Align crotonase (EC 4.2.1.150) (characterized)
to candidate RR42_RS03015 RR42_RS03015 enoyl-CoA hydratase
Query= metacyc::MONOMER-13469 (259 letters) >FitnessBrowser__Cup4G11:RR42_RS03015 Length = 265 Score = 167 bits (423), Expect = 2e-46 Identities = 103/255 (40%), Positives = 150/255 (58%), Gaps = 7/255 (2%) Query: 9 EKDGNVASITLNRPKALNALNAAT-LKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADI 67 E+ G++ ++T+N P+ N L T + + AI+ I D +V AVIITG+G AF +G +I Sbjct: 8 EQQGHIVTLTMNEPQRRNPLTGNTAVADFLEAIDRIHRDASVRAVIITGAGTAFSSGGNI 67 Query: 68 AEMK-----DLTAVEGRKFSVLG-NKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIR 121 +M+ + +E R+ LG ++ L NLE PVIAA+NG A+G G +L+ CD+R Sbjct: 68 RDMERQASGQVPGMEIRQDYRLGIQRLPLALFNLEVPVIAAVNGAAMGAGLDLACMCDMR 127 Query: 122 IASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKV 181 IAS +A+F + V LGI PG GG L R IG+ A EL +TG+VI+A +AL LV++V Sbjct: 128 IASEQAQFAESFVKLGIIPGDGGAWLLPRVIGLARAAELTFTGQVIDARQALEWNLVSRV 187 Query: 182 VEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDR 241 V PD+LL A L + I N P AVR+ K + + L +DT + A T D Sbjct: 188 VPPDQLLPTANELAERIAANPPHAVRLAKRLLREALHTRLDTLLELSAGFQALSHQTSDH 247 Query: 242 VEGMTAFVEKRDKAF 256 E ++AF++KR F Sbjct: 248 REAVSAFLDKRKPEF 262 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: 163 Number of extensions: 9 Number of successful extensions: 2 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: 265 Length adjustment: 25 Effective length of query: 234 Effective length of database: 240 Effective search space: 56160 Effective search space used: 56160 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