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

neocallimastigomycota vs early fungi: 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 (127537 sequences in 70280 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 2026-10-14T10:49:23. Source tables: studies/fungi/neocallimastigomycota_vs_early_fungi/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
Spizpunc	universe	8940	77.0%	62.6%	81.7%	68.6%	82.1%
Spizpunc	candidates	676	97.2%	75.1%	99.6%	91.9%	99.7%
Batrdend	universe	8610	68.0%	55.5%	75.5%	64.4%	75.9%
Batrdend	candidates	530	97.0%	74.5%	99.4%	93.4%	99.6%
Powehirt	universe	6533	88.3%	72.6%	92.2%	79.7%	92.5%
Powehirt	candidates	626	96.8%	73.3%	99.2%	92.8%	99.4%
Geravari	universe	8696	72.9%	59.8%	78.6%	65.8%	79.0%
Geravari	candidates	662	96.7%	74.6%	99.1%	91.7%	99.2%
Chytconf	universe	10661	80.1%	68.1%	86.9%	72.9%	87.3%
Chytconf	candidates	866	97.2%	77.4%	99.7%	91.0%	99.7%
Syncendo	universe	7895	64.4%	52.3%	69.6%	59.2%	70.0%
Syncendo	candidates	489	96.5%	72.8%	99.2%	91.8%	99.4%
Allomacr	universe	18611	65.4%	53.1%	72.9%	59.8%	73.3%
Allomacr	candidates	1133	96.6%	75.0%	99.6%	93.3%	99.7%
Cateangu	universe	12590	48.7%	39.4%	55.5%	44.3%	55.8%
Cateangu	candidates	670	96.6%	73.3%	99.4%	93.6%	99.4%
Rhizdele	universe	16971	60.9%	51.5%	66.8%	55.9%	67.1%
Rhizdele	candidates	836	96.4%	72.4%	99.0%	94.7%	99.4%
Mucocirc	universe	12143	74.1%	61.2%	78.5%	67.5%	78.7%
Mucocirc	candidates	878	97.5%	74.8%	99.8%	93.6%	99.9%
Umbevina	universe	9235	81.4%	67.2%	85.2%	73.5%	85.4%
Umbevina	candidates	755	97.5%	73.6%	99.5%	93.4%	99.6%
Sacccere	universe	6066	88.6%	66.3%	90.9%	94.8%	96.4%
Sacccere	candidates	402	98.8%	77.4%	100.0%	100.0%	100.0%
Neurcras	universe	9759	69.3%	54.9%	73.9%	62.6%	74.6%
Neurcras	candidates	650	96.8%	73.5%	99.5%	94.6%	99.5%
ALL_OUT	universe	136710	70.0%	57.3%	75.7%	64.4%	76.2%
ALL_OUT	candidates	9173	97.0%	74.5%	99.5%	93.3%	99.6%

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	3271	288 / 3151	73 / 477	689 / 6341	731 / 5815
whole_set	protein	9173	525 / 5060	105 / 532	1300 / 10615	1055 / 6985
Allomacr	family	737	19 / 444	22 / 254	54 / 1106	213 / 2416
Allomacr	protein	1133	64 / 787	33 / 311	152 / 1845	346 / 3038
Batrdend	family	496	2 / 235	11 / 200	17 / 622	156 / 1978
Batrdend	protein	530	12 / 307	16 / 215	32 / 785	177 / 2076
Cateangu	family	585	8 / 263	15 / 202	23 / 684	143 / 1943
Cateangu	protein	670	14 / 352	21 / 219	49 / 880	172 / 2050
Chytconf	family	637	20 / 387	17 / 245	47 / 969	180 / 2145
Chytconf	protein	866	43 / 590	22 / 280	100 / 1389	228 / 2408
Geravari	family	608	9 / 317	14 / 228	37 / 797	145 / 2044
Geravari	protein	662	19 / 372	16 / 241	55 / 928	170 / 2142
Mucocirc	family	656	13 / 384	15 / 231	37 / 906	170 / 2161
Mucocirc	protein	878	40 / 619	24 / 270	98 / 1435	252 / 2573
Neurcras	family	579	13 / 308	11 / 240	27 / 773	179 / 2541
Neurcras	protein	650	21 / 367	17 / 246	51 / 908	186 / 2632
Powehirt	family	591	6 / 297	8 / 222	12 / 748	147 / 1994
Powehirt	protein	626	9 / 358	15 / 234	22 / 880	154 / 2078
Rhizdele	family	645	14 / 397	18 / 231	39 / 938	198 / 2317
Rhizdele	protein	836	41 / 647	33 / 270	117 / 1498	277 / 2611
Sacccere	family	363	1 / 177	2 / 175	2 / 498	181 / 3454
Sacccere	protein	402	3 / 269	6 / 200	16 / 711	197 / 3712
Spizpunc	family	629	14 / 359	14 / 232	32 / 884	162 / 2444
Spizpunc	protein	676	17 / 424	19 / 245	44 / 1021	181 / 2536
Syncendo	family	465	6 / 249	13 / 201	23 / 629	118 / 1861
Syncendo	protein	489	13 / 296	14 / 214	39 / 735	123 / 1923
Umbevina	family	638	10 / 352	9 / 228	30 / 851	159 / 2137
Umbevina	protein	755	30 / 491	17 / 250	72 / 1138	185 / 2330

