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_029601857.1 C447_RS12510 zinc-dependent alcohol dehydrogenase family protein
Query= SwissProt::P0DOW0 (331 letters) >NCBI__GCF_000336675.1:WP_029601857.1 Length = 349 Score = 102 bits (255), Expect = 1e-26 Identities = 81/269 (30%), Positives = 126/269 (46%), Gaps = 17/269 (6%) Query: 1 MKTLTWTAKETMSILSAPAP-VPEPGWIALRVAGVGICGSELSGYLGHNELRKPPLVMGH 59 M+T T+ K + I P P V +R+ ICGS+L Y G + + + GH Sbjct: 1 MQTATYHGKGDVRIEERPDPEVKNATDAVVRITHTAICGSDLWYYRGQRDHPENSPI-GH 59 Query: 60 EFSGVVEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGIDFPGAYAE 119 E G+VE+VG V +V+ GD V A ++CG C C +G C + G D GA E Sbjct: 60 EPMGIVEDVGDAVRHVEPGDRVLAPFTISCGSCEFCRKGLTTSCVNGSSWGGDESGAQGE 119 Query: 120 RVLVP--SNQCYAVKDAIDG---------ALVEPLACAVRAVGLARIKVGDTAVVIGAGI 168 ++ VP V D L + + A A + GDTAVVIG G Sbjct: 120 KIRVPHAGGTLVRVPDRYKDNEKTLEALLPLTDVMCTGHHAAVSAGVDTGDTAVVIGDGA 179 Query: 169 IGLMTVRLLGLSGAKRIAVVDPNDERLKISQLWGATEMAPNLG-ALLTDNHPQSF---DC 224 +GL V GA+RI + +++RL+I++ +GATE+ G +T+ Q++ D Sbjct: 180 VGLCGVLASKRRGAERIIAMGHHEDRLEIAESFGATEIISARGEQAITEARDQTYGGADH 239 Query: 225 VIDAVGLSTTRRDSLNALIRGGRAVWIGL 253 V++ VG ++ + GG ++G+ Sbjct: 240 VLECVGTESSMETAAAVARPGGSVGYVGV 268 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: 327 Number of extensions: 28 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: 331 Length of database: 349 Length adjustment: 28 Effective length of query: 303 Effective length of database: 321 Effective search space: 97263 Effective search space used: 97263 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 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