Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate 5210422 Shew_2863 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__PV4:5210422 Length = 248 Score = 119 bits (298), Expect = 6e-32 Identities = 78/252 (30%), Positives = 134/252 (53%), Gaps = 13/252 (5%) Query: 10 YPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESAL-AVFRDKYPGTVATRADVSD 68 + G VLI+G A+G G++LA GA++ + D++++AL A+ + V R DVS Sbjct: 5 FEGKVVLITGAASGFGKLLAQRLAPQGAKLVLGDINDTALDALCSELGECAVGLRCDVSI 64 Query: 69 AAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHA 128 A+ A+ ++ E G LD+ +NNAGI+ P + A ++A+ + IN + Sbjct: 65 EAEQLALAQLAEESFGRLDIAINNAGISAPMKSLLATTEADMDLSFAINTKGVFFGMKAQ 124 Query: 129 VPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLP 188 +P++++ G +L++AS+AG G TPY A K A+VG+ ++ A E I+VNA+ P Sbjct: 125 IPLMQKHKCGAILNVASMAGINGAPKLTPYVAAKHAVVGITRTAALEFAAQGIQVNAICP 184 Query: 189 GIVEGPRM-DGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARN 247 P + +GV A EQ+ + ++R+ +V + L + +P Sbjct: 185 FFTPTPMVTEGVDPALIEQL-----------TRAVPMRRLADPNEVVSAMLHMVNPDNGF 233 Query: 248 VTGQAISVDGNV 259 +TGQAI++DG V Sbjct: 234 MTGQAIAIDGGV 245 Lambda K H 0.318 0.133 0.383 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: 137 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: 262 Length of database: 248 Length adjustment: 24 Effective length of query: 238 Effective length of database: 224 Effective search space: 53312 Effective search space used: 53312 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 (21.7 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