Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_092349901.1 BLU87_RS14010 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_900107645.1:WP_092349901.1 Length = 245 Score = 124 bits (310), Expect = 2e-33 Identities = 83/248 (33%), Positives = 129/248 (52%), Gaps = 16/248 (6%) Query: 16 LISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVF--RDKYPGT--VATRADVSDAAQ 71 LI+G + GIG +A A GA++ + A F K GT +A R DVS AA+ Sbjct: 8 LITGTSRGIGRGIATALAANGAKIVAAGTNLQATEDFVAELKAAGTEAIAVRCDVSVAAE 67 Query: 72 IEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPM 131 +E + K +E G +D+LVNNAGI G + + + +W A ++INL + + Sbjct: 68 VEQLVKTAKETFGRIDILVNNAGITRD-GLLLRMKEEDWDAVLDINLKGAFLCTRAVSKL 126 Query: 132 LKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIV 191 + + G +++I SV G+ G + Y A+K ++GL +S A EL + +I VNA+ PG + Sbjct: 127 MTKQRCGRIINIVSVVGQTGNPGQANYCASKAGLMGLTRSNAQELAKRNITVNAVAPGFI 186 Query: 192 EGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVTGQ 251 D +PE E RQ+ +I L R+ + ED++ LFL S A +TGQ Sbjct: 187 ATDMTD----------SLPE-EQRQDLAARIPLARLGSVEDISHAVLFLASDHAGYITGQ 235 Query: 252 AISVDGNV 259 I V+G + Sbjct: 236 VIGVNGGM 243 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: 142 Number of extensions: 6 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: 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