Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate AZOBR_RS29790 AZOBR_RS29790 3-ketoacyl-ACP reductase
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >FitnessBrowser__azobra:AZOBR_RS29790 Length = 250 Score = 109 bits (272), Expect = 6e-29 Identities = 78/254 (30%), Positives = 116/254 (45%), Gaps = 9/254 (3%) Query: 6 LLKPRPGLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGIA- 64 + K G ++ A G+GLA+AE F+ V + D+N A R + GIA Sbjct: 1 MTKRLDGKVALITGAAQGLGLAMAETFVREGGRVAVVDINGDAAKAVAERLGESAIGIAA 60 Query: 65 DVSKQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYF 124 +V++ A V+ I K G LD+LVNNAG G E + +++ + N+ S Y Sbjct: 61 NVTRMADVEMTIAATVEKFGRLDILVNNAGSTHANGPFENVTEEEFDRVFALNVKS-IYL 119 Query: 125 LRKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRV 184 KAV I+ + S AG P Y +TK A+ + KSLA EL P N+RV Sbjct: 120 YSKAVVATMRAQKSGVILNLGSTAGLRPRPGLVWYNATKGAVHNITKSLALELAPDNIRV 179 Query: 185 NAILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASP 244 A+ P E + A +G R + + L R+ D+A AL+LAS Sbjct: 180 CALAPVATETPLL-------ATFMGGDTPEKRARMMGIVPLGRLGQPTDVANAALYLASD 232 Query: 245 AGSNVTGQAISVDG 258 + +TG + +DG Sbjct: 233 EAAFLTGVVLEIDG 246 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: 136 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: 263 Length of database: 250 Length adjustment: 24 Effective length of query: 239 Effective length of database: 226 Effective search space: 54014 Effective search space used: 54014 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 17 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