Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_035219698.1 G491_RS0121185 3-oxoacyl-ACP reductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000429905.1:WP_035219698.1 Length = 479 Score = 108 bits (269), Expect = 3e-28 Identities = 87/252 (34%), Positives = 133/252 (52%), Gaps = 27/252 (10%) Query: 6 KVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGS--STEVQGYAL--D 61 K+ ++TG A G+G +A A GA++ ++D ++ DL S + ++ G AL D Sbjct: 240 KIALVTGAARGIGEQIARTMAGEGARVIVMDRPGEE------DLTSKLARKINGSALNCD 293 Query: 62 ITDEEDVVAGFAYILEDFGK--INVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVIN 119 IT + A +I E++GK ++V+V+NAG+ RD ML M D++ V+N Sbjct: 294 ITASDAPKAIKDHIAENYGKKGLDVIVHNAGVTRDKMLAN---------MDADRWNMVMN 344 Query: 120 VNLTGTFLCGREAAAAMIESGQAGVIVNISSLAK-AGNVGQSNYAASKAGVAAMSVGWAK 178 +NL +E M ++G+ IV +SS+A AGNVGQ+NYAASKAGV A Sbjct: 345 INLLALIASTKELLKIMPDNGR---IVCLSSIAGIAGNVGQTNYAASKAGVIGFVEALAP 401 Query: 179 ELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFII--EN 236 +A I AVAPG I T+MTAA+ E +L + + G +++A V F+ + Sbjct: 402 TVADRGITVNAVAPGFIETQMTAAIPFATREAGRRLASLSQGGLPQDVAQVVTFLASPQA 461 Query: 237 DYVNGRVFEVDG 248 V G V + G Sbjct: 462 SGVTGGVLRICG 473 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: 273 Number of extensions: 13 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: 479 Length adjustment: 29 Effective length of query: 223 Effective length of database: 450 Effective search space: 100350 Effective search space used: 100350 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: 49 (23.5 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