Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_058858690.1 AS188_RS09780 beta-ketoacyl-ACP reductase
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_001482365.1:WP_058858690.1 Length = 242 Score = 117 bits (292), Expect = 3e-31 Identities = 76/245 (31%), Positives = 121/245 (49%), Gaps = 19/245 (7%) Query: 15 VLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSDAAQIEA 74 VL++GG GIG +A A+ +AG V V S A G +A +ADV+DAA I+A Sbjct: 13 VLVTGGNRGIGRAIAQAFKDAGDNVAVTHRSGEAPE-------GFLAVQADVTDAASIDA 65 Query: 75 VFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPMLKE 134 FK G ++V+V NAGI T + + + ++Q ++ NLT +R A Sbjct: 66 AFKAVEAEFGPVEVVVANAGITRDTLLL-RMKEQDFQDVVDTNLTGAFRVVQRAAKGFMR 124 Query: 135 SSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIVEGP 194 G ++ I+SV G G + YAA+K +VG+ +S+ ELG ++ N + PG + Sbjct: 125 LKRGRVVLISSVVGLYGSPGQVNYAASKAGLVGMARSITRELGGRNVTANVVAPGFI--- 181 Query: 195 RMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTGQAIS 254 E + +++YL I R E+VAA+ ++ S A+ ++G I Sbjct: 182 --------NTEMTAALPEDTQRDYLASIPAGRFAEPEEVAAVVRWIASDEAKYISGAVIP 233 Query: 255 VDGNV 259 VDG + Sbjct: 234 VDGGL 238 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: 161 Number of extensions: 10 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: 242 Length adjustment: 24 Effective length of query: 238 Effective length of database: 218 Effective search space: 51884 Effective search space used: 51884 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: 46 (22.3 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