Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_019615251.1 G327_RS0113160 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_000381745.1:WP_019615251.1 Length = 251 Score = 93.6 bits (231), Expect = 4e-24 Identities = 74/252 (29%), Positives = 118/252 (46%), Gaps = 19/252 (7%) Query: 12 GLRVLISGGAAGIGEVLAAAYLEAGAQV----HVCDVSESALAVFRDKYPGTVATRADVS 67 G +++G G+G+ A +AGA + H+ A + + V Sbjct: 8 GKVAIVTGCNTGLGQGSAIGLAKAGADIVGIGHIPAPETQAQIEALGRKFHYITANLMVQ 67 Query: 68 DAAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHH 127 D Q+E + E +G +D+LVNNAGI +D S++ W ININ + F Sbjct: 68 D--QLENIVAETVEVMGRVDILVNNAGIIRREDFLD-FSESNWDDVININQKTVF-FLSQ 123 Query: 128 AVP--MLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNA 185 AV +K+ G +++IAS+ G Y A+K A++GL ++LA+EL + ++ VNA Sbjct: 124 AVAKQFVKQGKGGKIINIASMLSFQGGIRVPSYTASKSAVMGLTRALANELAQYEVNVNA 183 Query: 186 LLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAA 245 + PG + + + A + L +I R T ED+A +FL SPA+ Sbjct: 184 IAPGYMATDNTEALRADEARNAAI---------LERIPANRWGTPEDLAGPIVFLASPAS 234 Query: 246 RNVTGQAISVDG 257 V G I+VDG Sbjct: 235 DYVNGYTIAVDG 246 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: 137 Number of extensions: 9 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: 251 Length adjustment: 24 Effective length of query: 238 Effective length of database: 227 Effective search space: 54026 Effective search space used: 54026 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 24 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