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

serinales vs pichiales v2: functional enrichment (novelty)

One-sided hypergeometric test per term; Benjamini-Hochberg FDR within each scope, level and vocabulary. Candidates are the novelty candidates: gene families present in the IN group and absent from the OUT group. Universe: proteome. Background clustered: True (73331 sequences in 18151 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 2026-10-16T22:53:03. Source tables: studies/fungi/serinales_vs_pichiales_v2/analysis/enrichment/outputs/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.
Low annotation: the candidate set has less than 50% annotation for Pfam 34.4%, InterPro 41.3%, GO 23.5%, any vocabulary 42.6%. Enrichment for these vocabularies has low power.

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
Candalbi	universe	6040	84.2%	65.5%	88.1%	82.9%	90.2%
Candalbi	candidates	173	42.2%	15.0%	49.7%	41.6%	59.5%
Loddelon	universe	5779	82.1%	64.8%	86.1%	77.5%	86.6%
Loddelon	candidates	162	32.7%	16.1%	40.1%	21.0%	42.0%
Meyeguil	universe	5919	85.5%	68.6%	89.1%	80.3%	89.4%
Meyeguil	candidates	136	28.7%	13.2%	34.6%	16.9%	34.6%
Debahans	universe	6284	83.2%	65.2%	86.6%	78.1%	86.8%
Debahans	candidates	140	31.4%	12.1%	37.9%	21.4%	37.9%
Schestip	universe	5797	87.4%	69.0%	90.8%	82.2%	91.1%
Schestip	candidates	141	32.6%	12.8%	38.3%	22.0%	39.0%
Spatpass	universe	5973	83.9%	66.2%	87.4%	78.4%	87.7%
Spatpass	candidates	151	34.4%	17.2%	43.0%	25.2%	43.0%
Candtenu	universe	5540	85.3%	67.7%	88.4%	80.0%	88.7%
Candtenu	candidates	128	27.3%	12.5%	35.9%	18.0%	35.9%
Diutrugo	universe	5811	81.2%	64.5%	84.9%	75.5%	85.2%
Diutrugo	candidates	141	43.3%	18.4%	47.5%	24.8%	47.5%
Yamajaro	universe	5820	86.8%	68.5%	90.2%	81.0%	90.5%
Yamajaro	candidates	142	36.6%	14.8%	43.0%	22.5%	43.0%
Candauri	universe	5433	86.7%	68.6%	89.7%	79.6%	90.0%
Candauri	candidates	144	36.1%	15.3%	41.0%	22.2%	41.7%
Clavlusi	universe	5932	79.7%	63.0%	83.0%	74.8%	83.3%
Clavlusi	candidates	152	28.9%	11.8%	38.8%	20.4%	39.5%
Metsbicu	universe	5826	79.2%	61.3%	82.6%	74.5%	82.9%
Metsbicu	candidates	135	39.3%	16.3%	45.2%	23.0%	45.9%
Lizaspar	universe	5041	86.9%	68.5%	90.8%	81.8%	91.1%
Lizaspar	candidates	119	31.1%	12.6%	38.7%	22.7%	40.3%
ALL_IN	universe	75195	84.0%	66.2%	87.4%	79.0%	87.9%
ALL_IN	candidates	1864	34.4%	14.5%	41.3%	23.5%	42.6%

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	996	32 / 875	6 / 303	36 / 1781	10 / 3857
whole_set	protein	1864	57 / 4049	13 / 467	79 / 8479	87 / 6849
Candalbi	family	151	1 / 173	0 / 185	1 / 503	5 / 2838
Candalbi	protein	173	3 / 249	1 / 204	4 / 672	15 / 2967
Candauri	family	135	1 / 158	0 / 180	1 / 462	1 / 2010
Candauri	protein	144	2 / 207	1 / 194	3 / 576	7 / 2114
Candtenu	family	126	1 / 146	0 / 171	1 / 434	1 / 1879
Candtenu	protein	128	1 / 205	0 / 191	1 / 591	0 / 2031
Clavlusi	family	151	1 / 165	0 / 189	1 / 487	0 / 2433
Clavlusi	protein	152	1 / 210	0 / 199	1 / 590	1 / 2499
Debahans	family	137	1 / 172	0 / 181	2 / 495	0 / 2524
Debahans	protein	140	1 / 240	0 / 204	2 / 646	0 / 2649
Diutrugo	family	136	1 / 157	0 / 184	1 / 459	0 / 1890
Diutrugo	protein	141	2 / 224	1 / 205	2 / 595	4 / 2035
Lizaspar	family	119	0 / 148	0 / 172	0 / 454	0 / 1868
Lizaspar	protein	119	0 / 197	0 / 187	0 / 556	0 / 1969
Loddelon	family	159	1 / 172	0 / 181	1 / 488	0 / 2387
Loddelon	protein	162	1 / 225	0 / 200	1 / 601	1 / 2496
Metsbicu	family	134	0 / 142	0 / 175	0 / 429	0 / 2413
Metsbicu	protein	135	0 / 195	0 / 186	0 / 550	0 / 2507
Meyeguil	family	135	0 / 177	0 / 175	0 / 509	0 / 2477
Meyeguil	protein	136	0 / 226	0 / 190	0 / 628	0 / 2576
Schestip	family	137	0 / 167	1 / 182	0 / 486	0 / 2485
Schestip	protein	141	1 / 239	1 / 203	1 / 647	1 / 2640
Spatpass	family	145	1 / 172	0 / 182	1 / 500	0 / 2478
Spatpass	protein	151	2 / 224	1 / 196	3 / 617	5 / 2582
Yamajaro	family	139	1 / 169	0 / 174	1 / 476	0 / 1920
Yamajaro	protein	142	1 / 235	0 / 194	1 / 635	1 / 2050

