Align 2-oxopent-4-enoate hydratase; 2-keto-4-pentenoate hydratase; EC 4.2.1.80 (characterized)
to candidate H281DRAFT_01663 H281DRAFT_01663 2-keto-4-pentenoate hydratase
Query= SwissProt::Q9KWS4 (261 letters) >FitnessBrowser__Burk376:H281DRAFT_01663 Length = 269 Score = 299 bits (766), Expect = 4e-86 Identities = 157/254 (61%), Positives = 187/254 (73%), Gaps = 1/254 (0%) Query: 9 AALLNEAELSEKPIEPVRGHIEG-GIAQAYAIQQINVQRQLAAGRRVTGRKIGLTSAAVQ 67 AA L A+ S K + P+R + I AYAIQ++N +R+LA GRRV G KIGLTS AVQ Sbjct: 10 AAALATAQRSGKYLAPLRETYDQLSIDDAYAIQRVNTERRLAEGRRVVGCKIGLTSVAVQ 69 Query: 68 KQLGVDQPDFGTLFDSMAVNDGEEIAWSRTLQPKCEAEVALVIERDLDHENITLIDLIGA 127 KQLGVDQPDFG LFD M DGE I S QPK E+EVA VI RD+ +N T +D++ A Sbjct: 70 KQLGVDQPDFGMLFDDMGYGDGEPIPSSILTQPKVESEVAFVIGRDMTMDNPTQVDVLNA 129 Query: 128 TAYALPAIEVVGSRIANWDINILDTVADNASAGLYVLGHTPVKLEGLDLRLAGMVMERAG 187 YALPA+E+VGSRIA+W+I I DT+ADNAS+ YVLG P KL DLRL GMVMER G Sbjct: 130 IEYALPALEIVGSRIADWNIRITDTIADNASSSAYVLGTIPRKLSEFDLRLCGMVMERRG 189 Query: 188 QQVSLGVGAACLGHPLNAALWLARTLVKQGTPLKSGDVVLSGALGPLVAANPGDVFEARI 247 + VS+G GAACLG+P+NA +WLART+ G PLK+GD+VLSGALGP+V+ PGDVFE RI Sbjct: 190 EPVSVGAGAACLGNPVNAVVWLARTMASLGQPLKAGDLVLSGALGPMVSVVPGDVFETRI 249 Query: 248 QGLGSVRACFSPAS 261 GLGSVRA F P S Sbjct: 250 HGLGSVRAVFEPLS 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: 230 Number of extensions: 7 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: 269 Length adjustment: 25 Effective length of query: 236 Effective length of database: 244 Effective search space: 57584 Effective search space used: 57584 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 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