Align diisopropyl-fluorophosphatase (EC 3.1.8.2) (characterized)
to candidate Ac3H11_2081 Gluconolactonase (EC 3.1.1.17)
Query= BRENDA::Q03336 (299 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2081 Length = 316 Score = 129 bits (323), Expect = 1e-34 Identities = 88/289 (30%), Positives = 142/289 (49%), Gaps = 28/289 (9%) Query: 17 GESPVWEEASKCLLFVDIPSKTVCRWDSISNRVQRVGVDAPVSSVALRQSGGYVATIGTK 76 GESP W K L + DI + V W S R ++ + + A G V + Sbjct: 14 GESPFWHPTEKSLYWCDIQGQAVHAWHPESGRHRQWRMPSEPGCCAPAADGQLVIGLRNG 73 Query: 77 FCALNW-----EDQSVFILAMVDEDKKNN---RFNDGKVDPAGRYFAGTM-AEETAPAVL 127 F L+ + ++ LA++ ++ + R NDG+ D AGR++AG++ TAP Sbjct: 74 FYLLDTAKGSTDPTALTCLALLPPEQHDTAVLRLNDGRCDTAGRFWAGSVITPRTAP--- 130 Query: 128 ERHQGSLYSLFPD------HSVKKYFDQVDISNGLDWSLDHKIFYYIDSLSYTVDAFDYD 181 +L+ L D + V+ +NGL +S D + Y+ ++ + +D FD+D Sbjct: 131 ---NAALWCLQADAASATGYRVRHMAGDNFTANGLAFSPDDRTLYWSNTPEHRIDQFDFD 187 Query: 182 LPTGQISNRRTVYKMEKDEQ------IPDGMCIDVEGKLWVACYNGGRVIRLDPETGKRL 235 + TG ISNRR + ++ + PDG +DVEG WVA Y G V++L P G+ L Sbjct: 188 VDTGAISNRRPWVQFDRKVEGQPYGGRPDGAAVDVEGNYWVAMYEGACVLQLSP-AGEVL 246 Query: 236 QTVKLPVDKTTSCCFGGKDYSEMYVTCARDGMSAEGLLRQPDAGNIFKI 284 Q +++PV T CFGG+D +++T AR G E + AG++F + Sbjct: 247 QRIEVPVQCPTMVCFGGEDLRTLFITSARAGRPVEEREAEVPAGSLFSV 295 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: 306 Number of extensions: 15 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: 316 Length adjustment: 27 Effective length of query: 272 Effective length of database: 289 Effective search space: 78608 Effective search space used: 78608 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