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 351439 BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__Btheta:351439 Length = 259 Score = 120 bits (301), Expect = 3e-32 Identities = 77/249 (30%), Positives = 125/249 (50%), Gaps = 9/249 (3%) Query: 7 RYAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLN---GDALAA--TQAEIDATHVVA 61 R+ + ++TG A G+G+ RI++EGG V + DL+ D LAA TQA D + Sbjct: 3 RFENKVVVITGAAGGIGEATTRRIVSEGGKVVIADLSQERADKLAAELTQAGADVRPIY- 61 Query: 62 LDVSDHAAVAAAAKDSAAALGKVDILICSAGITGAT--VPVWEFPVDSFQRVIDINLNGL 119 ++ + + G++D+LI + G T + + + +D F V +NL Sbjct: 62 FSATELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLDIDYFDEVFHLNLCCT 121 Query: 120 FYCNREVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGV 179 Y +++V+P M +G G IVN+AS++G + N + Y ASKAGVI TK + ++ K + Sbjct: 122 MYLSQQVIPIMTTHGGGNIVNVASISGLTADANGTLYGASKAGVINLTKYIATQMGKKNI 181 Query: 180 IANALTPATFESP-ILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTAS 238 NA+ P +P LD L + + + LG E+ AA + F+AS + + T Sbjct: 182 RCNAVAPGLVLTPAALDNLNEEVRNIFLGQCATPYLGEPEDVAATIAFLASNDARYITGQ 241 Query: 239 TFDTSGGRT 247 T GG T Sbjct: 242 TIVVDGGLT 250 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: 177 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: 259 Length adjustment: 24 Effective length of query: 225 Effective length of database: 235 Effective search space: 52875 Effective search space used: 52875 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: 47 (22.7 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