Align 2-hydroxymuconate-6-semialdehyde hydrolase (EC 3.7.1.9) (characterized)
to candidate Ac3H11_413 N-formylglutamate deformylase (EC 3.5.1.68)
Query= BRENDA::G3KFX4 (282 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_413 Length = 331 Score = 83.6 bits (205), Expect = 5e-21 Identities = 77/263 (29%), Positives = 121/263 (46%), Gaps = 20/263 (7%) Query: 31 PVLLIHGSGPGVTAWANWRLVMPQLAQNRRVIAPDMLGFGYSDRPADGRYHQQRWVEHAI 90 P++L+HG W ++ P AQ R V+APD GFG S R D Y + Sbjct: 74 PLVLLHGIFAEKDHWVDF--ARPLTAQYR-VVAPDFPGFGESTRLDDQPYDYAAHTQRLG 130 Query: 91 GVLDALGIQQADIVGNSFGGGLALALAIRHPERVRRLVLMGSV-GVSFPITPGLDAV--W 147 +LDALGI++A + GNS GG +A A++HPE V + +G+ G+ P +D + Sbjct: 131 ALLDALGIEKAHLAGNSMGGTIAALFALQHPEHVASVAFIGAPHGIHSPKPSTMDRLIDA 190 Query: 148 GYEP----SFASMRRLMDVFAYDRSLVTNELAELRYQASIRPGFQESFAQMFPAPRQRWV 203 G P A+ +MD+ R + + QA++ G S +++ A + Sbjct: 191 GQRPLVAHDAATFSAMMDLVFEKRPFLPYPILHATEQAAL--GNAASNTRLWDAQLK--- 245 Query: 204 DGLASDEADIRALPHETLVIHGREDQVIPLAASLTLAEWIARAQLHVFGHCGHWTQIE-- 261 D ++ H L + G D+V + L L + + +AQL GH +E Sbjct: 246 DRYLLEQRLGGLQQHPVLALWGDSDRVFDRSGLLPLQKLLPQAQLEALPGVGHLPMMEAP 305 Query: 262 --HAERFARLVENFLAEADALHS 282 A+R+AR +E LA + AL S Sbjct: 306 ADTAQRYARFLEG-LAPSSALAS 327 Lambda K H 0.323 0.138 0.432 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: 279 Number of extensions: 15 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: 282 Length of database: 331 Length adjustment: 27 Effective length of query: 255 Effective length of database: 304 Effective search space: 77520 Effective search space used: 77520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 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