Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_017599726.1 D471_RS0116945 NAD(P)-dependent oxidoreductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000341125.1:WP_017599726.1 Length = 244 Score = 127 bits (320), Expect = 2e-34 Identities = 87/254 (34%), Positives = 137/254 (53%), Gaps = 24/254 (9%) Query: 7 VVVITGGAGGLGLAMAHNFAQAGAKLALIDVD--QDKLERACADLGSSTEVQGYALDITD 64 + ++TG A G+G A A + + V Q+ ++R A+ G + V D++D Sbjct: 1 MAIVTGAARGIGAATAERLGXRAVAVLDLKVSDAQEVVDRITAEGGRALAV---GCDVSD 57 Query: 65 EEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLTG 124 + V A + E G +LVNNAG+LRD +L K MS + + +V+NV+L G Sbjct: 58 ADQVAAAVDTVAERLGPPQILVNNAGVLRDNLLFK---------MSVEDWDTVMNVHLRG 108 Query: 125 TFLCGREAAAAMIESGQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKELARYN 184 FL R A A M E + G IVN+SS + GN GQ+NY+A+KAG+ + A EL ++ Sbjct: 109 AFLMSRAAQAHMTEH-KWGRIVNLSSSSAQGNRGQANYSAAKAGLQGFTKTLAIELGKFG 167 Query: 185 IRSAAVAPGVIATEMTAA------MKPEALERLEKL-VPVGRLGHAEEIASTVRFIIEN- 236 + AVAPG + T+MT A + +A++ + +PV R+G +IA+T+ F+ Sbjct: 168 VTCNAVAPGFVETDMTRATAERVGVDYDAMKEFKAAEIPVRRVGEPADIANTIAFLTGEA 227 Query: 237 -DYVNGRVFEVDGG 249 +V+G+V V GG Sbjct: 228 AGFVSGQVIYVAGG 241 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: 141 Number of extensions: 8 Number of successful extensions: 4 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: 244 Length adjustment: 24 Effective length of query: 228 Effective length of database: 220 Effective search space: 50160 Effective search space used: 50160 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: 46 (22.3 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