Align protocatechuate 3,4-dioxygenase type II α subunit (EC 1.13.11.3) (characterized)
to candidate Pf1N1B4_3235 Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3)
Query= metacyc::MONOMER-14209 (195 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3235 Length = 234 Score = 85.9 bits (211), Expect = 5e-22 Identities = 47/133 (35%), Positives = 71/133 (53%), Gaps = 6/133 (4%) Query: 45 GKHITLRGTVLDGDGLPVPDALIEIWQPDGLGRFS---GHHPLLKTAEFKGFGRAMCDAL 101 G+ I + G VLD +GLPVP L+EIWQ + GR++ H F G GR + DA Sbjct: 72 GERIIIHGRVLDENGLPVPGILVEIWQANAAGRYNHARDLHDAPLDPNFTGTGRTVTDAD 131 Query: 102 GLFSFETVKPGGAPM--RDGVIQAPHVAVSIFGKGLNRHLYTRVYFDDEEANKSDPVLNS 159 G + F+T+KPG P + H+ S+FG + L T++YF + DP+ N Sbjct: 132 GWYQFQTIKPGAYPWGNHHNAWRPAHIHFSLFGPSILTRLVTQMYFPGDPLLAYDPIYNC 191 Query: 160 IPE-DLRSKLIAK 171 +P+ + +LIA+ Sbjct: 192 VPDTSAKERLIAR 204 Lambda K H 0.320 0.140 0.425 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: 137 Number of extensions: 7 Number of successful extensions: 3 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: 195 Length of database: 234 Length adjustment: 22 Effective length of query: 173 Effective length of database: 212 Effective search space: 36676 Effective search space used: 36676 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: 45 (21.9 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