Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_035481637.1 B3C1_RS09380 acetoacetyl-CoA reductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000299915.1:WP_035481637.1 Length = 246 Score = 130 bits (327), Expect = 3e-35 Identities = 87/254 (34%), Positives = 131/254 (51%), Gaps = 22/254 (8%) Query: 4 KDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGY----- 58 K V ++TG GG+G A+ A+ G ++A + + E + QGY Sbjct: 3 KGNVALVTGANGGIGTAICRALAKEGYQVAALCRCPSRAEPWL----EQEKAQGYNPHLV 58 Query: 59 ALDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVI 118 DI D++ + + + + + G IN++VNNAGI RD K RM D + VI Sbjct: 59 IADIKDQDGIFSAVSVVEAELGAINLVVNNAGITRD---------KTLKRMQEDDWLEVI 109 Query: 119 NVNLTGTFLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWA 177 NLTG + R M+E Q G IVNISS+ + G +GQ+NYAA+KAG+ +++ A Sbjct: 110 QTNLTGAYHLCRAVVPLMLER-QYGRIVNISSINGEKGQMGQTNYAAAKAGLHGLTMSLA 168 Query: 178 KELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND 237 +E+A I ++PG IAT+M A+ E + + +PVGRLG EIA V F+ D Sbjct: 169 QEVASKGITVNTISPGYIATDMVMAVPEEIRQSIINQIPVGRLGEPSEIARIVTFLASPD 228 Query: 238 --YVNGRVFEVDGG 249 ++ G +GG Sbjct: 229 AGFITGSNLSANGG 242 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: 162 Number of extensions: 8 Number of successful extensions: 2 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: 246 Length adjustment: 24 Effective length of query: 228 Effective length of database: 222 Effective search space: 50616 Effective search space used: 50616 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