWRPAHIHFSIFGHGFAQRLITQM 182 +DPNFGG GRTITDE G YWF+T++PGAYPWPNGVNDWRPAHIHFS+FGHGFAQRLITQM Sbjct: 130 LDPNFGGCGRTITDEEGRYWFRTVRPGAYPWPNGVNDWRPAHIHFSVFGHGFAQRLITQM 189 Query: 183 YFEGDPLIWKCPIVKTIPDEDAIRRLIAPLDMNATLPMDMLAYKFDIVLRGRRSTLFENR 242 YFEGDP+IWKCPIV T+PD AI +LIA LD T+PMD AY+FDIVLRGRRST FENR Sbjct: 190 YFEGDPMIWKCPIVGTVPDRRAIEQLIAALDWGNTVPMDARAYRFDIVLRGRRSTFFENR 249 Query: 243 MEGN 246 EGN Sbjct: 250 PEGN 253 Lambda K H 0.322 0.142 0.457 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: 346 Number of extensions: 10 Number of successful extensions: 1 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: 246 Length of database: 253 Length adjustment: 24 Effective length of query: 222 Effective length of database: 229 Effective search space: 50838 Effective search space used: 50838 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: 46 (22.3 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