Align L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized)
to candidate WP_013722205.1 ALIDE2_RS12490 KR domain-containing protein
Query= SwissProt::Q9HK58 (254 letters) >NCBI__GCF_000204645.1:WP_013722205.1 Length = 253 Score = 118 bits (295), Expect = 1e-31 Identities = 74/243 (30%), Positives = 129/243 (53%), Gaps = 5/243 (2%) Query: 6 GKNAVITGGSRGIGRAIALGLAKQGANILISYASHDSEADEVLETASKYGVKAHKVKVDQ 65 GK A++TG RGIG A A LA+ GA + ++ A ++E + G + + +D Sbjct: 12 GKRALVTGAGRGIGLAAAAALAQAGAAVTLA-ARSENELRDACGRLRGEGGQCDYMVLDV 70 Query: 66 SDPYESIRFAEKAIETFGKVHILVDNAGICPFEDFFRISVDLFEKVWKVNVESHYFITQR 125 +D R ++ + G H+LV+NAG+ + ++ + + V +NV++ +++T+ Sbjct: 71 TDS----RAVDEQLAGQGAFHVLVNNAGMNRPKPLAQLQDEDIDAVLDLNVKAAFYVTRA 126 Query: 126 IAKNMIENKINGRILLISSISAHVGGEFQTHYTTTKSALNGFMHSIAIVLGKYGILVNSL 185 + + M I G ++ +SS HVG +T Y +K A+ G ++A LG GI VN++ Sbjct: 127 VTRRMAAEGIRGSVINVSSQMGHVGSLRRTLYCASKHAVEGMSKALAWELGAAGIRVNTV 186 Query: 186 EPGTILTDINKEDLSNQEKRAYMERRTVVGRLGLPEDMVAPALFLLSDDNTYVTGTELLA 245 P I TD+ R ++ R +GRLG E+++ +FL SD ++ +TG+ LL Sbjct: 187 CPTFIETDMTAAMFQEPGFRQWVTERIALGRLGRMEELMGAFVFLASDASSLMTGSALLL 246 Query: 246 DGG 248 DGG Sbjct: 247 DGG 249 Lambda K H 0.318 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: 140 Number of extensions: 7 Number of successful extensions: 2 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: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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 (21.7 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