Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate GFF2263 HP15_2213 3-ketoacyl-(acyl-carrier-protein) reductase
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__Marino:GFF2263 Length = 247 Score = 135 bits (339), Expect = 1e-36 Identities = 86/254 (33%), Positives = 133/254 (52%), Gaps = 14/254 (5%) Query: 1 MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSST-EVQGYA 59 M L+ K ++TG G+G A+A A GA++ + E DL S+ + G Sbjct: 1 MSLEGKTALVTGATRGIGQAIARALAAQGAEVVGTATSEAGAESITNDLQSAGYKGYGMV 60 Query: 60 LDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVIN 119 +++ D + AG + E G +LVNNAGI RD +L++ KD D + SV+ Sbjct: 61 MNVADPASIEAGLKELTEKSGAPLILVNNAGITRDNLLMRLKD---------DDWASVLE 111 Query: 120 VNLTGTFLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWAK 178 NL+ + + M ++ + G I+NISS+ A GN GQ NY A+KAGV + AK Sbjct: 112 TNLSSVYRTSKAVLRGMAKA-KWGRIINISSVVAGMGNAGQGNYCAAKAGVEGFTRSLAK 170 Query: 179 ELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEN-- 236 E++ I + VAPG I T+MT + + + +++P GRLG EE+A+ V F+ + Sbjct: 171 EMSNRGITANCVAPGFIDTDMTKKLDDKQRGAMLEIIPAGRLGEPEEVAAVVAFLASDAA 230 Query: 237 DYVNGRVFEVDGGI 250 YV G V+GG+ Sbjct: 231 GYVTGETINVNGGM 244 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: 179 Number of extensions: 15 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: 247 Length adjustment: 24 Effective length of query: 228 Effective length of database: 223 Effective search space: 50844 Effective search space used: 50844 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 Apr 09 2024. 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