Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_037577639.1 BS73_RS30360 SDR family oxidoreductase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000744815.1:WP_037577639.1 Length = 251 Score = 143 bits (360), Expect = 4e-39 Identities = 102/251 (40%), Positives = 134/251 (53%), Gaps = 14/251 (5%) Query: 6 KTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAF---GGTAIA 62 + IVTGASRGIGRA A AR G VV+ + RA A + AE + A G A+A Sbjct: 11 RLAIVTGASRGIGRAVAERLARDGTAVVVDY------RADAGAAAETVDAVHRAGARALA 64 Query: 63 VGADAADLDSGEKLVAAAVEAFGS-VDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGA 121 V AD D+ L AA FG D+LV NAG+ F + D+ Y TN A Sbjct: 65 VPADVTSPDAPAVLFDAAERHFGRPADILVCNAGVARFGALADLSDADYDLVFDTNTRSA 124 Query: 122 YFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYG 181 + + A+RR+ + GG I+ +SS +A+ A Y +KA +LMQS A LGP G Sbjct: 125 FRLFREASRRLPD---GGRIVLMSSGAAVSRRAGSGIYAASKAAADALMQSLAKELGPRG 181 Query: 182 IRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVT 241 I N+VLPG + T+ E ER+ + PLGRLGEP D+A + FL SD AR++T Sbjct: 182 ITVNSVLPGAVRTEALAAR-GRPEVLERILADTPLGRLGEPGDIAEVVAFLTSDAARWLT 240 Query: 242 GASLLVDGGLF 252 G +L GG F Sbjct: 241 GQTLHASGGEF 251 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: 169 Number of extensions: 12 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: 251 Length adjustment: 24 Effective length of query: 232 Effective length of database: 227 Effective search space: 52664 Effective search space used: 52664 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