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 GFF2310 Psest_2358 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__psRCH2:GFF2310 Length = 252 Score = 121 bits (304), Expect = 1e-32 Identities = 83/247 (33%), Positives = 124/247 (50%), Gaps = 12/247 (4%) Query: 7 RYAGRCAIVTGGASGLGKQVAARIIAEGGAVAL-----WDLNGDALAATQAEIDATHVVA 61 R+AG+ A++TG A+G+G+ A + AEG V + DL + A + Sbjct: 5 RFAGQTALITGAATGIGRATALALAAEGARVWINHRDQHDLANQLVEQITANGGDAWAIE 64 Query: 62 LDVSDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFY 121 DVSD AAVAA ++ A G +D+L+ +AG+ P E + V+ ++L G++ Sbjct: 65 ADVSDPAAVAAMF-ETIEAQGSLDLLVNNAGVI-LEKPFLETSEADWAMVLGVDLGGVYR 122 Query: 122 CNREVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIA 181 C R + M G IVN+AS G G AY +KAGVIG T+SL +E A G+ Sbjct: 123 CCRHALAQMQPRRSGAIVNVASDLGFLGREQYVAYCTAKAGVIGLTRSLAREFAADGIRV 182 Query: 182 NALTPATFESPILDQLPQSQVDYMRSK---IPMGRLGLVEESAAMVCFMASEECSFTTAS 238 N + P + ++ P+ D +K IPM RLG EE AA + F+ S + S+ T Sbjct: 183 NGVAPGPIATAMVS--PEHMSDEWMAKELAIPMARLGTPEEVAAAIVFLLSPQASYFTGQ 240 Query: 239 TFDTSGG 245 +GG Sbjct: 241 LLGPNGG 247 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: 143 Number of extensions: 9 Number of successful extensions: 4 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: 252 Length adjustment: 24 Effective length of query: 225 Effective length of database: 228 Effective search space: 51300 Effective search space used: 51300 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