Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_011842438.1 RSPH17029_RS17935 L-idonate 5-dehydrogenase
Query= SwissProt::P0DOW0 (331 letters) >NCBI__GCF_000015985.1:WP_011842438.1 Length = 345 Score = 123 bits (309), Expect = 6e-33 Identities = 102/305 (33%), Positives = 147/305 (48%), Gaps = 18/305 (5%) Query: 1 MKTLTWTAKETMSILSAPAPVPEPGWIALRVAGVGICGSELSGYLGH----NELRKPPLV 56 M+ A +SI P + G + L +A GICGS+L Y H N + + P++ Sbjct: 1 MRACVIRAARDLSIEPWAEPALQAGEVRLDLAWGGICGSDLH-YFQHGRVANSILREPMI 59 Query: 57 MGHEFSGVVEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIG--IDFP 114 +GHEFSG + EVG GV +K G V NP CG C C G C S R +G FP Sbjct: 60 LGHEFSGRIREVGPGVQWLKPGMAVAVNPSRPCGSCDQCSAGLTHLCRSMRFMGSAAHFP 119 Query: 115 ---GAYAERVLVPSNQCYAVKDAID---GALVEPLACAVRAVGLARIKVGDTAVVIGAGI 168 G +AER +V ++QC A+ + +D AL EP A A+ AV LA+I G + +V GAG Sbjct: 120 HTHGGFAERPVVLASQCVALPETVDLALAALSEPYAVALHAVELAQIAAGASVLVTGAGT 179 Query: 169 IGLMTVRLLGLSGAKRIAVVDPNDERL-KISQLWGA-TEMAPNLGAL-LTDNHPQSFDCV 225 IG + +GA R+ V D + L ++ ++ GA T + + A + D V Sbjct: 180 IGSLVAVAARQAGAGRLIVTDIAEPALARVRKVTGAETHLVGDPEATRAAEAAIGEVDVV 239 Query: 226 IDAVGLSTTRRDSLNALIRGGRAVWIGL--HEALTHLDGNQIVRDELEVRGSFCYTDDEF 283 ++A G+S ++ + GR V +G EA L G I L F DE Sbjct: 240 LEASGVSAALDMAIRCIRPRGRIVQVGFLPPEARLSLAGLLIREATLVGAYRFLGEFDEA 299 Query: 284 IRAVS 288 +R +S Sbjct: 300 VRQIS 304 Lambda K H 0.322 0.139 0.424 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: 270 Number of extensions: 17 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: 331 Length of database: 345 Length adjustment: 28 Effective length of query: 303 Effective length of database: 317 Effective search space: 96051 Effective search space used: 96051 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 (21.9 bits) S2: 49 (23.5 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