Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate BPHYT_RS27640 BPHYT_RS27640 acetoacetyl-CoA reductase
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__BFirm:BPHYT_RS27640 Length = 248 Score = 133 bits (335), Expect = 3e-36 Identities = 85/253 (33%), Positives = 138/253 (54%), Gaps = 16/253 (6%) Query: 6 KVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACA--DLGSSTEVQGYALDIT 63 +V ITGG GGLG A++ AG +A+ +++ + + Y D+T Sbjct: 5 RVAFITGGMGGLGAAVSRRLHDAGMVVAMSHSERNDHVATWLMHERDAGRRFHAYEADVT 64 Query: 64 DEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLT 123 + A +L++FG ++VLVNNAGI RD K MS D + +V+ +L Sbjct: 65 SFDSCAHCAARVLDEFGSVDVLVNNAGIARDSTFAK---------MSKDDWDAVLRTDLD 115 Query: 124 GTFLCGREAAAAMIESGQAGVIVNISSLAKA-GNVGQSNYAASKAGVAAMSVGWAKELAR 182 F + +M+ + G IVNI+S+ A G GQ+NYAA+KAG+ ++ A E+A+ Sbjct: 116 SMFNMTKPLLGSMVAQ-RFGRIVNIASVNGARGAFGQTNYAAAKAGIHGFTMSLALEVAK 174 Query: 183 YNIRSAAVAPGVIATEMTAAMKPEALE-RLEKLVPVGRLGHAEEIASTVRFIIEND--YV 239 + + V+PG +AT MTAA+ E +E ++ +PVGRLG +E+A+ V F+ +D +V Sbjct: 175 HGVTVNTVSPGYLATAMTAAVPKEVMETKILPQIPVGRLGQPDEVAALVAFLCSDDAAFV 234 Query: 240 NGRVFEVDGGIRL 252 G F ++GG+ + Sbjct: 235 TGANFAINGGMHM 247 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: 155 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 17 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