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 AZOBR_RS29790 AZOBR_RS29790 3-ketoacyl-ACP reductase
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__azobra:AZOBR_RS29790 Length = 250 Score = 125 bits (315), Expect = 7e-34 Identities = 89/257 (34%), Positives = 131/257 (50%), Gaps = 20/257 (7%) Query: 6 RSVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADV 65 + + G VA+ITG A GLGLA AE V +G ++D+ +A A++LG + + A+V Sbjct: 3 KRLDGKVALITGAAQGLGLAMAETFVREGGRVAVVDINGDAAKAVAERLGESAIGIAANV 62 Query: 66 TSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGT 125 T DV+ +A KFGR+D+ VN AG A+ + + T E+F RV +N+ Sbjct: 63 TRMADVEMTIAATVEKFGRLDILVNNAGSTHANGPF-----ENVTEEEFDRVFALNVKSI 117 Query: 126 FNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARD 185 + + V M + + GVI+N S A + G Y+A+KG + +T +A + Sbjct: 118 YLYSKAVVATM------RAQKSGVILNLGSTAGLRPRPGLVWYNATKGAVHNITKSLALE 171 Query: 186 LAPIGIRVMTIAPGLFGTPLLTSL-----PEKVCNFLASQVPFPSRLGDPAEYAH--LVQ 238 LAP IRV +AP TPLL + PEK + VP RLG P + A+ L Sbjct: 172 LAPDNIRVCALAPVATETPLLATFMGGDTPEKRARMMGI-VPL-GRLGQPTDVANAALYL 229 Query: 239 AIIENPFLNGEVIRLDG 255 A E FL G V+ +DG Sbjct: 230 ASDEAAFLTGVVLEIDG 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: 175 Number of extensions: 7 Number of successful extensions: 2 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: 250 Length adjustment: 24 Effective length of query: 237 Effective length of database: 226 Effective search space: 53562 Effective search space used: 53562 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