This reproduces tables from "DALI shines a light on remote homologs" by Holm et al. (2022).

Table 1. AlphaFold models validated by recently released PDB structures.

pfamid	pfam_description	accession	from	to	PDB hit	Z	rmsd	lali	%ide
PF03080	Neprosin	O64859	184	395	7zvaA	28.1	1.3	208	51
PF03706	Lysylphosphatidylglycerol synthase TM region	P75770	14	296	7duwA	26.6	2.4	239	26
PF03802	Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase	P0A6G5	13	177	7dcmA	27.6	0.9	165	99
PF04113	Gpi16 subunit, GPI transamidase component	E9QH65	77	628	7w72T	52.5	7.8	520	69
PF04114	Gaa1-like, GPI transamidase component	Q6AYM8	125	615	7w72A	42.3	1.1	465	93
PF04573	Signal peptidase subunit	I1JRE6	1	165	7p2pB	12.3	2.4	162	30
PF06703	Microsomal signal peptidase 25 kDa subunit (SPC25)	P58684	23	181	7p2qC	13.5	2.5	156	27
PF08014	Domain of unknown function (DUF1704)	Q7TQE7	265	511	7z5gB	33.9	0.7	247	66
PF09773	Meckelin (Transmembrane protein 67)	E9QB24	156	982	7fh1A	44.6	2.0	730	62
PF10510	Phosphatidylinositol-glycan biosynthesis class S protein	Q96S52	22	547	7w72S	44.4	2.7	511	92
PF11380	Stealth protein CR2, conserved region 2	Q54UF6	90	198	7dxiB	8.7	1.8	108	38
PF11744	Aluminium activated malate transporter	K7VD86	88	494	7vojA	35.0	2.0	338	47
PF12810	Glycine rich protein	Q9UM73	726	987	7ls0B	38.3	0.6	225	100
PF15778	UNC80 N-terminal	Q8N2C7	16	236	7sx3E	11.4	4.9	239	89
PF17517	IgGFc binding protein	Q9Y6R7	129	419	7wpqE	13.8	3.7	252	33

Table 2: Statistically significant sequence conservation in binomial test

pfamid	Bonf. p	pfam_description	PDB hit’s family	PDB hit	Z	%ide
PF03016	0.00141	Exostosin family with glycosyltransferase activities	PF05686 Glycosyltransferase family 90	5f84A	11.7	14
PF03690	0.0221	Uncharacterised protein family (UPF0160); DHH motif	PF01368 DHH family phosphoesterase (CL0137)	6mtzB	8.3	24
PF03942	0.00417	DTW domain	PF04034 RIbosome biogenesis protein, C-terminal	5apgA	9.8	21
PF04250	0.000649	Protein of unknown function (DUF429)	PF02075 Crossover junction endodeoxyribonuclease RuvC (CL0219)	6s16B	9.5	15
PF04293	0.00291	SpoVR like protein	PF05960 Bacterial protein of unknown function (DUF885)	3o0yA	13.2	14
PF04632	1.08E-10	Fusaric acid resistance protein family	PF11744 Aluminium activated malate transporter	7vq3A	12.7	19
PF06356	0.0330	Protein of unknown function (DUF1064)	PF08722 (CL0236) TnsA-like endonuclease	1t0fA	8.3	13
PF07759	1.94E-07	Protein of unknown function (DUF1615)	PF01464 Transglycosylase SLT domain (CL0037)	6cf9A	12.3	18
PF08889	7.61E-05	WbqC-like protein family	PF10079 Bacillithiol biosynthesis BshC	4wbdA	12.1	12
