Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_015944700.1 DHAF_RS18210 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_000021925.1:WP_015944700.1 Length = 260 Score = 146 bits (368), Expect = 5e-40 Identities = 96/249 (38%), Positives = 145/249 (58%), Gaps = 3/249 (1%) Query: 8 DGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAGQDLTEF 66 +GV V+T+N+P +NA+T E+ L L E E++ +R L++TGAG + F AG D+ +F Sbjct: 13 NGVGVITINKPP-VNALTLEVRGQLKETLNEVEKNTGIRVLVITGAGPKCFVAGADIKDF 71 Query: 67 GDR-KPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGASFT 125 ++ K + Y + L +P++ A+NG+A G G+ LAL D+R+A A Sbjct: 72 PNQFKEGPRENATIYKEMFSYLENTPRPVICALNGLALGGGLELALACDIRIADEKAKLG 131 Query: 126 TAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEKLMEE 185 V +GL+P G + L RLVG AKA+ELL + A+EAL +GLV+ VVPA + + E Sbjct: 132 LTEVLLGLLPGLGGTQRLARLVGPAKAKELLFSGKIVKADEALRIGLVNEVVPAGESLNE 191 Query: 186 ALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVRAFRE 245 AL LA++LA+G A K L+ + LSL +AL +E + +T+D EG+ AF Sbjct: 192 ALKLAEKLAKGAGIAMGYDKLLINKGLELSLADALEMEMHYVEKVFETEDLREGLDAFIN 251 Query: 246 KRPPRFQGR 254 KR F+ R Sbjct: 252 KREAVFKNR 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: 174 Number of extensions: 6 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: 260 Length adjustment: 24 Effective length of query: 230 Effective length of database: 236 Effective search space: 54280 Effective search space used: 54280 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