Align crotonase (EC 4.2.1.150) (characterized)
to candidate GFF3051 Psest_3109 Enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-13469 (259 letters) >FitnessBrowser__psRCH2:GFF3051 Length = 272 Score = 178 bits (451), Expect = 1e-49 Identities = 106/255 (41%), Positives = 147/255 (57%), Gaps = 2/255 (0%) Query: 6 IILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFVAG 64 + +EK G+ A IT+N P A N + +L + + + DD++YA++I+G G K F AG Sbjct: 19 LTVEKHGHTALITINHPPA-NTWDRESLIGLKQVVEHLNHDDDIYALVISGQGEKFFSAG 77 Query: 65 ADIAEMKDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIAS 124 AD+ D R+ + + F L + IAAINGFALGGG E +L+CD+RIA Sbjct: 78 ADLKLFADGDRNRAREMARRFGEAFEALRDFRGVSIAAINGFALGGGLECALACDLRIAE 137 Query: 125 SKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEP 184 +A+ G PE +G+ P GGTQ LA +G G AK +I G+ I AE ALRIGL+ +VVEP Sbjct: 138 QQAQMGLPEASVGLLPCAGGTQALAWLVGEGWAKRMILCGERITAETALRIGLIEQVVEP 197 Query: 185 DKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDRVEG 244 + A L I +P+AVR K I+ Q T A E E F E F ED +EG Sbjct: 198 GQARGHALLLAARIARQSPVAVRAIKPLIDGARQRLPHTFGAAEREAFVELFEAEDTLEG 257 Query: 245 MTAFVEKRDKAFKNK 259 + AF+EKRD ++N+ Sbjct: 258 VNAFLEKRDPRWRNR 272 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: 182 Number of extensions: 8 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: 272 Length adjustment: 25 Effective length of query: 234 Effective length of database: 247 Effective search space: 57798 Effective search space used: 57798 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