Align protocatechuate 3,4-dioxygenase (subunit 2/2) (EC 1.13.11.3) (characterized)
to candidate CCNA_02491 CCNA_02491 protocatechuate 3,4-dioxygenase beta chain
Query= BRENDA::Q0SH27 (237 letters) >FitnessBrowser__Caulo:CCNA_02491 Length = 235 Score = 268 bits (685), Expect = 7e-77 Identities = 127/228 (55%), Positives = 156/228 (68%), Gaps = 1/228 (0%) Query: 7 HFEAGHEANAPLLFPEYKTTRLRSPKNDLILIPQRLGEITGPVFGDADVAKGEN-DMTHA 65 +F+ P L Y +T RSP+ L+ IP L E TGP + G D+T Sbjct: 4 NFKREDAGQPPSLHAPYASTVPRSPRQPLVRIPHTLTETTGPSNAWPRLMGGAMADLTTQ 63 Query: 66 NGGEAQGQRIIVHGRVLDSAGKPIPDTLIEVWQANAGGRYRHKMDSWPAPLDPHFNGVAR 125 + QGQRIIV GRVLD G+P+P+T++E+WQANA GRY HK D W APLDP+F G R Sbjct: 64 HKAMPQGQRIIVSGRVLDEDGRPVPNTVMEIWQANAAGRYIHKKDQWDAPLDPNFTGAGR 123 Query: 126 CLTDKQGHYEFTTIKPGAYPWGNHHNAWRPAHIHFSLFGQAFTQRLVTQMYFPDDPFFFQ 185 +TD +G Y+F +I+PGAYPWGNHHNAWRPAHIH SL G AF RLVTQMYFPDDP Sbjct: 124 VITDDEGRYQFVSIRPGAYPWGNHHNAWRPAHIHLSLLGPAFATRLVTQMYFPDDPLIEI 183 Query: 186 DPIYNSVPEAARERMISTFDYDHTRDNWAVGFKFDIVLRGRDATPFED 233 DPI N+VP R+R++S FD + T+ NWA+G+ FD+VLRGRD TPFED Sbjct: 184 DPIANAVPLPYRQRLVSRFDIEATKPNWALGYLFDVVLRGRDQTPFED 231 Lambda K H 0.322 0.140 0.458 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: 237 Number of extensions: 8 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: 237 Length of database: 235 Length adjustment: 23 Effective length of query: 214 Effective length of database: 212 Effective search space: 45368 Effective search space used: 45368 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