Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_057506718.1 ABB28_RS00365 3-oxoacyl-ACP reductase
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >NCBI__GCF_001431535.1:WP_057506718.1 Length = 260 Score = 113 bits (283), Expect = 4e-30 Identities = 87/251 (34%), Positives = 123/251 (49%), Gaps = 16/251 (6%) Query: 12 GLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQ----AAIDEATSRFPKLHAGIADVS 67 G RV ++ G+ GIG IA AF A A V +C Q A +A + LH AD+S Sbjct: 16 GRRVAIAGGSKGIGRCIALAFAGAGASVSVCARGQQGLAALARDAQDQGTPLHTHAADLS 75 Query: 68 KQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRK 127 Q+ +++A LGG+DVLVNNA TG D W +++ +L + R Sbjct: 76 GLEQIGGWLENAAEALGGIDVLVNNA-----TGYGMADDEDGWAASLQVDLMAAVRASRL 130 Query: 128 AVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAI 187 A+P L+ ++D A I+ +SS+A + P PYA+ K A+ S A L +RVNAI Sbjct: 131 ALPWLRASTD-ACILNLSSIAAQQPRPGAAPYAAAKAALSHYTTSQALALAQYRIRVNAI 189 Query: 188 LPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGS 247 PG +E E D + A+ L KI R ++IA ALFL SP Sbjct: 190 APGSIEFE------DGLWDRRRVDDPALYHGTLAKIPFGRFGRPEEIAHAALFLCSPLAG 243 Query: 248 NVTGQAISVDG 258 +TG ++VDG Sbjct: 244 WITGHVLNVDG 254 Lambda K H 0.318 0.134 0.375 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: 138 Number of extensions: 9 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 263 Length of database: 260 Length adjustment: 25 Effective length of query: 238 Effective length of database: 235 Effective search space: 55930 Effective search space used: 55930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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