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 GFF1391 Psest_1428 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= SwissProt::P0DOW0 (331 letters) >FitnessBrowser__psRCH2:GFF1391 Length = 362 Score = 140 bits (353), Expect = 5e-38 Identities = 107/348 (30%), Positives = 163/348 (46%), Gaps = 37/348 (10%) Query: 1 MKTLTWTAKETMSILSAPAP-VPEPGWIALRVAGVGICGSELSGYLGHNELR-------- 51 M W ++ + + P P P+PGW+ +RV GICGS+L YL Sbjct: 7 MTAAVWHGRKDIRLEQVPLPGAPQPGWVQIRVHWCGICGSDLHEYLAGPVFIPVDAPHPL 66 Query: 52 ---KPPLVMGHEFSGVVEEVGHGVTNVKIGDLVTANPLVTCGRCIHCLRGERQRCESRRI 108 K ++GHEF G + +G GV GD V A+ CG+C C G+ CE Sbjct: 67 TGIKGQCILGHEFCGEIVAIGEGVEGYAPGDKVAADACQHCGQCRFCKTGQYNLCEQLAF 126 Query: 109 IGIDFPGAYAERVLVPSNQCYAVKDAID---GALVEPLACAVRAVGLARIKVGDTAVVIG 165 G+ GA+AE V VP+ Y + + GAL+EPLA + AV A +G+T VV+G Sbjct: 127 TGLMNNGAFAEFVNVPAELLYRLPEGFPLEAGALIEPLAVGMHAVKKAGSLLGETVVVVG 186 Query: 166 AGIIGLMTVRLLGLSGAKRIAVVDPNDER----LKISQLW----GATEMAPNLGALLTD- 216 AG IGL T+ +GA ++ ++ + R L++ W + + AL Sbjct: 187 AGTIGLCTIMCAKAAGAGQVIALEMSAARKAKALEVGANWVIDPSECDAIAEIKALTGGY 246 Query: 217 NHPQSFDCVIDAVGLSTTRRDSLNALIRGGRAVWIGLHEALTHLDGNQIVRDELEVRGSF 276 SF+C +G T + +++ + + GR V +G+ E + + +IV E +V GS Sbjct: 247 GAGVSFEC----IGHKATAKLAIDVIRKAGRCVMVGIFEEPSEFNFFEIVATEKQVIGSL 302 Query: 277 CYTDDEFIRAVSLINSQKF----LPVDRQWLDVRSLEEGPAAFKELVN 320 Y EF ++LI+ + L R LD LE+G F+EL N Sbjct: 303 AYA-GEFADVIALIDDGRIDVTPLITGRIGLD-NILEQG---FEELAN 345 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: 382 Number of extensions: 25 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: 331 Length of database: 362 Length adjustment: 29 Effective length of query: 302 Effective length of database: 333 Effective search space: 100566 Effective search space used: 100566 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