Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_012334629.1 M446_RS23635 NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_000019365.1:WP_012334629.1 Length = 248 Score = 140 bits (354), Expect = 2e-38 Identities = 87/252 (34%), Positives = 132/252 (52%), Gaps = 19/252 (7%) Query: 10 YPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSDA 69 + G R +++GGA+GIG +AA GA V + DV+ AL R + D++D Sbjct: 7 FQGRRAIVTGGASGIGLCVAARLAAEGAAVSLWDVNAEALGRARTEAGAADVQALDIADP 66 Query: 70 AQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAV 129 A++EA + LGGLDVLV +AGI GP G + W+ ++N+ + AV Sbjct: 67 ARVEAAMQASVAALGGLDVLVCSAGITGPNGPVRDYPVEAWRRVFDVNVHGLFYCNRAAV 126 Query: 130 PMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPG 189 P+L+ + +G ++++AS+AG+ G + Y+A+K A++GL KSL EL +DIRVN + P Sbjct: 127 PVLERTGYGRIVNVASIAGKEGNPNASAYSASKAAVIGLTKSLGKELARTDIRVNCVTPA 186 Query: 190 IVEGPRMDGVIRARAEQVGVPEAEMRQEY----LNKISLKRMVTAEDVAAMALFLCSPAA 245 V D +M QE+ L+KI + R T E+VAA+ +L S A Sbjct: 187 AVRTAIFD---------------QMTQEHIDFMLSKIPIGRFGTIEEVAALICWLASEEA 231 Query: 246 RNVTGQAISVDG 257 TG V G Sbjct: 232 SFSTGGVFDVSG 243 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: 166 Number of extensions: 8 Number of successful extensions: 1 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 24 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