Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_077275113.1 BW732_RS01410 acetoin reductase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_001998885.1:WP_077275113.1 Length = 258 Score = 137 bits (345), Expect = 2e-37 Identities = 86/254 (33%), Positives = 130/254 (51%), Gaps = 12/254 (4%) Query: 7 KTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKGDVA 66 K +VTG++ G+G+ A A+ G + ++ +S A++ V E + G I V GDV+ Sbjct: 3 KVAVVTGSAGGLGKGIAERLARDGFSIVLHDINSQKLAET-VEEFKTNGFETIGVTGDVS 61 Query: 67 DPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMVQAA 126 + + +AVETFG++DV+V+NAG+ LD+ ++ F +N++G F QAA Sbjct: 62 KKVDQESLITQAVETFGRLDVLVNNAGVDAVTPLLDITEKELQTIFNINVNGTVFGTQAA 121 Query: 127 AQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCNSVL 186 A Q ++QG G I+ SI+ + Y +K V S + A L KH I N+ Sbjct: 122 ATQFIKQGEKGKIINACSIAGHESYDMLGTYCASKHAVRSFTHTAAKELAKHQITVNAYC 181 Query: 187 PGTILTEI-----------NKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMA 235 PG TE+ ++ L E E A L R PED+A + FLASD A Sbjct: 182 PGIAKTEMWDRIDAAMVQHSQGRLKPGESFEQFTAGIALQRYQVPEDVANLVSFLASDEA 241 Query: 236 AYVTGAALLVDGGM 249 Y+TG A+L DGG+ Sbjct: 242 DYITGQAILTDGGL 255 Lambda K H 0.318 0.133 0.379 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: 6 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: 254 Length of database: 258 Length adjustment: 24 Effective length of query: 230 Effective length of database: 234 Effective search space: 53820 Effective search space used: 53820 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 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