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ESMC-SAE-Features

feature_id int64 0 16.4k	description stringlengths 43 3.53k	summary stringlengths 10 1.2k	activation_pattern stringlengths 0 1.23k	category stringclasses 14 values	exemplar_protein_families stringlengths 0 2.38k	uniref90_frequency int64 1.4M 208M	uniref90_idf float32 0 5	uniref90_max_activation float32 7.8 50.7	top_100_uniref_ids listlengths 100 100	top_swissprot_activations listlengths 20 20	decoder_nearest_neighbors listlengths 10 10	threshold float64 0 1.22 ⌀
0	Summary: Acidic, metal-coordinating catalytic segment for phosphate/diphosphate chemistry, firing primarily on the Nudix hydrolase signature (the Nudix box, E(x)7E(x)11EE) and secondarily on analogous E/D-rich motifs that bind Mg2+ and position pyrophosphate in related enzymes (e.g., IDI, PRPP/salvage enzymes) and DNA-...	Acidic, metal-coordinating catalytic segment for phosphate/diphosphate chemistry, firing primarily on the Nudix hydrolase signature (the Nudix box, E(x)7E(x)11EE) and secondarily on analogous E/D-rich motifs that bind Mg2+ and position pyrophosphate in related enzymes (e.g., IDI, PRPP/salvage enzymes) and DNA-processin...	Regional activation centered on short acidic stretches with strong residue-level peaks on catalytic Glu/Asp; in Nudix proteins the peak is typically near the N‑terminal Nudix box; spans range from single residues to a short loop/helix segment	Catalytic function	- Nudix hydrolases (MutT/NUDT1 8‑oxo‑dGTPase): activation on the conserved Nudix box that coordinates Mg2+ for diphosphatase activity - NAD‑capped RNA hydrolase (NudC): activation on the Nudix box that binds the NAD cap’s pyrophosphate - Viral mRNA decapping Nudix enzymes: activation on the Nudix signature that cleaves...	4,628,379	3.805359	13.757813	[ { "activation": 13.7578125, "uniref_id": "A0A1I5ZIT8" }, { "activation": 13.7109375, "uniref_id": "UPI002F91017D" }, { "activation": 13.6796875, "uniref_id": "A0A1G6BH86" }, { "activation": 13.640625, "uniref_id": "A0A7W7P4P0" }, { "activation": 13.6328125, "u...	[ { "activation": 11.051897048950195, "uniprot_id": "P45799" }, { "activation": 11.000073432922363, "uniprot_id": "A4WRA6" }, { "activation": 10.992526054382324, "uniprot_id": "D8KIT5" }, { "activation": 10.925203323364258, "uniprot_id": "Q9UKK9" }, { "activation": ...	[ 82, 334, 15309, 7546, 14504, 1546, 15772, 15444, 13061, 3365 ]	0.380352
1	Summary: Predominantly extracellular/secreted and cell-surface proteins with exposed, flexible low-complexity segments in the mature region (often Ser/Thr/Gly-rich or proteoglycan-like), frequently cysteine-rich; with a minority of metazoan lipid-binding proteins (including FABPs) that can be cytosolic Activation patte...	Predominantly extracellular/secreted and cell-surface proteins with exposed, flexible low-complexity segments in the mature region (often Ser/Thr/Gly-rich or proteoglycan-like), frequently cysteine-rich; with a minority of metazoan lipid-binding proteins (including FABPs) that can be cytosolic	Regional activation on extended contiguous stretches of exposed/disordered segments within the mature region—Gly/Thr-enriched repeats and Ser/Thr-rich O-glycosylated linkers when present, or flexible surface loops; weak in transmembranes and compact catalytic cores	Disorder	- Gram-positive adhesins and sortase-anchored cell-wall proteins: activation on Ser/Thr/Gly-rich repeat stalks between the signal peptide and LPXTG anchor - Type IV pilins and fimbrial/adhesin subunits: activation on extracellular low-complexity linker or repeat segments - Hemophores and iron-acquisition surface protei...	6,834,559	3.415573	18.828125	[ { "activation": 18.828125, "uniref_id": "A0A3M1ZTU0" }, { "activation": 18.328125, "uniref_id": "A0A956C9C0" }, { "activation": 18.203125, "uniref_id": "A0A6L3A521" }, { "activation": 18.03125, "uniref_id": "A0A952W8I6" }, { "activation": 18.03125, "uniref_id"...	[ { "activation": 12.867857933044434, "uniprot_id": "H8WEC0" }, { "activation": 11.957571029663086, "uniprot_id": "P9WI69" }, { "activation": 9.26235580444336, "uniprot_id": "O00834" }, { "activation": 7.776237487792969, "uniprot_id": "P46483" }, { "activation": 7.5...	[ 9518, 3158, 7101, 4124, 6534, 9879, 4894, 5095, 1267, 16078 ]	0.30678
