Align 2-hydroxymuconate semialdehyde hydrolase; HMSH; 2-hydroxymuconic semialdehyde hydrolase; EC 3.7.1.9 (characterized)
to candidate Pf1N1B4_4192 Hydrolase, alpha/beta fold family functionally coupled to Phosphoribulokinase
Query= SwissProt::P23106 (281 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4192 Length = 288 Score = 74.3 bits (181), Expect = 3e-18 Identities = 68/233 (29%), Positives = 108/233 (46%), Gaps = 18/233 (7%) Query: 55 SQTRRVIAPDMLGFGYSERPADGKYSQARWVEHAIGVLDALGIQQGDIVGNSFGGGLALA 114 ++ RRVI D G G S A + + A+G++ ALG + D++G S GG +A Sbjct: 65 AKNRRVITTDYRGIGGSGGAAP--LTVGEMADDAVGLIRALGFDKVDLLGFSLGGFVAQD 122 Query: 115 LAIRHPERVRRLVLMGSVGVSFPITAGLETAWGYTPSLANMRRLLDL-----FAHDRTLV 169 +A++ PERVRRL+L G+ G+++ T L ++ LL L + T Sbjct: 123 IAMKAPERVRRLILTGTGPAG---GTGIDSVGSVTWPLM-IKGLLTLRDPKFYLFFTTTA 178 Query: 170 NDELAELRYQASIRPGFQESFAAMFPPPRQNGVDDLAS----NETDIRALPNETLVIHGR 225 N + A Y ++ Q+ P + + + ++ L TL+ +G Sbjct: 179 NGQRAASEYLQRLKERQQDRDKGPTPRAFLRQLKAITAWGKQAPQELGRLRMPTLIANGD 238 Query: 226 EDRIIPLQASLTLAQWIPNAQLHVFGQCGHWTQIEHAERFARLVENFLAEADA 278 D ++P SL LA+ IPNAQL ++ GH + +H F V N LA DA Sbjct: 239 NDIMVPTVNSLELAKRIPNAQLIIYQDAGHGSIFQHHTDF---VANALAFLDA 288 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: 183 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 281 Length of database: 288 Length adjustment: 26 Effective length of query: 255 Effective length of database: 262 Effective search space: 66810 Effective search space used: 66810 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 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