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

chytrid vs mucoromycota: 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 (121980 sequences in 48216 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 2026-10-12T18:27:20. Source tables: studies/fungi/chytrid_vs_mucoromycota/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.
Low annotation: the candidate set has less than 50% annotation for GO 41.9%. 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
Mucocirc	universe	12143	74.1%	61.2%	78.5%	67.5%	78.7%
Mucocirc	candidates	959	52.3%	38.1%	63.8%	42.5%	64.1%
Rhizdele	universe	16971	60.9%	51.5%	66.8%	55.9%	67.1%
Rhizdele	candidates	1320	45.0%	32.7%	58.1%	37.8%	58.7%
Lichcory	universe	12138	68.9%	57.1%	74.0%	62.6%	74.2%
Lichcory	candidates	887	53.7%	40.9%	65.0%	43.1%	65.2%
Phycblak	universe	16154	52.4%	43.3%	58.3%	46.7%	58.5%
Phycblak	candidates	976	49.3%	36.0%	60.0%	38.8%	60.4%
Absiglau	universe	14825	71.1%	59.7%	77.2%	66.2%	77.4%
Absiglau	candidates	1130	53.2%	39.9%	65.8%	43.5%	66.2%
Syncrace	universe	11037	72.3%	59.4%	76.5%	66.0%	76.7%
Syncrace	candidates	859	51.6%	37.7%	62.5%	42.7%	62.6%
Choacucu	universe	11924	69.0%	56.5%	73.5%	62.9%	73.8%
Choacucu	candidates	895	51.8%	37.8%	64.7%	43.9%	65.2%
Hessvesi	universe	11058	69.9%	57.3%	74.3%	63.4%	74.4%
Hessvesi	candidates	874	48.3%	35.2%	58.2%	38.0%	58.5%
Umbevina	universe	9235	81.4%	67.2%	85.2%	73.5%	85.4%
Umbevina	candidates	647	53.5%	39.1%	66.0%	45.3%	66.3%
Mortisab	universe	9021	81.7%	67.5%	85.1%	74.3%	85.5%
Mortisab	candidates	623	52.6%	38.8%	61.6%	43.7%	62.3%
Thamspha	universe	6769	74.1%	59.4%	79.7%	68.4%	80.0%
Thamspha	candidates	125	69.6%	52.0%	79.2%	63.2%	79.2%
ALL_OUT	universe	131275	69.0%	57.0%	74.0%	62.9%	74.2%
ALL_OUT	candidates	9295	51.0%	37.6%	62.6%	41.9%	63.0%

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	4185	84 / 1724	19 / 397	132 / 3614	153 / 4052
whole_set	protein	9295	235 / 4592	56 / 496	424 / 9715	397 / 6140
Absiglau	family	921	10 / 427	3 / 237	21 / 972	12 / 2211
Absiglau	protein	1130	17 / 747	9 / 283	35 / 1655	52 / 2705
Choacucu	family	829	4 / 396	1 / 224	12 / 907	7 / 2419
Choacucu	protein	895	8 / 557	4 / 255	18 / 1284	19 / 2640
Hessvesi	family	799	6 / 332	1 / 214	10 / 798	7 / 2396
Hessvesi	protein	874	7 / 494	1 / 244	13 / 1138	24 / 2619
Lichcory	family	757	7 / 339	2 / 218	10 / 807	31 / 2292
Lichcory	protein	887	17 / 582	14 / 262	35 / 1311	70 / 2596
Mortisab	family	595	3 / 344	3 / 232	12 / 854	8 / 2129
Mortisab	protein	623	7 / 470	4 / 251	13 / 1129	29 / 2317
Mucocirc	family	834	8 / 380	4 / 229	19 / 896	27 / 2167
Mucocirc	protein	959	12 / 619	7 / 270	26 / 1435	46 / 2573
Phycblak	family	809	9 / 312	2 / 217	16 / 768	8 / 2037
Phycblak	protein	976	14 / 517	4 / 253	21 / 1241	24 / 2377
Rhizdele	family	1094	12 / 397	3 / 229	18 / 928	6 / 2304
Rhizdele	protein	1320	16 / 647	7 / 270	28 / 1498	34 / 2611
