Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate HSERO_RS20665 HSERO_RS20665 2,3-dehydroadipyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__HerbieS:HSERO_RS20665 Length = 262 Score = 145 bits (365), Expect = 1e-39 Identities = 87/250 (34%), Positives = 136/250 (54%), Gaps = 6/250 (2%) Query: 13 VMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQDLNDRNVD 72 V+ LTLNRP N+ ++ ++ L + E DD++R ++++G + F AG DLN+ + Sbjct: 19 VLHLTLNRPALRNALRNQSLREIVAALARAEEDDSVRVVVISGNEKAFAAGADLNEM-IH 77 Query: 73 PTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARSAKF 132 A L + + + R +A+ PKP++ AVNG A GAG L + DI IAAR AK Sbjct: 78 KDAIATQLDVRAQYW-----RAIARFPKPILAAVNGYALGAGCELLMHADIAIAARGAKI 132 Query: 133 VMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDETLAD 192 +G +P GGT L R G+ AM + L G +SA+QA + G++ +VVDD+ + Sbjct: 133 GQPEINVGTLPGAGGTQRLIRTVGKPLAMKMVLSGEFISADQALQAGLVAEVVDDDATLE 192 Query: 193 TAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREGVSAFL 252 LA +A + + L K+A+ + L+ L ER L SAD +EG++AF Sbjct: 193 RTLALAHSIAQKSPLAVRLAKEAMLQSFELGLEAGLLFERKSFSLMAASADRQEGIAAFQ 252 Query: 253 AKRSPQFTGK 262 KR+ F+G+ Sbjct: 253 EKRAAVFSGR 262 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: 126 Number of extensions: 7 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: 262 Length adjustment: 25 Effective length of query: 237 Effective length of database: 237 Effective search space: 56169 Effective search space used: 56169 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 17 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