Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_038208611.1 Q392_RS13970 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_000745855.1:WP_038208611.1 Length = 271 Score = 188 bits (477), Expect = 1e-52 Identities = 120/263 (45%), Positives = 150/263 (57%), Gaps = 10/263 (3%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQ 61 +L DGVL LTLNRPE NA+T + +AL L E E D VR ++LTGAG F AG Sbjct: 9 LLARLDDGVLTLTLNRPEARNAMTRAMNEALARQLAEAELDPAVRCVVLTGAGSGFCAGG 68 Query: 62 DLTEF--------GDRKPDYEAHLRRYNRVVEA--LSGLEKPLVVAVNGVAAGAGMSLAL 111 D+ G D H +R N+ A L + KP + A+ G AAGAG++LAL Sbjct: 69 DVKGMAAAGDGTVGALTIDEAIHRQRVNQRATAGRLYRMPKPTIAALPGAAAGAGLALAL 128 Query: 112 WGDLRLAAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALG 171 DLR+ A A TTAF R+G D G S+ L RLVG AKA+EL LS R++A+EAL LG Sbjct: 129 ACDLRVMASSAIMTTAFARVGFSGDYGGSYFLTRLVGAAKARELYFLSERVTADEALRLG 188 Query: 172 LVHRVVPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAG 231 L + V E+L E ++A+ LA GPT AY K+ L L + L LEA G Sbjct: 189 LANWVCTPEELAERTEAVARRLAAGPTVAYRYMKENLNRAVNGELDDCLDLEATHHIHCG 248 Query: 232 QTQDHEEGVRAFREKRPPRFQGR 254 QT+DH E RAF EKR P F+GR Sbjct: 249 QTEDHREAARAFVEKREPVFKGR 271 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: 175 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: 271 Length adjustment: 25 Effective length of query: 229 Effective length of database: 246 Effective search space: 56334 Effective search space used: 56334 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 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