Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate HSERO_RS20645 HSERO_RS20645 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::Q0KEY8 (284 letters) >FitnessBrowser__HerbieS:HSERO_RS20645 Length = 512 Score = 218 bits (555), Expect = 2e-61 Identities = 115/280 (41%), Positives = 171/280 (61%), Gaps = 1/280 (0%) Query: 6 VGIVGAGTMGNGIAQACAVVGLNVVMVDISDAAVQKGVATVASSLDRLIKKEKLTEADKA 65 V ++G+GTMG GIAQ AV G V++ D + A K + + ++LD+L+ K+KLT A Sbjct: 16 VAVIGSGTMGAGIAQVAAVAGHPVLLYDSREGAAGKAIGAICTNLDKLVSKDKLTPALAQ 75 Query: 66 SALARIKGSTSYDDLKATDIVIEAATENYDLKVKILKQIDGIVGENVIIASNTSSISITK 125 +A RI + S ++L D+VIEA E K ++ +++ IV I+A+NTSS+SIT+ Sbjct: 76 AASQRISVAQSLEELHQADLVIEAIVEQLAAKHELFGKLEAIVSTRCILATNTSSLSITQ 135 Query: 126 LAAVTSRADRFIGMHFFNPVPVMALVELIRGLQTSDTTHAAVEALSKQLGKYPITVKNSP 185 +AA +R +GMHFFNPVP+MALVE+I GL + + + GK P+ +++P Sbjct: 136 IAAGLQHPERVVGMHFFNPVPMMALVEIISGLASDAALAQCLHDTALAWGKTPVMARSTP 195 Query: 186 GFVVNRILCPMINEAFCVLGEGLASPEEIDEGMKLGCNHPIGPLALADMIGLDTMLAVME 245 GF+VNR+ P E +L EG A P ID M+ +GP L D+IG D AV + Sbjct: 196 GFIVNRLARPYYAEGLRMLHEGGAQPATIDAVMREAGGFRMGPFELMDLIGHDVNFAVTQ 255 Query: 246 -VLYTEFADPKYRPAMLMREMVAAGYLGRKTGRGVYVYSK 284 V + F DP++ P+++ +E+V AGYLGRK+GRG Y Y + Sbjct: 256 SVFHAYFNDPRFTPSLIQQELVHAGYLGRKSGRGFYRYGE 295 Score = 66.6 bits (161), Expect = 1e-15 Identities = 35/117 (29%), Positives = 65/117 (55%) Query: 153 LIRGLQTSDTTHAAVEALSKQLGKYPITVKNSPGFVVNRILCPMINEAFCVLGEGLASPE 212 L + Q +A V + + G +++ PG +V R +C ++NEA + +G+ + Sbjct: 391 LAKADQCRPQRYAEVAGVLQACGLDLSPMQDVPGMMVMRTVCMLVNEAADAVNQGVCNAA 450 Query: 213 EIDEGMKLGCNHPIGPLALADMIGLDTMLAVMEVLYTEFADPKYRPAMLMREMVAAG 269 + D M+ G N+P GPLA A+ IG+DT+ V+ L + + +YR + L++ + A+G Sbjct: 451 DADMAMRKGVNYPRGPLAWANEIGIDTVNQVLHHLCATYGEDRYRISPLLQRLYASG 507 Lambda K H 0.319 0.134 0.373 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: 335 Number of extensions: 9 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 284 Length of database: 512 Length adjustment: 30 Effective length of query: 254 Effective length of database: 482 Effective search space: 122428 Effective search space used: 122428 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: 50 (23.9 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