Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_110804536.1 C8J30_RS04555 enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_003217355.1:WP_110804536.1 Length = 258 Score = 210 bits (535), Expect = 2e-59 Identities = 116/259 (44%), Positives = 162/259 (62%), Gaps = 1/259 (0%) Query: 1 MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60 M ++T+ + E + I LNRP+ LNALN++LL EL A+ ++DP +R ++TG KA Sbjct: 1 MSYQTLIVEIEDGVALIRLNRPEALNALNSQLLGELAEALKTLDADPAVRCFVLTGSDKA 60 Query: 61 FCAGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDI 120 F AGADI + + + + G E D I KP IA + GYALGGG ELA+ CD Sbjct: 61 FAAGADIKEMADKSFTDMFLQDFFGTE-GDAILRTRKPIIAAVAGYALGGGCELAMMCDF 119 Query: 121 RIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNR 180 + AE A+ G PEINLG+ G GGTQRLTR +GK +++EM +TG + +AE+ GLV+R Sbjct: 120 ILCAENAKFGQPEINLGVVAGIGGTQRLTRFVGKSKSMEMHLTGRFMDAAEAERSGLVSR 179 Query: 181 VVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTED 240 V+PLA+L E A KIA KS I+ + K+ VNR ++ L G+ E + +F+TED Sbjct: 180 VLPLADLVPEALTTARKIAAKSAIATMVAKDCVNRAYETTLREGVLYERRVFHALFATED 239 Query: 241 KKEGVSAFLEKREPTFKGK 259 +KEG++AF EKR F K Sbjct: 240 QKEGMAAFTEKRPAKFTDK 258 Lambda K H 0.315 0.135 0.382 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: 161 Number of extensions: 5 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: 258 Length adjustment: 24 Effective length of query: 235 Effective length of database: 234 Effective search space: 54990 Effective search space used: 54990 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: 42 (22.0 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