gallery / domain / serinales_vs_pichiales_v2 / pairwise-diamond / enrichment (loss)

serinales vs pichiales v2: 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 (71861 sequences in 22669 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 2026-10-16T22:54:46. Source tables: studies/fungi/serinales_vs_pichiales_v2/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
Babjinos	universe	6393	79.0%	62.0%	82.1%	74.0%	82.4%
Babjinos	candidates	15	86.7%	60.0%	93.3%	73.3%	93.3%
Komaphaf	universe	5075	87.7%	68.1%	90.6%	82.5%	90.9%
Komaphaf	candidates	21	85.7%	76.2%	85.7%	57.1%	85.7%
Kuracaps	universe	6027	84.6%	67.4%	88.0%	79.2%	88.3%
Kuracaps	candidates	31	90.3%	64.5%	90.3%	64.5%	93.5%
Pichmemb	universe	5536	81.6%	64.9%	85.0%	77.1%	85.3%
Pichmemb	candidates	24	75.0%	54.2%	87.5%	54.2%	87.5%
Pichkudr	universe	5146	86.7%	68.2%	90.4%	81.9%	90.7%
Pichkudr	candidates	24	87.5%	66.7%	95.8%	62.5%	95.8%
Bretnaar	universe	5164	88.4%	70.2%	91.7%	82.9%	92.2%
Bretnaar	candidates	33	93.9%	72.7%	97.0%	63.6%	100.0%
Ogatpoly	universe	6801	68.1%	55.0%	70.8%	64.0%	71.0%
Ogatpoly	candidates	28	96.4%	64.3%	100.0%	64.3%	100.0%
Pachtann	universe	5643	85.8%	67.1%	88.9%	80.3%	89.3%
Pachtann	candidates	21	85.7%	66.7%	85.7%	57.1%	85.7%
Sacccere	universe	6066	88.6%	66.3%	90.9%	94.8%	96.4%
Sacccere	candidates	25	96.0%	64.0%	100.0%	100.0%	100.0%
Kluylact	universe	5071	90.6%	68.8%	93.2%	84.4%	93.8%
Kluylact	candidates	27	92.6%	66.7%	96.3%	70.4%	96.3%
Lachther	universe	5093	91.7%	69.8%	94.6%	85.0%	95.0%
Lachther	candidates	28	92.9%	64.3%	100.0%	67.9%	100.0%
Candglab	universe	5198	91.2%	68.9%	94.1%	89.9%	95.3%
Candglab	candidates	24	95.8%	66.7%	100.0%	75.0%	100.0%
Torudelb	universe	4974	92.9%	70.1%	95.3%	90.9%	96.5%
Torudelb	candidates	25	92.0%	68.0%	96.0%	88.0%	100.0%
ALL_OUT	universe	72187	85.4%	66.3%	88.3%	81.6%	89.2%
ALL_OUT	candidates	326	90.5%	66.0%	94.8%	69.0%	95.7%

