Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate Pf6N2E2_1959 Multiple polyol-specific dehydrogenase (EC 1.1.1.-)
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1959 Length = 257 Score = 117 bits (293), Expect = 2e-31 Identities = 78/253 (30%), Positives = 122/253 (48%), Gaps = 2/253 (0%) Query: 7 LKPRPGLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVN-QAAIDEATSRFPKLHAGIAD 65 +K G ++ A GIG + A+A+I A V I D+N + A A+ P+ +A D Sbjct: 1 MKRLEGKSALITGSARGIGRSFAQAYIGEGATVAIADINLERAQATASELGPQAYAVEMD 60 Query: 66 VSKQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFL 125 V++QA +D I + + G LD+LVNNA + + E+ ++ + N++ + L Sbjct: 61 VTRQASIDAAIAEVVARAGKLDILVNNAALFD-LAPITEITRESYDKLFAINVSGTLFTL 119 Query: 126 RKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVN 185 + A + II M+S AGR G Y +TK A++ L +S L + VN Sbjct: 120 QAAAKQMISQGHGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIKHKINVN 179 Query: 186 AILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPA 245 AI PGVV+GE D V + A P + ++ RM T +D+ MA+FLA Sbjct: 180 AIAPGVVDGEHWDGVDALFAKHENRPLGEKKRLVGLEVPYGRMGTAEDLVGMAIFLAGSE 239 Query: 246 GSNVTGQAISVDG 258 + Q +VDG Sbjct: 240 SDYIVAQTYNVDG 252 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: 130 Number of extensions: 6 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 239 Effective length of database: 233 Effective search space: 55687 Effective search space used: 55687 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