Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_086509100.1 BZY95_RS06195 KR domain-containing protein
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_002151265.1:WP_086509100.1 Length = 249 Score = 140 bits (354), Expect = 2e-38 Identities = 89/243 (36%), Positives = 133/243 (54%), Gaps = 7/243 (2%) Query: 16 LISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSDAAQIEAV 75 LI+ GIG A + GA+V D+ L D PG A R DV DA + A+ Sbjct: 9 LITAAGQGIGRATALRFAAEGARVIATDIDADKLRDLGDT-PGIEARRLDVLDAEAVTAL 67 Query: 76 FKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPMLKES 135 K L L+VL N AG +G + +SDA+W+ ++ +N+TA R +P + Sbjct: 68 AK----ELASLNVLFNCAGYVA-SGALLEVSDADWERSLALNVTAMLRLTRTLLPTMIAG 122 Query: 136 SHGHLLHIASVAGRL-GYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIVEGP 194 G ++++ASVA L G R Y TK A++GL KS+A++ + IR NA+ PG V+ P Sbjct: 123 GGGSIINMASVASSLTGVPNRCAYGTTKAAVLGLTKSIAADYIDRGIRCNAICPGTVDSP 182 Query: 195 RMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTGQAIS 254 + IR +AE+ G PEAE+ E+L + L R+ TAE++AA+A +L + + TG A Sbjct: 183 SLRQRIREQAERQGRPEAEVHAEFLARQPLGRLGTAEEIAALATYLAADESAYTTGTAQV 242 Query: 255 VDG 257 +DG Sbjct: 243 IDG 245 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: 151 Number of extensions: 10 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: 249 Length adjustment: 24 Effective length of query: 238 Effective length of database: 225 Effective search space: 53550 Effective search space used: 53550 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