Align protocatechuate 3,4-dioxygenase β subunit (EC 1.13.11.3) (characterized)
to candidate BWI76_RS13285 BWI76_RS13285 protocatechuate 3,4-dioxygenase subunit alpha
Query= metacyc::MONOMER-3185 (239 letters) >FitnessBrowser__Koxy:BWI76_RS13285 Length = 206 Score = 99.4 bits (246), Expect = 5e-26 Identities = 70/206 (33%), Positives = 103/206 (50%), Gaps = 16/206 (7%) Query: 40 IPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPI------GERIIVAGRVVDQYGKPV 93 +P++ S+T GP + H+G + N G + GERI + GRV+D G PV Sbjct: 5 LPETASQTAGP-YVHIGLAPDAAGFHIFERNFGPTLTTADTEGERITIEGRVIDGSGTPV 63 Query: 94 PNTLVEMWQANAGGRYRHKNDRYLA-PLDPNFGGVGRCLTD-SDGYYSFRTIKPGPYPWR 151 + L+E+WQANA GRY H +DR LD F G GR +D + G + F TIKPG R Sbjct: 64 RDVLLEIWQANAAGRYNHPDDRQQGKKLDTAFRGWGRSCSDFTSGVWRFETIKPGAVVGR 123 Query: 152 NGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMC-PIVKSIANPEAVQQLIAKLD 210 +G H++ + I L T++YF + P++ I Q LIA+ + Sbjct: 124 DGRT--MAPHVNLWVVARGINIGLNTRMYFSDEQDANQADPVLNLIEWEVRRQTLIAQRE 181 Query: 211 MNNANPMDCLAYRFDIVLRGQRKTHF 236 + + YRFDI L+G+ +T F Sbjct: 182 VRGTE----IVYRFDIYLQGENETVF 203 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: 164 Number of extensions: 12 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: 239 Length of database: 206 Length adjustment: 22 Effective length of query: 217 Effective length of database: 184 Effective search space: 39928 Effective search space used: 39928 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 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