Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_084517385.1 H567_RS0115475 hypothetical protein
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_000422285.1:WP_084517385.1 Length = 287 Score = 188 bits (477), Expect = 1e-52 Identities = 106/245 (43%), Positives = 152/245 (62%), Gaps = 3/245 (1%) Query: 12 VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGADLNEM--A 69 V +LT++RP NALN ++ +L + ++AA D + V VITG + F AGADL+ + A Sbjct: 43 VRVLTIDRPPV-NALNEEIVDELRDAVKAAMLDGRVRVLVITGAGKIFVAGADLDRLLAA 101 Query: 70 EKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLPE 129 + D + D L ++ KP+IAA+NG A G G ELA+ CDV +A +NAR GLPE Sbjct: 102 DMDAGRKMADGVKGLHREMRQGGKPVIAAINGMAAGGGLELAMACDVRIADQNARMGLPE 161 Query: 130 ITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYALQ 189 +TLG++PGAGGTQ L R VG A +M+ +G I A A Q GLV V + L+ AL+ Sbjct: 162 VTLGVLPGAGGTQMLPRLVGAGKAMEMMFTGMIIDANDALQLGLVEQVAIVESALDLALK 221 Query: 190 LASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKRT 249 +A++M +++PLA+ K A+ + + L GLA+E F L T D++EGI+AF +RT Sbjct: 222 MAARMVKNAPLAISEIKAAVYDTMSLPLDQGLAEETGRFARLCRTADKNEGITAFKSRRT 281 Query: 250 PDFKG 254 FKG Sbjct: 282 AVFKG 286 Lambda K H 0.318 0.130 0.356 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: 129 Number of extensions: 4 Number of successful extensions: 2 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: 255 Length of database: 287 Length adjustment: 25 Effective length of query: 230 Effective length of database: 262 Effective search space: 60260 Effective search space used: 60260 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 (21.8 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