Align 2-hydroxymuconate-6-semialdehyde hydrolase (EC 3.7.1.9) (characterized)
to candidate WP_042925300.1 C1M55_RS30820 alpha/beta fold hydrolase
Query= BRENDA::G3KFX4 (282 letters) >NCBI__GCF_002893965.1:WP_042925300.1 Length = 279 Score = 152 bits (385), Expect = 6e-42 Identities = 100/279 (35%), Positives = 154/279 (55%), Gaps = 24/279 (8%) Query: 10 IGREILAAGYRTNLHDQGEGFPVLLIHGSGPGVTAWANWRLVMPQLAQNRRVIAPDMLGF 69 +G+ + ++ + + GEG V+L+HG GPG T W+N+ + L+++ RV+ PDM G+ Sbjct: 8 VGKNVQTKSWKIHYIEAGEGPVVVLLHGGGPGATGWSNYAPNIEALSRHFRVVVPDMPGW 67 Query: 70 GYSDRPADGRYHQQRWVEHAIGVLDALGIQQADIVGNSFGGGLALALAIRHPERVRRLVL 129 G SD P D + + V + + DALGI++A +VGNS GG ++ AI HPER+ L+ Sbjct: 68 GDSD-PVD--FDKIDHVTVLVELFDALGIEKAALVGNSMGGHNSIRFAIEHPERISHLIT 124 Query: 130 MG-----------SVGVSFPITPGLDAVWGYEPSFASMRRLMDVFAYDRS-LVTNELAEL 177 MG S G S I DA +PS M +L+D+ +D+ + EL + Sbjct: 125 MGPPVQPKPFLFGSAGPSEGIKIMYDAY--LDPSPEGMAKLVDIMVFDQQRFASPELMKE 182 Query: 178 RYQASIR-PGFQESFAQMFP-APRQRWVDGLASDEADIRALPHETLVIHGREDQVIPLAA 235 R + +++ P E+ A+ P AP W+D S D+ A TL+IHGR+D+V Sbjct: 183 RSENALKHPEHLENVAKRIPFAPIPIWLD--QSRLGDVTA---PTLLIHGRDDRVATFEG 237 Query: 236 SLTLAEWIARAQLHVFGHCGHWTQIEHAERFARLVENFL 274 SL LA I ++ + CGHW Q+EHA+ F RLV +F+ Sbjct: 238 SLFLAAGIPNSRTVLINRCGHWAQLEHADEFNRLVTDFV 276 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: 233 Number of extensions: 15 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: 279 Length adjustment: 26 Effective length of query: 256 Effective length of database: 253 Effective search space: 64768 Effective search space used: 64768 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 24 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