Align protocatechuate 3,4-dioxygenase (subunit 2/2) (EC 1.13.11.3) (characterized)
to candidate WP_011427914.1 RHE_RS24305 protocatechuate 3,4-dioxygenase subunit alpha
Query= BRENDA::A0A193DXA9 (206 letters) >NCBI__GCF_000092045.1:WP_011427914.1 Length = 203 Score = 270 bits (691), Expect = 1e-77 Identities = 132/205 (64%), Positives = 156/205 (76%), Gaps = 2/205 (0%) Query: 2 VQPLNYFKETASQTAGPYVHIGCTPNFVGIEGVFEKDLGSGPLYNDKARGERISVRGTVY 61 +Q L Y KET SQTAGPYVHIG TPNF I GV++ DLG+ + NDK GERI+V G ++ Sbjct: 1 MQQLGYLKETPSQTAGPYVHIGLTPNFCDITGVYDSDLGT-QMVNDKTLGERITVTGRIF 59 Query: 62 DGAGMPLKDALIEIWQADTDGYYNSPSETRGKADPNFIGWGRSPGDMDTGEFVFETIKPG 121 DGAG ++DA+ EIWQAD+ G YNSPSE RG ADPNF GWGR P + G + FETIKPG Sbjct: 60 DGAGALVRDAVAEIWQADSAGLYNSPSELRGAADPNFAGWGRCPTRAEDGVYSFETIKPG 119 Query: 122 SVPFRDGRPMAPHITFWIVARGINIGLQTRMYFPEEQEANAADPVLARIEQKSRIATLVA 181 VPF+DGR APHIT WIVARGINIGL TRMYFPEE EANA+DP+L+RIE + R+AT++A Sbjct: 120 RVPFKDGRRQAPHITVWIVARGINIGLHTRMYFPEETEANASDPLLSRIEHRERVATMIA 179 Query: 182 KKEEGNVYRFDIRLQGEGETVFFDI 206 + +G FDI LQG ETVF DI Sbjct: 180 TR-DGATCHFDIHLQGPHETVFLDI 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: 210 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: 206 Length of database: 203 Length adjustment: 21 Effective length of query: 185 Effective length of database: 182 Effective search space: 33670 Effective search space used: 33670 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 Apr 09 2024. 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