Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_011384968.1 AMB_RS13020 KR domain-containing protein
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_000009985.1:WP_011384968.1 Length = 256 Score = 114 bits (285), Expect = 2e-30 Identities = 78/251 (31%), Positives = 117/251 (46%), Gaps = 6/251 (2%) Query: 9 PYPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSD 68 P G L++GG GIG +A L GA V + + L G A DV+D Sbjct: 6 PLAGRHALVTGGGRGIGAAIARQMLALGAVVTITGRDQGRLDAAATSL-GCSAVAMDVTD 64 Query: 69 AAQIEAVFKVQREHLGGLDVLVNNAGIA--GPTGGIDAISDAEWQATININLTAQYRFAH 126 A I+ F + G + +LVNNAGIA P D W + +LT + Sbjct: 65 APAIQNGFARAAQVQGPITILVNNAGIAKAAPFAKTDL---GLWDDILRTDLTGAFLCTQ 121 Query: 127 HAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNAL 186 A+P + E+ G ++++AS AG G A+ Y A K ++GL ++LA EL + VNA+ Sbjct: 122 AALPGMLEAGWGRVVNVASTAGLTGLAYCAAYCAAKHGLIGLTRALAVELASKPVTVNAV 181 Query: 187 LPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAAR 246 PG E + I + G E + KR++ E+VA +LC P + Sbjct: 182 CPGYTETDIVADTIANIVAKTGRTPEEALAGLVAANPQKRLIKPEEVAEAVAWLCLPGSA 241 Query: 247 NVTGQAISVDG 257 ++TGQ+I+V G Sbjct: 242 SITGQSIAVAG 252 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: 168 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: 256 Length adjustment: 24 Effective length of query: 238 Effective length of database: 232 Effective search space: 55216 Effective search space used: 55216 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