Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate PfGW456L13_4459 Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4459 Length = 267 Score = 90.1 bits (222), Expect = 4e-23 Identities = 60/201 (29%), Positives = 100/201 (49%), Gaps = 11/201 (5%) Query: 20 HAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSLVTPGPYSIEQLGRDVLA 79 H L+L + LG++ W+ QIP +RV+ D RGHGRS YSI D++A Sbjct: 18 HGTPLLLVHGLGSSTLDWEKQIPTLATRYRVIVPDVRGHGRSDKPQERYSIAGFSADLIA 77 Query: 80 LLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAAKI-----GDPSVWNPRI 134 L++ LN+ AH+ GLSMGG+IG LG++ + L L + N+A ++ D W R Sbjct: 78 LIEHLNLGPAHYVGLSMGGMIGFQLGVDQPQLLKSLCIVNSAPEVKLRSRDDYWQWFKRW 137 Query: 135 ETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQGYAANCAAVRDA 194 + A + ++ P QA+ + +++ + A Y A+ A+ Sbjct: 138 SLM----HALSLRTIGKALGSKLFPKPEQAD--LRQKMAERWAKNDKHAYLASFNAIVGW 191 Query: 195 DFREQLASITVPTLVIAGTED 215 +E+L+ +T PTL+++ D Sbjct: 192 GVQERLSKVTCPTLIVSADRD 212 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: 164 Number of extensions: 8 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: 267 Length adjustment: 25 Effective length of query: 241 Effective length of database: 242 Effective search space: 58322 Effective search space used: 58322 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 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