gallery / domain / yc_pseudo_powdery_mildew / pairwise-diamond / enrichment (loss)

yc pseudo powdery mildew: functional enrichment (loss)

One-sided hypergeometric test per term; Benjamini-Hochberg FDR within each scope, level and vocabulary. Candidates are the loss candidates: gene families present in the OUT group and absent from the IN group. Universe: proteome. Background clustered: True (33210 sequences in 19924 clusters, mmseqs easy-cluster --min-seq-id 0.3 -c 0.8). Family level: one unit per candidate family and per background cluster.

Sources: Pfam: 2026-01-27-Pfam38.2; InterPro entries: 110.0; GO: releases/2026-07-26; analysis generated 2026-10-24T14:48:05. Source tables: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/analysis/enrichment/outputs/loss/proteome_clustered. Full record: PROVENANCE. Run report: report.html.

Caveats

Annotation provenance is not fully recorded: PROVENANCE.yaml lists the per-species annotation files and their checksums, but not the UniProt release they come from.
GO results are secondary. GO annotations include computational evidence (IEA, IBA); the GO evidence column shows if a term has non-IEA support.
Candidate families (pipeline clustering of candidates) and background clusters (mmseqs clustering of the background proteome) are made by different runs, so family-level counts are not fully comparable.

Summary figure

Annotation coverage

Fraction of proteins with at least one term per vocabulary. Universe = all proteins of the species; candidates = the candidate set.

Species	Set	Proteins	Pfam	Pfam clan	InterPro	GO	Any
Botrcine	universe	11742	71.7%	58.1%	76.9%	61.6%	77.2%
Botrcine	candidates	1200	84.2%	72.7%	91.8%	60.8%	92.1%
Sclescle	universe	14445	52.5%	42.6%	57.2%	47.0%	57.6%
Sclescle	candidates	1085	80.4%	68.5%	91.1%	61.2%	91.5%
Anid	universe	10561	78.2%	64.8%	83.1%	71.4%	83.7%
Anid	candidates	1253	84.5%	74.3%	92.2%	68.2%	92.8%
ALL_OUT	universe	36748	66.0%	53.9%	71.0%	58.7%	71.4%
ALL_OUT	candidates	3538	83.1%	72.0%	91.7%	63.5%	92.2%

Tests summary

Per vocabulary: terms with FDR < 0.05 / terms tested. Protein level counts proteins; family level counts candidate families and background clusters.

Scope	Level	Cand. units	Pfam sig / tested	Pfam clan sig / tested	InterPro sig / tested	GO sig / tested
whole_set	family	1984	63 / 668	14 / 307	108 / 1455	59 / 3269
whole_set	protein	3538	190 / 1592	46 / 412	367 / 3484	215 / 4799
Anid	family	1040	17 / 352	12 / 242	51 / 848	19 / 2712
Anid	protein	1253	49 / 464	19 / 256	100 / 1090	57 / 2883
Botrcine	family	1031	26 / 377	13 / 242	52 / 874	42 / 2545
Botrcine	protein	1200	39 / 450	14 / 255	80 / 1064	73 / 2696
Sclescle	family	992	16 / 339	8 / 237	33 / 825	41 / 2394
Sclescle	protein	1085	23 / 401	13 / 246	59 / 973	61 / 2519

Top 25 Pfam terms (whole set, family level)

25 rows shown, ordered by FDR then p-value; 25 have FDR < 0.05 (bold).

