Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate AO356_29995 AO356_29995 3-hydroxybutyryl-CoA dehydrogenase
Query= BRENDA::Q0KEY8 (284 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29995 Length = 282 Score = 302 bits (774), Expect = 5e-87 Identities = 157/283 (55%), Positives = 204/283 (72%), Gaps = 1/283 (0%) Query: 1 MSIRTVGIVGAGTMGNGIAQACAVVGLNVVMVDISDAAVQKGVATVASSLDRLIKKEKLT 60 M+++ + ++GAGTMG+GIAQ CA G ++++DI + A+ +G+ V +LDR ++K L Sbjct: 1 MTLQHIAVIGAGTMGSGIAQTCAAAGHTLLLIDIHEQALGRGLQIVQKNLDRQVEKGTLL 60 Query: 61 EADKASALARIKGSTSYDDLKATDIVIEAATENYDLKVKILKQIDGIVGENVIIASNTSS 120 A L RI ST Y DL D+VIEAATE+ LK KIL+Q+D + +IASNTSS Sbjct: 61 PAQAIETLQRIHTSTHYTDLDQMDVVIEAATEDLLLKRKILQQVDTHARLDCLIASNTSS 120 Query: 121 ISITKLAAVTSRADRFIGMHFFNPVPVMALVELIRGLQTSDTTHAAVEALSKQLGKYPIT 180 +SIT+LAA +RF+G+HFFNPVP+M LVELIRGLQTSD T + AL +QLGK I Sbjct: 121 LSITQLAASIKHPERFMGIHFFNPVPIMGLVELIRGLQTSDATCSTAGALIEQLGKTAIH 180 Query: 181 VKNSPGFVVNRILCPMINEAFCVLGEGLASPEEIDEGMKLGCNHPIGPLALADMIGLDTM 240 +N PGF+VNRIL PMINEA VL E + ID M+LGCN PIGPLALAD+IGLDT+ Sbjct: 181 TQNRPGFMVNRILIPMINEAIFVLQEN-GDAQAIDASMRLGCNQPIGPLALADLIGLDTV 239 Query: 241 LAVMEVLYTEFADPKYRPAMLMREMVAAGYLGRKTGRGVYVYS 283 L +++ L T F DPKYRPA L++EMVAAG LG+K+GRG +VY+ Sbjct: 240 LGILDNLQTGFGDPKYRPAPLLKEMVAAGLLGKKSGRGFHVYN 282 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: 244 Number of extensions: 4 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: 284 Length of database: 282 Length adjustment: 26 Effective length of query: 258 Effective length of database: 256 Effective search space: 66048 Effective search space used: 66048 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 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