Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_024981780.1 BXU11_RS13235 3-oxoacyl-[acyl-carrier-protein] reductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_002017945.1:WP_024981780.1 Length = 248 Score = 132 bits (332), Expect = 7e-36 Identities = 89/255 (34%), Positives = 136/255 (53%), Gaps = 19/255 (7%) Query: 3 LKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACA---DLGS-STEVQGY 58 L+ KV +ITG + G+G +A FA+ GA +A +E A A +L + + +GY Sbjct: 4 LEGKVAIITGASRGIGKGIAEVFAKHGANIAF--TYSSSVESALALENELNTMGIKAKGY 61 Query: 59 ALDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVI 118 + D + +L DFG +++L+NNAGI +D +++ RMS F VI Sbjct: 62 QSNAADFNEAQTFVDAVLADFGSVDILINNAGITKDNLMM---------RMSEADFDQVI 112 Query: 119 NVNLTGTFLCGREAAAAMIESGQAGVIVNISSLAKA-GNVGQSNYAASKAGVAAMSVGWA 177 +VNL F + ++ +AG I+N+SS+ GN GQ+NYAASKAGV S A Sbjct: 113 DVNLKSVFNMTKAIQKTFLKQ-RAGSIINMSSVVGVKGNAGQTNYAASKAGVIGFSKSVA 171 Query: 178 KELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIE-- 235 EL NIR +APG I TEMTA + + ++ + +P+ R G +++A+ F Sbjct: 172 LELGSRNIRCNVIAPGFIETEMTAKLSDDVVKGWREGIPLKRGGSTDDVANACLFFASDM 231 Query: 236 NDYVNGRVFEVDGGI 250 + YV G+V V GG+ Sbjct: 232 SAYVTGQVLNVCGGM 246 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: 12 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 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