Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate N515DRAFT_1230 N515DRAFT_1230 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >FitnessBrowser__Dyella79:N515DRAFT_1230 Length = 254 Score = 87.0 bits (214), Expect = 3e-22 Identities = 82/252 (32%), Positives = 116/252 (46%), Gaps = 23/252 (9%) Query: 15 VFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDE-ATSRFPKLHAGI---ADVSKQA 70 VFVS GA GIG A E F + V D+++ + A S + HA D++ Sbjct: 15 VFVSGGATGIGAAFVEHFARQGSRVTFVDIDREHAEALAQSLAGERHAPRFLPCDITDLD 74 Query: 71 QVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKAVP 130 + I AR G + VLVNNA + Q++ +++ NL Q YF +AV Sbjct: 75 ALQASIAAAREAHGPVAVLVNNAA-NDVRHTFGDTTGEQFDRSIAINLRHQ-YFATQAVR 132 Query: 131 VLKETSDCASIIAMSSVAG---RLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAI 187 S+I + S GYP YA K A+ GLV LA ELG +R+NA+ Sbjct: 133 EDMRALGGGSVICLGSTGWMKKNAGYPI---YAMAKSAVHGLVNGLARELGHDRIRINAL 189 Query: 188 LPGVVEGERMDRVISARADALGIPFNAMREEYLKKIS-LRRMVTVDDIAAMALFLASPAG 246 +PG V E+ R+ DA G EE +K++ L + +D+A ALFL + Sbjct: 190 VPGWVITEKQRRL---WLDAAG-------EEEIKRVQCLPGYLMAEDLARAALFLGADDS 239 Query: 247 SNVTGQAISVDG 258 TGQ+ VDG Sbjct: 240 RMCTGQSFLVDG 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: 113 Number of extensions: 8 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: 254 Length adjustment: 24 Effective length of query: 239 Effective length of database: 230 Effective search space: 54970 Effective search space used: 54970 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