Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate Ga0059261_2534 Ga0059261_2534 3-hydroxyacyl-CoA dehydrogenase
Query= CharProtDB::CH_091789 (282 letters) >FitnessBrowser__Korea:Ga0059261_2534 Length = 289 Score = 275 bits (703), Expect = 8e-79 Identities = 144/281 (51%), Positives = 185/281 (65%) Query: 1 MKKVCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEA 60 MK V VIGAG MG+GIAQ A G+ V+L D+ ++G I K L++ V+K KI Sbjct: 1 MKTVGVIGAGQMGAGIAQVSAQAGYRVLLSDMDVARAEKGKAGIAKQLARAVEKEKITAK 60 Query: 61 TKVEILTRISGTVDLNMAADCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLS 120 L I + A CDLVIEAA ER +IK+ IFA++ + ILASNTSS+ Sbjct: 61 AADAALANIECVGGTDAFAPCDLVIEAATEREEIKRSIFANVGKVLSDTAILASNTSSIP 120 Query: 121 ITEVASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEVA 180 IT +A A+ P + +G+HFFNP PVM L+E+IRG+ATS T AV+ + K V Sbjct: 121 ITRLAQASPDPARFMGVHFFNPVPVMGLIELIRGLATSDATVAAVEAYGKTLNKRIVHAN 180 Query: 181 EAPGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPLELGDFIGLDICLA 240 +APGF+VNR+L+P++NEA L EG+A++ DID A++LG NHPMGP L DFIGLD CL Sbjct: 181 DAPGFIVNRVLMPLLNEACFALGEGVATIPDIDAAIQLGLNHPMGPFTLADFIGLDTCLE 240 Query: 241 IMDVLYSETGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDYS 281 I VL+ TGD K+RP LL KYV AGW GRK+G+GFYDYS Sbjct: 241 ITRVLFEGTGDPKFRPAPLLVKYVEAGWYGRKTGRGFYDYS 281 Lambda K H 0.319 0.137 0.386 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: 242 Number of extensions: 4 Number of successful extensions: 1 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: 282 Length of database: 289 Length adjustment: 26 Effective length of query: 256 Effective length of database: 263 Effective search space: 67328 Effective search space used: 67328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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