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)
PF00067	p450: Cytochrome P450	66 / 3127	122 / 41024	7.097	9.68e-38
PF05653	Mg_trans_NIPA: Magnesium transporter NIPA	32 / 3127	41 / 41024	10.239	4.05e-25
PF03109	ABC1: ABC1 atypical kinase-like domain	19 / 3127	20 / 41024	12.463	1.07e-17
PF00472	RF-1: RF-1 domain	18 / 3127	20 / 41024	11.807	7.90e-16
PF11815	DUF3336: Domain of unknown function (DUF3336)	16 / 3127	16 / 41024	13.119	7.90e-16
PF03169	OPT: OPT oligopeptide transporter protein	22 / 3127	32 / 41024	9.02	3.80e-15
PF07690	MFS_1: Major Facilitator Superfamily	70 / 3127	300 / 41024	3.061	9.22e-15
PF08022	FAD_binding_8: FAD-binding domain	24 / 3127	43 / 41024	7.322	1.03e-13
PF13621	Cupin_8: Cupin-like domain	21 / 3127	34 / 41024	8.103	3.85e-13
PF04083	Abhydro_lipase: Partial alpha/beta-hydrolase lipase region	14 / 3127	15 / 41024	12.245	7.96e-13
PF10436	BCDHK_Adom3: Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase	14 / 3127	15 / 41024	12.245	7.96e-13
PF21948	LplA-B_cat: Lipoyl protein ligase A/B catalytic domain	14 / 3127	15 / 41024	12.245	7.96e-13
PF00561	Abhydrolase_1: alpha/beta hydrolase fold	36 / 3127	105 / 41024	4.498	9.65e-13
PF07992	Pyr_redox_2: Pyridine nucleotide-disulphide oxidoreductase	27 / 3127	60 / 41024	5.904	9.65e-13
PF01734	Patatin: Patatin-like phospholipase	16 / 3127	23 / 41024	9.126	3.84e-11
PF01016	Ribosomal_L27: Ribosomal L27 protein	11 / 3127	11 / 41024	13.119	9.78e-11
PF07798	CCDC90-like: Coiled-coil domain-containing protein 90-like	15 / 3127	21 / 41024	9.371	1.07e-10
PF08030	NAD_binding_6: Ferric reductase NAD binding domain	19 / 3127	38 / 41024	6.56	8.01e-10
PF04389	Peptidase_M28: Peptidase family M28	18 / 3127	34 / 41024	6.946	8.01e-10
PF00394	Cu-oxidase: Multicopper oxidase	11 / 3127	12 / 41024	12.026	8.05e-10
PF22099	MRS2-like: Magnesium transporter MRS2-like	11 / 3127	12 / 41024	12.026	8.05e-10
PF01794	Ferric_reduct: Ferric reductase like transmembrane component	21 / 3127	47 / 41024	5.862	8.05e-10
PF03619	Solute_trans_a: Organic solute transporter Ostalpha	13 / 3127	18 / 41024	9.475	2.33e-09
PF02096	60KD_IMP: 60Kd inner membrane protein	11 / 3127	13 / 41024	11.101	4.40e-09
PF04116	FA_hydroxylase: Fatty acid hydroxylase	14 / 3127	22 / 41024	8.349	4.87e-09

