Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_010632153.1 RH97_RS09595 SDR family oxidoreductase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000246965.1:WP_010632153.1 Length = 314 Score = 139 bits (351), Expect = 5e-38 Identities = 86/246 (34%), Positives = 134/246 (54%), Gaps = 5/246 (2%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 L GK L+TG +GIG A AI A+ GADVAI+Y A A IE LGQR+I + G Sbjct: 68 LTGKVALITGGDSGIGAAVAIAFAKEGADVAISYLDEHEDANRTKARIEQLGQRSILLPG 127 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNAGI-CPFHAFLDMPVDVVERTFKVNLHGAYFM 122 DV D V + +++FG++D++V++ GI + LD+ + + TFKVN++ ++ Sbjct: 128 DVRDKIQCISIVEQTIQSFGRLDILVNHVGIQFQQPSLLDITDEQFDDTFKVNIYSHFYT 187 Query: 123 VQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRC 182 + A + G SI+ SS++A G YT TKA + ++ A L GIR Sbjct: 188 TRTALPYL---KPGSSIINTSSVTAFKGPSQLIDYTSTKAAIIGFTRALANNLIDKGIRV 244 Query: 183 NSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAA 242 N+V PG+ T + + ++ + + P+ R+ P +LA V+LASD + +VTG Sbjct: 245 NAVAPGSTWTPLQPSTYS-ADQVAILGSGNPMRRMAQPFELAPAYVYLASDDSRFVTGQT 303 Query: 243 LLVDGG 248 + V+GG Sbjct: 304 IHVNGG 309 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: 152 Number of extensions: 6 Number of successful extensions: 4 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: 314 Length adjustment: 26 Effective length of query: 228 Effective length of database: 288 Effective search space: 65664 Effective search space used: 65664 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