Term	Name	k / N cand.	n / M bg	Fold	FDR (BH)
PF24883	NPHP3_N: Nephrocystin 3, N-terminal	50 / 1598	82 / 11447	4.368	3.68e-20
PF22939	WHD_GPIID: GPI inositol-deacylase, winged helix domain	19 / 1598	23 / 11447	5.918	8.69e-11
PF00931	NB-ARC: NB-ARC domain	14 / 1598	14 / 11447	7.163	2.26e-10
PF00295	Glyco_hydro_28: Glycosyl hydrolases family 28	11 / 1598	12 / 11447	6.566	4.44e-07
PF03171	2OG-FeII_Oxy: 2OG-Fe(II) oxygenase superfamily	11 / 1598	12 / 11447	6.566	4.44e-07
PF14226	DIOX_N: non-haem dioxygenase in morphine synthesis N-terminal	11 / 1598	12 / 11447	6.566	4.44e-07
PF05368	NmrA: NmrA-like family	19 / 1598	37 / 11447	3.678	6.96e-06
PF03659	Glyco_hydro_71: Glycosyl hydrolase family 71	9 / 1598	10 / 11447	6.447	1.40e-05
PF13374	TPR_10: Tetratricopeptide repeat	17 / 1598	32 / 11447	3.806	1.40e-05
PF13424	TPR_12: Tetratricopeptide repeat	17 / 1598	33 / 11447	3.69	2.26e-05
PF00734	CBM_1: Fungal cellulose binding domain	15 / 1598	27 / 11447	3.98	2.82e-05
PF01408	GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold	11 / 1598	18 / 11447	4.378	2.61e-04
PF11951	Fungal_trans_2: Fungal specific transcription factor domain	36 / 1598	130 / 11447	1.984	0.001
PF04616	Glyco_hydro_43: Glycosyl hydrolases family 43	9 / 1598	15 / 11447	4.298	0.002
PF08386	Abhydrolase_4: TAP-like protein	6 / 1598	7 / 11447	6.14	0.002
PF11927	HODM_asu-like: Haem-dependent oxidative N-demethylase, alpha subunit-like	6 / 1598	7 / 11447	6.14	0.002
PF00248	Aldo_ket_red: Aldo/keto reductase family	12 / 1598	25 / 11447	3.438	0.002
PF00296	Bac_luciferase: Luciferase-like monooxygenase	5 / 1598	5 / 11447	7.163	0.002
PF04082	Fungal_trans: Fungal specific transcription factor domain	58 / 1598	251 / 11447	1.655	0.002
PF04479	RTA1: RTA1 like protein	8 / 1598	13 / 11447	4.408	0.003
PF01328	Peroxidase_2: Peroxidase, family 2	6 / 1598	8 / 11447	5.372	0.005
PF07519	Tannase: Tannase and feruloyl esterase	6 / 1598	8 / 11447	5.372	0.005
PF13450	NAD_binding_8: NAD(P)-binding Rossmann-like domain	11 / 1598	24 / 11447	3.283	0.005
PF13508	Acetyltransf_7: Acetyltransferase (GNAT) domain	9 / 1598	17 / 11447	3.792	0.005
PF13532	2OG-FeII_Oxy_2: 2OG-Fe(II) oxygenase superfamily	8 / 1598	14 / 11447	4.093	0.005

Top 25 InterPro terms (whole set, family level)

25 rows shown, ordered by FDR then p-value; 25 have FDR < 0.05 (bold).

