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 8502394 DvMF_3100 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__Miya:8502394 Length = 247 Score = 144 bits (363), Expect = 2e-39 Identities = 92/238 (38%), Positives = 129/238 (54%), Gaps = 6/238 (2%) Query: 13 AIVTGGASGLGKQVAARIIAEGGAVALWDLN----GDALAA-TQAEIDATHVVALDVSDH 67 A+VTGG+ G+GK VA + EG V L ++ +A+AA A + LDVSD Sbjct: 8 ALVTGGSRGIGKAVAETLAREGFQVYLTYVSKPEEAEAVAAGINAAGGSARAFRLDVSDA 67 Query: 68 AAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVV 127 AAVAA ++ +D+L+ +AGIT + + D F RV+D+NL+G F C RE Sbjct: 68 AAVAAFFQEEIREKVTLDVLVNNAGITKDGL-ILRMKDDDFDRVLDVNLSGAFTCLREAA 126 Query: 128 PFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPA 187 M GRIVN+ SV G+ GN YSA+KAG+IG TKS KELAG+ V NA+ P Sbjct: 127 KLMTRQRKGRIVNITSVVGQMGNAGQVNYSAAKAGLIGMTKSAAKELAGRNVTVNAVAPG 186 Query: 188 TFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGG 245 E+ + +L IP+ RLG ++ A V F+AS++ + T +GG Sbjct: 187 FIETDMTAKLTDEVRAAYIEAIPLRRLGQPQDIADAVAFLASDKAGYITGQVIAVNGG 244 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: 159 Number of extensions: 7 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: 247 Length adjustment: 24 Effective length of query: 225 Effective length of database: 223 Effective search space: 50175 Effective search space used: 50175 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 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