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	174	15 / 1262	6 / 318	30 / 2404	35 / 4466
whole_set	protein	326	34 / 4298	15 / 480	64 / 8828	88 / 7183
Babjinos	family	15	0 / 170	0 / 184	0 / 487	0 / 2443
Babjinos	protein	15	0 / 246	0 / 204	0 / 648	0 / 2598
Bretnaar	family	33	0 / 148	0 / 174	0 / 443	0 / 1868
Bretnaar	protein	33	0 / 199	0 / 188	0 / 559	0 / 2003
Candglab	family	24	0 / 152	0 / 169	0 / 447	0 / 3063
Candglab	protein	24	0 / 215	0 / 189	0 / 597	0 / 3216
Kluylact	family	27	0 / 149	0 / 173	0 / 448	0 / 1952
Kluylact	protein	27	0 / 187	0 / 184	0 / 536	0 / 2051
Komaphaf	family	21	0 / 145	0 / 172	0 / 438	0 / 2423
Komaphaf	protein	21	0 / 181	0 / 186	0 / 530	0 / 2522
Kuracaps	family	31	0 / 171	0 / 186	0 / 479	0 / 2465
Kuracaps	protein	31	0 / 237	0 / 201	0 / 622	0 / 2583
Lachther	family	28	0 / 147	0 / 175	0 / 443	0 / 1931
Lachther	protein	28	0 / 193	0 / 185	0 / 544	0 / 2056
Ogatpoly	family	28	0 / 169	0 / 181	0 / 480	0 / 2047
Ogatpoly	protein	28	0 / 207	0 / 194	0 / 585	0 / 2155
Pachtann	family	21	0 / 169	0 / 176	0 / 473	0 / 2075
Pachtann	protein	21	0 / 227	0 / 190	0 / 606	0 / 2230
Pichkudr	family	24	0 / 149	0 / 173	0 / 419	0 / 2013
Pichkudr	protein	24	0 / 202	0 / 191	0 / 543	0 / 2138
Pichmemb	family	24	0 / 153	0 / 176	0 / 451	0 / 2326
Pichmemb	protein	24	0 / 200	0 / 194	0 / 565	0 / 2420
Sacccere	family	25	0 / 169	0 / 175	0 / 486	0 / 3431
Sacccere	protein	25	0 / 269	0 / 200	0 / 711	0 / 3712
Torudelb	family	25	0 / 143	0 / 173	0 / 436	0 / 3145
Torudelb	protein	25	0 / 195	0 / 188	0 / 544	0 / 3235

Top 25 Pfam terms (whole set, family level)

25 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)
PF29832	SOV1_middle: SOV1 mitochondrial middle domain	7 / 151	7 / 14609	96.748	1.38e-11
PF01369	Sec7: Sec7 domain	7 / 151	17 / 14609	39.838	1.23e-07
PF00011	HSP20: Hsp20/alpha crystallin family	5 / 151	7 / 14609	69.106	9.59e-07
PF12330	Haspin_kinase: Haspin like kinase domain	4 / 151	5 / 14609	77.399	1.72e-05
PF08528	Whi5: Whi5 like	5 / 151	15 / 14609	32.249	7.70e-05
PF01417	ENTH: ENTH domain	5 / 151	17 / 14609	28.455	1.30e-04
PF17315	FMP23: Found in mitochondrial proteome	4 / 151	8 / 14609	48.374	1.34e-04
PF08539	HbrB: HbrB-like	4 / 151	9 / 14609	42.999	2.09e-04
PF02037	SAP: SAP domain	5 / 151	21 / 14609	23.035	2.76e-04
PF12709	Fungal_TACC: Fungal Transforming acidic coiled-coil (TACC) proteins	4 / 151	10 / 14609	38.699	2.77e-04
PF00498	FHA: FHA domain	6 / 151	42 / 14609	13.821	4.89e-04
PF04193	PQ-loop: PQ loop repeat	5 / 151	30 / 14609	16.125	0.001
PF01424	R3H: R3H domain	4 / 151	16 / 14609	24.187	0.002
PF10452	TCO89: TORC1 subunit TCO89	3 / 151	7 / 14609	41.464	0.003
PF08550	GATA_AreA: Nitrogen regulatory protein areA, GATA-like domain	4 / 151	24 / 14609	16.125	0.008
PF08737	Rgp1: Rgp1	2 / 151	5 / 14609	38.699	0.082
PF11470	TUG-UBL1: TUG ubiquitin-like domain	2 / 151	6 / 14609	32.249	0.115
PF20775	Tag1_N: Tag1 N-terminal domain	2 / 151	7 / 14609	27.642	0.151
PF12660	zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex	2 / 151	8 / 14609	24.187	0.189
PF01846	FF: FF domain	2 / 151	9 / 14609	21.5	0.219
PF22786	Tag1_C: Tag1 C-terminal domain	2 / 151	9 / 14609	21.5	0.219
PF02194	PXA: PXA domain	2 / 151	11 / 14609	17.591	0.301
PF02535	Zip: ZIP Zinc transporter	2 / 151	11 / 14609	17.591	0.301
PF02936	COX4: Cytochrome c oxidase subunit IV	2 / 151	12 / 14609	16.125	0.344
PF30880	PRTT-like_M: Transcriptional activator of proteases prtT middle domain	2 / 151	13 / 14609	14.884	0.388

