Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate GFF33 HP15_33 fumarylacetoacetate (FAA) hydrolase
Query= reanno::Smeli:SM_b21112 (281 letters) >FitnessBrowser__Marino:GFF33 Length = 300 Score = 123 bits (309), Expect = 4e-33 Identities = 87/262 (33%), Positives = 133/262 (50%), Gaps = 11/262 (4%) Query: 21 GIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGNPRLGPCVAGTGKFICIGLNY 80 G R + G S+ A A KL E NL E L A S L P G + +GLNY Sbjct: 23 GCARWILGAFSEWAVLA-SKGKLSE-KNLSAEQLQAASFT-LLAPIEPGA-RIFGVGLNY 78 Query: 81 SDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEKTDWEVELGIVIGKTAKYVSE 140 +H + G+ PP P+ ++K SA+VG +D++ P +E+ D+E+EL V+ + V Sbjct: 79 LEHLKKLGSEAPPHPLSYLKPDSAMVGHREDVLYPAVTEQLDYEIELVAVVARELANVQF 138 Query: 141 AEALDYVAGYCTVHDVSER-AFQTERHGQWTKGKSCDTFGPTGPWLVTKDEV--ADPQDL 197 + + GY +DVS R A Q K+ D P GPW+ T D V +L Sbjct: 139 PSSC--LLGYTVGNDVSARDAGQALGRLDLFTQKAMDRTTPVGPWIETADGVGGVGQPEL 196 Query: 198 AMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMGMKPPRYL 257 + + VNG+ Q G+T+ M++ +++YL LRPGD++ TG+ GV G++ +L Sbjct: 197 HLMMTVNGQVRQQGNTRDMIFSVDEILNYLDARCVLRPGDLVFTGSTSGV--GLETGTFL 254 Query: 258 KAGDVVELGIEGLGSQKQRVRA 279 K GD++E IE +G + A Sbjct: 255 KPGDLMEARIERIGVLSNSIAA 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: 288 Number of extensions: 23 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: 300 Length adjustment: 26 Effective length of query: 255 Effective length of database: 274 Effective search space: 69870 Effective search space used: 69870 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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