Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_028314216.1 G491_RS0107945 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >NCBI__GCF_000429905.1:WP_028314216.1 Length = 260 Score = 177 bits (448), Expect = 3e-49 Identities = 98/244 (40%), Positives = 146/244 (59%), Gaps = 1/244 (0%) Query: 16 LTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQDLNDRNVDPTG 75 + L+RP+ NSF+ EM +LA+ L ++ DD++R +L+TG G+ FCAG DL Sbjct: 16 VVLSRPKAFNSFHLEMITELAQELTRLAVDDSVRGVLITGEGKAFCAGGDLRWVTEFAEK 75 Query: 76 PAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARSAKFVMA 135 P +F+N +V + ++ KPV+ AVNGVAAG G +LAL D+ + +SA A Sbjct: 76 PGASFHTLAAQFHNAIVE-IRRMEKPVVAAVNGVAAGGGFSLALACDLRVMGKSAVLKQA 134 Query: 136 FSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDETLADTAQ 195 ++ GL D GGT+ LPR+ G ARA+ +A+ +SAE+A EWG+ +VV+DE + A+ Sbjct: 135 YTSSGLCIDGGGTYTLPRLVGMARALEIAVFDEPISAEKALEWGLATKVVEDEAVLQEAR 194 Query: 196 QLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREGVSAFLAKR 255 + L+ + +GL K +N A NTL+ QL+LER G D REG++AF KR Sbjct: 195 AMMGVLSKKSMHSIGLSKNLLNDAFNNTLEYQLELERQGLGACGDHPDGREGLAAFAEKR 254 Query: 256 SPQF 259 P+F Sbjct: 255 KPEF 258 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: 133 Number of extensions: 3 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: 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