Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_090448096.1 BLS63_RS22805 3-oxoacyl-ACP reductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_900100495.1:WP_090448096.1 Length = 248 Score = 140 bits (353), Expect = 2e-38 Identities = 86/252 (34%), Positives = 139/252 (55%), Gaps = 15/252 (5%) Query: 6 KVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYAL--DIT 63 ++ ++TGG GG+G A++ + G + + Q + A + + + + DIT Sbjct: 6 RIALVTGGMGGIGTAISRRLHRDGFIVVVGCSTQSTRQAAWLEQQGQDGYEFHCMSCDIT 65 Query: 64 DEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLT 123 D +D GFA + E+ G+I+VLVNNAGI RD RM+ + +VI NL Sbjct: 66 DWDDTCRGFAQVREEVGQIDVLVNNAGITRDSTF---------KRMTPADWNAVIATNLN 116 Query: 124 GTFLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWAKELAR 182 G F ++ +M+E G I+NISS+ + G GQ+NY+A+KAG+ ++ A+E+A Sbjct: 117 GLFNTSKQVLDSMVERSW-GRIINISSVNGQRGQFGQTNYSAAKAGIHGFTMALAREVAS 175 Query: 183 YNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFII--ENDYVN 240 + ++PG I TEMTA ++ + +E++ +P GRLG EEIAS V ++ E Y Sbjct: 176 KGVTVNTISPGYIRTEMTAVIREDVMEKIVAGIPAGRLGQPEEIASMVAWLAGEEAAYAT 235 Query: 241 GRVFEVDGGIRL 252 G F V+GG+ + Sbjct: 236 GADFSVNGGLNM 247 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: 166 Number of extensions: 11 Number of successful extensions: 2 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: 248 Length adjustment: 24 Effective length of query: 228 Effective length of database: 224 Effective search space: 51072 Effective search space used: 51072 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