Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate Dsui_1378 Dsui_1378 enoyl-CoA hydratase/carnithine racemase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__PS:Dsui_1378 Length = 258 Score = 121 bits (303), Expect = 2e-32 Identities = 78/245 (31%), Positives = 127/245 (51%), Gaps = 4/245 (1%) Query: 18 VLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENRA 77 ++TL+ P A NAL + +AL E D +I +VITG+D F AG +++ + + Sbjct: 16 LITLNRPKALNALCDPLVDELGDALTEFEADENIGCIVITGSDKAFAAGADISMMKDFSY 75 Query: 78 KDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVMS 137 D A D + ++ KPVIAAV G A G G LA++CD I+AAD A+F Sbjct: 76 MD----AYKGDYITRNWEKVKTCRKPVIAAVAGYALGGGCELAMSCDFIIAADSAQFGQP 131 Query: 138 YARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDAAV 197 ++G+ P GG+ L +A+ + A ++ + + + A G+V+++ + A+ Sbjct: 132 EVKLGILPGAGGTQRLPRAVGKAKAMDLCLSARMMDATEAERAGLVSRIVPADKLLEEAL 191 Query: 198 AWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLEKR 257 A+++ S V IK V A L+E L+ ER F A+ + EG++AF+EKR Sbjct: 192 GAAEKIASYSLPVVMMIKENVNRAFESSLNEGLLFERRQFHAAFALEDQKEGMAAFVEKR 251 Query: 258 APVYK 262 P +K Sbjct: 252 KPAFK 256 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: 138 Number of extensions: 4 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: 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 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