Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_013091878.1 BC1002_RS20360 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_000092885.1:WP_013091878.1 Length = 270 Score = 160 bits (406), Expect = 2e-44 Identities = 96/256 (37%), Positives = 142/256 (55%), Gaps = 4/256 (1%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQ 61 +L R+ VLVL+LN P NA+T E+ +AL AL++ + D ++ A++LTG G AF AG Sbjct: 5 ILSRREGAVLVLSLNNPAARNALTTEMYEALPVALEQAQHDADIGAIVLTGVGSAFCAGG 64 Query: 62 DLTEFGDRKP----DYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRL 117 DL R+ D A + + ++ A+ KP++ AV G AAGAG+S+AL DL + Sbjct: 65 DLNRLAQRRAMTPSDRRAGIEVLHHMIRAIRDCRKPVIAAVEGAAAGAGLSIALACDLLV 124 Query: 118 AAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVV 177 AA ASF+ A+V++GL PD+G + L V EL L +S E +LG+ +R+ Sbjct: 125 AARDASFSVAYVKVGLSPDAGATAFLSGCVSRQLLTELCLTGKPVSGERMHSLGVTNRLT 184 Query: 178 PAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHE 237 + + EA++LA+ LA GP RA A K L +L L LEA ++ + Sbjct: 185 EKQGALAEAIALAQTLASGPERASARIKSLCRRAGENTLDAQLDLEAQYMTESLGDDESA 244 Query: 238 EGVRAFREKRPPRFQG 253 EG+ AF KRP + G Sbjct: 245 EGIAAFFGKRPADYVG 260 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: 158 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: 270 Length adjustment: 25 Effective length of query: 229 Effective length of database: 245 Effective search space: 56105 Effective search space used: 56105 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