Align catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate BPHYT_RS33455 BPHYT_RS33455 protocatechuate 3,4-dioxygenase subunit beta
Query= BRENDA::Q8GAZ6 (300 letters) >FitnessBrowser__BFirm:BPHYT_RS33455 Length = 234 Score = 65.1 bits (157), Expect = 1e-15 Identities = 49/135 (36%), Positives = 63/135 (46%), Gaps = 19/135 (14%) Query: 120 NGNEPGETLVMRGRVLAENGEPVRDALVEVWHANHLGNYSH-FDKSQAEFN-----LRRS 173 NG GE +++ GRVL E PVR+ LVE+W AN G Y H D+ A + R Sbjct: 68 NGEPLGERIIVTGRVLDEGNRPVRNTLVEIWQANAAGRYVHKADQHDAPLDPNFLGAGRC 127 Query: 174 IRTDENGTYSFRSVVPIGYSVPPQGKTQQLLDLLGRHGHRPAHIHFFVSAPGY-RKLTTQ 232 I TD G Y F ++ P Y P G + RP HIHF + + +L TQ Sbjct: 128 I-TDNEGRYRFLTIKPGAY---PWGNHP--------NAWRPNHIHFSLFGDHFGSRLVTQ 175 Query: 233 INIEGDPYLWDDFAF 247 + GDP L D F Sbjct: 176 MYFPGDPLLAFDPIF 190 Lambda K H 0.317 0.137 0.407 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: 239 Number of extensions: 16 Number of successful extensions: 1 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: 300 Length of database: 234 Length adjustment: 25 Effective length of query: 275 Effective length of database: 209 Effective search space: 57475 Effective search space used: 57475 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 (21.6 bits) S2: 47 (22.7 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