Syncrace	family	789	5 / 341	2 / 215	12 / 823	7 / 2401
Syncrace	protein	859	8 / 528	7 / 251	15 / 1224	14 / 2692
Thamspha	family	118	1 / 178	0 / 173	0 / 510	0 / 1752
Thamspha	protein	125	1 / 236	0 / 189	0 / 628	0 / 1848
Umbevina	family	613	5 / 348	2 / 225	11 / 846	13 / 2132
Umbevina	protein	647	6 / 491	4 / 250	12 / 1138	28 / 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)
PF00339	Arrestin_N: Arrestin (or S-antigen), N-terminal domain	41 / 2215	83 / 24460	5.455	3.88e-18
PF13966	zf-RVT: zinc-binding in reverse transcriptase	41 / 2215	98 / 24460	4.62	4.12e-15
PF02752	Arrestin_C: Arrestin (or S-antigen), C-terminal domain	37 / 2215	82 / 24460	4.983	5.40e-15
PF13812	PPR_3: Pentatricopeptide repeat domain	31 / 2215	70 / 24460	4.89	3.44e-12
PF11223	DUF3020: SPP41, DUF3020	16 / 2215	19 / 24460	9.299	4.99e-12
PF13041	PPR_2: PPR repeat family	34 / 2215	87 / 24460	4.316	1.07e-11
PF14529	Exo_endo_phos_2: Endonuclease-reverse transcriptase	26 / 2215	53 / 24460	5.417	1.40e-11
PF04516	CP2: CP2 transcription factor	13 / 2215	14 / 24460	10.254	7.37e-11
PF27979	CON7_helical: CON7 transcription factor helical domain	11 / 2215	11 / 24460	11.043	6.29e-10
PF10342	Kre9_KNH: Kre9/KNH-like N-terminal Ig-like domain	29 / 2215	75 / 24460	4.27	6.57e-10
PF04082	Fungal_trans: Fungal specific transcription factor domain	42 / 2215	162 / 24460	2.863	4.12e-08
PF14542	Acetyltransf_CG: GCN5-related N-acetyl-transferase	9 / 2215	9 / 24460	11.043	5.80e-08
PF01535	PPR: PPR repeat	25 / 2215	69 / 24460	4.001	7.80e-08
PF27810	MSB2_C: MSB2 C-terminal domain	10 / 2215	12 / 24460	9.202	2.49e-07
PF08655	DASH_Ask1: DASH complex subunit Ask1	8 / 2215	8 / 24460	11.043	4.82e-07
PF10250	O-FucT: GDP-fucose protein O-fucosyltransferase	8 / 2215	8 / 24460	11.043	4.82e-07
PF00172	Zn_clus: Fungal Zn(2)-Cys(6) binuclear cluster domain	46 / 2215	209 / 24460	2.43	1.17e-06
PF08578	DUF1765: Protein of unknown function (DUF1765)	7 / 2215	7 / 24460	11.043	4.74e-06
PF08507	COPI_assoc: COPI associated protein	9 / 2215	12 / 24460	8.282	6.25e-06
PF13896	Glyco_transf_49: Glycosyl-transferase for dystroglycan	10 / 2215	16 / 24460	6.902	1.51e-05
PF12855	Ecl1: TORC1 inhibitor Ecl family	13 / 2215	28 / 24460	5.127	2.22e-05
PF03106	WRKY: WRKY DNA -binding domain	7 / 2215	8 / 24460	9.663	2.73e-05
PF23207	PH_SPO71: Prospore membrane adapter protein SPO71 PH domain	7 / 2215	8 / 24460	9.663	2.73e-05
PF01284	MARVEL: Membrane-associating domain	6 / 2215	6 / 24460	11.043	3.94e-05
PF10300	Iml2-TPR_39: Iml2/Tetratricopeptide repeat protein 39	12 / 2215	26 / 24460	5.097	5.87e-05

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)
IPR002885	Repeat:Pentatricopeptide repeat	56 / 2700	136 / 27833	4.245	1.09e-18
IPR011021	Domain:Arrestin-like, N-terminal	41 / 2700	83 / 27833	5.092	5.40e-17
IPR050357	Family:Arrestin domain-containing protein	43 / 2700	93 / 27833	4.766	1.13e-16
