Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_038200760.1 Q392_RS02230 3-oxoacyl-ACP reductase FabG
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000745855.1:WP_038200760.1 Length = 252 Score = 139 bits (351), Expect = 4e-38 Identities = 89/255 (34%), Positives = 137/255 (53%), Gaps = 15/255 (5%) Query: 3 LKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADL-GSSTEVQGYALD 61 L++KV ++TG G+G +A + AK+A++D + + E+ + + + + D Sbjct: 7 LENKVAIVTGAGQGIGAGIARAYGAQAAKVAVVDWNLETAEQVAQSIRDAGGQAAAFKCD 66 Query: 62 ITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVN 121 + D V A A ++ FG ++VLVNNAGI R ML K MS Q+Q VI+V+ Sbjct: 67 VADRAAVDAMVAAVVAKFGPVDVLVNNAGITRTAMLHK---------MSAHQWQQVIDVH 117 Query: 122 LTGTFLCGREAAAAMIESGQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKELA 181 LTG+F C + M+E + +I IS+ G +GQ NY ++KAG+ + A+ELA Sbjct: 118 LTGSFNCLQAVVDGMMERQRGWIINTISTAGILGTIGQINYGSAKAGLIGFTKSAARELA 177 Query: 182 RYNIRSAAVAPGVIATEMTAAMKPEA--LERLEKLVPVGRLGHAEEIASTVRFIIEN--D 237 RYNI VAPG AT MT ++ + +R +P+GR EEIA F+ Sbjct: 178 RYNIIVNCVAPGA-ATPMTETIRTDERFKQRTLDRIPLGRWAEPEEIAPVWVFLASEGAS 236 Query: 238 YVNGRVFEVDGGIRL 252 YV G++ VDGG+ + Sbjct: 237 YVTGQLIGVDGGMSI 251 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: 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: 252 Length of database: 252 Length adjustment: 24 Effective length of query: 228 Effective length of database: 228 Effective search space: 51984 Effective search space used: 51984 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