Term	Name	k / N cand.	n / M bg	Fold	FDR (BH)
IPR056884	Domain:Nephrocystin 3-like, N-terminal	50 / 1788	82 / 12613	4.301	1.70e-19
IPR054471	Domain:GPI inositol-deacylase, winged helix domain	19 / 1788	23 / 12613	5.827	2.54e-10
IPR002182	Domain:NB-ARC	14 / 1788	14 / 12613	7.054	6.14e-10
IPR036188	Homologous_superfamily:FAD/NAD(P)-binding domain superfamily	71 / 1788	218 / 12613	2.297	1.04e-09
IPR036291	Homologous_superfamily:NAD(P)-binding domain superfamily	109 / 1788	409 / 12613	1.88	3.69e-09
IPR029058	Homologous_superfamily:Alpha/Beta hydrolase fold	89 / 1788	314 / 12613	1.999	7.45e-09
IPR027443	Homologous_superfamily:Isopenicillin N synthase-like superfamily	15 / 1788	19 / 12613	5.569	8.16e-08
IPR053137	Family:Nucleotide-binding leucine-rich repeat (NLR)-like	21 / 1788	36 / 12613	4.115	1.62e-07
IPR000743	Family:Glycoside hydrolase, family 28	11 / 1788	12 / 12613	6.466	6.25e-07
IPR026992	Domain:Non-haem dioxygenase, N-terminal domain	11 / 1788	12 / 12613	6.466	6.25e-07
IPR044861	Domain:Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain	11 / 1788	12 / 12613	6.466	6.25e-07
IPR005123	Domain:Oxoglutarate/iron-dependent dioxygenase domain	16 / 1788	26 / 12613	4.341	3.73e-06
IPR000254	Domain:Cellulose-binding domain	17 / 1788	29 / 12613	4.135	3.73e-06
IPR032466	Homologous_superfamily:Metal-dependent hydrolase	21 / 1788	43 / 12613	3.445	6.27e-06
IPR011050	Homologous_superfamily:Pectin lyase fold/virulence factor	16 / 1788	27 / 12613	4.18	6.27e-06
IPR012334	Homologous_superfamily:Pectin lyase fold	16 / 1788	27 / 12613	4.18	6.27e-06
IPR008030	Domain:NmrA-like domain	19 / 1788	37 / 12613	3.622	8.08e-06
IPR007111	Domain:NACHT nucleoside triphosphatase	14 / 1788	22 / 12613	4.489	1.06e-05
IPR005197	Family:Glycoside hydrolase family 71	9 / 1788	10 / 12613	6.349	1.52e-05
IPR052523	Family:Acetyltransferase SAT19-like	15 / 1788	27 / 12613	3.919	4.15e-05
IPR050346	Family:Flavin-containing monooxygenases-like	11 / 1788	16 / 12613	4.85	6.86e-05
IPR035971	Homologous_superfamily:Cellulose-binding domain superfamily	14 / 1788	26 / 12613	3.798	1.50e-04
IPR023296	Homologous_superfamily:Glycosyl hydrolase, five-bladed beta-propeller domain superfamily	12 / 1788	21 / 12613	4.031	3.32e-04
IPR000683	Domain:Gfo/Idh/MocA-like oxidoreductase, N-terminal	11 / 1788	18 / 12613	4.311	3.32e-04
IPR051601	Family:Serine protease/Carboxylesterase S33	7 / 1788	8 / 12613	6.172	4.51e-04

Top 15 GO terms (whole set, family level) — secondary, computational evidence (IEA/IBA) included

15 rows shown, ordered by FDR then p-value; 15 have FDR < 0.05 (bold).

