Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_011765666.1 AZO_RS09770 NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_000061505.1:WP_011765666.1 Length = 269 Score = 124 bits (310), Expect = 3e-33 Identities = 77/252 (30%), Positives = 122/252 (48%), Gaps = 5/252 (1%) Query: 9 PYPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGT---VATRAD 65 P G +++G +GIGE +A GA + + L RDK G +A AD Sbjct: 14 PLAGRHAVVTGAGSGIGEAIAIELARLGATLTLVGRRAEPLNATRDKLAGQGHGIAV-AD 72 Query: 66 VSDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFA 125 ++D A I A G + +L+NNAG A + + A W + +NLT Y Sbjct: 73 ITDHAAIGAALAEAAAARGAIAILINNAG-AAKSAPLAKTEPALWNEMLTVNLTGTYNCT 131 Query: 126 HHAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNA 185 H +P ++ + G +++IAS AG +GYA+ + Y A K ++GL ++LA E+ + I VNA Sbjct: 132 HAVLPGMQATRWGRIVNIASTAGLVGYAYVSAYCAAKHGVIGLTRALALEVAKQGITVNA 191 Query: 186 LLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAA 245 + PG + P + G + + G + + R+V EDVA +LC P + Sbjct: 192 VCPGYTDTPLLGGAVDNIVAKTGRSSDDAKTTLAASNPQGRLVQPEDVARTVGWLCLPGS 251 Query: 246 RNVTGQAISVDG 257 + GQ+I V G Sbjct: 252 DAIHGQSIPVAG 263 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: 175 Number of extensions: 6 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: 269 Length adjustment: 25 Effective length of query: 237 Effective length of database: 244 Effective search space: 57828 Effective search space used: 57828 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