Align short chain enoyl-CoA hydratase subunit (EC 4.2.1.17) (characterized)
to candidate Echvi_0343 Echvi_0343 Enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-11697 (290 letters) >FitnessBrowser__Cola:Echvi_0343 Length = 258 Score = 122 bits (305), Expect = 1e-32 Identities = 86/257 (33%), Positives = 135/257 (52%), Gaps = 10/257 (3%) Query: 34 EYIITAKKGRNSNVGLIQLNRPKALNALCNGLIVELNQALQAFEEDPAVGAIVLTGGEKV 93 E++ +KGR +G + L+RP+ NAL ++ L AL E V +++ KV Sbjct: 3 EHVKFEQKGR---IGYVILSRPEKRNALNAAMVSGLQAALDRCEAIETVKVVIIKAEGKV 59 Query: 94 FAAGADIKE---MQSLTFQN--CYSGGFLSHWDQLTRVKKPVIAAVNGYALGGGCELAMM 148 F +GAD+++ MQ TF S G + +L K VIA V G+AL GGC L + Sbjct: 60 FCSGADLQDIERMQDNTFDENLADSEGLKKLFLRLYTFPKVVIAQVQGHALAGGCGLVSV 119 Query: 149 CDIIYAGEKAQFGQPEILIGTIPGAGGTQRLTRAVGKSLAMEMVLTGDRISAQDAKQAGL 208 CD YA A+ G E+ IG +P A L R +G+ A E++LTG+ + A AK+ GL Sbjct: 120 CDFAYAVPTAKLGYTEVRIGFVP-AMVLVFLVRKLGEGKAKELLLTGELLVAPAAKEIGL 178 Query: 209 VSKIFPVETVVEEAIQCAEK-IASNSKIVTAMAKESVNAAFEMTLAEGVKLEKKLFYSTF 267 + ++F + + AE+ I+ NS A+ K+ + A ++ L E ++ ++ Sbjct: 179 IQEVFEPAALDGAVQEIAERLISQNSGESMALTKKMIAAVQDLPLEEALEYAARMNAKAR 238 Query: 268 ATEDRKEGMAAFVEKRK 284 TED K G+AAF+ K+K Sbjct: 239 ETEDCKRGIAAFLGKKK 255 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: 176 Number of extensions: 11 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: 258 Length adjustment: 25 Effective length of query: 265 Effective length of database: 233 Effective search space: 61745 Effective search space used: 61745 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