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)
IPR001128	Family:Cytochrome P450	66 / 3239	122 / 46155	7.709	1.20e-39
IPR002401	Family:Cytochrome P450, E-class, group I	52 / 3239	76 / 46155	9.75	1.52e-38
IPR036396	Homologous_superfamily:Cytochrome P450 superfamily	66 / 3239	128 / 46155	7.348	2.32e-38
IPR017972	Conserved_site:Cytochrome P450, conserved site	48 / 3239	69 / 46155	9.913	2.93e-36
IPR036188	Homologous_superfamily:FAD/NAD(P)-binding domain superfamily	93 / 3239	285 / 46155	4.65	1.95e-34
IPR008521	Family:Magnesium transporter NIPA	32 / 3239	42 / 46155	10.857	8.03e-26
IPR029058	Homologous_superfamily:Alpha/Beta hydrolase fold	132 / 3239	732 / 46155	2.57	9.91e-21
IPR004147	Domain:ABC1 atypical kinase-like domain	19 / 3239	20 / 46155	13.537	1.68e-18
IPR050121	Family:Cytochrome P450 monooxygenase	29 / 3239	52 / 46155	7.947	1.55e-17
IPR011701	Family:Major facilitator superfamily	70 / 3239	300 / 46155	3.325	1.56e-16
IPR000352	Domain:Peptide chain release factor class I	18 / 3239	20 / 46155	12.825	1.56e-16
IPR021771	Domain:Triacylglycerol lipase, N-terminal	16 / 3239	16 / 46155	14.25	1.77e-16
IPR004813	Family:Oligopeptide transporter, OPT superfamily	22 / 3239	32 / 46155	9.797	6.10e-16
IPR002403	Family:Cytochrome P450, E-class, group IV	20 / 3239	28 / 46155	10.178	6.45e-15
IPR013112	Domain:Ferric reductase-like, FAD-binding domain	24 / 3239	43 / 46155	7.953	1.67e-14
IPR039028	Family:PDK/BCKDK protein kinase	16 / 3239	18 / 46155	12.666	1.67e-14
IPR045853	Homologous_superfamily:Peptide chain release factor class I superfamily	16 / 3239	18 / 46155	12.666	1.67e-14
IPR003016	Binding_site:2-oxo acid dehydrogenase, lipoyl-binding site	15 / 3239	16 / 46155	13.359	2.52e-14
IPR017927	Domain:FAD-binding domain, ferredoxin reductase-type	34 / 3239	91 / 46155	5.324	3.54e-14
IPR041667	Domain:Cupin-like domain 8	21 / 3239	34 / 46155	8.801	6.66e-14
IPR004648	Family:Tetrapeptide transporter, OPT1/isp4	17 / 3239	22 / 46155	11.011	1.32e-13
IPR039261	Homologous_superfamily:Ferredoxin-NADP reductase (FNR), nucleotide-binding domain	36 / 3239	106 / 46155	4.84	1.35e-13
IPR023753	Domain:FAD/NAD(P)-binding domain	27 / 3239	60 / 46155	6.412	1.56e-13
IPR006693	Domain:Partial AB-hydrolase lipase domain	14 / 3239	15 / 46155	13.3	2.34e-13
IPR018955	Domain:Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal	14 / 3239	15 / 46155	13.3	2.34e-13

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:0005739	cellular_component:mitochondrion	629 / 3005	2314 / 37183	3.363	1.16e-176	has_non_IEA	312
GO:0016491	molecular_function:oxidoreductase activity	515 / 3005	1790 / 37183	3.56	2.03e-153	has_non_IEA	120
GO:0005743	cellular_component:mitochondrial inner membrane	338 / 3005	861 / 37183	4.858	8.46e-143	has_non_IEA	133
GO:0019866	cellular_component:organelle inner membrane	338 / 3005	902 / 37183	4.637	1.14e-135	has_non_IEA	133
GO:0031966	cellular_component:mitochondrial membrane	393 / 3005	1206 / 37183	4.032	5.38e-135	has_non_IEA	148
GO:0098798	cellular_component:mitochondrial protein-containing complex	269 / 3005	608 / 37183	5.475	3.92e-128	has_non_IEA	121
GO:0003735	molecular_function:structural constituent of ribosome	261 / 3005	694 / 37183	4.654	4.26e-104	has_non_IEA	88
GO:0006412	biological_process:translation	263 / 3005	714 / 37183	4.558	1.62e-102	has_non_IEA	70
GO:0044391	cellular_component:ribosomal subunit	218 / 3005	549 / 37183	4.913	7.49e-92	has_non_IEA	102
GO:0000315	cellular_component:organellar large ribosomal subunit	130 / 3005	208 / 37183	7.734	2.33e-85	has_non_IEA	60
GO:0005762	cellular_component:mitochondrial large ribosomal subunit	130 / 3005	208 / 37183	7.734	2.33e-85	has_non_IEA	60
GO:0033108	biological_process:mitochondrial respiratory chain complex assembly	148 / 3005	302 / 37183	6.064	5.36e-77	has_non_IEA	59
GO:0032543	biological_process:mitochondrial translation	120 / 3005	215 / 37183	6.906	1.25e-70	has_non_IEA	59
GO:0009058	biological_process:biosynthetic process	668 / 3005	4369 / 37183	1.892	1.79e-62	has_non_IEA	219
GO:0016705	molecular_function:oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	138 / 3005	324 / 37183	5.27	5.12e-62	has_non_IEA	21

