Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate AO356_29975 AO356_29975 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29975 Length = 283 Score = 177 bits (450), Expect = 2e-49 Identities = 102/285 (35%), Positives = 158/285 (55%), Gaps = 6/285 (2%) Query: 1 MKLLRYGEPGQEKPGLLGSDGIIRDLS--GHVSDLAAGALDPSKLDELANLDVETLPA-- 56 MKL+ Y + G+ G++ DG++ V DLA + + E + VET A Sbjct: 1 MKLISYRKEGRAHFGVVSGDGVVELTRRFAQVPDLATFLANRLLVQEARKI-VETAQADY 59 Query: 57 VSGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPR 116 + +L + GK IC+G+NY HA E G V P+IF + ++ + LV P+ Sbjct: 60 SFSSIQLEAVIPNPGKVICVGINYVAHAEEAGRKVGEFPVIFQRFAETLLPHGEPLVRPK 119 Query: 117 GSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCD 176 SE+ D+E EL +VIGK ++ A+A+D+VAGY +D S R +Q H Q+ GK+ Sbjct: 120 VSEQFDFEAELAVVIGKGGAHIDPADAMDHVAGYTCFNDASVRDWQFHTH-QYGMGKTFR 178 Query: 177 TFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPG 236 G GPW++ E++D + L + +NGE +Q+GS + + HL+SY+S+ + PG Sbjct: 179 KTGALGPWIIPASEISDYRTLVVRGILNGEQLQEGSLSELAFDIPHLISYVSKALPWNPG 238 Query: 237 DIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRVRADA 281 DI++TGTP G+G KPP +LK GDV E+ I +G+ V +A Sbjct: 239 DILATGTPSGIGFKRKPPIFLKPGDVFEVVITEIGTLSNGVIDEA 283 Lambda K H 0.315 0.136 0.408 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: 267 Number of extensions: 15 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: 281 Length of database: 283 Length adjustment: 26 Effective length of query: 255 Effective length of database: 257 Effective search space: 65535 Effective search space used: 65535 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 47 (22.7 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