Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_036263857.1 DL86_RS15400 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_000746085.1:WP_036263857.1 Length = 259 Score = 125 bits (314), Expect = 9e-34 Identities = 85/262 (32%), Positives = 132/262 (50%), Gaps = 13/262 (4%) Query: 4 ETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFC 62 E + K E + + NRP NAL + + E L ++ ++DP I+V+I+TG G +AF Sbjct: 3 EDLLFKVEAGIAQVVFNRPRTRNALTSGMYEGLAAICAKVDADPAIKVLILTGAGDQAFA 62 Query: 63 AGADITQFNQL-TPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIR 121 +G DI +F Q +P + + + + +E TIA I G GGG +A CD+R Sbjct: 63 SGTDIAEFRQFASPDDVLAYEARIEAALSALERCRASTIAAIAGVCTGGGAMIAACCDLR 122 Query: 122 IAAEEAQLGLP-EINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNR 180 I E +LG+P LG RL +IG R ++++T + K+A GL+N Sbjct: 123 IGEPETKLGMPIARTLGNCLSMSNYARLAGLIGPARVKDLILTARLVGAKEAIAMGLLNE 182 Query: 181 VV-PLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVV---F 236 V L L ++A +P+SL KE + R + G A +S +V + Sbjct: 183 AVDQTKELLPRAHDLGRRVAGHAPLSLRATKEALLR------MRGQAPQSAAEDLVLMCY 236 Query: 237 STEDKKEGVSAFLEKREPTFKG 258 +ED +EGV+AFLEKR P ++G Sbjct: 237 LSEDFREGVAAFLEKRSPRWRG 258 Lambda K H 0.315 0.135 0.382 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: 120 Number of extensions: 9 Number of successful extensions: 5 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: 259 Length of database: 259 Length adjustment: 24 Effective length of query: 235 Effective length of database: 235 Effective search space: 55225 Effective search space used: 55225 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: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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