Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_090275068.1 BLU11_RS15910 3-hydroxyacyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_900105005.1:WP_090275068.1 Length = 697 Score = 123 bits (309), Expect = 9e-33 Identities = 83/200 (41%), Positives = 108/200 (54%), Gaps = 7/200 (3%) Query: 4 ETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAFAA 63 + + ++ Q VA+I +N P +NAL + L + EAD Q+ IVL F A Sbjct: 3 DVVTLERQGAVAVIRVNNPP-VNALGVAVREGLQNSFNAAEADAQVKAIVLVCEGNTFIA 61 Query: 64 GADIKEMAELTYPQI-YLDDFFADADRIATRRKPLIAAVAGYALGGGCELALLCDMIFAA 122 GADIKE + PQ L D + I KP IA + G ALGGG E+AL C A Sbjct: 62 GADIKEFGKP--PQAPSLPDVISG---IEAGSKPSIAVIHGTALGGGLEVALSCHYRIAR 116 Query: 123 DNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVFPA 182 +A+ G PEV LG+LPG GGTQRL R VG AKA+DM ++G + A EA G+V +F Sbjct: 117 KDAKVGLPEVKLGLLPGAGGTQRLPRVVGVAKALDMIVSGTPIGAVEANELGVVDELFDG 176 Query: 183 ESLLEETLKAARVIAEKSLP 202 E L A ++IAE P Sbjct: 177 ELLAAGLTFAEKLIAEGQGP 196 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: 377 Number of extensions: 13 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: 697 Length adjustment: 32 Effective length of query: 225 Effective length of database: 665 Effective search space: 149625 Effective search space used: 149625 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: 50 (23.9 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