Align 2-hydroxymuconate semialdehyde hydrolase; HMSH; EC 3.7.1.9; 2-hydroxymuconic semialdehyde hydrolase (uncharacterized)
to candidate Pf6N2E2_667 Dihydrolipoamide acetyltransferase component (E2) of acetoin dehydrogenase complex (EC 2.3.1.-)
Query= curated2:P19076 (283 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_667 Length = 370 Score = 83.2 bits (204), Expect = 8e-21 Identities = 77/259 (29%), Positives = 120/259 (46%), Gaps = 32/259 (12%) Query: 29 GFPLMMIHGSGPGVTAWANWRLVMPELAKSRRVIAPDMLGFGYSERPADAQYNRDVWVDH 88 G PL+++HG G + NW LA RRVIA D+ G G S + + + D Sbjct: 132 GTPLLLVHGFGGDLN---NWLFNHEALAAGRRVIALDLPGHGESGKVLQ-RGDLDELSGV 187 Query: 89 AVGVLDALEIEQADLVGNSFGGGIALALAIRHPERVRRLVLMGSAGVSFPITEGLDAVWG 148 + +LD L+I LVG+S GG ++L A P RVR L L+GSAG+ G + Sbjct: 188 VLALLDHLDINAVHLVGHSMGGAVSLNTARLAPRRVRSLTLIGSAGL------GSEINGS 241 Query: 149 YNPSFAEMR-------RLLDIFAFDRNLVN----DELAELRYQASIRPGFHESFAAMFPA 197 Y F E +L+ +F+ + LVN D++ + + + + + +F Sbjct: 242 YLQGFVEAANRNALKPQLVQLFS-NAELVNRQMLDDMLKYKRLEGVDAALQQLSSRLFAD 300 Query: 198 PRQRWVDGLASAEAAIRALPHETLVIHGREDQIIPLQTSLTLADWIARAQLHVFGQCGHW 257 RQ+ ++A TLV+ G +D IIP+ S L+ AQ+ V GH Sbjct: 301 GRQQ-----TDLREVVQAGQVPTLVVWGSDDAIIPVTHSEGLS-----AQVEVLPGQGHM 350 Query: 258 TQIEHAARFASLVGDFLAE 276 Q+E A + SL+ F+ + Sbjct: 351 VQMEAAEQVNSLILAFIQQ 369 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: 277 Number of extensions: 18 Number of successful extensions: 5 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: 370 Length adjustment: 28 Effective length of query: 255 Effective length of database: 342 Effective search space: 87210 Effective search space used: 87210 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: 48 (23.1 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