Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_086509903.1 BZY95_RS10660 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::P77467 (262 letters) >NCBI__GCF_002151265.1:WP_086509903.1 Length = 264 Score = 144 bits (363), Expect = 2e-39 Identities = 85/252 (33%), Positives = 127/252 (50%), Gaps = 8/252 (3%) Query: 13 VMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQDLNDRNVD 72 VM + NRP RLN+ + +++L L + ERD +RC++LTG GR FC G D+ + Sbjct: 17 VMEIRFNRPHRLNAVVEAFYSELLAALAEAERDPEVRCVILTGEGRAFCVGADMKEH--- 73 Query: 73 PTGPAPDLGMSVERFY---NPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARS 129 G A R+ N + + + PKPVI AVNG A GAGA +A+ D ++ A Sbjct: 74 --GSAQRTLFQRRRYLQLGNDVCEAILRHPKPVIAAVNGYALGAGAEMAVACDFIVMAEE 131 Query: 130 AKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDET 189 A+ + +G G + LLP++ G A L G ++ +A G+ + Sbjct: 132 AQIGFPETSIGTCVGGGVSKLLPQLVGLNMARQLLYTGRRIDGREAARVGLATSSHAADA 191 Query: 190 LADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREGVS 249 + AQ LA LA Q + ++K+ +N LD+QL E D +AD++EGV Sbjct: 192 MPAEAQALAESLARQAPVSIAMLKRLVNQGSDTGLDSQLQQELDAVFTCSTTADWQEGVD 251 Query: 250 AFLAKRSPQFTG 261 AF KR+PQF G Sbjct: 252 AFAEKRTPQFKG 263 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: 139 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: 264 Length adjustment: 25 Effective length of query: 237 Effective length of database: 239 Effective search space: 56643 Effective search space used: 56643 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