PF10070	9.41E-10	Probable inorganic carbon transporter subunit DabA	PF08936 Carboxysome shell carbonic anhydrase	2fgyA	13.5	13
PF10307	0.00428	HAD domain family 1 in Swiss Army Knife RNA repair proteins	PNKP1, component of bacterial RNA repair complex	4xruA	10.2	14
PF11001	0.0310	Protein of unknown function (DUF2841)	PF04873 Ethylene insensitive 3	4zdsA	12.0	20
PF11070	0.000261	Protein of unknown function (DUF2871)	PF00115 Cytochrome c and quinol oxidase polypeptide I (CL0714)	6lh3B	13.8	19
PF11765	0.00648	Hyphally regulated cell wall protein N-terminal	Adhesin-like wall protein 3b	7o9oA	28.6	18
PF11875	0.0404	DnaJ-like protein C11, C-terminal	PF02140 Galactose binding lectin domain	2zx0A	3.9	19
PF11904	0.00762	GPCR-chaperone. Adjust domain boundaries.	LolA/B superfamily of lipoprotein localization factors (CL0048)	2zf4F	4.4	15
PF12062	0.000201	heparan sulfate-N-deacetyse	Carbohydrate deacetylase Agd3	6nwzA	18.5	20
PF12222	1.64E-06	Peptide N-acetyl-beta-D-glucosaminyl asparaginase amidase A	PF09112, PF09113 Peptide-N-glycosidase F (CL0612)	4r4xA	18.4	17
PF12617	0.00701	Iron-Sulfur binding protein C terminal	PF01680 SOR/SNZ family (CL0036)	4wy0G	6.8	15
PF13258	2.41E-05	Domain of unknown function (DUF4049)	Tyrosine protein phosphatase WipA from Legionella	5n6xA	15.4	16
PF13898	0.0374	Deubiquitinating enzyme MINDY-3/4, conserved domain	Deubiquitinase	7bu0A	3.8	9
PF14033	0.0350	Protein of unknown function (DUF4246)	PF13640 2OG-Fe(i) oxygenase superfamily (CL0029)	6n1fA	13.0	9
PF14130	0.0200	Cap4 dsDNA endonuclease	N-terminal endonuclease domain	6vm6B	11.8	10
PF14646	4.99E-05	MYCBP-associated protein family	PapD-like domain 7 (cell cycle protein)	6fviA	10.8	17
PF14923	0.0211	Coiled-coil protein 142	PF07393 Exocyst complex component Sec10 (CL0294)	5h11A	13.4	9
PF14976	0.00943	FAM72 protein	PF03226 Yippe zinc-binding/DNA-binding Mis18, centromere assembly (CL0080)	5hj0C	10.0	13
PF15851	0.00453	Domain of unknown function (DUF4723)	Glycosylphosphatidulinositol-anchored high density lipoproterin-binding protein 1	6e7kC	11.1	24
PF16062	4.79E-06	Domain of unknown function (DUF4804)	Legionella effector protein MavL	6omiB	28.6	16
PF17659	1.69E-08	Family of unknown function (DUF5521)	PF16900 Replication protein A OB domain	4gnxC	13.1	18
PF17720	6.78E-07	Family of unknown function (DUF5565)	PF09414 RNA ligase (CL0078)	5cotA	7.3	18
PF18168	0.0289	Prim-pol family 5	PF01896 DNA primase small subunit (CL0243)	5l2xA	10.7	15
PF18658	0.0274	Spin-doc zinc-finger	PF19088 TUTase nucleotidyltransferase domain	6iw6A	4.2	14

