Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_011384978.1 AMB_RS13070 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >NCBI__GCF_000009985.1:WP_011384978.1 Length = 256 Score = 154 bits (388), Expect = 2e-42 Identities = 90/264 (34%), Positives = 142/264 (53%), Gaps = 10/264 (3%) Query: 1 MMEFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGF 60 M E +L V+ L +NRP+ N+ N E+ LAE + + D ++R +++TG F Sbjct: 1 MTEVLLEKPFDSVVLLRINRPDAKNALNGEVRRLLAEHMTTLGADPSVRAIVMTGNQEAF 60 Query: 61 CAGQDLNDRNVDPTGPAPDLGMS--VERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLA 118 AG D+ D ++G ++R + L R +A PKPVI AVNG A G G L Sbjct: 61 AAGADIKDM--------AEVGAIELMQRNNHLLWRAIANCPKPVIAAVNGYAWGGGCELV 112 Query: 119 LGGDIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEW 178 + DI++A +A F K+G++P GGT L R G+ +AM + + G +S +A + Sbjct: 113 MHADIIVAGENASFSQPEVKVGIMPGAGGTQRLTRAVGKFKAMLMVMTGQAISGVEAGQM 172 Query: 179 GMIWQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLA 238 G+ VV D + D A ++A+ ++ P + IK+ + + + +LDT L LER +L Sbjct: 173 GLASVVVPDAEVVDKALEIAKTISRMPPVAIAQIKEVLLAGQDASLDTALMLERKAFQLL 232 Query: 239 GRSADYREGVSAFLAKRSPQFTGK 262 SAD +EG+ AF+ KR P + GK Sbjct: 233 FASADQKEGMKAFIEKRKPTYQGK 256 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: 125 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: 256 Length adjustment: 24 Effective length of query: 238 Effective length of database: 232 Effective search space: 55216 Effective search space used: 55216 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