Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_008486155.1 B3C1_RS16220 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000299915.1:WP_008486155.1 Length = 249 Score = 161 bits (407), Expect = 1e-44 Identities = 99/248 (39%), Positives = 141/248 (56%), Gaps = 3/248 (1%) Query: 1 MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIA 60 M L GK LVTGAS G+G+A A+G A++GA+V I + +G VA+I ALG +A A Sbjct: 1 MFALNGKRALVTGASRGLGQAMALGLAENGAEV-ICASSREGGCDDTVAKILALGGKARA 59 Query: 61 VKGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAY 120 + D+ D Q Q +A+ G VDV+V+N G A LD P+D + KVNL+ A+ Sbjct: 60 LAADLGDSQAVQALAEQALAA-GPVDVLVNNGGCIYREAALDFPLDAFDAVIKVNLNAAF 118 Query: 121 FMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGI 180 + Q + MV +G G IV ++S+ + GG YT +K + L ++ A G+HGI Sbjct: 119 QLSQLLGRAMVTKG-SGKIVNIASMLSYSGGIRVPAYTASKHAIAGLTKALANEWGQHGI 177 Query: 181 RCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTG 240 + N++ PG T+ + D E+ +E R P GR G P+DL G +VFLAS + YV G Sbjct: 178 QVNAIAPGYFRTDNTQALQDDAERSSEIEKRIPAGRWGNPDDLKGAVVFLASKASDYVNG 237 Query: 241 AALLVDGG 248 L VDGG Sbjct: 238 HILAVDGG 245 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: 132 Number of extensions: 8 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: 249 Length adjustment: 24 Effective length of query: 230 Effective length of database: 225 Effective search space: 51750 Effective search space used: 51750 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 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