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_012968735.1 KVAR_RS18790 short chain dehydrogenase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000025465.1:WP_012968735.1 Length = 261 Score = 115 bits (287), Expect = 1e-30 Identities = 80/213 (37%), Positives = 115/213 (53%), Gaps = 19/213 (8%) Query: 7 SVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQA----KKLGNNCVFAP 62 +++G VA +TG SG+G A L GA V DL + GG A+ + +G Sbjct: 12 NLQGRVAFVTGAGSGIGQTIACSLASAGARVVCFDLRDDGGLAETVSHIESIGGQACSYT 71 Query: 63 ADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNL 122 DV D++ A+ALAK +FGR+D+AVN AGIA A+ +K E +QRV+D+NL Sbjct: 72 GDVRQIADLRAAVALAKNRFGRLDIAVNAAGIANANPALEMKS------EQWQRVIDINL 125 Query: 123 MGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVG--QAAYSASKGGIVGMTL 180 G +N + A M + GG G IIN AS++ G QA Y+ SK G++ ++ Sbjct: 126 TGVWNSCKAEAELM----LESGG--GSIINIASMSGIIVNRGLDQAHYNCSKAGVIHLSK 179 Query: 181 PIARDLAPIGIRVMTIAPGLFGTPLLTSLPEKV 213 +A + GIRV +I+PG TP+ T PE V Sbjct: 180 SLAMEWVGKGIRVNSISPGYTATPMNTR-PEMV 211 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: 159 Number of extensions: 9 Number of successful extensions: 3 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: 261 Length adjustment: 25 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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 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