Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_012536362.1 AFE_RS03745 3-oxoacyl-ACP reductase FabG
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000021485.1:WP_012536362.1 Length = 240 Score = 118 bits (295), Expect = 1e-31 Identities = 86/250 (34%), Positives = 133/250 (53%), Gaps = 18/250 (7%) Query: 6 KVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACAD--LGSSTEVQGYALDIT 63 K ++TGG+GG+G A+ A G ++ + + +A AD + + + A D+T Sbjct: 3 KRALVTGGSGGIGAAICKKLAADGLQVIIHTHRNPEKAQALADSIVATGGDATLLAFDVT 62 Query: 64 DEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLT 123 D + A LE G I VLVNNAGI D V +S Q+Q VI+V+L Sbjct: 63 DAQATTAALQDELEA-GPIQVLVNNAGI---------HDDAVFPALSARQWQGVIDVSLN 112 Query: 124 GTFLCGREAAAAMIESGQAGVIVNISSLAK-AGNVGQSNYAASKAGVAAMSVGWAKELAR 182 G F + MI + + G I+NI+S+A GN GQ NY+A+K + A + A E+A Sbjct: 113 GFFHVTQAVLMPMIRT-RWGRIINITSVAALTGNRGQVNYSAAKGALHAATKSLALEVAN 171 Query: 183 YNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND--YVN 240 I AVAPG+IATEM+A P ++ + ++VP+ R G EE+A V F+ Y++ Sbjct: 172 RGITVNAVAPGIIATEMSANAFP--IDAIAQMVPMKRAGRPEEVADLVGFLASEQAAYIS 229 Query: 241 GRVFEVDGGI 250 G++ ++G + Sbjct: 230 GQIISINGAM 239 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: 127 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: 240 Length adjustment: 24 Effective length of query: 228 Effective length of database: 216 Effective search space: 49248 Effective search space used: 49248 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