Align protocatechuate 3,4-dioxygenase (subunit 2/2) (EC 1.13.11.3) (characterized)
to candidate H281DRAFT_03865 H281DRAFT_03865 protocatechuate 3,4-dioxygenase, beta subunit
Query= BRENDA::Q0SH27 (237 letters) >FitnessBrowser__Burk376:H281DRAFT_03865 Length = 234 Score = 253 bits (646), Expect = 2e-72 Identities = 118/216 (54%), Positives = 151/216 (69%), Gaps = 2/216 (0%) Query: 19 LFPEYKTTRLRSPKNDLILIPQRLGEITGPVFGDADVAKGENDMTH--ANGGEAQGQRII 76 ++P Y ++ R P LI + ++L + PV+G D+ ++D+T GE G+RII Sbjct: 18 IYPGYGSSVKRGPTRPLIPLKEKLRDQRVPVYGTEDLGALDSDLTRNAVRNGEPLGERII 77 Query: 77 VHGRVLDSAGKPIPDTLIEVWQANAGGRYRHKMDSWPAPLDPHFNGVARCLTDKQGHYEF 136 V GRVLD G+P+ +TL+E+WQANA GRY HKMD APLDP+F G RC+TD +G Y F Sbjct: 78 VTGRVLDEGGRPVRNTLVEIWQANAAGRYVHKMDQHDAPLDPNFLGAGRCITDNEGRYRF 137 Query: 137 TTIKPGAYPWGNHHNAWRPAHIHFSLFGQAFTQRLVTQMYFPDDPFFFQDPIYNSVPEAA 196 TIKPGAYPWGNH NAWRP HIHFSLFG+ F RLVTQMYFP DP DPI+ PE A Sbjct: 138 LTIKPGAYPWGNHPNAWRPNHIHFSLFGEHFGSRLVTQMYFPGDPLLAFDPIFQGTPEQA 197 Query: 197 RERMISTFDYDHTRDNWAVGFKFDIVLRGRDATPFE 232 R+R+I+ F D T++ +A+G+ FDIVLRGR+ TP E Sbjct: 198 RDRLIAKFSLDTTQEAYALGYDFDIVLRGRNETPME 233 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: 243 Number of extensions: 10 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: 234 Length adjustment: 23 Effective length of query: 214 Effective length of database: 211 Effective search space: 45154 Effective search space used: 45154 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