IPR014752	Homologous_superfamily:Arrestin-like, C-terminal domain superfamily	55 / 2700	148 / 27833	3.831	1.94e-16
IPR050815	Family:Transcription factor, fungi	44 / 2700	105 / 27833	4.32	2.80e-15
IPR011022	Domain:Arrestin-like, C-terminal domain	39 / 2700	86 / 27833	4.675	6.61e-15
IPR026960	Domain:Reverse transcriptase zinc-binding domain	41 / 2700	98 / 27833	4.313	2.95e-14
IPR039327	Family:C2H2 finger domain transcription factor CON7-like	14 / 2700	14 / 27833	10.309	2.55e-12
IPR040167	Family:Transcription factor CP2-like	14 / 2700	14 / 27833	10.309	2.55e-12
IPR050987	Family:ABC-transporter-regulating transcription factor-like	39 / 2700	104 / 27833	3.866	9.10e-12
IPR021386	Domain:SPP41, DUF3020	16 / 2700	19 / 27833	8.681	1.41e-11
IPR052982	Family:Remodeling of fungal cell wall protein 1	21 / 2700	36 / 27833	6.013	1.95e-10
IPR007604	Domain:CP2 transcription factor	13 / 2700	14 / 27833	9.572	2.33e-10
IPR060579	Domain:C2H2 finger domain transcription factor CON7, helical domain	11 / 2700	11 / 27833	10.309	1.81e-09
IPR018466	Domain:Cell wall synthesis protein KRE9/Knh1-like, N-terminal	29 / 2700	75 / 27833	3.986	5.07e-09
IPR031165	Domain:Yjdj-type Gcn5-related N-acetyltransferase	9 / 2700	9 / 27833	10.309	1.60e-07
IPR039295	Family:Signaling mucin MSB2	9 / 2700	9 / 27833	10.309	1.60e-07
IPR036864	Homologous_superfamily:Zn(2)-C6 fungal-type DNA-binding domain superfamily	55 / 2700	240 / 27833	2.362	2.33e-07
IPR001138	Domain:Zn(2)Cys(6) fungal-type DNA-binding domain	56 / 2700	249 / 27833	2.318	3.20e-07
IPR014756	Homologous_superfamily:Immunoglobulin E-set	42 / 2700	161 / 27833	2.689	3.20e-07
IPR007219	Domain:Xylanolytic transcriptional activator-like, regulatory domain	42 / 2700	163 / 27833	2.656	4.56e-07
IPR060624	Domain:MSB2-like, C-terminal domain	10 / 2700	12 / 27833	8.59	6.56e-07
IPR013964	Family:DASH complex subunit Ask1	8 / 2700	8 / 27833	10.309	1.17e-06
IPR019378	Family:GDP-fucose protein O-fucosyltransferase	8 / 2700	8 / 27833	10.309	1.17e-06
IPR001849	Domain:Pleckstrin homology domain	59 / 2700	282 / 27833	2.157	1.63e-06

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
GO:0140110	molecular_function:transcription regulator activity	269 / 1815	1759 / 21652	1.824	4.93e-20	IEA_only
GO:0003700	molecular_function:DNA-binding transcription factor activity	237 / 1815	1510 / 21652	1.872	5.41e-19	IEA_only
GO:0042729	cellular_component:DASH complex	32 / 1815	62 / 21652	6.157	1.37e-15	IEA_only
GO:0000981	molecular_function:DNA-binding transcription factor activity, RNA polymerase II-specific	184 / 1815	1166 / 21652	1.883	1.29e-14	IEA_only
GO:0070086	biological_process:ubiquitin-dependent endocytosis	26 / 1815	52 / 21652	5.965	3.33e-12	IEA_only
GO:0001216	molecular_function:DNA-binding transcription activator activity	51 / 1815	182 / 21652	3.343	3.33e-12	IEA_only
