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_026128216.1 D471_RS0129645 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000341125.1:WP_026128216.1 Length = 262 Score = 93.2 bits (230), Expect = 5e-24 Identities = 63/194 (32%), Positives = 96/194 (49%), Gaps = 15/194 (7%) Query: 9 KGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLG---NNCVFAPADV 65 +G ++TG SG+G ATA R++ +G + V D+ +G + K G D+ Sbjct: 5 EGRRVLVTGAGSGIGQATALRVLSEGGAVVAADVSEAGLKDTLDKAGPAAERLGTVVVDI 64 Query: 66 TSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGT 125 E V+ A+ A + G +D VN AGI +S T + + DF +L VNL+GT Sbjct: 65 ADETSVRAAVRSAAAQLGGLDALVNAAGILRSSHT------ERTSAADFTHILRVNLVGT 118 Query: 126 FNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARD 185 F VIR + + G+ ++N +S +A AAY+ASKGG+ MT +A + Sbjct: 119 FLVIREALPHLRE------GRGPAVVNFSSTSAAFAHPYMAAYAASKGGVQSMTHALASE 172 Query: 186 LAPIGIRVMTIAPG 199 A GIR + PG Sbjct: 173 YAADGIRFTAVQPG 186 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: 174 Number of extensions: 9 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: 262 Length adjustment: 25 Effective length of query: 236 Effective length of database: 237 Effective search space: 55932 Effective search space used: 55932 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