Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_083769281.1 AFER_RS05300 hypothetical protein
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_000023265.1:WP_083769281.1 Length = 277 Score = 117 bits (294), Expect = 2e-31 Identities = 84/252 (33%), Positives = 126/252 (50%), Gaps = 8/252 (3%) Query: 6 IILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGA 65 ++LE+ V +TLN NAL+ A L + A+ + + D++V A++IT +G F AGA Sbjct: 23 LLLERRDGVVRMTLNDVARRNALSPALLDALHGALREGSSDEDVRAMVITNAGSVFCAGA 82 Query: 66 DIAEMKDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASS 125 D+A VL +E KPVI I G A GGG L+ +CDI IASS Sbjct: 83 DLAAAGTSAGDHATLADVL-----LAIEESPKPVIGRIGGHAFGGGLGLAAACDISIASS 137 Query: 126 KAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPD 185 +A+FG EV LG+ P L + + A EL T + A A+ GL+ + VEP Sbjct: 138 EARFGFTEVRLGVAPAIISVVCLPK-LRRSDALELFLTAERFEATRAVASGLITRAVEPA 196 Query: 186 KLLEEAKALVDAIIVNAPIAVRMCK-AAINQGLQCDIDTGVAYEAEVFGECFATEDRVEG 244 +L E ++ A++ AP A+ + K A+ + + A E+ FA + EG Sbjct: 197 RLDAEVDEVIAAVLRGAPGALAVAKRLALGHDREASREAYAAM-TELSQALFAGAEAAEG 255 Query: 245 MTAFVEKRDKAF 256 + AF E+R A+ Sbjct: 256 IAAFRERRAAAW 267 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: 146 Number of extensions: 12 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: 259 Length of database: 277 Length adjustment: 25 Effective length of query: 234 Effective length of database: 252 Effective search space: 58968 Effective search space used: 58968 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 24 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