Align 2-hydroxymuconate semialdehyde hydrolase; HMSH; 2-hydroxymuconic semialdehyde hydrolase; EC 3.7.1.9 (characterized)
to candidate WP_025765335.1 X939_RS0121495 alpha/beta hydrolase
Query= SwissProt::P23106 (281 letters) >NCBI__GCF_000566685.1:WP_025765335.1 Length = 268 Score = 76.3 bits (186), Expect = 7e-19 Identities = 79/263 (30%), Positives = 120/263 (45%), Gaps = 29/263 (11%) Query: 26 QGEGFPALLIHG-SGPASPPGPTGAGSFRSSQTRRVIAPDMLGFGYSERPADGKYSQARW 84 +GEG P LLI G + P S GP A Q I D G G+S++PA G Y+ A Sbjct: 16 KGEGEPLLLIMGITAPGSVWGPHVADWQEHFQC---IVADNRGVGFSDKPA-GPYTSAMM 71 Query: 85 VEHAIGVLDALGIQQGDIVGNSFGGGLALALAIRHPERVRRLVLMGSVGVSFPITAG--- 141 + G+LD LG++ +VG S G +A LAIRHP +V+ LVLM G Sbjct: 72 ADDYAGLLDHLGMENVSVVGCSMGSIIAQQLAIRHPHKVKSLVLMCPWARCDSYAKGVFQ 131 Query: 142 --LETAWGYTPSLANMRRLLDLFAH---DRTLVNDELAELRYQASIRPGFQESFAAMFPP 196 + +TP+ ++ L +F+ D+ V E+ E R P FP Sbjct: 132 QMINAKARFTPAEFSLHIQLLIFSKSHWDKPQVLKEMEEGRLADGENP---------FPQ 182 Query: 197 PRQNGVDDLAS---NETDIRAL---PNETLVIHGREDRIIPLQASLTLAQWIPNAQLHVF 250 P +G++ A+ + + AL + TLVI G D P+ + +++ I +QL+++ Sbjct: 183 P-LHGLEGQAAACIHHDALAALAEVKSPTLVIGGDADIFTPVWMAREVSEAIKGSQLYLY 241 Query: 251 GQCGHWTQIEHAERFARLVENFL 273 GH E+ F V +L Sbjct: 242 EGLGHGFHFENTPDFNPRVREWL 264 Lambda K H 0.320 0.137 0.416 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: 181 Number of extensions: 11 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: 281 Length of database: 268 Length adjustment: 25 Effective length of query: 256 Effective length of database: 243 Effective search space: 62208 Effective search space used: 62208 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 (21.8 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