Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_026039138.1 RH97_RS13020 SDR family oxidoreductase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000246965.1:WP_026039138.1 Length = 299 Score = 122 bits (305), Expect = 1e-32 Identities = 83/252 (32%), Positives = 128/252 (50%), Gaps = 8/252 (3%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L K +++G GIGRAAA AR+GARV I + D+ A + I A G + Sbjct: 53 LTGKVAVISGGDSGIGRAAALAFAREGARVAIIYLNEDKD---AEWTKQRIEALGSECLP 109 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGI-CPFHSFLDMPRELYLKTVGTNLNGA 121 + AD + ++ E + A + FG V +LVNN + S ++ + L T TN+ Sbjct: 110 IRADLRESEASETVAAQVIRHFGGVSILVNNCAVQFVRQSLTEISDDQLLNTFKTNIFSY 169 Query: 122 YFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYG 181 ++ +A + G +II +S++A G Y+ TK ++SL +S + L P G Sbjct: 170 FYLTRAILPHLTS---GSSIINTASVTAYRGSKTLIDYSATKGAIVSLTRSLSQNLVPQG 226 Query: 182 IRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVT 241 IR NAV PG I T + + +K + +P+ R G+P +LA V+LASD +RY+T Sbjct: 227 IRVNAVAPGPIWTPLIVASFKE-DKVGTFGTDMPMKRPGQPFELAPAYVYLASDDSRYMT 285 Query: 242 GASLLVDGGLFV 253 G L + GG V Sbjct: 286 GQVLHIGGGEMV 297 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: 159 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: 299 Length adjustment: 25 Effective length of query: 231 Effective length of database: 274 Effective search space: 63294 Effective search space used: 63294 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