Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate AZOBR_RS18155 AZOBR_RS18155 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__azobra:AZOBR_RS18155 Length = 248 Score = 134 bits (338), Expect = 1e-36 Identities = 92/255 (36%), Positives = 135/255 (52%), Gaps = 8/255 (3%) Query: 9 VEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAG-RGFCAGQDLN 67 V+ V T+TL+RP++LN+ EM AQL + + DD IRC++LTGAG R FC G D+ Sbjct: 1 VDGFVATITLDRPQKLNAVTPEMAAQLVAAVARCNADDDIRCVVLTGAGPRAFCCGSDI- 59 Query: 68 DRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAA 127 R +D A + + Y +R L K P I AVNG A G G A+ DI IA+ Sbjct: 60 -RELDRYDTAWNFRNRED--YCDAIRGLRK---PSIAAVNGYAFGGGLETAMSCDIRIAS 113 Query: 128 RSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDD 187 +A+F KLG I G L G + A + L G+ + A++A WG++ +VV Sbjct: 114 ENAQFGAPEIKLGWIGGGGVAAFLSHSIGTSNAAMMILTGDPIPADKALAWGLVSEVVPA 173 Query: 188 ETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREG 247 + L AQ++A +A++ K + +A T ++ ++ ERD Q + +AD EG Sbjct: 174 DRLLARAQEIAAIVASRAPIAAETAKLNLKAAHTMPVEKAIEYERDLQTICFATADAAEG 233 Query: 248 VSAFLAKRSPQFTGK 262 +AF KRSP F K Sbjct: 234 RAAFKEKRSPVFRRK 248 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: 136 Number of extensions: 8 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: 248 Length adjustment: 24 Effective length of query: 238 Effective length of database: 224 Effective search space: 53312 Effective search space used: 53312 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 Apr 09 2024. 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