Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_013074532.1 BTUS_RS02380 3-oxoacyl-[acyl-carrier-protein] reductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000092905.1:WP_013074532.1 Length = 245 Score = 191 bits (485), Expect = 1e-53 Identities = 112/255 (43%), Positives = 154/255 (60%), Gaps = 13/255 (5%) Query: 1 MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYAL 60 M +KDKVVVITGGA G+G A A F + GA++ D D + +L S V Y + Sbjct: 1 MRVKDKVVVITGGARGIGKATAEKFLEEGARVVFCDRDAEAGRETLEELRSLGPVSFYPV 60 Query: 61 DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINV 120 D+T EED++ ++E +++VL+NNAGI DG+L K + + + V+ V Sbjct: 61 DVTAEEDILDFIGKVVEVHDRVDVLINNAGITMDGLLTKLAE---------EAWHKVLAV 111 Query: 121 NLTGTFLCGREAAAAMIESGQAGVIVNISSLAKA-GNVGQSNYAASKAGVAAMSVGWAKE 179 NLTG FLC + A MIE G+ GVI+N SS+ GN GQ+NYAA+KAGV ++ WAKE Sbjct: 112 NLTGVFLCTKAVAPFMIERGR-GVILNASSVVGLYGNFGQTNYAATKAGVIGLTRTWAKE 170 Query: 180 LARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND-- 237 L IR AVAPG IAT+MTA + + LER+ + P+ LG E+IAS F+ ++ Sbjct: 171 LGPKGIRVNAVAPGFIATDMTAKVPEKILERMREQTPLRTLGRPEDIASAYLFLASDEAR 230 Query: 238 YVNGRVFEVDGGIRL 252 Y+NG V VDGG+ L Sbjct: 231 YINGAVLSVDGGLVL 245 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: 176 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: 245 Length adjustment: 24 Effective length of query: 228 Effective length of database: 221 Effective search space: 50388 Effective search space used: 50388 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