Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_059151871.1 V474_RS12920 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >NCBI__GCF_001046635.1:WP_059151871.1 Length = 255 Score = 129 bits (323), Expect = 8e-35 Identities = 88/247 (35%), Positives = 132/247 (53%), Gaps = 13/247 (5%) Query: 18 VLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGA-DNFFCAGGNLNRLLENR 76 V+TL+ P RNAL ++ A E D ++R ++TG+ D FCAGG+L ++E Sbjct: 16 VITLNRPEQRNALTAEVREGLRAAWARFEADDALRIAILTGSGDKAFCAGGDLKEMVETG 75 Query: 77 AKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVM 136 P D+ A + LS KP IAAV+G A G+ +A ACDL VA+ AKF + Sbjct: 76 MAVPPR-----DMYALPYDTIELS-KPTIAAVNGVAFAGGWMIAQACDLCVASTAAKFAI 129 Query: 137 SYARVGLTPDGGGSWF--LAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARD 194 + +VG G W L + +++ E+++ GKPI AAR +E+G+VN+L +PG D Sbjct: 130 TEVKVGR----GSPWAAPLIHMIGQRIFMEIVLTGKPIDAARAYEIGLVNRLAQPGAVLD 185 Query: 195 AAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFL 254 AA+ A E+ + +P SV + V + S L A R + + ++ EG AF Sbjct: 186 AAIELAREVLEGAPLSVKAARETVMLSTEMGRSAALAAARSAHEHTYNSQDAQEGPRAFA 245 Query: 255 EKRAPVY 261 EKR PV+ Sbjct: 246 EKRRPVW 252 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: 153 Number of extensions: 11 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: 255 Length adjustment: 24 Effective length of query: 238 Effective length of database: 231 Effective search space: 54978 Effective search space used: 54978 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