Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_011020528.1 MA_RS02500 NAD(P)-dependent oxidoreductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000007345.1:WP_011020528.1 Length = 258 Score = 115 bits (287), Expect = 1e-30 Identities = 80/252 (31%), Positives = 124/252 (49%), Gaps = 12/252 (4%) Query: 2 DLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTE-VQGYAL 60 + + KV ++TG G G ++A GA +AL+ L+ C + SS + + Sbjct: 11 EFEGKVAIVTGAGTGNGESIAERLYAGGASVALVSRHIAPLDDICNRIDSSGKRTFPIEV 70 Query: 61 DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINV 120 D+ D V + I+E FGKI++ VNNAGI + + ++ VI Sbjct: 71 DVRDPHSVQIAVSSIIERFGKIDIAVNNAGITGPA-------NTPLQDLDIEIWRDVIET 123 Query: 121 NLTGTFLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWAKE 179 +LTG F C + AM+++G +G IVN+SS G G + Y +K GV ++ A E Sbjct: 124 DLTGVFYCMKYEIPAMLKNG-SGAIVNMSSANGLVGLAGMAAYTTAKHGVIGLTRSAALE 182 Query: 180 LARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEN--D 237 LA NIR AVAPG +AT EA++ + P+ RL EE+A V +++ Sbjct: 183 LAESNIRVCAVAPGYVATPRIIDSGKEAMDYMAAAHPMKRLATREEVADLVAYLLSERAA 242 Query: 238 YVNGRVFEVDGG 249 ++ G V +DGG Sbjct: 243 FITGSVHCIDGG 254 Lambda K H 0.317 0.134 0.369 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: 146 Number of extensions: 8 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: 252 Length of database: 258 Length adjustment: 24 Effective length of query: 228 Effective length of database: 234 Effective search space: 53352 Effective search space used: 53352 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