Align 2-hydroxymuconate semialdehyde hydrolase; HMSH; EC 3.7.1.9; 2-hydroxymuconic semialdehyde hydrolase (uncharacterized)
to candidate WP_003945808.1 C1M55_RS04155 alpha/beta fold hydrolase
Query= curated2:P19076 (283 letters) >NCBI__GCF_002893965.1:WP_003945808.1 Length = 292 Score = 154 bits (388), Expect = 3e-42 Identities = 100/271 (36%), Positives = 145/271 (53%), Gaps = 17/271 (6%) Query: 19 IRTNLHDSGAGFP--LMMIHGSGPGVTAWANWRLVMPELAKSRRVIAPDMLGFGYSERPA 76 ++ + H++G G ++++HG GPG ++W+N+ +P LAKS VIA D G+G S++P Sbjct: 23 LKLHFHEAGVGNDKTIVLLHGGGPGASSWSNFARNIPVLAKSFHVIAVDQPGYGQSDKPT 82 Query: 77 DAQYNRDVWVDHAVGVLDALEIE-QADLVGNSFGGGIALALAIRHPERVRRLVLMGSAGV 135 + +LD LEI + DL+GNS GGG A+ A+ +P+R RLVLMG G+ Sbjct: 83 EHPQYFVHSASALNDLLDTLEITGRVDLLGNSLGGGAAVRFALDYPDRAGRLVLMGPGGL 142 Query: 136 SFPI-----TEGLDAV--WGYNPSFAEMRRLLDIFAFDRNLVNDELAELRYQASIRPGFH 188 S + TEG+ + + Y P+ + L I FD+ L+ EL + R+ A+ P Sbjct: 143 SVNLFAPDPTEGVKNLGKFSYQPTRENLEAFLRIMVFDQKLITPELVDERFAAASTP--- 199 Query: 189 ESFAAMFPAPRQRWVDG---LASAEAAIRALPHETLVIHGREDQIIPLQTSLTLADWIAR 245 ES AA A + + G L L L+I GRED++ PL +L I R Sbjct: 200 ESLAAA-KAMGKSFSSGDFELGMLWREAYKLRQRVLLIWGREDRVNPLDGALVALKMIPR 258 Query: 246 AQLHVFGQCGHWTQIEHAARFASLVGDFLAE 276 AQLHVFG CGHW Q+E F L DFL + Sbjct: 259 AQLHVFGGCGHWAQLEKFDEFNRLATDFLLD 289 Lambda K H 0.323 0.137 0.424 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: 255 Number of extensions: 16 Number of successful extensions: 4 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: 283 Length of database: 292 Length adjustment: 26 Effective length of query: 257 Effective length of database: 266 Effective search space: 68362 Effective search space used: 68362 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 (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