2	Summary: Glycine-rich, acidic (Asp/Glu) and often histidine-bearing flexible capping/loop segments at the mouths of active sites or ligand-binding clefts that bind/position anionic cofactors or substrates (phosphate- or carboxylate-bearing; often Mg2+-assisted) and act as lids/gates across diverse folds; the same acidi...	Glycine-rich, acidic (Asp/Glu) and often histidine-bearing flexible capping/loop segments at the mouths of active sites or ligand-binding clefts that bind/position anionic cofactors or substrates (phosphate- or carboxylate-bearing; often Mg2+-assisted) and act as lids/gates across diverse folds; the same acidic Gly-ric...	Regional activation over contiguous mid-sequence blocks (≈15–50 residues), peaking on Gly clusters adjacent to Asp/Glu or His–Asp pairs; often one or a few such segments per protein	Ligand-binding site	- One‑carbon/folate enzymes (glycine cleavage T protein, folate‑linked demethylases, GAR transformylase/GART): activation on THF-binding/capping loops with Gly clusters and acidic residues that cradle the folate phosphate/carboxylates. - Purine biosynthesis AIRS/PurM and related enzymes: activation on β–α loops in the ...	9,601,427	3.075654	22.734375	[ { "activation": 22.734375, "uniref_id": "A0A4S2EWG0" }, { "activation": 22.703125, "uniref_id": "UPI0024BC8F7B" }, { "activation": 22.671875, "uniref_id": "A0A7X6UYK5" }, { "activation": 22.609375, "uniref_id": "A0A9D2INP9" }, { "activation": 22.578125, "unire...	[ { "activation": 21.305940628051758, "uniprot_id": "Q681Y3" }, { "activation": 20.359771728515625, "uniprot_id": "Q4FP21" }, { "activation": 19.548770904541016, "uniprot_id": "P48728" }, { "activation": 19.227611541748047, "uniprot_id": "Q9UI17" }, { "activation": ...	[ 6453, 353, 1933, 4121, 15196, 10049, 4215, 14972, 14024, 12232 ]	0.187933
3	Summary: Acidic, Ser/Thr-rich low-complexity segments on the non-lumenal side of membrane proteins—juxtamembrane loops and terminal tails that function as flexible regulatory/assembly and trafficking regions, often carrying phosphorylation sites and acidic motifs; typically disordered or only modestly structured, thoug...	Acidic, Ser/Thr-rich low-complexity segments on the non-lumenal side of membrane proteins—juxtamembrane loops and terminal tails that function as flexible regulatory/assembly and trafficking regions, often carrying phosphorylation sites and acidic motifs; typically disordered or only modestly structured, though sometim...	Regional activation across long contiguous stretches (≈20–50 aa), frequently multiple per protein, typically immediately flanking a transmembrane helix; strongest at clusters of Asp/Glu interspersed with Ser/Thr and Gly/Pro; minimal activation within hydrophobic transmembranes.	Membrane-associated	Viral Vpu: cytoplasmic acidic, serine-rich disordered C-terminal tail with phosphoserines; Mitochondrial calcium uniporter (MCU): acidic, partly helical/coiled C-terminal region directly after TM2 implicated in oligomerization/regulation; NADPH oxidase/DUOX/RBOH: cytosolic N-terminal regulatory segments enriched for ac...	26,165,785	2.073112	16.84375	[ { "activation": 16.84375, "uniref_id": "UPI00194225C9" }, { "activation": 16.609375, "uniref_id": "UPI0030DB5CEF" }, { "activation": 16.546875, "uniref_id": "A0A1R4JNN4" }, { "activation": 16.46875, "uniref_id": "UPI00048F70B9" }, { "activation": 16.34375, "un...	[ { "activation": 14.78911304473877, "uniprot_id": "Q75007" }, { "activation": 14.782535552978516, "uniprot_id": "P08806" }, { "activation": 14.743574142456055, "uniprot_id": "P19554" }, { "activation": 13.964645385742188, "uniprot_id": "Q1A244" }, { "activation": 1...	[ 5207, 13482, 8819, 4627, 15458, 10956, 11224, 11353, 4818, 6971 ]	0.435727
4	Summary: Intrinsically disordered, low‑complexity effector regions of metazoan transcriptional regulators and cofactors (activation/repression and cofactor‑binding segments), enriched in proline/serine/glutamine/glycine and PTM/SLiM hotspots, with little or no activation on folded DNA‑binding or SAM domains. Activation...	Intrinsically disordered, low‑complexity effector regions of metazoan transcriptional regulators and cofactors (activation/repression and cofactor‑binding segments), enriched in proline/serine/glutamine/glycine and PTM/SLiM hotspots, with little or no activation on folded DNA‑binding or SAM domains.	Broad, contiguous regional activation across long N‑ or C‑terminal IDRs (often hundreds of residues; low pLDDT), with occasional peaks at short helices/coils and known linear motifs or PTM clusters; near‑zero activation over structured domains such as POU/homeobox, HMG box, SAM, and other folded cores. PolyQ tracts may...	Disorder	- POU-class homeobox transcription factors (e.g., BRN2/POU3F2): strong activation on the N‑terminal low‑complexity activation region; inactive on POU‑specific and homeobox DNA‑binding domains. - TCF/LEF HMG box transcription factors (e.g., POP‑1): activation on the N‑terminal disordered regulatory region (includes phos...	4,760,752	3.77716	16.171875	[ { "activation": 16.171875, "uniref_id": "A0A9J7M6S5" }, { "activation": 16.0625, "uniref_id": "A0A7K6F9T6" }, { "activation": 16.03125, "uniref_id": "A0A7K8D2G4" }, { "activation": 16.015625, "uniref_id": "A0A8C0VFA7" }, { "activation": 15.984375, "uniref_id":...	[ { "activation": 15.344257354736328, "uniprot_id": "Q96NU1" }, { "activation": 15.296398162841797, "uniprot_id": "Q1RNF8" }, { "activation": 14.820014953613281, "uniprot_id": "P54259" }, { "activation": 14.220223426818848, "uniprot_id": "Q8R089" }, { "activation": ...	[ 1591, 6987, 6850, 7540, 10694, 3507, 6711, 11789, 10467, 5408 ]	0.347705
