Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_057507779.1 ABB28_RS05820 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >NCBI__GCF_001431535.1:WP_057507779.1 Length = 259 Score = 135 bits (339), Expect = 1e-36 Identities = 85/251 (33%), Positives = 132/251 (52%), Gaps = 5/251 (1%) Query: 13 VMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAG-RGFCAGQDLNDRNV 71 + T+T+ RPE+LN+ N E LA +Q +D +R ++LTGAG + F AG D+++ N Sbjct: 13 IRTVTVQRPEKLNALNGETLRALAAAFEQAAQDPAVRVVILTGAGPKAFVAGADISEMNT 72 Query: 72 DPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARSAK 131 D + +R L+R++ ++PKPVI VNG A G G LA+ + IA +A+ Sbjct: 73 LSAVEGRDFSLLGQR----LMRQIERMPKPVIARVNGFALGGGLELAMACHLRIAVDTAR 128 Query: 132 FVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDETLA 191 LGLIP GG+ L R+ GRA A+ L LLG + A +A + G++ +V + L Sbjct: 129 LGQPEITLGLIPGFGGSQRLLRLCGRAAALELCLLGTPIDAARALQLGLVNEVASADDLD 188 Query: 192 DTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREGVSAF 251 LA LA + + A++ +L++ L+ E L + D REG SAF Sbjct: 189 ARVAGLAERLANAAPLAVRALLDAVHVGGECSLESGLEYESAQFGLLFATHDMREGTSAF 248 Query: 252 LAKRSPQFTGK 262 L +R+ F + Sbjct: 249 LERRAAMFQNR 259 Lambda K H 0.321 0.136 0.403 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: 148 Number of extensions: 11 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: 262 Length of database: 259 Length adjustment: 25 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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 (21.8 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