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)
IPR063435	Domain:SOV1, middle domain	7 / 161	7 / 15485	96.18	2.77e-11
IPR050923	Family:Cellular Process Regulator and RNA Processing Protein	6 / 161	6 / 15485	96.18	1.38e-09
IPR000904	Domain:Sec7 domain	7 / 161	17 / 15485	39.604	9.87e-08
IPR023394	Homologous_superfamily:Sec7, C-terminal domain superfamily	7 / 161	17 / 15485	39.604	9.87e-08
IPR035999	Homologous_superfamily:Sec7 domain superfamily	7 / 161	17 / 15485	39.604	9.87e-08
IPR031107	Family:Small heat shock protein	5 / 161	6 / 15485	80.15	2.72e-07
IPR002068	Domain:Alpha crystallin/Hsp20 domain	5 / 161	7 / 15485	68.7	8.10e-07
IPR039198	Family:Srl3/Whi5	5 / 161	8 / 15485	60.113	1.87e-06
IPR005282	Family:Lysosomal cystine transporter	5 / 161	10 / 15485	48.09	7.37e-06
IPR024604	Domain:Serine/threonine-protein kinase haspin, C-terminal	4 / 161	5 / 15485	76.944	1.22e-05
IPR038882	Family:Respiratory complex factor Rcf3	4 / 161	5 / 15485	76.944	1.22e-05
IPR008978	Homologous_superfamily:HSP20-like chaperone	5 / 161	14 / 15485	34.35	4.25e-05
IPR013734	Conserved_site:Transcription factor Nrm1/Whi5	5 / 161	15 / 15485	32.06	5.83e-05
IPR035283	Domain:Protein Fmp23	4 / 161	8 / 15485	48.09	1.31e-04
IPR013745	Family:TORC2 component Bit61/PRR5	4 / 161	9 / 15485	42.747	2.18e-04
IPR024312	Domain:TACC, C-terminal, fungi	4 / 161	10 / 15485	38.472	3.38e-04
IPR003034	Domain:SAP domain	5 / 161	23 / 15485	20.909	4.67e-04
IPR013809	Domain:ENTH domain	5 / 161	25 / 15485	19.236	6.85e-04
IPR036361	Homologous_superfamily:SAP domain superfamily	5 / 161	27 / 15485	17.811	9.69e-04
IPR006603	Repeat:PQ-loop repeat	5 / 161	30 / 15485	16.03	0.002
IPR000253	Domain:Forkhead-associated (FHA) domain	6 / 161	51 / 15485	11.315	0.002
IPR008984	Homologous_superfamily:SMAD/FHA domain superfamily	6 / 161	52 / 15485	11.098	0.002
IPR001374	Domain:R3H domain	4 / 161	17 / 15485	22.631	0.003
IPR036867	Homologous_superfamily:R3H domain superfamily	4 / 161	18 / 15485	21.373	0.003
IPR018857	Family:TORC1 complex, subunit TCO89	3 / 161	7 / 15485	41.22	0.003