5	Summary: Intrinsically disordered regulatory regions of transcription factors—especially fungal TFs—composed of low‑complexity Ser/Thr/Pro- and Gln/Asn‑rich segments that host short linear regulatory motifs (e.g., SP/TP phosphorylation clusters, YPX[LI] interaction/processing motifs, degron/processing boxes, occasional...	Intrinsically disordered regulatory regions of transcription factors—especially fungal TFs—composed of low‑complexity Ser/Thr/Pro- and Gln/Asn‑rich segments that host short linear regulatory motifs (e.g., SP/TP phosphorylation clusters, YPX[LI] interaction/processing motifs, degron/processing boxes, occasional Lys/Arg‑...	Broad regional activation over long, low‑pLDDT IDRs flanking or trailing DNA‑binding domains; minimal/absent signal on structured DBDs. Superimposed residue‑level peaks at protease boxes/cleavage sites and other SLiMs within the IDRs. Often spans N‑ or C‑terminal tails and large internal regulatory stretches.	Disorder	pH‑response TF PacC/RIM101: strong activation across the C‑terminal inhibitory propeptide, including the signaling protease box, cleavage site, and YPX[LI] motifs; no activation on the N‑terminal C2H2 zinc fingers. Myb‑like transcription factors: activation on the C‑terminal disordered regulatory tail outside the Myb r...	6,227,829	3.508538	16.140625	[ { "activation": 16.140625, "uniref_id": "A0A367K883" }, { "activation": 16.046875, "uniref_id": "UPI0023007FF6" }, { "activation": 15.9921875, "uniref_id": "A0A1C7NB31" }, { "activation": 15.953125, "uniref_id": "I1BSX4" }, { "activation": 15.9296875, "uniref_...	[ { "activation": 14.969688415527344, "uniprot_id": "P78871" }, { "activation": 14.574922561645508, "uniprot_id": "P34233" }, { "activation": 13.977060317993164, "uniprot_id": "Q753Y2" }, { "activation": 13.935336112976074, "uniprot_id": "Q5A5Q6" }, { "activation": ...	[ 1170, 2673, 5705, 2655, 13464, 6773, 14292, 8500, 8979, 5727 ]	0.6411
6	Summary: Alpha-helical segments in transporter systems: predominantly hydrophobic transmembrane helices and adjacent loop–helix boundary motifs in multi-pass membrane proteins (EC 7 translocases; ABC and non-ABC) and 7TM receptors; also tolerates amphipathic helices within associated ABC ATPase (NBD) subunits Activatio...	Alpha-helical segments in transporter systems: predominantly hydrophobic transmembrane helices and adjacent loop–helix boundary motifs in multi-pass membrane proteins (EC 7 translocases; ABC and non-ABC) and 7TM receptors; also tolerates amphipathic helices within associated ABC ATPase (NBD) subunits	Regional activation across many segments per protein (multiple TMs); strong signal on long hydrophobic alpha-helices; residue-level peaks at loop→TM transitions (N/C caps), at Trp/Tyr interface positions, and at Ser/Thr/Gly within hydrophobic runs; occasional activation on amphipathic helices in cytosolic ABC NBDs	Membrane-associated	- ABC heavy‑metal tolerance transporters (permease/TMD): activation on TM helices and at cytoplasmic loop→TM starts within the ABC transmembrane type‑1 domain - Peptide antibiotic transporter SbmA: activation within a TM helix, at a periplasmic loop→TM transition, and on a periplasmic helical segment - Bacteriocin/pept...	11,381,374	2.905587	22.515625	[ { "activation": 22.515625, "uniref_id": "UPI001BD4A070" }, { "activation": 22.375, "uniref_id": "A0A6I3IVE1" }, { "activation": 22.375, "uniref_id": "A0AB36JQY9" }, { "activation": 22.375, "uniref_id": "UPI000A7DAC9B" }, { "activation": 22.328125, "uniref_id":...	[ { "activation": 21.230918884277344, "uniprot_id": "O07549" }, { "activation": 21.20414161682129, "uniprot_id": "P0AAG5" }, { "activation": 19.838315963745117, "uniprot_id": "Q0P9C4" }, { "activation": 19.750431060791016, "uniprot_id": "Q9X2W0" }, { "activation": 1...	[ 3128, 6489, 8166, 5625, 3594, 1527, 11268, 9427, 7943, 5789 ]	0.300471