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_in1	near_miss_in2	n_Spizpunc	n_Batrdend	n_Powehirt	n_Geravari	n_Chytconf	n_Syncendo	n_Allomacr	n_Cateangu	n_Rhizdele	n_Mucocirc	n_Umbevina	n_Sacccere	n_Neurcras	n_Pirofinn	n_Anaerobu	n_Neocalif	n_Neolanat	n_Neoconst	n_PiroE2sp
Arp2/3 ARPC2 (P34-Arc)	PF04045		14	14	14	0	0	1	1	1	1	1	1	2	1	1	1	1	1	1	1	1	2	2	2	1
Arp2/3 ARPC3 (P21-Arc)	PF04062		13	13	13	0	0	1	1	1	1	1	1	2	1	0	1	1	1	1	1	1	2	2	2	1
Arp2/3 ARPC4	PF05856		14	14	14	0	0	1	1	1	1	1	1	1	1	2	1	1	1	1	1	1	2	2	2	0
Arp2/3 ARPC5 (P16-Arc)	PF04699		15	15	15	1	0	1	1	1	1	2	1	2	1	1	1	1	1	1	1	1	2	2	2	1
Arp2/3 ARPC1 (description only)		arp2/3 complex.*(41\|p41\|subunit 1)\|ARPC1	1	1	1	0	0	0	0	0	0	0	1	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	91	91	91	1	0	6	6	7	6	6	7	13	7	7	6	7	7	6	6	7	7	6	7	0
WAVE complex NCKAP1	PF09735		8	8	0	0	0	1	1	1	1	0	1	2	1	0	0	0	0	0	1	1	1	1	1	1
WAVE complex CYFIP (FragX_IP)	PF05994		10	10	1	0	0	1	1	1	1	0	1	4	1	0	0	0	0	0	1	1	1	1	1	2
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
SCAR/WAVE (SCAR_helical)	PF27569		6	6	0	0	0	1	1	1	1	0	1	0	1	0	0	0	0	0	1	1	1	1	1	0
WASP family (WH1)	PF00568		19	19	10	0	0	1	1	1	1	1	1	4	1	1	3	2	1	1	1	2	6	6	6	3
WH2 motif (WASP, WAVE, others)	PF02205		19	14	6	0	2	1	3	1	1	1	1	2	1	1	2	2	2	1	2	2	3	3	3	2
Formin FH2	PF02181		60	59	53	0	0	4	4	4	4	5	3	9	3	9	8	4	2	1	7	7	11	11	11	5
Formin Drf_GBD / Drf_FH3 / Drf_DAD	PF06371\|PF06367\|PF06345		58	58	47	0	0	4	3	3	4	3	2	7	3	11	8	7	1	2	7	6	10	13	11	6
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
Coronin (description only)		coronin	29	29	28	0	0	3	1	3	4	4	1	4	1	3	1	2	1	1	4	4	0	0	0	0
Cortactin (HS1_rep)	PF02218		1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
Myosin 2 tail (Myosin_tail_1)	PF01576		7	7	6	0	0	1	1	1	1	1	1	1	0	0	0	0	0	0	2	1	2	0	3	2
Myosin head (all myosins)	PF00063		133	133	133	0	0	9	7	9	7	13	6	21	8	19	17	8	5	4	14	12	24	23	24	12

Page written by bin/generate_enrichment_page.py.