Align protocatechuate 3,4-dioxygenase, beta chain; EC 1.13.11.3 (characterized)
to candidate WP_011654839.1 RL_RS30190 protocatechuate 3,4-dioxygenase subunit alpha
Query= CharProtDB::CH_121290 (241 letters) >NCBI__GCF_000009265.1:WP_011654839.1 Length = 203 Score = 88.6 bits (218), Expect = 9e-23 Identities = 66/206 (32%), Positives = 106/206 (51%), Gaps = 21/206 (10%) Query: 40 IAETLSEVTAPHFS-------ADKFGPKDNDLILNYAKDGLPIGERVIVHGYVRDQFGRP 92 + ET S+ P+ D G D+DL + D +GER+ V G + D G Sbjct: 7 LKETPSQTAGPYVHIGLTPNFCDISGVYDSDLGVAMVNDKT-LGERITVTGRIFDGAGAL 65 Query: 93 VKNALVEVWQANASGRYRHPNDQYIGAMDPNFGGCGRMLT-DDNGYYVFRTIKPGPYPWR 151 V++A++E+WQA+++G Y P++ GA DPNF G GR T ++G Y F T+KPG P++ Sbjct: 66 VRDAVIEIWQADSAGLYNSPSEMR-GAADPNFTGWGRCPTRAEDGVYSFETVKPGRVPFK 124 Query: 152 NRINEWRPAHIHFSLIADGWAQRLISQFYFEGDTLIDSC-PILKTIPSEQQRRALIALED 210 + + HI F ++A G L ++ YF +T ++ P+L I ++ ++A D Sbjct: 125 D--GRRQAPHITFWIVARGINIGLHTRMYFPEETEANAADPLLLRIEHRERVATMVATRD 182 Query: 211 KSNFIEADSRCYRFDITLRGRRATYF 236 C+ FDI L+G + T F Sbjct: 183 -------GVTCH-FDIHLQGPKETVF 200 Lambda K H 0.321 0.139 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: 162 Number of extensions: 9 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: 241 Length of database: 203 Length adjustment: 22 Effective length of query: 219 Effective length of database: 181 Effective search space: 39639 Effective search space used: 39639 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 24 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