7	Summary: Specific heptad-register signal in long alpha-helical coiled-coils: the feature marks one solvent-exposed position of the (abcdefg)n repeat (consistent with charged/polar e/g faces) across extended coiled-coil scaffolds common in eukaryotic cytoskeletal, centrosomal, nucleoporin, and endomembrane tether protei...	Specific heptad-register signal in long alpha-helical coiled-coils: the feature marks one solvent-exposed position of the (abcdefg)n repeat (consistent with charged/polar e/g faces) across extended coiled-coil scaffolds common in eukaryotic cytoskeletal, centrosomal, nucleoporin, and endomembrane tether proteins.	Residue-level sharp peaks recurring every 7 residues across long coiled-coil segments (often hundreds to >1000 aa); minimal in globular domains and unstructured regions unless they harbor latent coiled-coil propensity; activated residues are enriched for E/Q/K/R/S/T, consistent with a solvent-exposed coiled-coil face.	Structural motif	- Golgin-84 (Golgi tether): periodic peaks on the N-terminal cytosolic coiled-coil heptad register. - Restin homolog (cytoskeletal coiled-coil): continuous 7-residue–spaced peaks across the long C-terminal coiled-coil. - Cep290 (centrosomal/ciliary scaffold): heptad-pattern peaks throughout annotated coiled-coils and c...	9,479,694	3.088413	20.390625	[ { "activation": 20.390625, "uniref_id": "A0A850GJI8" }, { "activation": 20.359375, "uniref_id": "A0A2S9XEN9" }, { "activation": 20.109375, "uniref_id": "A0A956C7V5" }, { "activation": 19.9375, "uniref_id": "UPI0035D4CAA0" }, { "activation": 19.890625, "uniref_...	[ { "activation": 16.945043563842773, "uniprot_id": "Q9VJE5" }, { "activation": 16.81955909729004, "uniprot_id": "Q1D823" }, { "activation": 16.67233657836914, "uniprot_id": "I1RGD4" }, { "activation": 16.52066993713379, "uniprot_id": "O94488" }, { "activation": 16....	[ 10979, 14900, 11423, 534, 4316, 1650, 9, 8058, 14528, 931 ]	0.920796
8	Summary: Membrane-embedded transmembrane helical bundles of large multi-pass transporters/channels, with strongest preference for sterol/lipid-handling systems (sterol-sensing domain proteins and lipid exporters) and related multi-TM secretion/transport assemblies Activation pattern: Domain-/regional-level activation c...	Membrane-embedded transmembrane helical bundles of large multi-pass transporters/channels, with strongest preference for sterol/lipid-handling systems (sterol-sensing domain proteins and lipid exporters) and related multi-TM secretion/transport assemblies	Domain-/regional-level activation concentrated in long, contiguous hydrophobic segments corresponding to transmembrane helices; broad coverage across entire TM bundles (e.g., the 5-helix sterol-sensing domain and additional TM clusters), with minimal signal in luminal/cytosolic loops; in large eukaryotic proteins, acti...	Membrane-associated	- Sterol-sensing domain proteins (Dispatched/Patched/NPC1/SCAP): activation spans the SSD 5-TM unit and adjacent TM clusters that form sterol/lipid conduits - ABC lipid transporters (ABCA family): activation across both transmembrane domains (two ∼6-helix bundles), often strongest in the C-terminal TMD - Mycobacterial ...	4,040,523	3.941191	21.65625	[ { "activation": 21.65625, "uniref_id": "A0A852VXV7" }, { "activation": 21.125, "uniref_id": "A0A6V8CE66" }, { "activation": 20.984375, "uniref_id": "A0A5N9HZR9" }, { "activation": 20.875, "uniref_id": "A0A7M3ML86" }, { "activation": 20.71875, "uniref_id": "A0A...	[ { "activation": 19.143085479736328, "uniprot_id": "P9WJU7" }, { "activation": 18.018360137939453, "uniprot_id": "Q9VNJ5" }, { "activation": 18.008285522460938, "uniprot_id": "P9WJU5" }, { "activation": 17.91112518310547, "uniprot_id": "A0A0H3KP92" }, { "activation...	[ 11118, 3223, 14639, 5875, 268, 6389, 12486, 15465, 5428, 13715 ]	0.176626
9	Summary: Recognition of repetitive helical segments and hydrophobic/amphipathic motifs—most prominently the X/Y positions of collagen G–X–Y triple-helical repeats, but also contiguous hydrophobic alpha-helical transmembrane segments and proline/glycine-rich low-complexity stretches; predominant in secreted and membrane...	Recognition of repetitive helical segments and hydrophobic/amphipathic motifs—most prominently the X/Y positions of collagen G–X–Y triple-helical repeats, but also contiguous hydrophobic alpha-helical transmembrane segments and proline/glycine-rich low-complexity stretches; predominant in secreted and membrane proteins...	Regional activation over stretches: dense, domain-scale activation across collagenous triple-helix regions with zero or minimal signal on the invariant glycine (G) and peaks at X/Y (especially proline/hydrophobic residues); contiguous activation across single-pass or multi-pass transmembrane alpha-helices and amphipath...	Repeat	- Fibrillar collagens: strong activation along the triple-helical G–X–Y domain, peaking at X/Y positions (especially proline/hydroxyproline-like Y), with minimal signal on G. - Light-harvesting complex alpha subunits (photosynthetic bacteria): activation along their single transmembrane alpha-helix. - YhhN/TMEM86 lysop...	50,660,038	1.412428	8.367188	[ { "activation": 8.3671875, "uniref_id": "UPI002169DC94" }, { "activation": 8.359375, "uniref_id": "A0A352SCY4" }, { "activation": 8.3515625, "uniref_id": "U1S1F5" }, { "activation": 8.25, "uniref_id": "A0A973J484" }, { "activation": 8.1328125, "uniref_id": "A0...	[ { "activation": 6.0440354347229, "uniprot_id": "P86327" }, { "activation": 5.8930463790893555, "uniprot_id": "Q28487" }, { "activation": 5.683255195617676, "uniprot_id": "A0A182BSS4" }, { "activation": 5.659261703491211, "uniprot_id": "P29164" }, { "activation": 5...	[ 14900, 1650, 2304, 11423, 7, 8419, 4697, 6680, 4316, 10583 ]	0.371393
