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_058930114.1 AU252_RS07090 SDR family NAD(P)-dependent oxidoreductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_001484605.1:WP_058930114.1 Length = 269 Score = 257 bits (657), Expect = 2e-73 Identities = 148/269 (55%), Positives = 183/269 (68%), Gaps = 18/269 (6%) Query: 8 VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKL-----------GN 56 V G VA+ITGGASGLG ATA+RL GAS VL+DLP+S G A A +L G Sbjct: 3 VLGTVALITGGASGLGAATAKRLFDAGASVVLIDLPSSAGPAYAAELNASALNAAGGSGA 62 Query: 57 NCVFAPADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQR 116 VFAPADVT+E +VQ A+ A G + + VNCAG+A K L + L+ F R Sbjct: 63 RAVFAPADVTNEAEVQAAVDTAVA-LGPLRIVVNCAGVATPGKM--LGRDGVLPLDTFNR 119 Query: 117 VLDVNLMGTFNVIRLVAGEMGQNEP---DQGG-QRGVIINTASVAAFEGQVGQAAYSASK 172 V+ VNL+GTFNV+RL A M EP D GG +RGV+INTASVAAF+GQ+GQ AY+ASK Sbjct: 120 VVQVNLVGTFNVLRLAAASMVSTEPVSTDLGGAERGVMINTASVAAFDGQIGQPAYAASK 179 Query: 173 GGIVGMTLPIARDLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAE 232 G + MTLP+AR+LA +RV+TIAPG+F TP++ +L ++ L QVP PSRLG PAE Sbjct: 180 GAVAAMTLPLARELARSLVRVVTIAPGIFETPMMATLSDEAQASLGQQVPHPSRLGRPAE 239 Query: 233 YAHLVQAIIENPFLNGEVIRLDGAIRMQP 261 YA+LV I+EN +NGE IRLDGAIRM P Sbjct: 240 YANLVAHIVENAMINGETIRLDGAIRMGP 268 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: 217 Number of extensions: 7 Number of successful extensions: 5 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: 269 Length adjustment: 25 Effective length of query: 236 Effective length of database: 244 Effective search space: 57584 Effective search space used: 57584 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 Apr 09 2024. 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