Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate 206645 3-oxoacyl-(acyl-carrier-protein) reductase
Query= uniprot:Q8EGC1 (252 letters) >MicrobesOnline__882:206645 Length = 259 Score = 156 bits (395), Expect = 3e-43 Identities = 96/250 (38%), Positives = 150/250 (60%), Gaps = 21/250 (8%) Query: 9 VITGGAGGLGLAMAHNFAQAGAKLALIDVDQ-DKLERACADL----GSSTEVQGYALDIT 63 ++TGG+ G+G A+A A+AG ++ L V + D+ E A + GS+T + LD++ Sbjct: 21 IVTGGSRGIGKAVAETLARAGLQVFLTYVSKPDEAEAVAAGIRDAGGSAT---AFRLDVS 77 Query: 64 DEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLT 123 D V A F ++D +++VLVNNAGI +DG++++ KD + F+ V++VNL Sbjct: 78 DAAAVAAFFQSEIKDKVRLDVLVNNAGITKDGLIMRMKD---------EDFERVLDVNLC 128 Query: 124 GTFLCGREAAAAMIESGQAGVIVNISSLA-KAGNVGQSNYAASKAGVAAMSVGWAKELAR 182 G F C REA+ M + G I+NI+S+ + GN GQ+NY A+KAG+ ++ AKELA Sbjct: 129 GAFTCLREASKLMTRQ-RLGRIINITSVVGQMGNAGQANYCAAKAGLIGLTKSAAKELAA 187 Query: 183 YNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEN--DYVN 240 N+ AVAPG I T+MTA + E + + +P+ RLG A++IA V F+ Y+ Sbjct: 188 RNVTVNAVAPGFIETDMTAGLPEEVRKAYVEAIPLRRLGSAQDIADAVAFLASERASYIT 247 Query: 241 GRVFEVDGGI 250 G+V V+GG+ Sbjct: 248 GQVLAVNGGM 257 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: 191 Number of extensions: 14 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: 259 Length adjustment: 24 Effective length of query: 228 Effective length of database: 235 Effective search space: 53580 Effective search space used: 53580 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 17 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