Align diisopropyl-fluorophosphatase (EC 3.1.8.2) (characterized)
to candidate RR42_RS33665 RR42_RS33665 gluconolactonase
Query= BRENDA::Q03336 (299 letters) >FitnessBrowser__Cup4G11:RR42_RS33665 Length = 300 Score = 139 bits (349), Expect = 1e-37 Identities = 93/286 (32%), Positives = 142/286 (49%), Gaps = 12/286 (4%) Query: 17 GESPVWEEASKCLLFVDIPSKTVCRWDSISNRVQRVGVDAPVSSVALRQSGGYVATIGTK 76 GESP W+ ++CL + DIP++T+ W + + ++ + +A +GG+VA + + Sbjct: 18 GESPFWDTQTQCLYWSDIPARTLFEWRAANAAIRTWELPEMAGCIAPASAGGFVAGMQSG 77 Query: 77 FCALNWEDQSVFI---LAMVDEDKKNNRFNDGKVDPAGRYFAGTMAEETAPAVLERHQGS 133 L + LA V + RFNDG+ D GR++AGTM + PA + GS Sbjct: 78 LFHLQPQPDGSMASRRLASVAHPAPSMRFNDGRCDRQGRFWAGTMHLDMHPA---QSIGS 134 Query: 134 LYSLFPDHSVKKYFDQVDISNGLDWSLDHKIFYYIDSLS--YTVDAFDYDLPTGQISNRR 191 +Y F +++ + + + NG+ WS D + Y DS + AFDYD G S RR Sbjct: 135 VYR-FDARGLQQQIEGLIVPNGMAWSPDGRTMYLSDSHPDVQAIWAFDYDAANGVASRRR 193 Query: 192 TVYKMEKDEQIPDGMCIDVEGKLWVACYNGGRVIRLDPETGKRLQTVKLPVDKTTSCCFG 251 M + PDG +DV+G W+ + G V R PE G+ +++ LPV K C FG Sbjct: 194 LWIDMRQYPGRPDGAAVDVDGCYWICGNDAGVVHRFTPE-GRLDRSIALPVKKPAMCAFG 252 Query: 252 GKDYSEMYVTCARDGMSAEGLLRQPDAGNIFKITGLGVKGIAPYSY 297 G D ++VT R A QP AG +F + GV GIA ++ Sbjct: 253 GADMKTLFVTSIRPA-DASVQAEQPLAGGVFAVRP-GVAGIAERAF 296 Lambda K H 0.319 0.137 0.423 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: 275 Number of extensions: 23 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: 299 Length of database: 300 Length adjustment: 27 Effective length of query: 272 Effective length of database: 273 Effective search space: 74256 Effective search space used: 74256 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 (21.8 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