Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_012049785.1 SWIT_RS18205 enoyl-CoA hydratase/isomerase family protein
Query= uniprot:A0A2Z5MCI7 (262 letters) >NCBI__GCF_000016765.1:WP_012049785.1 Length = 263 Score = 138 bits (347), Expect = 1e-37 Identities = 76/241 (31%), Positives = 127/241 (52%) Query: 19 LTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENRAK 78 LTL+ P A NAL D+ A + A E DP+IR V +TGA FCAGG++ + K Sbjct: 17 LTLNRPEAANALDIDLARALVTAALDCEHDPAIRCVTLTGAGRLFCAGGDVAYMAGAGDK 76 Query: 79 DPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVMSY 138 + A+ L +S L SKP++ V+G AAGAG+ +AL+ D+++ A A F +Y Sbjct: 77 TAAATAELASTLHLAMSHLARMSKPLVTIVNGPAAGAGYGMALSGDVVLMARSASFTPAY 136 Query: 139 ARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDAAVA 198 +G++PDGG +W L + + + A E+++ + +GA +G++ + A Sbjct: 137 GMLGVSPDGGLTWLLPRLVGLRRAQEIILTNRKVGAEEAEAMGLITRAVDDDALAAEGAA 196 Query: 199 WADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLEKRA 258 A +L + ++ ++ L+ + HL E +++ R+G EG++AFL KR Sbjct: 197 IAAKLAASATYAIGSVRALLLDSYANSWETHLELEARGIASAISGRDGREGVAAFLAKRK 256 Query: 259 P 259 P Sbjct: 257 P 257 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: 155 Number of extensions: 4 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: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 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