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 BWI76_RS23705 BWI76_RS23705 3-oxoacyl-ACP reductase
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Koxy:BWI76_RS23705 Length = 244 Score = 118 bits (296), Expect = 1e-31 Identities = 83/250 (33%), Positives = 127/250 (50%), Gaps = 20/250 (8%) Query: 13 AVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKL---GNNCVFAPADVTSEK 69 A++TG A G+G A+ L +GA ++ D ++ GEA A L G +F ++ + Sbjct: 8 AIVTGAARGIGFGIAQVLAREGARVIIADR-DAHGEAAAASLRESGAQALFISCNIGDKA 66 Query: 70 DVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVI 129 V+ + A+ FG VD+ VN AGI + + L + D+ V+DVNL GTF + Sbjct: 67 QVEALFSQAEEAFGAVDIVVNNAGINRDAMLHKLSEA------DWDTVIDVNLKGTFLCM 120 Query: 130 RLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPI 189 + A M + G IIN AS A++ G VGQ YSASK G+VGMT R+LA Sbjct: 121 QQAAIRMRERGA------GRIINIAS-ASWLGNVGQTNYSASKAGVVGMTKTACRELAKK 173 Query: 190 GIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN--PFLN 247 G+ V I PG T + +PE V + +++P G+ + V + + ++N Sbjct: 174 GVTVNAICPGFIDTDMTRGVPENVWQIMINKIP-AGYAGEAKDVGECVAFLASDGARYIN 232 Query: 248 GEVIRLDGAI 257 GEVI + G + Sbjct: 233 GEVINVGGGM 242 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: 154 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: 244 Length adjustment: 24 Effective length of query: 237 Effective length of database: 220 Effective search space: 52140 Effective search space used: 52140 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 Sep 17 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