Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate GFF2305 PS417_11755 diacetyl reductase
Query= metacyc::MONOMER-11802 (255 letters) >FitnessBrowser__WCS417:GFF2305 Length = 259 Score = 94.7 bits (234), Expect = 2e-24 Identities = 82/265 (30%), Positives = 126/265 (47%), Gaps = 24/265 (9%) Query: 1 MHIANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARE---LGDNARFAV 57 M I K +V+GA G+G A A L + GA + LVD+N +EA A E LG A V Sbjct: 1 MAITGKVALVTGAGQGIGRAIALRLAQDGADIALVDINGARLEAVASEVVALGRQASVFV 60 Query: 58 ADISDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIG 117 AD+S + +AV+ A G +VN AG+ + +L + P + + + +N+ G Sbjct: 61 ADVSKREQVVAAVEHAHQTLGGFDIIVNNAGVAQIDSLL-EVSPEQVE---RTLGINVQG 116 Query: 118 SFNLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAAR 177 L + AA A + G+ IIN SIA ++G Y+A+K A+ +LT AA+ Sbjct: 117 V--LWGIQAAGKKFKALKQKGK---IINACSIAGHEGFALLGVYSATKFAVRALTQAAAK 171 Query: 178 ELARFGIRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPPR-------LGR---PQEYA 227 ELA GI V PG+ T M + + A V + LGR P++ A Sbjct: 172 ELASAGITVNAYCPGVVGTDMWVEIDKRMAEITGADVGATYKKYVDGIALGRAETPEDVA 231 Query: 228 ALARHII--ENSMLNGEVIRLDGAL 250 L ++ ++ + G+ +DG L Sbjct: 232 GLVSYLAGPDSDYMTGQSPLIDGGL 256 Lambda K H 0.318 0.131 0.358 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: 121 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: 255 Length of database: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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