Table 3: Related known functions

pfamid	pfam_description	PDB hit’s family	PDB hit	Z	%ide	Type
PF01548	Transposase	PF02075 Crossover junction endodeoxyribonuclease RuvC (CL0219)	4ld0B	11.7	15	E
PF01955	Adenosylcobinamide amidohydrolase	PF03576 Peptidase family S58 (CL0635)	5xyoA	11.0	6	E
PF03859	CG-1 domain	PF08549 SWI/SNF and RSC complexes subunit Ssr4 N-terminal (Holm 2022a)	7k7vA	9.7	25	B
PF04479	RTA1 like protein. 7 transmembrane helices.	PF01036 Bacteriorhodopsin-like protein (CL0192)	1x0k1	13.0	10	T
PF04666	DUF659 Protein of unknown function (transposase-like proteins with no known function)	DNA transposase	2apcA	18.2	14	E
PF04709	Anti-Mullerian hormone, N terminal region	PF00688 TGF-beta propeptide	6sf2F	6.0	20	B
PF04724	Glycosyltransferase family 17	PF00535 Glycosyl transferase family 2	6e4qA	10.7	10	E
PF04765	Protein of unknown function (DUF616). A number of the members are thought to be glycosyltransferases.	PF03414 Glycosyltransferase family 6	2vs3A	10.6	7	E
PF04833	COBRA-like protein	PF00553 Cellulose-binding domain	6qfsA	8.4	21	B
PF05123	S-layer like family, N-terminal region	PF07752 S-layer protein	3u2gA	3.2	12	S
PF05124	S-layer like family, C-terminal region	PDB protein’s sequence assigned to the same Pfam family, but link is missing from pdbmap.	6npsA	6.5	16	S
PF05428	Corticotropin-releasing factor binding protein (CRF-BP)	PF00431 CUB domain (CL0164). Involved in binding interaction partners.	6fzwD	8.9	21	B
PF05458	Cd27 binding protein (Siva). Zinc finger.	PF02318 FYVE-like zinc finger (CL0390)	2cjsC	6.1	10	B
PF06081	Aromatic acid exporter family member 1	PF06081 Aromatic acid exporter family member 1	7vg3B	13.3	25	T
PF06189	5'-nucleotidase	Polynucleotide kinase	5ujoB	9.6	14	E
PF06420	Mitochondrial genome maintenance MGM101	PF04098 Rad52/22 family double-strand break repair protein	5xs0G	12.4	16	B
PF06524	NOA36 protein (zinc finger protein 330)	PF00643 B-box zinc finger	6imqA	4.5	17	B
PF07906	ShET2 enterotoxin, N-terminal region. Is a cysteine protease (Pearson et al., 2017)	Ubiquitin-specific protease (Schlieker et al., 2007)	2j7qA	9.6	8	E
PF07958	Protein of unknown function (DUF1688). Involved in uracil catabolism	PF09171 N-glycosylase/DNA lyase	1xqpA	11.9	12	E
PF09317	Acyl-CoA dehydrogenase, C-terminal, bacterial type	C-terminal domain of acyl-CoA dehydrogenase	3owaA	11.6	12	E
PF10113	FeGP cofactor biosynthesis protein, fibrillarin family	PF04055 Radical SAM superfamily (CL0036)	3t7vA	19.8	16	E
PF10238	E2 transcripion factor associated phosphoprotein	PF03228 Yippee zinc-binding/DNA-binding Mis18, centromere assembly	5hj0C	9.2	15	B
PF10337	Putative ER transporter, 6TM, N-terminal	PF11447 Aluminium activated malate transporter	7vojA	16.3	11	T
PF10343	Potential Queuosine, Q, salvage protein family. DNA glycosidase activity has been suggested.	PF09171 N-glycosylase/DNA lyase	1xqoA	12.8	9	E
PF11726	Inovirus Gp2. Involved in viral DNA replication via phospho-Tyr mechanism.	HUH-endonuclease superfamily	2x3gA	7.8	11	E
PF12141	Beta-mannosyltransferases	PF04041 beta-1,4-mannooligosaccharide phosphorylase (CL0143)	3tawA	20.8	11	E
PF14249	Tocopherol cyclase	Diels-Alderase (pericyclase)	7dmnA	21.7	8	E
PF14616	Transcription regulator Rua1, C-terminal	Transcriptional regularot KAISO	2lt7A	3.0	18	B
PF15051	FAM198 protein. UniProt annotates query protein as Golgi associated kinase 1b.	PF06702 Golgi casein kinase, C-terminal, Fam20	5yh3A	18.3	18	E
PF15083	Colipase-like	PF01114 Colipase, N-terminal domain; PF02740 Colipase, C-terminal domain (CL0621)	1lpbA	3.2	22	B
PF15704	Mitochondrial ATP synthase subunit	Mitochondrial ATP synthase associated protein ASA4	6rdq4	9.0	13	B
PF16094	Proteasome assembly chaperone 4	PF09754 Pac2 family (proteasome assembly chaperone)	3wz2A	17.5	8	B
PF16887	Domain of unknown function (DUF5081). Believed to be involved in type VII secretion system.	PF14011 EspG family (secretion-associated proteins)	4w4lC	11.3	8	T
PF17184	Rit1 N-terminal domain of tRNA modifying enzyme	PF00156 Phosphoribosyltransferase domain (CL0533)	7kl7A	4.4	9	E
PF18143	HAD domain phosphoesterases in Swiss Army Knife RNA repair proteins	Inorganic pyrophosphatase, member of the haloacid dehalogenase superfamily (CL0137)	3qu2D	8.2	10	E
PF19043	Nuclear cap binding complex subunit CBP66	PF07065 Cell division cycle protein 123	4zgoA	16.4	14	B
PF19306	Helicase Lhr winged helix domain	Winged helix domain of ATP-dependent DNA helicase (Jones et al., 2018).	5v9xA	14.1	25	B

