Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_017547482.1 C792_RS0100525 SDR family oxidoreductase
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_000330705.1:WP_017547482.1 Length = 257 Score = 139 bits (351), Expect = 5e-38 Identities = 85/254 (33%), Positives = 141/254 (55%), Gaps = 7/254 (2%) Query: 10 YPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPG---TVATRADV 66 + G V+I+GG+ GIG+ A +L+ GA+V + D++E +L R++ +A +ADV Sbjct: 5 FEGQVVIITGGSGGIGKQTALQFLQEGAKVTIVDINEESLTSAREELSRQGEVLAVQADV 64 Query: 67 SDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAH 126 SD A +E + E G +DVL NNAGI G G + ++A +N+ + Sbjct: 65 SDEADVENYIRATVEKFGKVDVLFNNAGIIGKVGSLVDQEYDNFKAVTGVNMNGVFLGLK 124 Query: 127 HAVP-MLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNA 185 HA+ M+K+ + G +++ SV G ++ Y+ATK A+VGL K+ A E +IRVN+ Sbjct: 125 HAIKQMIKQGTPGSIINTGSVDSFRGSPEQSAYSATKHAVVGLTKTAAVEAAGHNIRVNS 184 Query: 186 LLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAA 245 + P V+ P M V +R ++ A +R+++ + I L R + D+A + LFL S + Sbjct: 185 IHPAPVDTPMMAHVEESRDKK---NSASVREKFTSGIPLNRYADSSDIADLVLFLASDDS 241 Query: 246 RNVTGQAISVDGNV 259 + VTG S+DG + Sbjct: 242 KFVTGSQYSIDGGM 255 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: 141 Number of extensions: 7 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: 262 Length of database: 257 Length adjustment: 24 Effective length of query: 238 Effective length of database: 233 Effective search space: 55454 Effective search space used: 55454 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