Align protocatechuate 3,4-dioxygenase (subunit 2/2) (EC 1.13.11.3) (characterized)
to candidate 3610095 Dshi_3476 protocatechuate 3,4-dioxygenase, alpha subunit (RefSeq)
Query= BRENDA::A0A193DXA9 (206 letters) >FitnessBrowser__Dino:3610095 Length = 204 Score = 257 bits (657), Expect = 9e-74 Identities = 124/205 (60%), Positives = 151/205 (73%), Gaps = 2/205 (0%) Query: 1 MVQPLNYFKETASQTAGPYVHIGCTPNFVGIEGVFEKDLGSGPLYNDKARGERISVRGTV 60 MVQ L+Y KET SQTAGPYVHIGCTPN G+ G ++ D G+ L +G+ I++RGT+ Sbjct: 1 MVQALSYLKETPSQTAGPYVHIGCTPNHAGLTGFYDTDPGA-VLKTGSVKGQEITLRGTI 59 Query: 61 YDGAGMPLKDALIEIWQADTDGYYNSPSETRGKADPNFIGWGRSPGDMDTGEFVFETIKP 120 +DGAG PL+DA++EIWQAD G + S + RG ADP+F GWGR D DTGEF FET+KP Sbjct: 60 FDGAGAPLRDAMVEIWQADAAGRFAS-GDPRGGADPHFTGWGRCACDADTGEFGFETVKP 118 Query: 121 GSVPFRDGRPMAPHITFWIVARGINIGLQTRMYFPEEQEANAADPVLARIEQKSRIATLV 180 G VPF DGR APHI+ WIVARGIN+GLQTR YF +E AN DP+L+RIE + RI TL+ Sbjct: 119 GRVPFIDGRLQAPHISLWIVARGINLGLQTRAYFADEVTANTEDPILSRIEHRHRIPTLL 178 Query: 181 AKKEEGNVYRFDIRLQGEGETVFFD 205 E VYRFDI LQG+ ET+FFD Sbjct: 179 VLPEASGVYRFDIHLQGDRETIFFD 203 Lambda K H 0.318 0.139 0.426 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: 200 Number of extensions: 8 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: 206 Length of database: 204 Length adjustment: 21 Effective length of query: 185 Effective length of database: 183 Effective search space: 33855 Effective search space used: 33855 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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