Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate RR42_RS16375 RR42_RS16375 short-chain dehydrogenase
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__Cup4G11:RR42_RS16375 Length = 257 Score = 149 bits (375), Expect = 7e-41 Identities = 98/256 (38%), Positives = 135/256 (52%), Gaps = 11/256 (4%) Query: 1 MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAI----NYAHSDGPAQSCVAEIEALGQ 56 M+ LEGK+VLVTGAS+GIGRA A+ + GA + + G + V +E G Sbjct: 1 MRRLEGKSVLVTGASSGIGRAIALRFGREGARLVLADITETVREGGVPTADVLRLE--GH 58 Query: 57 RAIAVKGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNL 116 ++ DVA A VA AV +G++DV+V++A I + +D R VNL Sbjct: 59 EVEFIRTDVAQESDADAAVAHAVRRYGRLDVLVNDAAISAGKPLTETTIDEWNRVMAVNL 118 Query: 117 HGAYFMVQAAAQQMVRQG----HGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTA 172 G + M +AA M++Q G IV VSS +V Y +KAGV L + A Sbjct: 119 TGVFLMSRAAVSAMLKQEVCREARGRIVNVSSQHGMVCAPRNVAYGTSKAGVVYLTRQIA 178 Query: 173 IALGKHGIRCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLAS 232 + GI CN+V PG I+T A EY EARTP+ RLG P+D+A +FLAS Sbjct: 179 VDYADQGIICNAVAPGKIVTG-KAGPAASAAALEYSEARTPMPRLGRPDDVASAALFLAS 237 Query: 233 DMAAYVTGAALLVDGG 248 D A ++TG L++DGG Sbjct: 238 DEATFITGENLMIDGG 253 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: 139 Number of extensions: 7 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: 257 Length adjustment: 24 Effective length of query: 230 Effective length of database: 233 Effective search space: 53590 Effective search space used: 53590 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