Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_011840637.1 RSPH17029_RS04240 glucose 1-dehydrogenase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000015985.1:WP_011840637.1 Length = 254 Score = 152 bits (383), Expect = 8e-42 Identities = 101/252 (40%), Positives = 143/252 (56%), Gaps = 17/252 (6%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALS-LAEEIAAFGGTAI 61 L + +VTGASRG+G+A A A GA +V+ AGAL A I A G A+ Sbjct: 11 LTGRRAMVTGASRGLGQAIALGLAEAGADLVLTARA-----AGALEETAARIRALGREAL 65 Query: 62 AVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAG---ICPFHSFLDMPRELYLKTVGTNL 118 + D +D S VAA +EA G +D+LVNNAG +CP + + EL+ + + TNL Sbjct: 66 CLALDQSDPAS----VAAPMEAAGRIDILVNNAGTEEVCPSEA---VTPELWDRILDTNL 118 Query: 119 NGAYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALG 178 GA+F QAAAR M +G+G +I+ + S+++ VG Y +K+GLL + ++ A Sbjct: 119 RGAFFVTQAAARGMLARGQG-SIVNLCSLTSFVGVPTAVPYGSSKSGLLGMTRALAAEWA 177 Query: 179 PYGIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMAR 238 P G+R NA+ PG T + + + + + M +R+P GR GE DL G VFLASD + Sbjct: 178 PRGVRVNAMAPGYFRTALTEVFYQNEDWAQAMQARIPQGRFGEGRDLVGAAVFLASDASA 237 Query: 239 YVTGASLLVDGG 250 YVTG L VDGG Sbjct: 238 YVTGQCLGVDGG 249 Lambda K H 0.319 0.136 0.383 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: 160 Number of extensions: 10 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: 256 Length of database: 254 Length adjustment: 24 Effective length of query: 232 Effective length of database: 230 Effective search space: 53360 Effective search space used: 53360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. 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