Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_011779220.1 MVAN_RS09985 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >NCBI__GCF_000015305.1:WP_011779220.1 Length = 266 Score = 173 bits (439), Expect = 3e-48 Identities = 99/254 (38%), Positives = 137/254 (53%), Gaps = 1/254 (0%) Query: 10 EKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQDLNDR 69 + V+ +TL+RP R NS + M L L DD++R + LTGAG FC+G D Sbjct: 13 DDAVLRITLDRPTRRNSLSHAMIDDLVGTLTSAASDDSVRAIHLTGAGDDFCSGADWVTT 72 Query: 70 NVDPTGPAP-DLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAAR 128 N P P +L + N +V +A + PV+C V G A G GA LAL D +A Sbjct: 73 NSSDRKPRPGNLVRRIPHAANRVVELVATIQLPVVCTVRGWAVGLGANLALAADFTLATP 132 Query: 129 SAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDE 188 A F G PD G TWLLPR+AG RA + LLG +++ A +WG+I Q V + Sbjct: 133 EANLWEPFIDRGFSPDSGSTWLLPRLAGVTRAKRMLLLGEKVTGADAADWGLIHQAVPAD 192 Query: 189 TLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREGV 248 + A++L LA+ PT +GL KQAIN TL + E LA R+AD++EG+ Sbjct: 193 EIDAAAEELVTRLASGPTVAIGLAKQAINYGMHATLPQSMAHELASLELACRTADFKEGL 252 Query: 249 SAFLAKRSPQFTGK 262 +AF A+R+P F G+ Sbjct: 253 AAFRARRAPDFEGR 266 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: 162 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: 266 Length adjustment: 25 Effective length of query: 237 Effective length of database: 241 Effective search space: 57117 Effective search space used: 57117 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