Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_013459741.1 SULKU_RS04455 KR domain-containing protein
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000183725.1:WP_013459741.1 Length = 232 Score = 74.7 bits (182), Expect = 2e-18 Identities = 61/186 (32%), Positives = 90/186 (48%), Gaps = 21/186 (11%) Query: 14 VITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQT 73 VITG A G+GL TA + + LD + E +K+ G + D++ + ++ Sbjct: 5 VITGAAQGIGLGTARLFASRNWRVIGLDCNENLLEKASKETGFEPILC--DLSDPQQIEK 62 Query: 74 ALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLVA 133 A +DV VN A I+ + +T L ++ RVL VNL F + RL+A Sbjct: 63 AAE----SIHTLDVLVNNAAISANTDP------KTLLLSEWNRVLGVNLTAPFLLSRLLA 112 Query: 134 GEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRV 193 + + +G I+N AS A + AYSASKGGI+ +T +A LAP IRV Sbjct: 113 DKFESS-------KGSIVNIASTRALMSEPHTEAYSASKGGILSLTHALAMSLAP--IRV 163 Query: 194 MTIAPG 199 I+PG Sbjct: 164 NAISPG 169 Lambda K H 0.318 0.135 0.385 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: 125 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: 261 Length of database: 232 Length adjustment: 24 Effective length of query: 237 Effective length of database: 208 Effective search space: 49296 Effective search space used: 49296 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: 46 (22.3 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