Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_012404884.1 BPHY_RS28295 3-hydroxybutyryl-CoA dehydrogenase
Query= BRENDA::Q0KEY8 (284 letters) >NCBI__GCF_000020045.1:WP_012404884.1 Length = 288 Score = 357 bits (916), Expect = e-103 Identities = 179/280 (63%), Positives = 223/280 (79%) Query: 3 IRTVGIVGAGTMGNGIAQACAVVGLNVVMVDISDAAVQKGVATVASSLDRLIKKEKLTEA 62 I T+GIVGAGTMGNGIAQ AV GL VV++D++DAA+ KGVAT+ SL +L++K K+ A Sbjct: 5 IETIGIVGAGTMGNGIAQVAAVAGLKVVLIDVTDAALSKGVATLTGSLAKLVEKGKVEAA 64 Query: 63 DKASALARIKGSTSYDDLKATDIVIEAATENYDLKVKILKQIDGIVGENVIIASNTSSIS 122 + +AL RI+ ST Y L + DIV+EAATEN +LKV+ILKQI+ +V ++ I+ASNTSSIS Sbjct: 65 ARDAALTRIETSTDYQRLASADIVVEAATENAELKVRILKQIESVVSDDTIVASNTSSIS 124 Query: 123 ITKLAAVTSRADRFIGMHFFNPVPVMALVELIRGLQTSDTTHAAVEALSKQLGKYPITVK 182 IT LAA R +RF+GMHFFNPVP++ LVE+IRG+QTSD T AV L+++LGK P++VK Sbjct: 125 ITALAATIGRPERFVGMHFFNPVPLLPLVEVIRGVQTSDDTATAVRELTERLGKTPVSVK 184 Query: 183 NSPGFVVNRILCPMINEAFCVLGEGLASPEEIDEGMKLGCNHPIGPLALADMIGLDTMLA 242 N+PGFVVNRIL PMINEAF +L EG A+ EEID GM+LG NHPIGPLALAD+IGLD L+ Sbjct: 185 NAPGFVVNRILVPMINEAFFLLAEGTATAEEIDAGMRLGANHPIGPLALADLIGLDVCLS 244 Query: 243 VMEVLYTEFADPKYRPAMLMREMVAAGYLGRKTGRGVYVY 282 VM+V +F D KYR L+RE+VAAG LGRKTG GVY Y Sbjct: 245 VMDVFLKDFGDSKYRACPLLRELVAAGRLGRKTGHGVYRY 284 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: 254 Number of extensions: 7 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: 284 Length of database: 288 Length adjustment: 26 Effective length of query: 258 Effective length of database: 262 Effective search space: 67596 Effective search space used: 67596 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 24 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