Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate RR42_RS21790 RR42_RS21790 short-chain dehydrogenase
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__Cup4G11:RR42_RS21790 Length = 252 Score = 159 bits (401), Expect = 7e-44 Identities = 101/248 (40%), Positives = 143/248 (57%), Gaps = 5/248 (2%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIA--V 61 + GK VL TG ++GIGRA A G A+HGA + + + G A S AE+EA V Sbjct: 1 MAGKVVLNTGGASGIGRAMAHGFARHGARLMLLDLDAQGLA-SAKAELEAAYPEVQVEIV 59 Query: 62 KGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYF 121 K + DP + A FG++D++++NAGI L++ D R ++L G +F Sbjct: 60 KASITDPDAVEQACAATEARFGRIDILLNNAGISMNKPSLELTPDDWRRAIDIDLSGVFF 119 Query: 122 MVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIR 181 QAAA++MVRQG GGSI++ +S+ L + Y KAGV SL +S A ++ IR Sbjct: 120 CTQAAARRMVRQG-GGSILSTASMWGLASSARRLAYCAAKAGVVSLTKSLAAEWAEYNIR 178 Query: 182 CNSVLPGTILTEINKDDLADQE-KREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTG 240 N+V PG T + + LA + E + ARTPL R GAPE++A +FLASD AA++TG Sbjct: 179 VNAVCPGYTSTALMETLLASKAIDGEALLARTPLRRFGAPEEMAEVALFLASDSAAFITG 238 Query: 241 AALLVDGG 248 AL+ DGG Sbjct: 239 HALVSDGG 246 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: 133 Number of extensions: 6 Number of successful extensions: 3 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: 252 Length adjustment: 24 Effective length of query: 230 Effective length of database: 228 Effective search space: 52440 Effective search space used: 52440 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: 46 (22.3 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