Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_002721912.1 RSPH17029_RS00050 enoyl-CoA hydratase
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_000015985.1:WP_002721912.1 Length = 258 Score = 335 bits (858), Expect = 7e-97 Identities = 167/258 (64%), Positives = 213/258 (82%), Gaps = 1/258 (0%) Query: 1 MTFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKA 60 M +ETL+V+I++ VALI LNRP ALNALN +++SEL ALG + + ++ CIVLTGS KA Sbjct: 1 MAYETLIVEIEDYVALIRLNRPDALNALNSKMMSELADALGAADRNEKVRCIVLTGSEKA 60 Query: 61 FAAGADIKEMAELTYPQIYLDDFF-ADADRIATRRKPLIAAVAGYALGGGCELALLCDMI 119 FAAGADIKEMAE ++ ++ DFF +D++ + RKP++AAVAGYALGGGCELA++CD I Sbjct: 61 FAAGADIKEMAEQSFVDVFGSDFFTSDSEAMLRVRKPIVAAVAGYALGGGCELAMMCDFI 120 Query: 120 FAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARV 179 AAD A+FGQPE+NLGV+ G+GGTQRLTR VGK+K+MDM LTGR MDAAEAER GLV+RV Sbjct: 121 IAADTAKFGQPEINLGVVAGLGGTQRLTRFVGKSKSMDMHLTGRFMDAAEAERCGLVSRV 180 Query: 180 FPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQ 239 PA++L+EE +KAA I+EKSL M +KE+VNR++ETTL EG+ FERR+FHA+FAT DQ Sbjct: 181 VPAKNLMEEAMKAASKISEKSLLTAMAVKEAVNRSYETTLREGVLFERRLFHALFATEDQ 240 Query: 240 KEGMAAFSEKRKPEFTNR 257 KEGMAAF EKR P+F ++ Sbjct: 241 KEGMAAFLEKRTPQFRDK 258 Lambda K H 0.321 0.135 0.375 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: 218 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: 257 Length of database: 258 Length adjustment: 24 Effective length of query: 233 Effective length of database: 234 Effective search space: 54522 Effective search space used: 54522 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. 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