Align protocatechuate 3,4-dioxygenase (subunit 1/2) (EC 1.13.11.3) (characterized)
to candidate GFF244 PGA1_c02560 protocatechuate 3,4-dioxygenase beta chain
Query= BRENDA::A0A193DXP2 (246 letters) >FitnessBrowser__Phaeo:GFF244 Length = 241 Score = 342 bits (876), Expect = 5e-99 Identities = 159/242 (65%), Positives = 192/242 (79%), Gaps = 3/242 (1%) Query: 5 PPETGPFFARNRDIHPLAYAPGYKTSILRSPQRALISLEGTKSEITGPVFGHGMLNPLDN 64 PP+ +++R+R HP A+ P YKTS+ RSP+ L+SLE T SEITGP F + P DN Sbjct: 3 PPD---YYSRDRRWHPPAFTPDYKTSVSRSPRLPLLSLENTASEITGPTFAPTDIAPGDN 59 Query: 65 DLILNYARPGEMPVGPRILVHGRVLDERGRGVDGALVEFWQANAGGRYRHKKESYLAAID 124 DL+ N+AR G P+G RIL+HGRV+DE R V LVE WQANA GRYRHKK+ YL A+D Sbjct: 60 DLLTNFARAGGSPIGERILLHGRVVDENARPVPNTLVEIWQANASGRYRHKKDGYLGALD 119 Query: 125 PNFGGVGRTITDENGYYWFKTIQPGAYPWPNGVNDWRPAHIHFSIFGHGFAQRLITQMYF 184 PNFGG GR +TD+NG Y F+T++PGAYPW NG+NDWRPAHIH S+FG FAQRLITQ+YF Sbjct: 120 PNFGGCGRVLTDDNGAYAFRTVKPGAYPWRNGINDWRPAHIHVSVFGSAFAQRLITQLYF 179 Query: 185 EGDPLIWKCPIVKTIPDEDAIRRLIAPLDMNATLPMDMLAYKFDIVLRGRRSTLFENRME 244 EGDPLI +CPIV TIPD A+++LIA LDMN T P+DM+AY+FDIVLRGRRST+FENRME Sbjct: 180 EGDPLIARCPIVSTIPDPAAVQQLIARLDMNETRPLDMIAYRFDIVLRGRRSTMFENRME 239 Query: 245 GN 246 GN Sbjct: 240 GN 241 Lambda K H 0.322 0.142 0.457 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: 293 Number of extensions: 10 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: 246 Length of database: 241 Length adjustment: 23 Effective length of query: 223 Effective length of database: 218 Effective search space: 48614 Effective search space used: 48614 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