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 Pf1N1B4_5603 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= SwissProt::P0DOW0 (331 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5603 Length = 399 Score = 72.0 bits (175), Expect = 2e-17 Identities = 73/232 (31%), Positives = 95/232 (40%), Gaps = 32/232 (13%) Query: 27 IALRVAGVGICGSELSGYLGHNELRKPPLVMGHEFSGVVEEVGHGVTNVKIGDLVTANPL 86 + LRV ICGS+ G + LV+GHE +G V E G V NV+IGDLV+ Sbjct: 37 VILRVVSTNICGSDQHMVRGRTTAQVG-LVLGHEITGEVIEKGRDVENVQIGDLVSVPFN 95 Query: 87 VTCGRCIHCLRGERQRC---ESRRIIGI-------DFPGAYAERVLVPSNQCYAVK-DAI 135 V CGRC C C R G D+ G AE VLVP +K Sbjct: 96 VACGRCRSCKEQHTGVCLTVNPARPGGAYGYVDMGDWVGGQAEYVLVPYADFNLLKLPDR 155 Query: 136 DGAL--VEPLAC-------AVRAVGLARIKVGDTAVVIGAGIIGLMTVRLLGLSGAKRIA 186 D A+ + L C A + G T + GAG +GL L GA + Sbjct: 156 DKAMEKIRDLTCLSDILPTGYHGAVTAGVGPGSTVYIAGAGPVGLAAAASARLLGAAVVI 215 Query: 187 VVDPNDERL--------KISQLWGATEMAPNLGALLTDNHPQSFDCVIDAVG 230 V D N RL +I+ L T + + +L + DC +DAVG Sbjct: 216 VGDVNPLRLAHAKAQGFEIADLTLDTPLHEQIANMLGE---PEVDCAVDAVG 264 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: 356 Number of extensions: 20 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: 331 Length of database: 399 Length adjustment: 29 Effective length of query: 302 Effective length of database: 370 Effective search space: 111740 Effective search space used: 111740 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 17 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