Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_049776088.1 XAUT_RS04520 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= uniprot:A0A2Z5MCI7 (262 letters) >NCBI__GCF_000017645.1:WP_049776088.1 Length = 258 Score = 128 bits (321), Expect = 1e-34 Identities = 82/247 (33%), Positives = 130/247 (52%), Gaps = 4/247 (1%) Query: 12 ESESTLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNR 71 + E + LTL+ P NA +++ + ALD+ D + RAV++TGA FCAG +L Sbjct: 6 QHEGWVELTLNRPDRLNAFTEELHRSLAAALDAAA-DDACRAVLLTGAGRGFCAGQDLGD 64 Query: 72 LLENRAKDPSVQAQSIDLLAE-WISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAAD 130 +A+ P +I+ I +R KPV+ AV+G AAGAG ++A ACD+++AA Sbjct: 65 --RAKAEGPLDLGATIEAFYNPLIRRIRALRKPVVCAVNGVAAGAGANIAFACDIVLAAR 122 Query: 131 DAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPG 190 AKF+ ++A++GL PD GG++FL + + A +++ +P+ A + G++ K Sbjct: 123 SAKFIQAFAKIGLVPDSGGTFFLPRLIGDARARALMLLAEPVSAEKAESWGLIWKAVDDA 182 Query: 191 TARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGI 250 D A A A L +A K + A+ L L ERD + + EG+ Sbjct: 183 ALMDEARALASHLASQPTQGLALTKQALNASAGNALDAQLDLERDLQREAGRTPDYREGV 242 Query: 251 SAFLEKR 257 SAF+EKR Sbjct: 243 SAFMEKR 249 Lambda K H 0.317 0.132 0.377 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: 173 Number of extensions: 8 Number of successful extensions: 4 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: 258 Length adjustment: 24 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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