Align short chain enoyl-CoA hydratase subunit (EC 4.2.1.17) (characterized)
to candidate GFF12 HP15_12 enoyl-CoA hydratase/isomerase
Query= metacyc::MONOMER-11697 (290 letters) >FitnessBrowser__Marino:GFF12 Length = 270 Score = 176 bits (447), Expect = 4e-49 Identities = 102/252 (40%), Positives = 150/252 (59%), Gaps = 10/252 (3%) Query: 43 RNSNVGLIQLNRPKALNALCNGLIVELNQALQAFEEDPAVGAIVLTG-GEKVFAAGADIK 101 R+ NVG + LNRPK +NA+ + + V + +AL+ FE+D + IV+ G GE+ AGADIK Sbjct: 19 RDGNVGWVILNRPKQINAINDEIRVGVPEALEQFEKDKEIRVIVIRGEGERGLCAGADIK 78 Query: 102 EMQ----SLTFQNCYSGGFLSHW-DQLTRVKKPVIAAVNGYALGGGCELAMMCDIIYAGE 156 E + SL + + W + + + KPVI A++GY +GGG ELA+ CDI YA Sbjct: 79 ERRGPENSLQVRKRME---CARWIESIDQTTKPVIVAIHGYCMGGGLELALACDIRYASP 135 Query: 157 KAQFGQPEILIGTIPGAGGTQRLTRAVGKSLAMEMVLTGDRISAQDAKQAGLVSKIFPV- 215 A PE +G IPG GGTQRL+R V A++M+L+GDR+ A A+ GLV+++ Sbjct: 136 NAVMALPETGLGLIPGGGGTQRLSRVVAPGHALDMLLSGDRLDAARARSIGLVTRVAETQ 195 Query: 216 ETVVEEAIQCAEKIASNSKIVTAMAKESVNAAFEMTLAEGVKLEKKLFYSTFATEDRKEG 275 E++++E + A+KIA + T K + A+ E+ L G+ LE LF TED +E Sbjct: 196 ESLLQEVSELAQKIAMKPPLATTYVKRAARASLELELKRGLDLELDLFALLAPTEDAREA 255 Query: 276 MAAFVEKRKANF 287 +AF E+R NF Sbjct: 256 ASAFSERRSPNF 267 Lambda K H 0.319 0.133 0.378 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: 160 Number of extensions: 6 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: 290 Length of database: 270 Length adjustment: 26 Effective length of query: 264 Effective length of database: 244 Effective search space: 64416 Effective search space used: 64416 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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