Align crotonase (EC 4.2.1.150) (characterized)
to candidate Ac3H11_2719 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-13469 (259 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2719 Length = 271 Score = 157 bits (396), Expect = 3e-43 Identities = 97/262 (37%), Positives = 146/262 (55%), Gaps = 8/262 (3%) Query: 6 IILEKDGNVASITLNRPKALNAL-NAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAG 64 +++E+DG V + LNRP+ NAL + A + E+ A I D ++ A+++TG G AF AG Sbjct: 10 LLIERDGPVLTARLNRPETRNALTDPAHMDELVALCRQIRADHSIKALVLTGEGSAFCAG 69 Query: 65 ADIAEMKDLTAV-EGRKFSVLGN------KIFRKLENLEKPVIAAINGFALGGGCELSLS 117 ++ +M+ + G + V + +I L L+ PVIAA+NG A+G G +L+ Sbjct: 70 GNVKDMQQRGGIFAGSPYEVRDSYRDTIQRIPLALYELDVPVIAAVNGPAIGAGLDLACM 129 Query: 118 CDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGL 177 CDIRIAS KA F + V +GI PG GG L R IG+ A L +TG I+A +AL GL Sbjct: 130 CDIRIASDKALFAESFVKVGIVPGDGGAWLLPRVIGMPKASLLAFTGDTIDAAKALSWGL 189 Query: 178 VNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFA 237 V V D+LL +A+AL I +N A+R+ K + +G +DT + + Sbjct: 190 VADVFPADQLLGQAQALAQRIALNPSHALRLTKRLLREGQHVRLDTLLELSSAYQALSHH 249 Query: 238 TEDRVEGMTAFVEKRDKAFKNK 259 TED +E + AF++KR F + Sbjct: 250 TEDHLEAVNAFLDKRPAQFTGR 271 Lambda K H 0.318 0.136 0.376 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: 158 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: 259 Length of database: 271 Length adjustment: 25 Effective length of query: 234 Effective length of database: 246 Effective search space: 57564 Effective search space used: 57564 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 (21.7 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