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_046010133.1 OLEAN_RS16510 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000967895.1:WP_046010133.1 Length = 253 Score = 257 bits (656), Expect = 2e-73 Identities = 136/254 (53%), Positives = 180/254 (70%), Gaps = 4/254 (1%) Query: 8 VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTS 67 +KG+ AV+TGGASGLG ATA L QGA L D+ +A AK++G V+ DVTS Sbjct: 3 IKGVPAVVTGGASGLGEATARFLASQGAKVALFDVQMDKAQAVAKEIGGIAVYC--DVTS 60 Query: 68 EKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFN 127 + + A+ AK G +AVNCAGI + ++G TL+ F +V+ VNL+G+FN Sbjct: 61 AESAEQAMQTAKEAHGDCGIAVNCAGIGNPGRIIG-REGPM-TLDFFSKVIQVNLIGSFN 118 Query: 128 VIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLA 187 ++RL A +M + + G+RGVII+TASVAAFEGQ+GQAAY+ASKGGIV MTLP AR+LA Sbjct: 119 ILRLAADQMKNRKANDNGERGVIISTASVAAFEGQIGQAAYAASKGGIVAMTLPAARELA 178 Query: 188 PIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLN 247 G+RV+ IAPGLF TP++ S +++ + LAS +PFPSRLG PAE+A LV+ I+ENP LN Sbjct: 179 KFGVRVLAIAPGLFMTPMMESFSQEIQDSLASTLPFPSRLGKPAEFARLVRDIVENPILN 238 Query: 248 GEVIRLDGAIRMQP 261 GEVIR+D A+RM P Sbjct: 239 GEVIRIDSALRMAP 252 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: 212 Number of extensions: 7 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: 253 Length adjustment: 24 Effective length of query: 237 Effective length of database: 229 Effective search space: 54273 Effective search space used: 54273 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