Align 2-hydroxymuconate semialdehyde hydrolase; HMSH; EC 3.7.1.9; 2-hydroxymuconic semialdehyde hydrolase (uncharacterized)
to candidate RR42_RS31825 RR42_RS31825 3-oxoacyl-ACP reductase
Query= curated2:P19076 (283 letters) >FitnessBrowser__Cup4G11:RR42_RS31825 Length = 282 Score = 120 bits (302), Expect = 3e-32 Identities = 88/274 (32%), Positives = 131/274 (47%), Gaps = 20/274 (7%) Query: 18 GIRTNLHDSGAGFPLMMIHGSGPGVTAWANWRLVMPELAKSR-RVIAPDMLGFGYSERPA 76 G+R + D+GAG P++ IHGSGPG + +N++ P A + R + D+ G+G S +PA Sbjct: 20 GLRLHYLDAGAGEPVVFIHGSGPGASGHSNFKHNAPAFAAAGFRTVVVDLPGYGQSSKPA 79 Query: 77 DAQYNRDVWVDHAVGVLDALEIEQADLVGNSFGGGIALALAIRHPERVRRLVLMGSAGVS 136 D +Y D +V L AL + + LVGNS GG IAL A+ +PE V RLV+M GV Sbjct: 80 DVEYTLDFFVAALRAQLLALALPRCVLVGNSLGGAIALKYALDYPEHVSRLVMMAPGGVE 139 Query: 137 FPIT----EGLDAV----WGYNPSFAEMRRLLDIFAFDRNLVNDELAELRYQASIRPGFH 188 T EG++ + G + + MR+LL + D LV D L + R A + Sbjct: 140 DRETYFRMEGIEKMVSLFTGGHMNPDTMRQLLTLLVHDATLVTDALVDER-MAVCKAQPR 198 Query: 189 ESFAAMFPAPRQRWVDGLASAEAAIRALPHETLVIHGREDQIIPLQTSLTLADWIARAQL 248 E A M + + + + L G ED+ P +L A+ Sbjct: 199 EVLATM----------KVPNLTERLGEIACPVLGFWGTEDRFNPAGGALKFLQGCRDARF 248 Query: 249 HVFGQCGHWTQIEHAARFASLVGDFLAEADAAAI 282 + +CGHW +EH+ F FLA+ AA+ Sbjct: 249 VLINRCGHWVMVEHSDYFNRECLGFLADTAEAAV 282 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: 194 Number of extensions: 13 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: 283 Length of database: 282 Length adjustment: 26 Effective length of query: 257 Effective length of database: 256 Effective search space: 65792 Effective search space used: 65792 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 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