Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_047093910.1 AAV99_RS08330 3-hydroxybutyrate dehydrogenase
Query= SwissProt::Q1NEI6 (249 letters) >NCBI__GCF_001013305.1:WP_047093910.1 Length = 251 Score = 139 bits (350), Expect = 5e-38 Identities = 95/253 (37%), Positives = 138/253 (54%), Gaps = 23/253 (9%) Query: 10 GRCAIVTGGASGLGKQVAARIIAEGGAVALWDL-NGDALAATQAEIDATHVVA--LDVSD 66 G+ A+VTG SG+G +A + AEG +V + + D +A AEI ATH A +DV + Sbjct: 5 GKRALVTGSTSGIGLAIAKALAAEGASVVINGFGDADEIAGICAEIGATHSGANLMDVGE 64 Query: 67 HAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREV 126 + A A G +DIL+ +AG+ PV EFPV+ + +VI +NL +F+ R Sbjct: 65 IETMMAEA-------GPLDILVNNAGMQHVC-PVEEFPVEKWHQVIALNLTAVFHTTRLA 116 Query: 127 VPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTP 186 VP M E G+GRI+N AS K +P SAY+ASK GV GFTK++ ELA GV AN ++P Sbjct: 117 VPAMREKGWGRIINTASAHSKTASPFKSAYNASKHGVDGFTKTVALELAETGVTANCISP 176 Query: 187 ATFESPILD-QLP---------QSQV--DYMRSKIPMGRLGLVEESAAMVCFMASEECSF 234 +P+++ Q+P + QV D + +K P + VEE A+ F+ E Sbjct: 177 GYVWTPLIEGQIPDTMKARGLTEEQVINDVLLAKQPTKKFVQVEEVGALATFLCRTEMGN 236 Query: 235 TTASTFDTSGGRT 247 T + + GG T Sbjct: 237 VTGANWSIDGGWT 249 Lambda K H 0.318 0.132 0.381 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: 147 Number of extensions: 8 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: 249 Length of database: 251 Length adjustment: 24 Effective length of query: 225 Effective length of database: 227 Effective search space: 51075 Effective search space used: 51075 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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