Term	Name	k / N cand.	n / M bg	Fold	FDR (BH)	GO evidence	Families with non-IEA
GO:0016491	molecular_function:oxidoreductase activity	218 / 1203	937 / 9824	1.9	8.23e-20	has_non_IEA	92
GO:0003824	molecular_function:catalytic activity	700 / 1203	4500 / 9824	1.27	4.36e-17	has_non_IEA	290
GO:0004553	molecular_function:hydrolase activity, hydrolyzing O-glycosyl compounds	75 / 1203	236 / 9824	2.595	8.69e-13	has_non_IEA	33
GO:0016798	molecular_function:hydrolase activity, acting on glycosyl bonds	80 / 1203	261 / 9824	2.503	8.69e-13	has_non_IEA	35
GO:0000272	biological_process:polysaccharide catabolic process	44 / 1203	101 / 9824	3.558	1.88e-12	has_non_IEA	33
GO:0016052	biological_process:carbohydrate catabolic process	59 / 1203	166 / 9824	2.902	2.47e-12	has_non_IEA	44
GO:0005975	biological_process:carbohydrate metabolic process	110 / 1203	433 / 9824	2.075	5.73e-12	has_non_IEA	53
GO:0005976	biological_process:polysaccharide metabolic process	51 / 1203	143 / 9824	2.912	1.17e-10	has_non_IEA	40
GO:0050660	molecular_function:flavin adenine dinucleotide binding	68 / 1203	227 / 9824	2.446	1.98e-10	has_non_IEA	9
GO:0045488	biological_process:pectin metabolic process	19 / 1203	26 / 9824	5.968	3.45e-10	has_non_IEA	17
GO:0045490	biological_process:pectin catabolic process	19 / 1203	26 / 9824	5.968	3.45e-10	has_non_IEA	17
GO:0005576	cellular_component:extracellular region	93 / 1203	376 / 9824	2.02	2.21e-09	has_non_IEA	42
GO:0016787	molecular_function:hydrolase activity	269 / 1203	1560 / 9824	1.408	4.50e-08	has_non_IEA	120
GO:0043531	molecular_function:ADP binding	14 / 1203	18 / 9824	6.352	7.05e-08	IEA_only	0
GO:0030248	molecular_function:cellulose binding	18 / 1203	31 / 9824	4.742	3.18e-07	IEA_only	0

Actin cytoskeleton controls

Known actin-related families and how many of their proteins pass each filter. Protein ID columns are left out.

control	pfam_ids	desc_regex	OUT_universe	OUT_in_matrix	OUT_pass_outgroup_rule	near_miss_in2	n_Botrcine	n_Sclescle	n_Anid	n_Blumgram	n_Blumhord	n_Erysneca	n_Podoxant
Arp2/3 ARPC2 (P34-Arc)	PF04045		3	3	3	0	1	1	1	1	1	0	1
Arp2/3 ARPC3 (P21-Arc)	PF04062		3	3	3	0	1	1	1	0	1	1	1
Arp2/3 ARPC4	PF05856		3	3	3	0	1	1	1	1	1	0	1
Arp2/3 ARPC5 (P16-Arc)	PF04699		3	3	3	0	1	1	1	1	0	1	1
Arp2/3 ARPC1 (description only)		arp2/3 complex.*(41\|p41\|subunit 1)\|ARPC1	0	0	0	0	0	0	0	0	0	0	0
Arp2 / Arp3 (description only)		actin-related protein (2\|3)\b\|\bARP[23]\b	18	18	18	0	5	6	7	4	4	3	0
WAVE complex NCKAP1	PF09735		0	0	0	0	0	0	0	0	0	0	0
WAVE complex CYFIP (FragX_IP)	PF05994		0	0	0	0	0	0	0	0	0	0	0
WAVE complex ABI	PF07815\|PF27594		0	0	0	0	0	0	0	0	0	0	0
SCAR/WAVE (SCAR_helical)	PF27569		0	0	0	0	0	0	0	0	0	0	0
WASP family (WH1)	PF00568		3	3	3	0	1	1	1	0	1	1	1
WH2 motif (WASP, WAVE, others)	PF02205		5	5	5	3	1	1	3	0	0	1	1
Formin FH2	PF02181		3	3	3	0	1	1	1	0	1	1	1
Formin Drf_GBD / Drf_FH3 / Drf_DAD	PF06371\|PF06367\|PF06345		6	6	6	0	2	2	2	2	2	2	1
Ena/VASP (VASP_tetra)	PF08776		0	0	0	0	0	0	0	0	0	0	0
Coronin (description only)		coronin	3	3	3	0	1	1	1	1	1	1	0
Cortactin (HS1_rep)	PF02218		0	0	0	0	0	0	0	0	0	0	0
Myosin 2 tail (Myosin_tail_1)	PF01576		0	0	0	0	0	0	0	0	0	1	0
Myosin head (all myosins)	PF00063		13	13	13	0	4	4	5	3	4	4	3

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