10	Summary: Specific transmembrane alpha‑helical segments of multi‑pass solute transporters/efflux pumps, especially DMT/EamA (SLC35 and plastidic phosphate/nucleotide‑sugar transporters) and mitochondrial carriers (SLC25), characterized by hydrophobic helices enriched in aromatic anchors and occasional helix‑kink residue...	Specific transmembrane alpha‑helical segments of multi‑pass solute transporters/efflux pumps, especially DMT/EamA (SLC35 and plastidic phosphate/nucleotide‑sugar transporters) and mitochondrial carriers (SLC25), characterized by hydrophobic helices enriched in aromatic anchors and occasional helix‑kink residues (Gly/Pr...	Regional activation concentrated on one or a few individual transmembrane helices per protein, appearing as long contiguous blocks within those helices; residue‑level peaks frequently at aromatic residues (W/Y/F) and sometimes at kink/packing residues (G/P, occasionally H); minimal activation in soluble domains or targ...	Membrane-associated	- Plastidic Xylulose‑5‑phosphate/phosphate translocator (pPT; DMT/EamA repeat carrier): strong activation on specific EamA-domain TM helices, with negligible signal on the chloroplast transit peptide and most other helices. - Bacterial guanidinium exporter (SMR family): primary activation on the C‑terminal part of TM2 ...	8,163,288	3.237918	25.8125	[ { "activation": 25.8125, "uniref_id": "J2RS97" }, { "activation": 25.796875, "uniref_id": "UPI00298D3AB3" }, { "activation": 25.796875, "uniref_id": "UPI00247630B0" }, { "activation": 25.765625, "uniref_id": "A0A2T5AXM6" }, { "activation": 25.71875, "uniref_id...	[ { "activation": 24.473054885864258, "uniprot_id": "D7A5Q8" }, { "activation": 24.180133819580078, "uniprot_id": "B0B8F4" }, { "activation": 23.602218627929688, "uniprot_id": "P0ADP5" }, { "activation": 23.49236488342285, "uniprot_id": "P46136" }, { "activation": 2...	[ 12225, 5037, 15380, 1370, 2596, 5846, 6816, 3258, 9479, 1930 ]	0.215546
11	Summary: Charge-rich, low-complexity linker and terminal segments—typically acidic (Asp/Glu-enriched) but also tolerating basic/His runs—that are flexible/disordered or weakly helical and lie outside catalytic cores; these extensions are common in subunits of large macromolecular assemblies (ribosome, F1-ATP synthase, ...	Charge-rich, low-complexity linker and terminal segments—typically acidic (Asp/Glu-enriched) but also tolerating basic/His runs—that are flexible/disordered or weakly helical and lie outside catalytic cores; these extensions are common in subunits of large macromolecular assemblies (ribosome, F1-ATP synthase, chaperone...	Regional activation across long, contiguous stretches, with a strong preference for C-terminal tails and inter-domain linkers; often lower predicted structural confidence (IDR-like), sometimes forming short/loose helices; little to no activation in compact catalytic cores.	Disorder	• Holliday junction branch migration protein RuvA: activation on the low-confidence flexible linker between domains II and III and into the C-terminal region. • Peptide deformylase: exclusive activation on the C-terminal tail/helix outside the catalytic/metal-binding core. • Ribosomal proteins and rRNA biogenesis fac...	9,059,907	3.133706	21.546875	[ { "activation": 21.546875, "uniref_id": "A0A923W9B7" }, { "activation": 21.390625, "uniref_id": "A0A975EJR3" }, { "activation": 21.296875, "uniref_id": "UPI003626A34D" }, { "activation": 21.28125, "uniref_id": "A0A4Q2YDQ8" }, { "activation": 21.265625, "uniref...	[ { "activation": 19.206684112548828, "uniprot_id": "P0AB28" }, { "activation": 17.867006301879883, "uniprot_id": "A0A1D6HQ92" }, { "activation": 17.418704986572266, "uniprot_id": "Q9LT27" }, { "activation": 11.9529447555542, "uniprot_id": "P56930" }, { "activation"...	[ 1500, 7847, 146, 1447, 15166, 1855, 1801, 11458, 11355, 7931 ]	0.256214
