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_110207257.1 DNK54_RS12225 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_003194585.1:WP_110207257.1 Length = 254 Score = 287 bits (735), Expect = 1e-82 Identities = 152/250 (60%), Positives = 185/250 (74%), Gaps = 3/250 (1%) Query: 12 VAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDV 71 VA++TGGASGLG AT E L+ +G AV+LDLP GE AK+LG+ F PADV SE+DV Sbjct: 7 VALVTGGASGLGRATVEALLAKGGRAVILDLPGGAGETTAKELGDAVRFVPADVRSEEDV 66 Query: 72 QTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRL 131 + A+A A + G + V VNCAG A KT + + + + FQR++++NL+GTFNVIRL Sbjct: 67 KAAIAAAS-ELGELRVVVNCAGTGDAIKTVG-RGNEPYPYDKFQRIIEINLLGTFNVIRL 124 Query: 132 VAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGI 191 A M + G +RGVI+NTASVAAF+GQ+GQAAYSASKGG+VGMTLPIARDL+ +GI Sbjct: 125 TAAHMAGLDL-LGEERGVIVNTASVAAFDGQIGQAAYSASKGGVVGMTLPIARDLSTLGI 183 Query: 192 RVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVI 251 RV+TIAPGLF TPLL SLPE+ L QVP PSRLGDPAEY L ++ENP LNGE I Sbjct: 184 RVVTIAPGLFDTPLLASLPEEARRSLGQQVPHPSRLGDPAEYGALAAHVVENPMLNGETI 243 Query: 252 RLDGAIRMQP 261 RLDGAIRM P Sbjct: 244 RLDGAIRMAP 253 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: 264 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