Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_176342813.1 BZY95_RS08205 SDR family NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_002151265.1:WP_176342813.1 Length = 247 Score = 142 bits (357), Expect = 9e-39 Identities = 84/246 (34%), Positives = 131/246 (53%), Gaps = 7/246 (2%) Query: 12 GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSDAAQ 71 G RV+I+GG +GIG +A A+ EAGA V + L ++P ADV+ A Sbjct: 6 GKRVVITGGGSGIGADMALAFAEAGADVTIIGRRREPLETTACRHPAIACEIADVTREAD 65 Query: 72 IEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPM 131 + A+F E LG +D+++ NAG A + + +WQ +++NLT + + Sbjct: 66 MVALF----ERLGEVDIVIANAG-AAESAPLARTGLDQWQRMLDVNLTGVFLTLREGLKR 120 Query: 132 LKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIV 191 +++ G L+ +AS AG GYA+ PY A K +VGL+++LA E+ E DI VNAL PG Sbjct: 121 VRDG--GRLIAVASTAGLKGYAYVAPYCAAKHGVVGLVRALAQEVAERDITVNALCPGFT 178 Query: 192 EGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTGQ 251 E P ++ + + G A+ R + R++ +V A AL+LC P + + GQ Sbjct: 179 ETPLLEASVATIVAKTGQSPAQARAHLQSTNPSGRLIQPAEVTATALWLCGPHSGAIHGQ 238 Query: 252 AISVDG 257 AIS+ G Sbjct: 239 AISISG 244 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: 174 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: 247 Length adjustment: 24 Effective length of query: 238 Effective length of database: 223 Effective search space: 53074 Effective search space used: 53074 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 Apr 09 2024. 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