Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate 3608139 Dshi_1544 3-hydroxybutyrate dehydrogenase (RefSeq)
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__Dino:3608139 Length = 257 Score = 111 bits (277), Expect = 2e-29 Identities = 81/253 (32%), Positives = 123/253 (48%), Gaps = 12/253 (4%) Query: 12 GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSES----ALAVFRDKYPGTVAT--RAD 65 G +I+G +GIG +A AGA V + ++ ALA + G A +AD Sbjct: 5 GKTAVITGSNSGIGLGIAWELARAGADVVLNSFTDREEDHALADEIARETGVYARYIKAD 64 Query: 66 VSDAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFA 125 +S A+ E G D+LVNNAGI ID +W A I IN+ + + Sbjct: 65 MSKGDDCRALI----ESAGTCDILVNNAGIQH-VAPIDEFPVDKWDAIIAINMNSAFHTT 119 Query: 126 HHAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNA 185 A+PM++++ G +++IAS G ++ Y A K +VG+ K++A E + I NA Sbjct: 120 AAALPMMRKAGWGRVVNIASAHGLTASPYKAAYVAAKHGVVGMTKTVALETAQEPITCNA 179 Query: 186 LLPGIVEGPRMDGVIRARAEQVGVPEAE-MRQEYLNKISLKRMVTAEDVAAMALFLCSPA 244 + PG V P ++ I E+ + E ++Q L + K T E + +FLCS A Sbjct: 180 ICPGYVLTPLVEAQIPNTMEKYDMGREEVIKQVMLERQPSKEFATVEQLGGTCVFLCSDA 239 Query: 245 ARNVTGQAISVDG 257 A +TG ISVDG Sbjct: 240 AAQITGTTISVDG 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: 162 Number of extensions: 9 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 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