Align 4-oxalocrotonate decarboxylase; EC 4.1.1.77 (characterized)
to candidate WP_010443489.1 G7G_RS0121215 hydratase/decarboxylase
Query= SwissProt::Q9KWS3 (256 letters) >NCBI__GCF_000192475.1:WP_010443489.1 Length = 258 Score = 96.7 bits (239), Expect = 4e-25 Identities = 69/218 (31%), Positives = 104/218 (47%), Gaps = 14/218 (6%) Query: 22 QLTGDDAVTVREAAEIQRLLIAHRIERGARQVGLKMGFTSRAKMAQMGVSDLIWGRLTSD 81 QLT D+A ++ A+ ++ L +G ++VG K+GFT+R GV IWG++ +D Sbjct: 31 QLTLDEAYSI--ASRVREL-------QGKKRVGRKVGFTNRTIWPVYGVDQPIWGQVYAD 81 Query: 82 MWVEEGGEIDLAHYVHPRVEPEICYLLGKRLEGNVTPLEALAAVEAVAPAMEIIDSRYRD 141 ++LA Y PR+EPEI L + + VE VAP EI+ S Y D Sbjct: 82 GLFSTDQPVNLARYSEPRIEPEIVVGLKHAPTAEMNNEQLAGCVEWVAPGFEIVQSIYPD 141 Query: 142 FKFSLPDVIADNASSSGFVVG----AWHKPETDVSNLGMVMSFDGRAVELGTSAAILGSP 197 +KFS+ D IA V+G A T ++ + + + G A+E G LG P Sbjct: 142 WKFSVEDSIAAQGLHGCLVLGDKIAATQDVLTGLAEVPIALFKGGEAIESGKGENALGGP 201 Query: 198 IRALVAAARLAAQQGEALEAGSLILAGAATAAVALRPG 235 I L L + + + L+ G L+ G T A + PG Sbjct: 202 IEVLAHLVSLLS-EADQLQGGELVTTGTLTDAWPVSPG 238 Lambda K H 0.318 0.132 0.372 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: 122 Number of extensions: 6 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: 256 Length of database: 258 Length adjustment: 24 Effective length of query: 232 Effective length of database: 234 Effective search space: 54288 Effective search space used: 54288 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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