Align crotonase (EC 4.2.1.150) (characterized)
to candidate Pf1N1B4_267 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-13469 (259 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_267 Length = 263 Score = 108 bits (270), Expect = 1e-28 Identities = 79/251 (31%), Positives = 114/251 (45%), Gaps = 3/251 (1%) Query: 9 EKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADIA 68 E+ G+V I L+R NA + L E+ A + D ++ G G+ F AG D+ Sbjct: 12 ERHGHVLMIGLDRVAKRNAFDLNLLNELSLAYGEFEADSEARVAVVFGHGEHFTAGLDLV 71 Query: 69 EMKDLTAVEGRKFSVLGNKIFRKLEN--LEKPVIAAINGFALGGGCELSLSCDIRIASSK 126 A EG + G + L + KPVI A G+ L G EL L+ DI + +S Sbjct: 72 SAGAALA-EGWQAPPGGCDPWGVLAGPRVSKPVIVAAQGYCLTVGIELMLAADINLCASN 130 Query: 127 AKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDK 186 +F Q EV GI P G T RL + G G A + TG +A +AL +GLV +V+ + Sbjct: 131 TRFAQKEVQRGIFPFGGATLRLHQVAGWGNAMRWLLTGDEFDAHDALHLGLVQEVMASED 190 Query: 187 LLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDRVEGMT 246 LL A L + I AP+ V+ + Q T + +ED EG+ Sbjct: 191 LLPRAIELAERIARQAPLGVQATLMSARQARYEGEMTAAQALPALVKNLLNSEDAKEGVR 250 Query: 247 AFVEKRDKAFK 257 + +EKR FK Sbjct: 251 SMIEKRPGVFK 261 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: 133 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: 263 Length adjustment: 25 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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