Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_028585316.1 G494_RS0115915 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >NCBI__GCF_000429965.1:WP_028585316.1 Length = 259 Score = 132 bits (332), Expect = 7e-36 Identities = 89/260 (34%), Positives = 140/260 (53%), Gaps = 8/260 (3%) Query: 5 ILSHV-EKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAG 63 +LS V ++ V T+TLNRPE+LN+FN + +LA+ L+ ++ + +R +L+ GAG+ FCAG Sbjct: 6 LLSDVNDRFVGTITLNRPEQLNTFNSGLAGELAQALRAMDEEPAVRVILVKGAGKAFCAG 65 Query: 64 QDLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDI 123 D+N+ A + +E PL+ +A+L KPVI V GVAA G L D+ Sbjct: 66 IDVNELE---GKSAMEYRAWIEHMEQPLI-TIARLKKPVIAQVQGVAAANGMGLVAAADL 121 Query: 124 VIAARSAKFVMAFSKLGLIPDCGGTWL-LPRVAGRARAMGLALLGNQLSAEQAHEWGMIW 182 IAA + K + +GL +C G + + R GR +A+ L L G+ + A +A E G++ Sbjct: 122 AIAADNTKMGLTAINVGL--NCVGPIVPVARCVGRKKALELLLYGDLIKAPEAKELGLLN 179 Query: 183 QVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSA 242 ++V E L D A A LA + + + KQ ++E Q DL + + Sbjct: 180 RIVAKEELEDAALAWAETLAKKSPVAVQIAKQGYYASEDMDYFRQFDLMNEAFARLCTTD 239 Query: 243 DYREGVSAFLAKRSPQFTGK 262 D +EGV AF +R+P + K Sbjct: 240 DAKEGVRAFFERRNPVWQEK 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: 161 Number of extensions: 8 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: 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