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_017617176.1 CDO52_RS11130 3-oxoacyl-ACP reductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_002263495.1:WP_017617176.1 Length = 254 Score = 127 bits (319), Expect = 2e-34 Identities = 96/256 (37%), Positives = 133/256 (51%), Gaps = 21/256 (8%) Query: 9 KGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSE 68 +G VAVITG SG+G ATA RL +G + V +DL GEA AK+ G ++ ADVT E Sbjct: 5 EGRVAVITGAGSGIGKATALRLASEGGTVVAVDLDRDAGEAVAKETGG--LYIAADVTDE 62 Query: 69 KDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNV 128 + V+ A A K +GRVDVA N AGI+ L G +E +++V +VNL + Sbjct: 63 EAVKAAFAEVKEVYGRVDVAFNNAGISPPDDDSILDTG----IEAWRKVQEVNLTSVYLC 118 Query: 129 IRLVAGEMGQNEPDQGGQRGVIINTAS-VAAFEGQVGQAAYSASKGGIVGMTLPIARDLA 187 + M +QG +G I+NTAS VA Q +Y+ASKGG++ M+ + A Sbjct: 119 CKYALPYM----REQG--KGAIVNTASFVATMGAATSQISYTASKGGVLAMSRELGVQFA 172 Query: 188 PIGIRVMTIAPGLFGTPLLTSL----PEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN 243 G+RV ++PG TPLL L PE+ L VPF R +P E A V + + Sbjct: 173 RDGVRVNALSPGPVNTPLLKELFAKDPERAQRRLV-HVPF-GRFAEPEEIASAVAFLASD 230 Query: 244 --PFLNGEVIRLDGAI 257 F+ +DG I Sbjct: 231 DASFITASNFLVDGGI 246 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: 173 Number of extensions: 11 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: 254 Length adjustment: 24 Effective length of query: 237 Effective length of database: 230 Effective search space: 54510 Effective search space used: 54510 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