Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_041098458.1 SUTH_RS08230 3-oxoacyl-ACP reductase FabG
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000828635.1:WP_041098458.1 Length = 248 Score = 160 bits (404), Expect = 3e-44 Identities = 96/257 (37%), Positives = 148/257 (57%), Gaps = 15/257 (5%) Query: 1 MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLER-ACADLGSSTEVQGYA 59 M LKD+V ++TG G+G ++A +A+ GAK+A++D++ + E+ A A +G+ G A Sbjct: 1 MQLKDRVAIVTGAGQGIGASVAAAYAREGAKVAVVDMNGEAAEKVAAAIVGAGGTAIGVA 60 Query: 60 LDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVIN 119 D++ E V A A + ++G+I++LVNNAGI R ML K M+ +Q+ V+ Sbjct: 61 CDVSSREQVEAMAAKVNAEWGRIDILVNNAGITRTAMLHK---------MTIEQWNQVVG 111 Query: 120 VNLTGTFLCGREAAAAMIESGQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKE 179 V+LTG F C + MIE +I S+ G +GQ NY+A+KAG+ M+ AKE Sbjct: 112 VHLTGAFNCLQAVVGGMIERKYGRIIYVTSAAGVLGTIGQINYSAAKAGILGMTKSTAKE 171 Query: 180 LARYNIRSAAVAPGVIATEMTAAMKPEALERLEKL--VPVGRLGHAEEIASTVRFIIE-- 235 LARYNI + A+APG AT MT ++ + + + L +P+GR EEIA F Sbjct: 172 LARYNITANAIAPGA-ATPMTEVIRTDEKFKDKYLDRIPLGRWAEPEEIAPVFLFFASDA 230 Query: 236 NDYVNGRVFEVDGGIRL 252 + YV G++ DGG+ + Sbjct: 231 SAYVTGQILAADGGMTI 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: 154 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: 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 Apr 09 2024. 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