Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_028315560.1 G491_RS0117880 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >NCBI__GCF_000429905.1:WP_028315560.1 Length = 260 Score = 160 bits (406), Expect = 2e-44 Identities = 97/261 (37%), Positives = 140/261 (53%), Gaps = 5/261 (1%) Query: 3 EFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAG-RGFC 61 E +LS E V+TLTLNRP+ +NSFN M L + + D +R +++TGAG R FC Sbjct: 4 ELVLSQTEDQVLTLTLNRPKVMNSFNFAMLHALKAAVDKARFDPEVRVIIITGAGDRAFC 63 Query: 62 AGQDLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGG 121 AG DL +R + ++ + + LPKPVI AVNG+A G G LALG Sbjct: 64 AGADLKERATLTPVQVKEFIYTIRNLFTDI----ENLPKPVIAAVNGIALGGGTELALGC 119 Query: 122 DIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMI 181 DI +AA +A + + L +IP GGT LPR+ G+ +A L G ++ A++A E GM+ Sbjct: 120 DIRLAAETAAMGLTETTLAIIPGAGGTQRLPRLIGKGKAKELIFTGRRVDAQEALELGMV 179 Query: 182 WQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRS 241 QVV ++L D A+ +A + + K AIN L T L +E + + S Sbjct: 180 NQVVPGDSLLDAAKDMAAAIRKNGPIAVTQAKYAINQGMETDLSTGLAIESNAYWITIPS 239 Query: 242 ADYREGVSAFLAKRSPQFTGK 262 D EG++AF KR P + G+ Sbjct: 240 KDRLEGLAAFREKRKPVYKGE 260 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: 118 Number of extensions: 5 Number of successful extensions: 3 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: 260 Length adjustment: 25 Effective length of query: 237 Effective length of database: 235 Effective search space: 55695 Effective search space used: 55695 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