Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate SMc02037 SMc02037 oxidoreductase
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >FitnessBrowser__Smeli:SMc02037 Length = 256 Score = 120 bits (302), Expect = 2e-32 Identities = 82/253 (32%), Positives = 129/253 (50%), Gaps = 17/253 (6%) Query: 12 GLRVFVSAGAAGIGLAIAEAFIEAQAEVYIC----DVNQAAIDEATSRFPKLHAGIADVS 67 G FV+ G+ GIG A AEA EA A V I D + A+ + + + AD+S Sbjct: 10 GRAAFVTGGSRGIGFACAEALGEAGARVAISARSRDEGEKAVRQLRQKGIEAIYLPADIS 69 Query: 68 KQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRK 127 ++ Q++ A +LGGLD+LVNNAGIA ++ +L+P W+ ++TNL F+ R Sbjct: 70 NESAAQQVVRQAAAELGGLDILVNNAGIARHCDSL-KLEPETWDEVINTNLTGLFWCCRA 128 Query: 128 AVPVLKETSDCASIIAMSSVAGRLGY--PFRTPYASTKWAIVGLVKSLAAELGPSNVRVN 185 A+ + + SI+ + S++G + + Y ++K + L KSLA E SN+R+N Sbjct: 129 AIETM-SAAGRGSIVNIGSISGYISNLPQNQVAYNASKAGVHMLTKSLAGEFAKSNIRIN 187 Query: 186 AILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPA 245 A+ PG +E G+ + +L L R ++AA LFLAS A Sbjct: 188 AVAPGYIETAMTQG---------GLDDPEWSKIWLGMTPLGRAGKASEVAAAVLFLASDA 238 Query: 246 GSNVTGQAISVDG 258 S +TG +++DG Sbjct: 239 ASYITGSVLTIDG 251 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: 142 Number of extensions: 8 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: 256 Length adjustment: 24 Effective length of query: 239 Effective length of database: 232 Effective search space: 55448 Effective search space used: 55448 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