Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_011842425.1 RSPH17029_RS17815 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_000015985.1:WP_011842425.1 Length = 261 Score = 125 bits (315), Expect = 7e-34 Identities = 92/259 (35%), Positives = 129/259 (49%), Gaps = 14/259 (5%) Query: 1 MVLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAG 60 ++L+E + V LTLNRPE LNA++ +L AL + E R +R +++ GAG+AF AG Sbjct: 4 ILLREDRGAVATLTLNRPEALNALSDAMLAALKEQFRALAEHRTIRVVVIRGAGKAFCAG 63 Query: 61 QDLTEF------GDRKPDYEAHL-RRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWG 113 DL E DR Y + L R V++A+ L +P++ V+G+A AG L Sbjct: 64 HDLREMQAARQSDDRGAAYFSDLFSRCAEVMQAIPALPQPVIAEVHGIATAAGCQLVASC 123 Query: 114 DLRLAAVGASFTTAFVRIGL---VPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALAL 170 D+ +AA G F V IGL P L+ +PR V A E+L + A+ A + Sbjct: 124 DMAVAAHGTRFGVNGVNIGLFCSTPMVALTRAVPRKV----AFEMLTTGEFIEADRAREV 179 Query: 171 GLVHRVVPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQA 230 GLV+R VP E L E LA +A T A K+ + + L A L + Sbjct: 180 GLVNRTVPPEDLAAEVQKLAAVVAGKLTAAVRTGKRAFYDQAGMGLGAAYTLTGAVMADN 239 Query: 231 GQTQDHEEGVRAFREKRPP 249 +D EEGV AF EKR P Sbjct: 240 MMWRDTEEGVAAFLEKRAP 258 Lambda K H 0.318 0.135 0.371 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: 147 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: 254 Length of database: 261 Length adjustment: 24 Effective length of query: 230 Effective length of database: 237 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 Apr 10 2024. 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