Align 2-hydroxymuconate-6-semialdehyde hydrolase (EC 3.7.1.9) (characterized)
to candidate RR42_RS27870 RR42_RS27870 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase
Query= BRENDA::G3KFX4 (282 letters) >FitnessBrowser__Cup4G11:RR42_RS27870 Length = 294 Score = 99.0 bits (245), Expect = 1e-25 Identities = 90/275 (32%), Positives = 128/275 (46%), Gaps = 29/275 (10%) Query: 16 AAGYRTN-LHDQGEGFPVL-LIHGSGPGVTAWANWRLVMPQLAQNRRVIAPDMLGFGYSD 73 A G RT LH G P L L+HG G A+ + A++ V A DM+G G++D Sbjct: 22 AKGIRTRYLHAGSSGKPALILLHGVGGHAEAYVR---NLQSHAEHFDVWAIDMIGHGWTD 78 Query: 74 RPADGRYHQQRWVEHAIGVLDALGIQQADIVGNSFGGGLALALAIRHPERVRRLVLMGSV 133 +PA GR +V+H I V+D LGI +A G S GG +A LAI HPERV RLVL + Sbjct: 79 KPAGGREISD-YVDHVIRVMDTLGIARAAFSGESLGGWVAARLAIDHPERVERLVLNTAG 137 Query: 134 G-VSFPI------TPGLDAVWGYEPSFASMRRLMDVFAYDRSLVTNELAELRYQASIRPG 186 G + P+ T + AV EP + ++ + D++ ++L R +PG Sbjct: 138 GSQADPVVMERLKTLSMRAV--EEPGWDFIKARVQWLMADKAKAFDDLIATRQAIYAQPG 195 Query: 187 FQESFAQMFPAPRQRWV-DGLASDEADIRALPH------ETLVIHGREDQVIPLAASLTL 239 M A R V + + + +I H TLV+ +D ++ + Sbjct: 196 -------MVEAQRGNMVLQDMETRQRNILRAEHYGRIKAPTLVLWTSDDPTADVSEGRRI 248 Query: 240 AEWIARAQLHVFGHCGHWTQIEHAERFARLVENFL 274 A I A V CGHW Q E A+ F R+ NFL Sbjct: 249 ATMIPGALFTVMDGCGHWPQFEDADTFNRIHLNFL 283 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: 254 Number of extensions: 16 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: 282 Length of database: 294 Length adjustment: 26 Effective length of query: 256 Effective length of database: 268 Effective search space: 68608 Effective search space used: 68608 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: 47 (22.7 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