Align 2-oxopent-4-enoate hydratase; 2-keto-4-pentenoate hydratase; EC 4.2.1.80 (characterized)
to candidate WP_009397184.1 BLS63_RS10120 2-oxo-3-hexenedioate decarboxylase
Query= SwissProt::Q9KWS4 (261 letters) >NCBI__GCF_900100495.1:WP_009397184.1 Length = 264 Score = 173 bits (438), Expect = 4e-48 Identities = 100/256 (39%), Positives = 145/256 (56%), Gaps = 1/256 (0%) Query: 3 EQNAKLAALLNEAELSEKPIEPVRG-HIEGGIAQAYAIQQINVQRQLAAGRRVTGRKIGL 61 EQ LA + AEL I V + E A AY IQ +R+ A G ++ G K+GL Sbjct: 8 EQVLALAEHIENAELQAHDIHKVTNDYPEMTFADAYDIQWEIRRRKEARGNKIVGLKMGL 67 Query: 62 TSAAVQKQLGVDQPDFGTLFDSMAVNDGEEIAWSRTLQPKCEAEVALVIERDLDHENITL 121 TS A Q+GV+ P +G L D +V DG + S+ + PK EAE+++V + L + Sbjct: 68 TSWAKMAQMGVETPIYGFLADYFSVPDGGVVDCSKLIHPKIEAEISVVTKAPLQGPGCHI 127 Query: 122 IDLIGATAYALPAIEVVGSRIANWDINILDTVADNASAGLYVLGHTPVKLEGLDLRLAGM 181 D+I A Y +P +EV+ SR N+ +++ VADNAS+ ++ G LE +DLR G+ Sbjct: 128 GDVIAAVDYVIPTVEVIDSRYENFKFDLISVVADNASSTRFITGGQMANLEDVDLRTLGV 187 Query: 182 VMERAGQQVSLGVGAACLGHPLNAALWLARTLVKQGTPLKSGDVVLSGALGPLVAANPGD 241 VME+ G+ V LG GAA LGHPL++ LA L ++G + +G +++G + V+ PGD Sbjct: 188 VMEKNGEVVELGAGAAVLGHPLSSVAMLANLLAERGEHIPAGTFIMTGGITAAVSVEPGD 247 Query: 242 VFEARIQGLGSVRACF 257 R QGLGSV A F Sbjct: 248 NITVRYQGLGSVSARF 263 Lambda K H 0.317 0.134 0.384 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: 159 Number of extensions: 9 Number of successful extensions: 1 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: 261 Length of database: 264 Length adjustment: 25 Effective length of query: 236 Effective length of database: 239 Effective search space: 56404 Effective search space used: 56404 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