Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate 3607555 Dshi_0967 fumarylacetoacetate (FAA) hydrolase (RefSeq)
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Dino:3607555 Length = 294 Score = 170 bits (431), Expect = 3e-47 Identities = 92/244 (37%), Positives = 146/244 (59%), Gaps = 3/244 (1%) Query: 31 SDLAAGALDPSKLDELANLDVETLPAVSGNPRLGPCVAGTGKFICIGLNYSDHAAETGAT 90 +DL A DP + + A L + + +A G IC+GLNY +H E G Sbjct: 34 TDLMALTRDPELVTKAAGLVGQGPQTQVADITPALPIAHPGTIICLGLNYVEHIREGGYE 93 Query: 91 VPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGY 150 +P P +FM+ ++I+ +V P SE D+E EL +++G+ +++ E AL++V GY Sbjct: 94 IPGYPALFMRGRNSIMPSGAPMVRPACSETLDYEAELMLIVGEGGRHIPEDAALEHVFGY 153 Query: 151 CTVHDVSERAFQTERHGQWTKGKSCDTFGPTGPWLVTKDEVAD-PQDLAMWLKVNGETMQ 209 T +D S R +Q + H QWT GK+ D G GP +VT DE+ + + L + +V E +Q Sbjct: 154 TTFNDGSVREYQRKTH-QWTPGKNFDATGAVGPIVVTPDELPEGAKGLKIESRVGNEILQ 212 Query: 210 DGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMGMKP-PRYLKAGDVVELGIE 268 +T+ M++GAA +S +S++ +L PGD+I+ GTPPGVG KP PR+L+ G+V+E+ IE Sbjct: 213 SSNTENMIWGAAKTLSIISEYTTLEPGDLIALGTPPGVGHAKKPGPRWLRPGEVIEVEIE 272 Query: 269 GLGS 272 G+G+ Sbjct: 273 GIGT 276 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: 291 Number of extensions: 17 Number of successful extensions: 4 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: 294 Length adjustment: 26 Effective length of query: 255 Effective length of database: 268 Effective search space: 68340 Effective search space used: 68340 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