12	Summary: Long, low-complexity, intrinsically disordered terminal regions (often proline/glycine-rich) used as regulatory, adaptor-binding, and oligomerization segments that scaffold signaling and large macromolecular assemblies across taxa; these are strongly enriched in innate immune and microbial defense systems, but...	Long, low-complexity, intrinsically disordered terminal regions (often proline/glycine-rich) used as regulatory, adaptor-binding, and oligomerization segments that scaffold signaling and large macromolecular assemblies across taxa; these are strongly enriched in innate immune and microbial defense systems, but also occ...	Regional activation over tens to hundreds of residues, with a strong bias for N- or C-terminal stretches; frequently coincides with predicted disorder/low pLDDT and low-complexity composition; in some families, contiguous coverage includes the SEFIR/TIR module or the C-terminal catalytic lobe of nucleotidyl cyclases; t...	Disorder	- Interferon regulatory factors and other antiviral transcription factors: activation on disordered C-terminal transactivation/regulatory regions (e.g., IRF2/IRF3 C-termini), not the N-terminal DNA-binding domain. - TIR/SEFIR family (IL-17 receptors, ACT1; plant/bacterial TIR/Thoeris): activation on the cytosolic SEFIR...	7,143,808	3.371319	24.1875	[ { "activation": 24.1875, "uniref_id": "UPI002AF6C780" }, { "activation": 24.109375, "uniref_id": "UPI00360A451C" }, { "activation": 23.984375, "uniref_id": "UPI00363A6DC8" }, { "activation": 23.9375, "uniref_id": "A0A085ZFS2" }, { "activation": 23.890625, "uni...	[ { "activation": 20.718738555908203, "uniprot_id": "A0A2T5Y4G4" }, { "activation": 20.31635093688965, "uniprot_id": "A0A381HAP5" }, { "activation": 14.84177303314209, "uniprot_id": "Q833J1" }, { "activation": 8.529245376586914, "uniprot_id": "P0DXN8" }, { "activati...	[ 3730, 14537, 5460, 12817, 2641, 3028, 1286, 14688, 1567, 7154 ]	0.164847
13	Summary: Low-complexity, Ser/Thr/Pro-rich intrinsically disordered segments found in N-terminal tails, propeptides, targeting presequences (signal/transit peptides), and flexible linkers—serving as mucin-like O-glycosylated stalks in secreted/viral proteins, as phosphorylation/degron-rich regulatory regions in cytosoli...	Low-complexity, Ser/Thr/Pro-rich intrinsically disordered segments found in N-terminal tails, propeptides, targeting presequences (signal/transit peptides), and flexible linkers—serving as mucin-like O-glycosylated stalks in secreted/viral proteins, as phosphorylation/degron-rich regulatory regions in cytosolic protein...	Regional activation over contiguous clusters, typically starting near the N-terminus and spanning disordered tails/linkers/presequences; strong preference for S/T runs and SP/TP dipeptides; D/E and Gly frequently co-occur but are not required (transit peptides can be acidic-poor); low activation in well-folded cores bu...	Compositional bias	- Viral structural/attachment proteins: activation on Ser/Thr/Pro-rich mucin-like stalks and propeptides. - Integrin alpha subunits: activation on N-terminal prodomain/extracellular low-complexity segments. - Cystatins (stefins/type 2 cystatins): activation on flexible N-terminal segments and PEST-/PTS-like tracts. - C...	49,268,642	1.440277	14.296875	[ { "activation": 14.296875, "uniref_id": "A0A7X1F9E5" }, { "activation": 14.2734375, "uniref_id": "UPI0025EB4A01" }, { "activation": 14.2265625, "uniref_id": "UPI0013EA073C" }, { "activation": 14.21875, "uniref_id": "A0A0Q4KT97" }, { "activation": 14.2109375, "...	[ { "activation": 10.025796890258789, "uniprot_id": "P03630" }, { "activation": 9.904528617858887, "uniprot_id": "P14016" }, { "activation": 9.788032531738281, "uniprot_id": "P44853" }, { "activation": 9.748165130615234, "uniprot_id": "P03614" }, { "activation": 9.3...	[ 14228, 5157, 5301, 7807, 6038, 12564, 12631, 6763, 7270, 777 ]	0.372983
14	Summary: Terminus-proximal functional modules: the feature highlights a protein’s principal functional region—either the core of a folded domain or, in intrinsically disordered segments, embedded short linear interaction motifs—often at disorder-to-order boundaries and including catalytic/binding determinants (e.g., ac...	Terminus-proximal functional modules: the feature highlights a protein’s principal functional region—either the core of a folded domain or, in intrinsically disordered segments, embedded short linear interaction motifs—often at disorder-to-order boundaries and including catalytic/binding determinants (e.g., active-site...	