Align diisopropyl-fluorophosphatase (EC 3.1.8.2) (characterized)
to candidate WP_086510992.1 BZY95_RS16570 SMP-30/gluconolactonase/LRE family protein
Query= BRENDA::Q03336 (299 letters) >NCBI__GCF_002151265.1:WP_086510992.1 Length = 304 Score = 123 bits (308), Expect = 6e-33 Identities = 93/295 (31%), Positives = 150/295 (50%), Gaps = 18/295 (6%) Query: 6 IECVLRENYRCGESPVW----EEASKCLLFVDIPSKTVCRWDSISNRVQRVGVDAPVSSV 61 I+ + R + G P+W EA + LLFVDI + + D S + ++ + Sbjct: 15 IQRIWRGRAQLGGGPLWCPGQGEAGR-LLFVDILRRALYVHDFASGTTRGWPLEEACCWL 73 Query: 62 ALRQSG-GYVATIGTKFCALNWEDQSVFILA--MVDEDKKNNRFNDGKVDPAGRYFAGTM 118 R G G++A + ++ L E+ I+ + E+ NRFN+ VD GR + G+M Sbjct: 74 VPRADGDGFIAGLASRLVHLRLEEHGPRIVDDWVTPEEPAGNRFNNAAVDTLGRLWFGSM 133 Query: 119 AEETAPAVLERHQGSLYSLFPDHSVKKYFDQVDISNGLDWSLDHKIFYYIDSLSYTVDAF 178 +E + E QG+LY L +++ ++NG S D + Y+ D+ + V A+ Sbjct: 134 SENEQESG-EPGQGALYRL-DGAGLRRVDHGYGVANGPAVSPDGRTLYHSDTAAGIVYAY 191 Query: 179 DYDLPTGQISNRRTVYKMEKDEQIPDGMCIDVEGKLWVACYNGGRVIRLDPETGKRLQTV 238 + G+++ RR + + PDGM DVEG LWVA + GGRV R P+ G +T+ Sbjct: 192 EL-AADGELTGRREHLRFHGAQGYPDGMTCDVEGGLWVAHWGGGRVSRFLPD-GTLDETL 249 Query: 239 KLPVDKTTSCCFGGKDYSEMYVTCARDGMSAEGLLRQPDAGNIFKITGLGVKGIA 293 LP + TSC FGG + ++Y+T A DG E L AG++F++ GV+G+A Sbjct: 250 LLPASRVTSCAFGGPELDQLYITTAADGRDQEAL-----AGSLFRVAP-GVRGLA 298 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: 270 Number of extensions: 17 Number of successful extensions: 3 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: 304 Length adjustment: 27 Effective length of query: 272 Effective length of database: 277 Effective search space: 75344 Effective search space used: 75344 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 24 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