Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_057507562.1 ABB28_RS04910 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >NCBI__GCF_001431535.1:WP_057507562.1 Length = 265 Score = 119 bits (298), Expect = 6e-32 Identities = 87/247 (35%), Positives = 128/247 (51%), Gaps = 7/247 (2%) Query: 18 VLTLSNPGARN-ALHPDMYAAGIEALDSVERDPSIRAVVITG-ADNFFCAGGNLNRLLEN 75 V+TL NP A +H AA + + ++ D SI A+VI+G + FF AG +LN+ Sbjct: 22 VITLHNPPAHTWTVHS--LAALRDLVAALNADRSIYALVISGEGEKFFSAGADLNQFASG 79 Query: 76 RAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFV 135 A+ E +S R S IAA++G A G G ALACDL + + A+ Sbjct: 80 DRGAAREAARRFGEAFEALSGFRGVS---IAAINGYAMGGGLECALACDLRIIEEHAQVA 136 Query: 136 MSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDA 195 + A VGL P GG+ L + + A +++ G+ I A +G+ + G A+ Sbjct: 137 LPEATVGLLPCAGGTQNLPRLVGEGWAKRMILLGERIDADTAVRIGLAEQKAGKGEAKAL 196 Query: 196 AVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLE 255 A+ WA + GK SP S+A KTLV + T + LVAER+ FV + +EG+SAFLE Sbjct: 197 ALEWAKKAGKQSPTSIAACKTLVQSTRTGTHAAALVAEREAFVDLFDSADQVEGVSAFLE 256 Query: 256 KRAPVYK 262 KR+ +K Sbjct: 257 KRSAQWK 263 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: 139 Number of extensions: 5 Number of successful extensions: 1 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: 265 Length adjustment: 25 Effective length of query: 237 Effective length of database: 240 Effective search space: 56880 Effective search space used: 56880 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 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