Predominantly regional/domain-level activation in long contiguous blocks, frequently near a terminus; can split into several short segments within a domain; superimposed residue-level peaks at catalytic or binding residues; may extend into adjacent low-complexity coils when these harbor binding motifs	Domain	- Transcription-related regulator with large N-terminal IDR: activation confined to the structured C-terminal domain (ignores extensive disordered N-terminus) - Proteasome subunit DSS1/SEM1 (Rpn15): activation across disordered N-terminal ubiquitin-binding SLiMs (UBS I/II) within low-pLDDT regions - Photosystem II PsbP...	7,715,843	3.29429	22.203125	[ { "activation": 22.203125, "uniref_id": "A0A1C5HR93" }, { "activation": 22.1875, "uniref_id": "A0A0D1YAD5" }, { "activation": 22.140625, "uniref_id": "A0A5D0UYT9" }, { "activation": 22.125, "uniref_id": "A0A917VBP5" }, { "activation": 22.046875, "uniref_id": "...	[ { "activation": 19.772228240966797, "uniprot_id": "P30047" }, { "activation": 19.231605529785156, "uniprot_id": "Q12467" }, { "activation": 18.898269653320312, "uniprot_id": "Q14699" }, { "activation": 17.011259078979492, "uniprot_id": "Q96CX2" }, { "activation": ...	[ 8862, 7504, 1256, 2868, 6992, 15512, 15743, 15355, 7178, 9480 ]	0.143008
15	Summary: Intrinsically disordered, low‑complexity repeat and linker tracts (rich in Ser/Thr/Pro/Gly/Asn) that act as flexible stalks/spacers in secreted and cell‑surface proteins—especially in Gram‑positive bacteria—connecting or flanking structured modules (e.g., catalytic domains, LysM, NEAT, Ig‑like, CBMs) rather th...	Intrinsically disordered, low‑complexity repeat and linker tracts (rich in Ser/Thr/Pro/Gly/Asn) that act as flexible stalks/spacers in secreted and cell‑surface proteins—especially in Gram‑positive bacteria—connecting or flanking structured modules (e.g., catalytic domains, LysM, NEAT, Ig‑like, CBMs) rather than the fo...	Extended regional activation across very long, repetitive low‑complexity segments; strongest just after the signal peptide and in inter‑domain linkers/stalks; repeated activation between tandem domains; little to no activation on well‑folded domains.	Disorder	- Staphylococcal autolysins with LysM repeats: activation on the long N‑terminal disordered region around the signal peptide cleavage and on short glycine/low‑complexity linkers between LysM repeats; not on the catalytic or LysM domains. - MSCRAMM adhesins (e.g., clumping factors, Sdr family): activation on serine/aspa...	8,203,838	3.232963	19.796875	[ { "activation": 19.796875, "uniref_id": "UPI00290388ED" }, { "activation": 19.453125, "uniref_id": "UPI0022B78D87" }, { "activation": 19.4375, "uniref_id": "UPI0019057AE9" }, { "activation": 19.40625, "uniref_id": "UPI0028FF730E" }, { "activation": 19.390625, ...	[ { "activation": 18.24134063720703, "uniprot_id": "P0DJM0" }, { "activation": 17.992229461669922, "uniprot_id": "P16952" }, { "activation": 17.795677185058594, "uniprot_id": "P17953" }, { "activation": 17.07499885559082, "uniprot_id": "Q8Y3L4" }, { "activation": 16...	[ 14681, 14413, 12785, 10780, 4884, 11481, 9087, 6795, 9268, 6205 ]	0.285472
16	Summary: Detector for the mature cores of small, proteolytically processed and post‑translationally modified peptide effectors—especially RiPPs (lantibiotics, lasso peptides, thiopeptides, bacteriocins/pheromones)—and analogous cysteine‑rich toxin/effector segments. It responds to short Cys/Ser/Thr/Gly/Pro‑rich stretch...	Detector for the mature cores of small, proteolytically processed and post‑translationally modified peptide effectors—especially RiPPs (lantibiotics, lasso peptides, thiopeptides, bacteriocins/pheromones)—and analogous cysteine‑rich toxin/effector segments. It responds to short Cys/Ser/Thr/Gly/Pro‑rich stretches that h...	Strong, localized activation over short windows (tens of residues) that align with the mature peptide/core or a Cys‑centered modification motif; little to no activation on N‑terminal leaders/propeptides. Peaks typically start at or just after the cleavage site (often Gly/Gly or the first residue of the core) and center...	Post-translational modification	- Lantibiotic core peptides (lanthipeptides): activation spans the mature core containing dehydrated Ser/Thr and lanthionine/thioether crosslinks (e.g., flavovirin). - Lasso peptides: activation on the core beginning at the conserved Gly and covering the isopeptide bond and aromatic lock residues (e.g., Astexin‑1). - C...	9,672,609	3.068267	14.070313	[ { "activation": 14.0703125, "uniref_id": "A0AAE3R652" }, { "activation": 13.7734375, "uniref_id": "A0A512AU80" }, { "activation": 13.421875, "uniref_id": "A0A5M6CTI6" }, { "activation": 13.421875, "uniref_id": "UPI002665E1EF" }, { "activation": 13.265625, "uni...	[ { "activation": 9.594944953918457, "uniprot_id": "P29399" }, { "activation": 8.95433235168457, "uniprot_id": "P0DQL4" }, { "activation": 8.867847442626953, "uniprot_id": "P43683" }, { "activation": 8.629541397094727, "uniprot_id": "P29827" }, { "activation": 8.437...	[ 14993, 5563, 6258, 15924, 15052, 1472, 14495, 14008, 2765, 5171 ]	0.371451
