Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate GFF3169 PGA1_c32200 fumarylacetoacetate hydrolase family protein
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Phaeo:GFF3169 Length = 284 Score = 138 bits (347), Expect = 2e-37 Identities = 90/275 (32%), Positives = 135/275 (49%), Gaps = 6/275 (2%) Query: 1 MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANLDV--ETLPAVS 58 MK Y GQ G DG+I LS LD + L L V E+ Sbjct: 1 MKFASYSAAGQAFYGAATDDGMIA-LSPDFPQWPT-LLDVVRAGGLDQLIVTAESRSVTH 58 Query: 59 GNPRLGPCVAGTGKFICIGLNYSDHAAE--TGATVPPEPIIFMKATSAIVGPNDDLVLPR 116 + + + + +C+G+N+ D AE G+ P +F + S G N L+ P Sbjct: 59 TDVQYDMVLPNARRILCVGVNFPDRNAEYKDGSEQPKYMSLFPRFASGFTGHNRPLIRPP 118 Query: 117 GSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCD 176 S D+E E+ IVIGK + +++A+A D++A ++ + R + T+GK+ D Sbjct: 119 ESHMLDYEGEVAIVIGKGGRRIAQADAYDHIAALTICNEGTIRDWVRHAKFNVTQGKNWD 178 Query: 177 TFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPG 236 G GPWLV + A D + +VNG+ QD M++ + Y+S FM+L PG Sbjct: 179 NSGAIGPWLVPFRDPAQLDDARITTRVNGDVRQDDVLSRMMHPIRREIEYISTFMTLEPG 238 Query: 237 DIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLG 271 DII TGTP G G + PP++LK GDVVE+ + G+G Sbjct: 239 DIIVTGTPTGSGARLDPPQFLKPGDVVEVEVTGIG 273 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: 266 Number of extensions: 14 Number of successful extensions: 2 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: 284 Length adjustment: 26 Effective length of query: 255 Effective length of database: 258 Effective search space: 65790 Effective search space used: 65790 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