Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_086008421.1 MVAN_RS09935 3-oxoacyl-ACP reductase FabG
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000015305.1:WP_086008421.1 Length = 250 Score = 164 bits (415), Expect = 2e-45 Identities = 101/253 (39%), Positives = 144/253 (56%), Gaps = 13/253 (5%) Query: 3 LKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYALDI 62 L + VITGGA GLG A+A F + GA++ L DV+ D A LG + D+ Sbjct: 8 LTGQTAVITGGAQGLGFAIAQRFVEEGARVVLGDVNLDATVAAAEKLGGEDVARAVRCDV 67 Query: 63 TDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNL 122 TD +V A A ++ FG ++++VNNAGI RD + K M+ +QF VI V+L Sbjct: 68 TDSAEVDALIAAAVDGFGSLDIMVNNAGITRDATMRK---------MTEEQFDQVIAVHL 118 Query: 123 TGTFLCGREAAAAMIESGQAGVIVNISSLA-KAGNVGQSNYAASKAGVAAMSVGWAKELA 181 GT+ G AAAA++ + G IVN+SS++ K G VGQ+NY+A+KAG+ M+ +KELA Sbjct: 119 KGTWN-GLRAAAAVMREQKRGAIVNMSSISGKVGMVGQTNYSAAKAGIVGMTKAASKELA 177 Query: 182 RYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIE--NDYV 239 +R A+ PG+I + MT AM + VP+GR G EE+A+ F+ + Y+ Sbjct: 178 YLGVRVNAIQPGLIRSAMTEAMPQRIWDSKVAEVPMGRAGEPEEVANVALFLASDLSSYM 237 Query: 240 NGRVFEVDGGIRL 252 G V EV GG L Sbjct: 238 TGTVLEVTGGRHL 250 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: 159 Number of extensions: 9 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: 250 Length adjustment: 24 Effective length of query: 228 Effective length of database: 226 Effective search space: 51528 Effective search space used: 51528 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