Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate WP_010443808.1 G7G_RS0122440 alpha/beta fold hydrolase
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >NCBI__GCF_000192475.1:WP_010443808.1 Length = 266 Score = 109 bits (273), Expect = 5e-29 Identities = 72/224 (32%), Positives = 106/224 (47%), Gaps = 7/224 (3%) Query: 13 YQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSLVTPGPYSIEQ 72 +++ GPE APV+V+ + LG N W IPA FRVL +D GHG+S P S+ Sbjct: 10 FKMTGPEDAPVVVMIHGLGLNQDCWQWTIPALPDRFRVLTYDLFGHGQSAPPPECPSLSM 69 Query: 73 LGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAAKIGDPS--VW 130 R + +LLD I+ A G S+GG+I + + +R+ LV+ ++ K D + Sbjct: 70 FSRQLESLLDHCAIQNAVIAGFSLGGMIARRFAQDVPQRVSALVILHSPHKRTDAAQKAI 129 Query: 131 NPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQGYAANCAA 190 R+E DGP A V +A++ RWFT F Q+NP + + D + A Y Sbjct: 130 LKRVEQARLDGPKATV---EAALDRWFTDAFRQSNPRMMNTVRDWVMANDKAIYHTIYRV 186 Query: 191 VRDA--DFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRG 232 + D + I+ P LVI G ED P I + G Sbjct: 187 LVDGIDEIVAPSPPISCPALVITGDEDFGNGPEMANAIASEIAG 230 Lambda K H 0.321 0.136 0.410 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: 185 Number of extensions: 9 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: 266 Length of database: 266 Length adjustment: 25 Effective length of query: 241 Effective length of database: 241 Effective search space: 58081 Effective search space used: 58081 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 (21.9 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