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_017601550.1 D471_RS0127265 3-oxoacyl-ACP reductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000341125.1:WP_017601550.1 Length = 254 Score = 115 bits (289), Expect = 7e-31 Identities = 91/258 (35%), Positives = 127/258 (49%), Gaps = 27/258 (10%) Query: 10 GLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEK 69 G VAVITG SG+G ATA RL +GA V +D+ GG+ A+ G +F DVT E+ Sbjct: 6 GRVAVITGAGSGIGRATALRLAEEGARIVAVDVDEEGGKRVAEDTGG--LFVRTDVTDEE 63 Query: 70 DVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVI 129 V+ A A A+ +G VDVA N AGI+ L G ++ ++RV +VNL + Sbjct: 64 QVREAFATARSAYGSVDVAFNNAGISPPDDDSILTTG----MDAWRRVQEVNLTSVYLCC 119 Query: 130 RLVAGEMGQNEPDQGGQRGVIINTAS-VAAFEGQVGQAAYSASKGGIVGMTLPIARDLAP 188 + M + RG I+NTAS VA Q +Y+ASKGG++ ++ + A Sbjct: 120 KYALPHMRERG------RGSIVNTASFVATMGAATSQISYTASKGGVLALSRELGVQFAR 173 Query: 189 IGIRVMTIAPGLFGTPLLTSL----PEKVCNFLASQVPFPSRLGDPAEYAHLVQAII--- 241 GIRV ++PG TPLL L PE+ L VP LG AE + A+ Sbjct: 174 EGIRVNALSPGPVNTPLLQELFAKDPERAQRRLV-HVP----LGRFAEVTEIAAAVAFLA 228 Query: 242 --ENPFLNGEVIRLDGAI 257 + F+ +DG I Sbjct: 229 SDDASFITASNFLVDGGI 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: 155 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: 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