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 Dsui_2228 Dsui_2228 Zn-dependent alcohol dehydrogenase
Query= SwissProt::P0DOW0 (331 letters) >FitnessBrowser__PS:Dsui_2228 Length = 340 Score = 97.1 bits (240), Expect = 6e-25 Identities = 87/289 (30%), Positives = 127/289 (43%), Gaps = 18/289 (6%) Query: 20 PVPE--PGWIALRVAGVGICGSELSGYLGHNELRKP-PLVMGHEFSGVVEEVGHGVTNVK 76 PVPE PG + ++V G+C ++L G ++ P + GHE G V VG GVT+VK Sbjct: 23 PVPEVPPGQVLVKVVASGVCHTDLHAADGDWPVKPSLPFIPGHEGVGYVAAVGAGVTHVK 82 Query: 77 IGDLVTANPLVT-CGRCIHCLRGERQRCESRRIIGIDFPGAYAERVLVPSNQCYAVKDAI 135 GD V L T CG C HC+ G C+S+++ G G YAE VL + D + Sbjct: 83 EGDRVGVPWLHTACGHCEHCITGWETLCDSQQMTGYTVNGGYAEYVLADPGYVGKLPDTL 142 Query: 136 DGALVEPLACA----VRAVGLARIKVGDTAVVIGAGIIGLMTVRLLGLSGAKRIAVVDPN 191 + A P+ CA + + + K GD + G G +G M V+ G IA VD Sbjct: 143 EFAPAAPVLCAGVTVYKGLKVLECKPGDWVAISGIGGLGHMAVQYAKAMGFHVIA-VDVA 201 Query: 192 DERLKISQLWGATEMAPNLGALLTDNHPQSFDCVIDAVGLSTTR------RDSLNALIRG 245 DE+L +++ GA L A D + + A G+ T +L L + Sbjct: 202 DEKLALAKTLGAD---VTLNAARVDPVAEIQKQIKGAHGILVTAVSRSAFGQALGMLHKR 258 Query: 246 GRAVWIGLHEALTHLDGNQIVRDELEVRGSFCYTDDEFIRAVSLINSQK 294 G +GL L +V + VRGS T + A++ K Sbjct: 259 GTMSLVGLPPGDFGLPIFDVVLNAKTVRGSIVGTRKDLEEALAFAGEGK 307 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: 322 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 331 Length of database: 340 Length adjustment: 28 Effective length of query: 303 Effective length of database: 312 Effective search space: 94536 Effective search space used: 94536 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