Align 2-deoxy-3-keto-D-ribonate cleavage enzyme (characterized)
to candidate RR42_RS10310 RR42_RS10310 NADPH:quinone reductase
Query= reanno::Burk376:H281DRAFT_00641 (312 letters) >FitnessBrowser__Cup4G11:RR42_RS10310 Length = 297 Score = 171 bits (432), Expect = 3e-47 Identities = 108/319 (33%), Positives = 162/319 (50%), Gaps = 44/319 (13%) Query: 5 SRKVIISCAITGATHVPSMSEFLPITPEQIRDQAIEAAQAGAAIIHLHARDPVDGRPTPS 64 SRKVI++CA+TG +P+TP QI D +EAA+AGA++ H+H RDP G + Sbjct: 2 SRKVILTCAVTGNAPFNRKHPAMPVTPVQIADACVEAAKAGASVAHIHVRDPDTGAGSRD 61 Query: 65 PEIFKAFVPAI-AEATDAVINITTG-----------------GSTRMTLEERLAYPRLAR 106 P +FK V + A TD V+N+T G S + + ER+ + L Sbjct: 62 PALFKEVVDRVRASGTDIVLNLTCGLGAFLLPDPEDESRALPDSDVIPVAERVRHLELCL 121 Query: 107 PEMCSLNMGSMNFSIHPVAAKISSWRYGWEKDYIEGMEDMIFRNTFRDIRNILLELGESG 166 PE+ SL++ + N +EG + ++ NT R +R + E G Sbjct: 122 PEIASLDITTGN--------------------QVEGKLEFVYLNTTRTLRAMAKRFQELG 161 Query: 167 TRFEFECYDVGHLYNLAHFVDQGLVKPPFFIQSVFGILGGLGADPENMLLMRSTADRLFG 226 + E E + G + + GL+ Q V G+L G A E M+ RS Sbjct: 162 VKPELEVFSAGDILFGNSMIADGLINGVPLFQMVLGVLWGAPATTETMIYQRSLIP---- 217 Query: 227 RENYHFSVLGAGRHQMPLVTMSAIMGGNVRVGLEDSVYLAKGVKAETNAQQVRKIRRILE 286 N ++ G R +MP+V SA++GGNVRVGLED++YL++GV A TN Q V + R I+E Sbjct: 218 -ANAQWAAFGIARDEMPMVAQSALLGGNVRVGLEDNLYLSRGVFA-TNGQLVERARTIIE 275 Query: 287 ELSLEIATPADARKMLGLK 305 L + +ATPA+AR ++ L+ Sbjct: 276 YLGMSVATPAEARDIMELR 294 Lambda K H 0.321 0.137 0.400 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: 225 Number of extensions: 13 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: 312 Length of database: 297 Length adjustment: 27 Effective length of query: 285 Effective length of database: 270 Effective search space: 76950 Effective search space used: 76950 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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