Align (S)-3-hydroxybutanoyl-CoA dehydrogeanse (EC 1.1.1.35) (characterized)
to candidate H281DRAFT_05521 H281DRAFT_05521 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-19851 (285 letters) >FitnessBrowser__Burk376:H281DRAFT_05521 Length = 283 Score = 324 bits (830), Expect = 2e-93 Identities = 164/278 (58%), Positives = 211/278 (75%) Query: 8 IGVIGAGTMGNGIAQVCAVAGLNVTMLDVDDAALKRGMDTIIRNLDRMVAKEKLTASARD 67 +G+IGAGTMGNGIAQ A+AG++V ++DV AAL G T++ +L R+ +K L + + Sbjct: 6 VGIIGAGTMGNGIAQTVALAGIDVVLIDVSQAALASGFATMVTSLQRLTSKGILEPALSE 65 Query: 68 AALAKISTGLDYGALQSADMVIEAATENLGLKLKILRQVANCVGKDAIIATNTSSISITQ 127 AALA+I +DY +L+ A++VIEAATEN+ LK IL++V V AIIA+NTSSISIT+ Sbjct: 66 AALARIERSMDYASLRDAELVIEAATENVALKRDILKKVEAVVSSGAIIASNTSSISITE 125 Query: 128 LGAVLDAPECFIGIHFFNPVPLMSLLEVIRGVQTSDATHAATMAFAQKVGKAPITVRNSP 187 + A LD P F+G+HFFNPVPL+ L+EVIRG+QT++ + FA+ + K PI+V NSP Sbjct: 126 MAATLDDPSRFVGMHFFNPVPLLPLVEVIRGLQTAEDVANSVEQFARDLNKTPISVNNSP 185 Query: 188 GFVVNRILCPMINEAIFVLQEGLASAEGIDVGMRLGCNHPIGPLALADMIGLDTLLSIMG 247 GFVVNRIL PMINEA FVL EG+ASA ID G++LG NHPIGPL LAD+IGLD LS+M Sbjct: 186 GFVVNRILVPMINEAFFVLAEGVASAAEIDAGLKLGANHPIGPLGLADLIGLDVCLSVMD 245 Query: 248 VLYDEFNDPKYRPALLLKEMVAAGRLGRKTKQGFYSYS 285 VL ++ D KYR + LL+EMVAAGRLGRK+KQG YSYS Sbjct: 246 VLTNDLGDQKYRASPLLREMVAAGRLGRKSKQGVYSYS 283 Lambda K H 0.321 0.137 0.388 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: 265 Number of extensions: 10 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: 285 Length of database: 283 Length adjustment: 26 Effective length of query: 259 Effective length of database: 257 Effective search space: 66563 Effective search space used: 66563 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 (21.9 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