Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_012385265.1 BIND_RS11625 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_000019845.1:WP_012385265.1 Length = 245 Score = 128 bits (322), Expect = 1e-34 Identities = 78/249 (31%), Positives = 127/249 (51%), Gaps = 13/249 (5%) Query: 12 GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTV-ATRADVSDAA 70 G L++G + G+G+ +A A GA V + L + V D+SD+A Sbjct: 6 GKTALVTGASGGLGQAIARALHRQGAVVALSGTRREQLEGLAAELENNVHVLPCDLSDSA 65 Query: 71 QIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVP 130 +EA+ LG LD+LVNNAGI + + D+EW A + +NLTA +R A ++ Sbjct: 66 AVEALVPAAEAALGSLDILVNNAGITRDNLFM-RMKDSEWDAVLAVNLTATFRLARASLK 124 Query: 131 MLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGI 190 + + +G ++ + SV G G A + YAA+K ++G+ KSLA+E+ ++ VN + PG Sbjct: 125 GMMKRRYGRIIGVTSVVGVTGNAGQGNYAASKAGMIGMSKSLAAEVASRNVTVNCVAPGF 184 Query: 191 VEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTG 250 +E P V + + L + + R+ T +DVAA ++L S A VTG Sbjct: 185 IESP-----------MTAVLNEKQKAAILANVPMGRLGTGDDVAAAIVYLASSEASYVTG 233 Query: 251 QAISVDGNV 259 Q + V+G + Sbjct: 234 QTLHVNGGM 242 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: 157 Number of extensions: 8 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: 245 Length adjustment: 24 Effective length of query: 238 Effective length of database: 221 Effective search space: 52598 Effective search space used: 52598 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