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_011613843.1 TERY_RS21945 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000014265.1:WP_011613843.1 Length = 252 Score = 76.3 bits (186), Expect = 6e-19 Identities = 72/250 (28%), Positives = 108/250 (43%), Gaps = 14/250 (5%) Query: 12 VAVITGGASGLGLATAERLVGQGASAVLLDLPNS-GGEAQAKKLGNN-CVFAPADVTSEK 69 V +ITG +SG+ AT + L GA +L E K+G + C A++ + Sbjct: 8 VILITGASSGISAATVQTLASAGAKVILHYYHKQLVAETIGDKIGKDKCYLLKANLAEKN 67 Query: 70 DVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVI 129 A +D+ VN AGI V + +++ +Q L VNL+ ++ Sbjct: 68 AAVKLWQEAIAWRNHIDILVNNAGIFVGA---SVEDEMDIWANAWQETLQVNLIAVADLC 124 Query: 130 RLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAA-YSASKGGIVGMTLPIARDLAP 188 R Q G IIN AS AAF G Q Y+ASKGG++ MT IAR A Sbjct: 125 REAIRHF------QTRNGGTIINIASRAAFRGDDPQHIHYAASKGGVISMTRTIARGFAK 178 Query: 189 IGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN--PFL 246 I +APG T + S ++V A++ +L P + A++V + P Sbjct: 179 DNILAYAVAPGFVRTERVESYLQEVGEEFATRDIPLGKLATPEDVANVVAFLASGLAPHT 238 Query: 247 NGEVIRLDGA 256 G I ++GA Sbjct: 239 TGATIDINGA 248 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: 137 Number of extensions: 7 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: 252 Length adjustment: 24 Effective length of query: 237 Effective length of database: 228 Effective search space: 54036 Effective search space used: 54036 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