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 PfGW456L13_2522 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2522 Length = 248 Score = 117 bits (294), Expect = 2e-31 Identities = 88/248 (35%), Positives = 123/248 (49%), Gaps = 24/248 (9%) Query: 12 VAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDV 71 VAV+TGGASG+GLA R +GA + LD+ G A A G +F DV E V Sbjct: 8 VAVVTGGASGIGLACVRRFSAEGAQVIGLDI----GSAPADFPG---LFMTLDVRDEAQV 60 Query: 72 QTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRL 131 Q + +FGR+DV VN AG+A T ++QRV+D+NL G+ + Sbjct: 61 QQVMQEVISRFGRIDVLVNAAGVADQGSVTQT------TTANWQRVMDINLTGSMLTSKY 114 Query: 132 VAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGI 191 M + + G IIN S+ +G G AY+ SKGGI +T +A D I Sbjct: 115 ALASMVEQ------RNGSIINVGSIFGLQGCDGNVAYNVSKGGINQLTRSMAIDYGYANI 168 Query: 192 RVMTIAPGLFGTPLLTSLPEKVC--NFLASQVPFPSRLGDPAEYAH--LVQAIIENPFLN 247 RV + PGL TP+ + + + F ASQ +R G P E A+ L A E F++ Sbjct: 169 RVNGLCPGLIETPMTSMVRDNDAFHAFFASQ-HMLNRSGQPEEVANVALFLASDEASFVS 227 Query: 248 GEVIRLDG 255 G++I +DG Sbjct: 228 GQMIAVDG 235 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: 158 Number of extensions: 12 Number of successful extensions: 4 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: 248 Length adjustment: 24 Effective length of query: 237 Effective length of database: 224 Effective search space: 53088 Effective search space used: 53088 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 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