Align Enoyl-CoA hydratase (characterized, see rationale)
to candidate WP_041242954.1 GLOV_RS14360 crotonase
Query= uniprot:A0A2Z5MEB0 (258 letters) >NCBI__GCF_000020385.1:WP_041242954.1 Length = 254 Score = 204 bits (520), Expect = 1e-57 Identities = 111/254 (43%), Positives = 156/254 (61%), Gaps = 2/254 (0%) Query: 7 LVETRGRVGLVTLSRPKALNALNDALMDELGVALREFDADDAIGAIVLTGS-EKAFAAGA 65 +VET+ + +T++RP ++NA+ + EL V ++E A + A+++TG+ EKAF AG Sbjct: 1 MVETKDGIATITVNRPASMNAMTVTTLQELSVVVQELSASAVVRAVIITGAGEKAFIAGG 60 Query: 66 DIGMMSTYSYMDVYKGDYITRNW-ETVRSIRKPIIAAVAGFALGGGCELAMMCDMIFAAD 124 DI M+ + + + + KP IAAV G+ALGGGCELA+ CDM AA+ Sbjct: 61 DIAMLQKLGPVAARELALLAHGLCRAIEQSPKPFIAAVNGYALGGGCELALCCDMRIAAE 120 Query: 125 TAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAA 184 A+FGQPEI +G +PG GG+QRLPR V K +A+++ LT +DA EA R GLV++V+PAA Sbjct: 121 NARFGQPEINIGTLPGFGGSQRLPRLVGKGRALEMILTGDMIDAQEAWRIGLVNKVVPAA 180 Query: 185 SLIDESIAAGATIAEFPLPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGM 244 L+ + A +A L A+ + KE V E L +E LF FAT DQ+EGM Sbjct: 181 ELMAAANAVAQKLAGKSLMALKLCKEVVVNGLEMDLDRACSYEADLFALSFATADQQEGM 240 Query: 245 AAFVEKRKPVFKHR 258 AAF+EKR PVF R Sbjct: 241 AAFLEKRAPVFSDR 254 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: 178 Number of extensions: 7 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: 254 Length adjustment: 24 Effective length of query: 234 Effective length of database: 230 Effective search space: 53820 Effective search space used: 53820 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