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_011384506.1 AMB_RS10625 3-oxoacyl-[acyl-carrier-protein] reductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000009985.1:WP_011384506.1 Length = 245 Score = 102 bits (255), Expect = 6e-27 Identities = 77/253 (30%), Positives = 123/253 (48%), Gaps = 17/253 (6%) Query: 10 GLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEK 69 G A++TG + G+G A A+ L +GA+ L +A A +LG PA+++ Sbjct: 6 GKTALVTGASGGIGGAIAKALHARGATVGLHGTRREALDALAAELGERVHVLPANLSDAA 65 Query: 70 DVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVI 129 V+ A+ G VD+ VN AG+ +K ED+Q VLDVNL F + Sbjct: 66 AVEQLAKDAEAAMGSVDILVNNAGLTKDGLVLRMKD------EDWQTVLDVNLTAAFRLS 119 Query: 130 RL-VAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAP 188 R V G+M + + G IIN S+ G GQ Y+ASK G++GM+ +A+++A Sbjct: 120 RAAVKGQMKR-------RWGRIINITSIVGVTGNPGQVNYAASKAGMIGMSKALAQEVAS 172 Query: 189 IGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLV--QAIIENPFL 246 I V +APG + + L ++ L + +P R+G E A V A E ++ Sbjct: 173 RNITVNCVAPGFVSSAMTDVLSDEQKTKLNAGIP-AGRMGTADEIAAAVVYLASAEAAYV 231 Query: 247 NGEVIRLDGAIRM 259 G+ + ++G + M Sbjct: 232 TGQTLHVNGGMAM 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: 156 Number of extensions: 6 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: 245 Length adjustment: 24 Effective length of query: 237 Effective length of database: 221 Effective search space: 52377 Effective search space used: 52377 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