Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate GFF829 PGA1_c08430 short chain dehydrogenase / reductase
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__Phaeo:GFF829 Length = 257 Score = 201 bits (511), Expect = 1e-56 Identities = 110/247 (44%), Positives = 153/247 (61%), Gaps = 3/247 (1%) Query: 14 RVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSDAAQIE 73 RVLI+ G +GIG +A + AG QV V DVS ALA D G T D +D A ++ Sbjct: 8 RVLITAGGSGIGRAMAEGFAAAGHQVWVTDVSAEALA---DVPEGWRTTVVDATDEAGVK 64 Query: 74 AVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPMLK 133 +F GGLDVL NAGIAGPT I+ I+ +W+ +++NL + A +A PM+K Sbjct: 65 GLFAEITVEWGGLDVLCANAGIAGPTALIEDIALEDWRTCVSVNLEGCFLAAKYAAPMMK 124 Query: 134 ESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIVEG 193 + G ++ +S AG+ GY R PYA+ KWA++GLMK+LA ELG IR N + PG VEG Sbjct: 125 AAKAGAIIVTSSTAGQYGYPNRAPYASAKWAVIGLMKTLAMELGPFGIRANVICPGAVEG 184 Query: 194 PRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTGQAI 253 PRM+GV+ A G+ ++ + Y + S++ V A+D+A MA+FL S AAR V+GQ I Sbjct: 185 PRMEGVLEREAAAKGMTRDQVYEGYASGTSMRSFVEAQDIANMAVFLGSDAARLVSGQVI 244 Query: 254 SVDGNVE 260 +VDG+ E Sbjct: 245 AVDGHTE 251 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: 194 Number of extensions: 6 Number of successful extensions: 2 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