Table 4: Putative function transfer

pfamid	pfam_description	PDB hit’s family	PDB-id	Z	%ide	shared motif
PF00674	DUP family	Myb-like DNA-binding domain	2m3aA	5.3	18	Conserved Pro, Trp
PF04755	Plastid lipid associated protein and fibrillins	PF00061 Lipocalin / cytosolic fatty-acid binding protein	2wq9A	9.5	11	Conserved Trp
PF04937	DUF659 Protein of unknown function	Transposase	2bw3A	7.9	13	Conserved Trp, Asp, Cys
PF05212	Protein of unknown function (DUF707)	PF00535 glycosyltransferase family 2	6h2nB	12.7	7	Conserved DxD contact substrate
PF05444	Protein of unknown function (DUF753)	LY6/PLAUR domain	6ionA	5.4	23	Five conserved disulphide bridges
PF05912	Caenorhabditis elegans protein of unknown function (DUF870)	PF01060 Transthyretin-like family (CL0287)	3uafA	9.5	17	C, HxC form conserved disulphide bridge
PF07505	Protein of unknown function (DUF5131)	Spore photoproduct lyase	4rh1A	14.1	11	Three conserved Cys and Asp
PF07712	Stress up-regulated Nod 19	Pf01082 & PF03712 Copper type II ascorbate-dependent monooxygenase, N-terminal & C-terminal domains (CL0612)	6alaA	17.1	11	Conserved HH, HxH, M contact cofactor
PF08795	Putative papain-like cysteine peptidase (DUF1796)	PF08942 Domain of unknown function (DUF1919)	2g6tA	7.3	11	Conserved catalytic dyad Cys30/Cys119, His90/His192
PF09725	Folate-sensitive fragile site protein Fra10Ac1	N-terminal zinc finger domain of transcription repressor Val1	5yugE	2.7	16	Conserved CCCC zinc finger
PF09887	Uncharacterized protein conserved in archaea (DUF2114)	PF03702 Anhydro-N-acetylmuramic acid kinase (CL0108)	4bgbB	18.5	13	GN, G, D - Asp233/Asp165 contact substrate
PF09892	Uncharacterized protein conserved in archaea (DUF2119)	PF04952 Succinylglutamate desuccinylase / Aspartoacylase family	3cdxF	10.6	13	Conserved calcium binding residues GxHGxE, H, E
PF09909	Uncharacterized protein conserved in bacteria (DUF2138)	Fusion of (i) the treponema porin (t-por) family, and (ii) PF14032 PknH-like extracellular domain (CL0619)	3k8iA, 4esqA	7.9, 6.2	9, 7	Structural modeling suggests it is a fusion of porin and extracellular sensor domain
PF10118	Predicted metal-dependent hydrolase	PF00268 ribonucleotide reductase, small chain	1w69A	14.0	13	Conserved E, H, E, H in active site
PF10170	Cysteine-rich domain	PF02318 FYVE-like zinc finger (CL0390)	2cjsC	4.4	23	Two CCCC zinc fingers
PF10223	Uncharacterized conserved protein (DUF2181)	PF03009 phosphodiesterase (CL0384)	4oecB	16.3	19	Conserved H, ExD, H bind Mg ion
PF10561	C2orf69	PF00756 Putative esterase	6gi0A	6.0	10	Conserved GxSxGG motif in catalytic site (Perraud et al., 2018)
PF10936	Protein of unknown function (DUF2617)	PF01536 Adenosylmethionine decarboxylase	1jl0A	8..1	12	Conserved catalytic His (Ekstrom et al., 2001)
PF10974	Protein of unknown function (DUF2804)	PF07143 CrtC N-terminal lipcalin domain; PF17186 Lipocalin-like domain	2ichA	20.2	10	Conserved Trp
PF11296	Protein of unknown function (DUF3097)	Class 2 old family nuclease	6nk8A	9.7	10	Conserved Asp, Glu bind Mg
PF11443	Domain of unknown function (DUF2828)	PF05731 TROVE domain – RNA binding protein	1yvrA	16.9	11	Large common core (403 residues)
PF12038	Domain of unknown function (DUF3524)	PF13579 Glycosyl transferase 4-like domain.	6kihD	13.5	15	essential His near UDP at domain interface
PF14001	YdfZ protein.	KOW domain, involved in RNA binding	5oikZ	7.7	18	DxxxN, GxxG
PF15016	Domain of unknown function (DUF4520)	PF00659 POLO box duplicated region	4x9vA	11.8	13	Structural resemblance
PF15025	Domain of unknown function (DUF4524)	PF00659 POLO box duplicated region	4xb0A	9.3	11	Structural resemblance
PF15094	Domain of unknown function (DUF4556).	Zona pellucida sperm-binding protein	6gf6B	5.6	12	Conserved disulphide bridge
PF15474	Meiotically up-regulated gene family	PF09044 KP4 killer toxin.	1kptA	10.2	19	Two conserved disulphide bridges
PF15749	MRN-interacting protein	PF09082 Domain of unknown function (DUF1922)	1gh9A	2.9	17	Conserved CCCC zinc finger
PF15866	Domain of unknown function (DUF4729)	PF03145 Seven in absentia protein family (CL0389(	4ca1A	11.5	9	Conserved CCHH zinc finger
PF16044	Domain of unknown function (DUF4796)	PF05903 PPPDE peptidase domain (CL0125)	3ebqA	7.6	12	Conserved H, C bind metal ion
PF17249	Family of unknown function (DUF5318)	PF03367 ZPR1 zinc-finger domain (CL0167)	2qkdA	3.6	17	Conserved CCCC zinc finger