Align protocatechuate 3,4-dioxygenase β subunit (EC 1.13.11.3) (characterized)
to candidate GFF243 PGA1_c02550 protocatechuate 3,4-dioxygenase alpha chain
Query= metacyc::MONOMER-3185 (239 letters) >FitnessBrowser__Phaeo:GFF243 Length = 214 Score = 85.5 bits (210), Expect = 8e-22 Identities = 71/214 (33%), Positives = 105/214 (49%), Gaps = 17/214 (7%) Query: 37 LVSIPQSISETTGPNFSHLGF--GAHDHDL----LLNFNNGGLPIGERIIVAGRVVDQYG 90 + S+ ++ S+T GP + H+G GA D+ L G G+RI + GRV+D G Sbjct: 1 MTSLKETPSQTAGP-YVHIGLAPGAAGFDIYETELGQDIAGPEAKGQRIRIEGRVLDGTG 59 Query: 91 KPVPNTLVEMWQANAGGRYRHKN----DRYLAPLDPNFGGVGRCLTDSD-GYYSFRTIKP 145 P+ + L+E+WQANA G Y H+ + ++ F G GR ++D D G + F T+KP Sbjct: 60 TPLKDVLIEVWQANAKGIYAHRETPQPEGEPQQVEAGFRGWGRVISDFDTGDWQFETVKP 119 Query: 146 GPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGD-PLIPMCPIVKSIANPEAVQQ 204 GP R + HI+ I I L T+LYFE + P++K I Sbjct: 120 GPV--RGRDSRMMAPHINLWIVARGINLGLNTRLYFEEEHEANGNDPVLKLIEQTARRST 177 Query: 205 LIAKLDM--NNANPMDCLAYRFDIVLRGQRKTHF 236 L+A+ M + L YRFDI L+G +T F Sbjct: 178 LLARRQMQADTGTAETPLVYRFDIHLQGPDETVF 211 Lambda K H 0.321 0.140 0.452 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: 180 Number of extensions: 10 Number of successful extensions: 4 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: 239 Length of database: 214 Length adjustment: 22 Effective length of query: 217 Effective length of database: 192 Effective search space: 41664 Effective search space used: 41664 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: 46 (22.3 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