Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_068003992.1 PsAD2_RS06355 SDR family oxidoreductase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_001623255.1:WP_068003992.1 Length = 263 Score = 162 bits (410), Expect = 7e-45 Identities = 100/253 (39%), Positives = 140/253 (55%), Gaps = 9/253 (3%) Query: 1 MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60 M L K IVTG ++GIG A A+ GA+V+I + G A +L+E FG A Sbjct: 1 MKLDRKVAIVTGGAQGIGYAIAQRFLEDGAKVMISDADERAGEAAQEALSE----FGHVA 56 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 LD +VA ++ FG +DVLVNNAG+ FL + + + + + NL G Sbjct: 57 FCHCDVGVRLDV-RNMVANTLDEFGDIDVLVNNAGVTAAGDFLTLSEDDFDRVLQVNLKG 115 Query: 121 AYFTVQAAARRMKEQ----GRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIA 176 A+ QA AR M E+ G G II +SS+++++ Q YT +K GL L A+A Sbjct: 116 AFLCSQAVARHMVEKIEEGGSAGIIINISSVNSVLAIPEQVPYTVSKGGLNQLTNVSAVA 175 Query: 177 LGPYGIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDM 236 L YGIR N + PG+I TD+ K + D K ++ SR PLGRLG+P ++AG FLASD Sbjct: 176 LAKYGIRVNGIGPGSIETDMLKAVVQDESKMNKVLSRTPLGRLGQPSEIAGVASFLASDD 235 Query: 237 ARYVTGASLLVDG 249 A YV+G ++ DG Sbjct: 236 ASYVSGQTIFADG 248 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: 167 Number of extensions: 7 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: 256 Length of database: 263 Length adjustment: 24 Effective length of query: 232 Effective length of database: 239 Effective search space: 55448 Effective search space used: 55448 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 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