17	Summary: Long, charge-enriched amphipathic α‑helical scaffolds and associated charged IDRs in eukaryotic peripheral‑membrane and cytosolic adaptor/scaffold proteins that bind extended polyanionic surfaces (acidic membranes, F‑actin, nucleic acids) or short cargo/peptide motifs, often in a Ca2+-regulated manner (e.g., a...	Long, charge-enriched amphipathic α‑helical scaffolds and associated charged IDRs in eukaryotic peripheral‑membrane and cytosolic adaptor/scaffold proteins that bind extended polyanionic surfaces (acidic membranes, F‑actin, nucleic acids) or short cargo/peptide motifs, often in a Ca2+-regulated manner (e.g., annexin‑li...	Predominantly long, domain‑spanning activation over helix‑rich cores (sometimes multiple blocks in multi‑domain proteins); compositionally enriched for mixed acidic/basic and aliphatic residues consistent with amphipathic helices; additionally, strong activation on extended charged, low‑pLDDT disordered tails (e.g., C‑...	Domain	- Annexins/annexin‑like: activation across the α‑helical annexin core repeats that mediate Ca2+‑dependent binding to acidic phospholipid membranes. - Actin cytoskeleton regulators (gelsolin/villin/flightless): activation over G‑domain helical bundles involved in Ca2+‑regulated actin and PIP2 interactions. - ADF‑H famil...	5,385,785	3.653802	21.15625	[ { "activation": 21.15625, "uniref_id": "A0A7S2BLQ7" }, { "activation": 21.03125, "uniref_id": "A0A914GTJ6" }, { "activation": 21.015625, "uniref_id": "A0A6G0RV74" }, { "activation": 20.921875, "uniref_id": "A0A5N4C1A1" }, { "activation": 20.84375, "uniref_id":...	[ { "activation": 18.699111938476562, "uniprot_id": "P17063" }, { "activation": 18.567176818847656, "uniprot_id": "Q9NFS4" }, { "activation": 18.163284301757812, "uniprot_id": "C0HJG9" }, { "activation": 17.720613479614258, "uniprot_id": "P08133" }, { "activation": ...	[ 1216, 8405, 14937, 3499, 1334, 3236, 7147, 4917, 15961, 3725 ]	0.23308

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ESMC Sparse Autoencoder Features Table

This dataset contains a Parquet table of the 16,384 features from the ESMC-6B-sae-layer60-k64-codebook16384, that was used for analysis in the ESMC paper and to construct the ESM Atlas. This table provides descriptions of the precomputed features that can be activated through the spotlight SAE model, assisting users for downstream interpretation of the insights revealed by ESMC.

Download the table here.

The features descriptions are in the table below.

Feature	Description
`feature_id`	The feature index.
`description`	Full description of the concept the feature activates on, produced by a multi-agent system based on activations of the feature in Swissprot. This description has 3 sections which are used to derive the `summary`, `activation_pattern`, and `exemplar_protein_families` columns. Note that these represent our best understanding of what each feature represents but are not necessarily comprehensive and may not capture nuances of features that have complex meaning or limited activation in Swissprot.
`summary`	Summary of the biological concept that is activated.
`activation_pattern`	The residue-level activation pattern of the feature with respect to the concepts described in the summary (ex. is the activation diffuse across an entire domain, or is it highly localized to one or more residues in specific locations).
`exemplar_protein_families`	Some of the common protein families/functions that the feature is found in. These are derived from the Swissprot data used to generate the description. These should not be considered exhaustive.
`threshold`	The activation threshold above which the feature description can be relied upon for accuracy.
`category`	Agent-generated categorization of the feature into 1 of 12 categories based on its description. Categories include things like "catalytic function", "compositional bias", and "structural motif".
`uniref90_frequency`	Frequency of activation of this feature in Uniref90 (total 208M proteins).
`uniref90_idf`	Inverse document frequency (IDF) of this feature in Uniref90 (derived from the frequency by `log(N / freq`), used for feature normalization.
`uniref90_max_activation`	Maximum activation value in Uniref90 (used alongside IDF for feature normalization).
`top_100_uniref_ids`	Top 100 proteins in Uniref90 by activation strength of this feature.
`top_swissprot_activations`	Top 100 proteins in a non-redundant subset of Swissprot (30% sequence identity clustered and filtered to high annotation score).
`decoder_nearest_neighbors`	10 nearest neighbor features in the SAE decoder latent space, i.e. the most semantically similar features according to the model.

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