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:0032012	biological_process:regulation of ARF protein signal transduction	7 / 111	18 / 13320	46.667	3.04e-07	IEA_only	0
GO:0038201	cellular_component:TOR complex	7 / 111	33 / 13320	25.455	1.84e-05	has_non_IEA	1
GO:0015184	molecular_function:L-cystine transmembrane transporter activity	5 / 111	11 / 13320	54.545	2.43e-05	has_non_IEA	1
GO:0072354	molecular_function:histone H3T3 kinase activity	4 / 111	5 / 13320	96.0	2.53e-05	IEA_only	0
GO:0000099	molecular_function:sulfur amino acid transmembrane transporter activity	5 / 111	14 / 13320	42.857	6.18e-05	has_non_IEA	1
GO:0140996	molecular_function:histone H3 kinase activity	4 / 111	7 / 13320	68.571	1.17e-04	IEA_only	0
GO:0051056	biological_process:regulation of small GTPase mediated signal transduction	7 / 111	53 / 13320	15.849	1.55e-04	IEA_only	0
GO:0072349	molecular_function:modified amino acid transmembrane transporter activity	5 / 111	18 / 13320	33.333	1.55e-04	has_non_IEA	1
GO:0035173	molecular_function:histone kinase activity	4 / 111	8 / 13320	60.0	1.55e-04	IEA_only	0
GO:0030118	cellular_component:clathrin coat	5 / 111	19 / 13320	31.579	1.58e-04	IEA_only	0
GO:0030125	cellular_component:clathrin vesicle coat	5 / 111	19 / 13320	31.579	1.58e-04	IEA_only	0
GO:0031929	biological_process:TOR signaling	7 / 111	59 / 13320	14.237	2.05e-04	has_non_IEA	1
GO:0033309	cellular_component:SBF transcription complex	5 / 111	24 / 13320	25.0	4.72e-04	has_non_IEA	1
GO:0035556	biological_process:intracellular signal transduction	18 / 111	589 / 13320	3.667	5.26e-04	has_non_IEA	4
GO:0031930	biological_process:mitochondria-nucleus signaling pathway	4 / 111	14 / 13320	34.286	0.001	has_non_IEA	1

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	n_Babjinos	n_Komaphaf	n_Kuracaps	n_Pichmemb	n_Pichkudr	n_Bretnaar	n_Ogatpoly	n_Pachtann	n_Sacccere	n_Kluylact	n_Lachther	n_Candglab	n_Torudelb	n_Candalbi	n_Loddelon	n_Meyeguil	n_Debahans	n_Schestip	n_Spatpass	n_Candtenu	n_Diutrugo	n_Yamajaro	n_Candauri	n_Clavlusi	n_Metsbicu	n_Lizaspar
Arp2/3 ARPC2 (P34-Arc)	PF04045		13	13	13	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
Arp2/3 ARPC3 (P21-Arc)	PF04062		13	13	13	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	1	1	1
Arp2/3 ARPC4	PF05856		13	13	13	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
Arp2/3 ARPC5 (P16-Arc)	PF04699		13	13	13	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Arp2 / Arp3 (description only)		actin-related protein (2\|3)\b\|\bARP[23]\b	87	87	87	7	8	7	7	5	6	7	7	7	6	6	7	7	7	7	7	6	6	7	5	7	7	6	6	4	7
WAVE complex NCKAP1	PF09735		0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
WASP family (WH1)	PF00568		13	13	13	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1
WH2 motif (WASP, WAVE, others)	PF02205		22	22	22	1	2	2	2	2	1	1	1	2	2	2	2	2	2	3	0	2	2	1	0	2	2	2	1	1	1
Formin FH2	PF02181		26	26	26	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	1	2	2	2	2
Formin Drf_GBD / Drf_FH3 / Drf_DAD	PF06371\|PF06367\|PF06345		22	22	22	2	2	2	2	1	2	1	2	1	2	2	1	2	2	2	2	2	2	2	0	2	0	2	2	2	2
Ena/VASP (VASP_tetra)	PF08776		0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Coronin (description only)		coronin	13	13	13	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	1	0	1	1	1	1	1	0	1	1
Cortactin (HS1_rep)	PF02218		0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Myosin head (all myosins)	PF00063		43	43	43	3	3	3	2	4	3	3	3	5	3	3	5	3	3	3	3	3	3	3	0	3	3	3	3	2	3

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