Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate HSERO_RS19365 HSERO_RS19365 oxidoreductase
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__HerbieS:HSERO_RS19365 Length = 254 Score = 122 bits (305), Expect = 1e-32 Identities = 80/247 (32%), Positives = 122/247 (49%), Gaps = 7/247 (2%) Query: 12 GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSDAAQ 71 G VLI+ A GIG + GA+V D+S+ L D+ G + D Sbjct: 10 GKTVLITAAAQGIGRASTELFAREGARVIATDISKPHL----DELAGIAGVETHLLDVTD 65 Query: 72 IEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPM 131 +A K +G +DVL N AG G I D W + N+N A + +P Sbjct: 66 -DAAIKALVAKIGTIDVLFNCAGYVA-AGNILECDDKAWDFSFNLNAKAMFHTIRAVLPG 123 Query: 132 LKESSHGHLLHIASVAGRL-GYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGI 190 + G +++IAS A + G A R Y A+K A+VGL KS+A++ IR NA+ PG Sbjct: 124 MLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVAQGIRCNAICPGT 183 Query: 191 VEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTG 250 +E P ++ I +A++ G E E+R ++ + + R+ AE+VAA+AL+L S + TG Sbjct: 184 IESPSLNQRISTQAKETGKSEEEVRAAFVGRQPMGRIGKAEEVAALALYLASDESNFTTG 243 Query: 251 QAISVDG 257 +DG Sbjct: 244 SIHMIDG 250 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: 143 Number of extensions: 6 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: 254 Length adjustment: 24 Effective length of query: 238 Effective length of database: 230 Effective search space: 54740 Effective search space used: 54740 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