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)
PF29124	MSC3_beta: Meiotic sister-chromatid recombination protein 3 beta-sheet domain	10 / 343	10 / 11248	32.793	4.41e-13
PF05730	CFEM: CFEM domain	13 / 343	20 / 11248	21.315	4.41e-13
PF29143	PGA45_C: GPI-anchored protein 45 C-terminal domain	9 / 343	10 / 11248	29.514	5.84e-11
PF29116	PET130: Mitochondrial protein PET130	7 / 343	8 / 11248	28.694	3.94e-08
PF28466	DUF8407: Domain of unknown function (DUF8407)	6 / 343	6 / 11248	32.793	1.12e-07
PF29045	YOL036W_C: YOL036W-like C-terminal domain	6 / 343	6 / 11248	32.793	1.12e-07
PF11214	Med2: Mediator complex subunit 2	5 / 343	5 / 11248	32.793	3.20e-06
PF29044	FGR15_N: Filamentous growth regulator 15 N-terminal domain	7 / 343	13 / 11248	17.658	3.70e-06
PF29481	SKG1: SKG1 domain	6 / 343	9 / 11248	21.862	5.82e-06
PF02257	RFX_DNA_binding: RFX DNA-binding domain	6 / 343	12 / 11248	16.397	5.33e-05
PF00498	FHA: FHA domain	9 / 343	35 / 11248	8.432	5.72e-05
PF11488	Lge1: Transcriptional regulatory protein LGE1	5 / 343	8 / 11248	20.496	8.95e-05
PF15511	CENP-T_C: Centromere kinetochore component CENP-T histone fold	5 / 343	8 / 11248	20.496	8.95e-05
PF13094	CENP-Q: CENP-Q, a CENPA-CAD centromere complex subunit	5 / 343	10 / 11248	16.397	3.56e-04
PF11957	efThoc1: THO complex subunit 1 transcription elongation factor	4 / 343	6 / 11248	21.862	6.64e-04
PF17053	GEP5: Genetic interactor of prohibitin 5	4 / 343	6 / 11248	21.862	6.64e-04
PF18497	RNase_3_N: Ribonuclease III N-terminal domain	4 / 343	7 / 11248	18.739	0.001
PF01399	PCI: PCI domain	6 / 343	21 / 11248	9.369	0.001
PF03134	TB2_DP1_HVA22: TB2/DP1, HVA22 family	4 / 343	10 / 11248	13.117	0.007
PF07954	DUF1689: Protein of unknown function (DUF1689)	4 / 343	10 / 11248	13.117	0.007
PF08508	DUF1746: Fungal domain of unknown function (DUF1746)	3 / 343	5 / 11248	19.676	0.011
PF29317	AIM44: Altered inheritance of mitochondria protein 44	3 / 343	5 / 11248	19.676	0.011
PF20789	4HBT_3C: Acyl-CoA thioesterase C-terminal domain	3 / 343	6 / 11248	16.397	0.019
PF27837	Fyv8: Protein Fyv8	3 / 343	6 / 11248	16.397	0.019
PF12657	TFIIIC_delta: Transcription factor IIIC subunit delta bet-propeller domain	3 / 343	7 / 11248	14.054	0.027

