Align 2-oxopent-4-enoate hydratase; 2-keto-4-pentenoate hydratase; EC 4.2.1.80 (characterized)
to candidate AO356_28650 AO356_28650 2-keto-4-pentenoate hydratase
Query= SwissProt::Q9KWS4 (261 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28650 Length = 254 Score = 107 bits (268), Expect = 2e-28 Identities = 70/203 (34%), Positives = 102/203 (50%), Gaps = 9/203 (4%) Query: 33 IAQAYAIQQINVQRQLAAGRRVTGRKIGLTSAAVQKQLGVDQPDFGTLFDSMAVNDGEEI 92 + Y +Q+ ++R+ A G R+TG K+ A Q + G+D+P G L D+M V G + Sbjct: 31 LPMGYTLQREALRRRQAGGERLTGWKVAFAGRAAQDRFGIDEPVLGALTDAMVVEPGRGV 90 Query: 93 AWSRTLQPKCEAEVALVIERDLDHENITLIDLIGATAYALPAIEVVGSRIANWDINILDT 152 + +R +QPK E E+A V+ R L + D++ A + PA E+ R W + Sbjct: 91 SLARLIQPKLEIELAFVLGRTLVPGFYSDEDILAAVSEIAPAFEIADCRWQGWRFGVGAF 150 Query: 153 VADNASAGLYVLG----HTPVKLEGLDLRLAGMVMERAGQQVSLGVGAACLGHPLNAALW 208 +ADNA+AGLY LG P +L L+ RLA G G A P W Sbjct: 151 LADNAAAGLYCLGPRVRFHPEQLAHLNYRLA-----CDGVPCGEGNAQAREDTPQANLCW 205 Query: 209 LARTLVKQGTPLKSGDVVLSGAL 231 L R L+ G +++G VVLSGAL Sbjct: 206 LVRRLLADGQCVEAGQVVLSGAL 228 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: 156 Number of extensions: 10 Number of successful extensions: 3 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: 254 Length adjustment: 24 Effective length of query: 237 Effective length of database: 230 Effective search space: 54510 Effective search space used: 54510 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