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_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_002117405.1:WP_085770280.1 Length = 246 Score = 110 bits (274), Expect = 4e-29 Identities = 83/252 (32%), Positives = 117/252 (46%), Gaps = 15/252 (5%) Query: 10 GLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEK 69 G A++TG +SGLGLA A L GA+ L E A +L P +++ Sbjct: 6 GKTALVTGASSGLGLAIARTLHQAGATVGLSGTRREALETLAGELKERAHILPCNLSDRA 65 Query: 70 DVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVI 129 + + A+G G VD+ VN AGI +K ED+ VL VNL F + Sbjct: 66 ETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKD------EDWDAVLAVNLTAAFRLS 119 Query: 130 RLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPI 189 R V M + + G IIN SVA G GQA YSA+K G+ GMT +A ++A Sbjct: 120 RAVLRGMMRK------RHGRIINITSVAGAVGNPGQANYSAAKAGLTGMTKSLANEVASR 173 Query: 190 GIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEY--AHLVQAIIENPFLN 247 G+ V +APG+ +P+ L E L +P R G E A L A E F+ Sbjct: 174 GVTVNCVAPGVIESPMTQVLNEAQRERLLKLIPM-ERFGSADEIGAAVLYLASDEAAFIT 232 Query: 248 GEVIRLDGAIRM 259 G+ + ++G + M Sbjct: 233 GQTLHINGGMAM 244 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: 134 Number of extensions: 5 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: 246 Length adjustment: 24 Effective length of query: 237 Effective length of database: 222 Effective search space: 52614 Effective search space used: 52614 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 Apr 09 2024. 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