Align 2-oxopent-4-enoate hydratase (EC 4.2.1.80) (characterized)
to candidate 14488 b0350 2-keto-4-pentenoate hydratase (VIMSS)
Query= BRENDA::P77608 (269 letters) >FitnessBrowser__Keio:14488 Length = 269 Score = 535 bits (1379), Expect = e-157 Identities = 269/269 (100%), Positives = 269/269 (100%) Query: 1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRK 60 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRK Sbjct: 1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRK 60 Query: 61 VGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATD 120 VGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATD Sbjct: 61 VGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATD 120 Query: 121 ITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKN 180 ITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKN Sbjct: 121 ITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKN 180 Query: 181 CAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVN 240 CAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVN Sbjct: 181 CAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVN 240 Query: 241 AGDRFEAHIEGIGSVAATFSSAAPKGSLS 269 AGDRFEAHIEGIGSVAATFSSAAPKGSLS Sbjct: 241 AGDRFEAHIEGIGSVAATFSSAAPKGSLS 269 Lambda K H 0.319 0.135 0.399 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: 403 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: 269 Length of database: 269 Length adjustment: 25 Effective length of query: 244 Effective length of database: 244 Effective search space: 59536 Effective search space used: 59536 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 (21.7 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