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 PfGW456L13_3426 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3426 Length = 273 Score = 120 bits (301), Expect = 3e-32 Identities = 77/249 (30%), Positives = 124/249 (49%), Gaps = 11/249 (4%) Query: 6 GRYAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGD-ALAATQAEIDATH---VVA 61 G+ AGR AI+TG GLG + A + + G ++A+ D+N + A A Q+ + H +A Sbjct: 4 GKLAGRVAIITGSGGGLGAECARVLASHGASIAVVDINFEGATAVAQSLVAEGHQALAIA 63 Query: 62 LDVSDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWE-----FPVDSFQRVIDINL 116 DVS V A G++DIL +A I A + + ++ R I +NL Sbjct: 64 TDVSSEDDVRAMVAQVKERFGRIDILHNNAAILNAEQRQLDRDFVNLDMQAWDRAIAVNL 123 Query: 117 NGLFYCNREVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAG 176 G C + V+P MLENG G I+ S G +G+ + + Y+ SKAG++ + + + Sbjct: 124 RGAVLCTKHVIPVMLENGKGSIIFATSGLGMQGDMSLTGYATSKAGLMMLPRMVASQYGK 183 Query: 177 KGVIANALTPATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTT 236 +G+ NA+ +P +P+ +D +R LG + A +V F+AS+E SF T Sbjct: 184 QGIRGNAVQIGL--APSEHAMPEPLLDILRDNHCTAELGTPRQIADVVAFLASDESSFVT 241 Query: 237 ASTFDTSGG 245 +T GG Sbjct: 242 GTTLVADGG 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: 164 Number of extensions: 6 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: 273 Length adjustment: 25 Effective length of query: 224 Effective length of database: 248 Effective search space: 55552 Effective search space used: 55552 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