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)
IPR062021	Domain:Meiotic sister-chromatid recombination protein 3, beta-sheet domain	10 / 414	10 / 12158	29.367	3.36e-12
IPR008427	Domain:Extracellular membrane protein, CFEM domain	13 / 414	20 / 12158	19.089	3.82e-12
IPR063250	Domain:GPI-anchored protein 45, C-terminal	9 / 414	10 / 12158	26.43	3.26e-10
IPR051735		8 / 414	10 / 12158	23.494	3.19e-08
IPR062383	Family:Mitochondrial protein PET130	7 / 414	8 / 12158	25.696	1.40e-07
IPR059451	Domain:Domain of unknown function DUF8407	6 / 414	6 / 12158	29.367	3.83e-07
IPR062062	Domain:YOL036W-like, C-terminal domain	6 / 414	6 / 12158	29.367	3.83e-07
IPR021017	Family:Mediator complex, subunit Med2, fungi	5 / 414	5 / 12158	29.367	9.96e-06
IPR062451	Domain:Filamentous growth regulator 15. N-terminal domain	7 / 414	13 / 12158	15.813	1.44e-05
IPR063222	Domain:SKG1-like domain	6 / 414	9 / 12158	19.578	2.06e-05
IPR000999	Domain:Ribonuclease III domain	7 / 414	17 / 12158	12.092	1.18e-04
IPR021581	Domain:Transcription regulator LGE1, helical region	5 / 414	8 / 12158	18.354	3.15e-04
IPR035425	Domain:CENP-T/Histone H4, histone fold	5 / 414	8 / 12158	18.354	3.15e-04
IPR008984	Homologous_superfamily:SMAD/FHA domain superfamily	9 / 414	37 / 12158	7.143	3.83e-04
IPR003150	Domain:DNA-binding RFX-type, winged-helix domain	6 / 414	14 / 12158	12.586	3.84e-04
IPR000253	Domain:Forkhead-associated (FHA) domain	9 / 414	38 / 12158	6.955	3.84e-04
IPR036910	Homologous_superfamily:High mobility group box domain superfamily	8 / 414	29 / 12158	8.101	3.84e-04
IPR036389	Homologous_superfamily:Ribonuclease III, endonuclease domain superfamily	7 / 414	21 / 12158	9.789	3.84e-04
IPR025212	Family:Centromere protein Q	5 / 414	10 / 12158	14.684	9.17e-04
IPR052145		5 / 414	11 / 12158	13.349	0.001
IPR011032	Homologous_superfamily:GroES-like superfamily	8 / 414	35 / 12158	6.712	0.001
IPR021861	Family:THO complex, subunit THOC1	4 / 414	6 / 12158	19.578	0.001
IPR031455	Family:Genetic interactor of prohibitin 5	4 / 414	6 / 12158	19.578	0.001
IPR040540	Domain:Ribonuclease III, N-terminal domain	4 / 414	7 / 12158	16.781	0.003
IPR017956	Conserved_site:AT hook, DNA-binding motif	4 / 414	8 / 12158	14.684	0.006

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

15 rows shown, ordered by FDR then p-value; 10 have FDR < 0.05 (bold).

Term	Name	k / N cand.	n / M bg	Fold	FDR (BH)	GO evidence	Families with non-IEA
GO:0004525	molecular_function:ribonuclease III activity	7 / 230	22 / 10340	14.304	6.09e-04	has_non_IEA	1
GO:0032296	molecular_function:double-stranded RNA-specific ribonuclease activity	7 / 230	22 / 10340	14.304	6.09e-04	has_non_IEA	1
GO:0097745	biological_process:mitochondrial tRNA 5'-end processing	5 / 230	9 / 10340	24.976	7.86e-04	IEA_only	0
GO:0005576	cellular_component:extracellular region	16 / 230	170 / 10340	4.231	0.001	has_non_IEA	7
GO:0000964	biological_process:mitochondrial RNA 5'-end processing	5 / 230	13 / 10340	17.291	0.004	IEA_only	0
GO:0099116	biological_process:tRNA 5'-end processing	5 / 230	16 / 10340	14.049	0.010	IEA_only	0
GO:0020037	molecular_function:heme binding	9 / 230	69 / 10340	5.864	0.010	has_non_IEA	4
GO:0046906	molecular_function:tetrapyrrole binding	9 / 230	69 / 10340	5.864	0.010	has_non_IEA	4
GO:0090646	biological_process:mitochondrial tRNA processing	5 / 230	20 / 10340	11.239	0.026	IEA_only	0
GO:0016042	biological_process:lipid catabolic process	8 / 230	65 / 10340	5.533	0.035	has_non_IEA	2
GO:0008541	cellular_component:proteasome regulatory particle, lid subcomplex	5 / 230	24 / 10340	9.366	0.055	IEA_only	0
GO:0000963	biological_process:mitochondrial RNA processing	5 / 230	26 / 10340	8.645	0.075	IEA_only	0
GO:0010467	biological_process:gene expression	5 / 230	29 / 10340	7.751	0.110	IEA_only	0
GO:0140053	biological_process:mitochondrial gene expression	5 / 230	29 / 10340	7.751	0.110	IEA_only	0
GO:0019825	molecular_function:oxygen binding	4 / 230	18 / 10340	9.99	0.147	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	IN_universe	IN_in_matrix	IN_pass_ingroup_rule	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	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
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		12	12	12	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	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	82	82	81	7	7	7	6	6	7	5	7	7	6	6	4	7	7	8	7	7	5	6	7	7	7	6	6	7	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		12	12	12	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
WH2 motif (WASP, WAVE, others)	PF02205		19	19	19	2	3	0	2	2	1	0	2	2	2	1	1	1	1	2	2	2	2	1	1	1	2	2	2	2	2
Formin FH2	PF02181		25	25	25	2	2	2	2	2	2	2	2	1	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2
Formin Drf_GBD / Drf_FH3 / Drf_DAD	PF06371\|PF06367\|PF06345		22	22	22	2	2	2	2	2	2	0	2	0	2	2	2	2	2	2	2	2	1	2	1	2	1	2	2	1	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	9	9	9	1	0	0	1	0	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	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		35	35	35	3	3	3	3	3	3	0	3	3	3	3	2	3	3	3	3	2	4	3	3	3	5	3	3	5	3

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