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_068462532.1 APY04_RS10945 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_001541235.1:WP_068462532.1 Length = 251 Score = 106 bits (265), Expect = 4e-28 Identities = 81/258 (31%), Positives = 124/258 (48%), Gaps = 20/258 (7%) Query: 8 VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKL---GNNCVFAPAD 64 +K +A++TG A+G+GLAT ERL +GA + D+ +G E A L G + D Sbjct: 4 LKDKIALVTGSAAGIGLATIERLAAEGAHVYVTDVDGAGAEKAAAALVAKGLHATAMTVD 63 Query: 65 VTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMG 124 V+ +DV + + + GR+DV VN AGI V + N+ D+ R+ +VNL G Sbjct: 64 VSRGQDVTALVRAIEQQHGRLDVVVNNAGINVRTDFRNMSDA------DWVRLREVNLDG 117 Query: 125 TFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIAR 184 + R M + + +IN AS+ G AAY A+KG + +T +A Sbjct: 118 MVRIARDTFPLM------KASGKASLINLASIMGHRGMRTLAAYGATKGAMSALTRGLAV 171 Query: 185 DLAPIGIRVMTIAPGLFGTPLLTSL--PEKVCNFLASQVPFPSRLGDPAEYAHLVQ--AI 240 + AP GIRV +APG T L + E L Q P R G + A+ V A Sbjct: 172 EYAPFGIRVNALAPGFIETALTERVLRIEAFSKALLEQTPL-RRFGSGEDVANAVLFFAS 230 Query: 241 IENPFLNGEVIRLDGAIR 258 E+ ++ G + +DG ++ Sbjct: 231 DESAYITGAELAIDGGMQ 248 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: 157 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: 251 Length adjustment: 24 Effective length of query: 237 Effective length of database: 227 Effective search space: 53799 Effective search space used: 53799 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