Align 2-deoxy-3-keto-D-ribonoate cleavage enzyme (characterized)
to candidate GFF5130 PS417_26280 NADPH:quinone reductase
Query= reanno::WCS417:GFF1426 (310 letters) >FitnessBrowser__WCS417:GFF5130 Length = 295 Score = 176 bits (447), Expect = 5e-49 Identities = 116/321 (36%), Positives = 163/321 (50%), Gaps = 47/321 (14%) Query: 4 NRPVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRPSQD 63 N VIITCA+TGA T S SPH+P+T ++IA AA+ AA+AGA +VH H RDP G+ S+D Sbjct: 2 NHDVIITCALTGAGDTTSRSPHVPVTPKQIAAAAVEAAKAGATVVHCHVRDPETGKFSRD 61 Query: 64 PALFAEFLPQIKAAS-DVVINITTG------------------GAPTMGVEERLQPVMQF 104 AL+ E + +I+ A D+++N+T G +G RL V + Sbjct: 62 VALYREVMERIREADIDIIVNLTAGMGGDLEIGGGENPMAFGPNTDLVGPLTRLAHVEEL 121 Query: 105 KPELASLNMGSMNFGLYEMLNRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNACAEN 164 PE+ +L+ G++NFG D I+ +T + E Sbjct: 122 LPEICTLDCGTLNFG----------------------DGDTIYVSTPAQLRAGAKRIQEL 159 Query: 165 RTRFEIECYDIGHLYTAAHFLERGLLKPPLFIQSVFGLRGGIGGHPEDLAHMRRTADRLF 224 + E+E +D GHL+ A ++ GLL PLF Q G+ G P D M+ D L Sbjct: 160 GVKAELEIFDTGHLWFAKQMIKEGLLDDPLF-QLCLGIPWGA---PADTTTMKAMVDNL- 214 Query: 225 GSDYVWSILGAGRGQIPLATMGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIRTVIE 284 +D VW+ G GR Q+P+A + +G N RVGLED+LW G L A+N V R ++ Sbjct: 215 PADAVWAGFGIGRMQMPMAAQAVLLGGNVRVGLEDNLWLDKGVL-ATNGQLVERASEILS 273 Query: 285 ALGHRVATPDEAREILGLKGR 305 LG RV TP E R +GL R Sbjct: 274 RLGARVMTPAEGRVKMGLTKR 294 Lambda K H 0.321 0.138 0.416 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: 245 Number of extensions: 14 Number of successful extensions: 5 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: 310 Length of database: 295 Length adjustment: 27 Effective length of query: 283 Effective length of database: 268 Effective search space: 75844 Effective search space used: 75844 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