Align Enoyl-CoA hydratase (characterized, see rationale)
to candidate WP_156424864.1 AQZ52_RS04030 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MEB0 (258 letters) >NCBI__GCF_001519075.1:WP_156424864.1 Length = 277 Score = 150 bits (379), Expect = 3e-41 Identities = 99/266 (37%), Positives = 143/266 (53%), Gaps = 21/266 (7%) Query: 4 ENILVETRGRVGLVTLSRPKALNALNDALMDELGVALREFDADDAIGAIVLTGSEKAFAA 63 E+I VE RGRV +TL+RP LNA+N + +EL A F ADD V+TG + F A Sbjct: 22 EHITVEQRGRVTRITLARPAVLNAINARMHEELEEAFNAFAADDGQWVAVVTGQGRGFCA 81 Query: 64 GADIGMMSTYSYMDVYKGDY--ITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDMIF 121 G+D+ ++ + Y + ++ KPIIAAV G ALGGG E+A+ CD+I Sbjct: 82 GSDLKAVAAEGFRSYPAHGYAGLIERFDC----DKPIIAAVNGLALGGGFEVALACDLII 137 Query: 122 AADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVI 181 AA++A+FG PE ++G + GG RL R + +AM + L+AR +DAAE ER G V+ V+ Sbjct: 138 AAESARFGLPEPRVGAVALGGGLHRLARQIGLKRAMGMILSARPVDAAEGERLGFVTEVV 197 Query: 182 PAASLID------ESIAAGATIAEFPLPAVMMVKESVNRAYE---TTLAEGVHFERRLFH 232 P L E+I GA + ++ K++V R + A F Sbjct: 198 PDTDLESAVERWVEAILLGAPL------SIRASKQAVMRGLDEAGVAAAMAAQPGYPAFA 251 Query: 233 SLFATEDQKEGMAAFVEKRKPVFKHR 258 + A+ D +EG AF EKR PV++ R Sbjct: 252 AWSASADLREGTTAFAEKRPPVWQGR 277 Lambda K H 0.322 0.135 0.383 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: 205 Number of extensions: 12 Number of successful extensions: 3 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: 258 Length of database: 277 Length adjustment: 25 Effective length of query: 233 Effective length of database: 252 Effective search space: 58716 Effective search space used: 58716 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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