GO:0001228	molecular_function:DNA-binding transcription activator activity, RNA polymerase II-specific	51 / 1815	182 / 21652	3.343	3.33e-12	IEA_only
GO:0072686	cellular_component:mitotic spindle	28 / 1815	75 / 21652	4.454	1.90e-09	IEA_only
GO:0031625	molecular_function:ubiquitin protein ligase binding	27 / 1815	77 / 21652	4.183	2.01e-08	IEA_only
GO:0044389	molecular_function:ubiquitin-like protein ligase binding	27 / 1815	77 / 21652	4.183	2.01e-08	IEA_only
GO:0009986	cellular_component:cell surface	16 / 1815	28 / 21652	6.817	2.36e-08	IEA_only
GO:0098657	biological_process:import into cell	54 / 1815	250 / 21652	2.577	2.54e-08	IEA_only
GO:0005034	molecular_function:osmosensor activity	9 / 1815	9 / 21652	11.929	6.26e-08	IEA_only
GO:0001402	biological_process:signal transduction involved in filamentous growth	9 / 1815	11 / 21652	9.76	2.39e-06	IEA_only
GO:0007231	biological_process:osmosensory signaling pathway	9 / 1815	11 / 21652	9.76	2.39e-06	IEA_only

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	candidates	near_miss_in1	near_miss_in2	n_Mucocirc	n_Rhizdele	n_Lichcory	n_Phycblak	n_Absiglau	n_Syncrace	n_Choacucu	n_Hessvesi	n_Umbevina	n_Mortisab	n_Thamspha	n_Batrdend	n_Batrsala	n_Spizpunc	n_Powehirt	n_Geravari	n_Syncendo	n_Syncmicr	n_Chytconf	n_Polystew	n_Rhizglob	n_Rhizrose
Arp2/3 ARPC2 (P34-Arc)	PF04045		12	12	12	0	0	0	1	1	1	1	2	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
Arp2/3 ARPC3 (P21-Arc)	PF04062		10	10	10	0	0	0	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
Arp2/3 ARPC4	PF05856		11	11	11	0	0	0	1	2	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1
Arp2/3 ARPC5 (P16-Arc)	PF04699		10	10	10	0	0	0	1	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	2	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	1	0	0	0	1	0	0	0	0	0
Arp2 / Arp3 (description only)		actin-related protein (2\|3)\b\|\bARP[23]\b	69	69	69	0	0	0	6	7	5	5	8	5	8	7	7	7	4	6	7	6	7	6	7	6	6	8	5	6
WAVE complex NCKAP1	PF09735		0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	0	1	0	1
WAVE complex CYFIP (FragX_IP)	PF05994		0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	0	1	0	1
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
SCAR/WAVE (SCAR_helical)	PF27569		0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	0	1	0	1
WASP family (WH1)	PF00568		21	21	21	2	1	2	3	1	1	1	2	3	2	3	2	2	1	1	1	1	1	1	1	1	1	1	1	1
WH2 motif (WASP, WAVE, others)	PF02205		20	20	18	0	0	2	2	1	2	0	3	2	2	3	2	3	0	3	1	1	1	1	1	1	1	1	0	1
Formin FH2	PF02181		65	64	63	1	0	0	8	9	7	3	9	6	6	7	4	4	2	4	6	4	4	4	3	4	5	6	5	5
Formin Drf_GBD / Drf_FH3 / Drf_DAD	PF06371\|PF06367\|PF06345		81	81	80	17	0	0	8	11	7	6	10	7	8	8	7	7	2	3	4	4	3	4	2	3	3	4	3	7
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
Coronin (description only)		coronin	21	21	21	0	0	0	1	3	2	2	3	2	1	2	2	2	1	1	1	3	3	4	1	2	4	2	2	4
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
Myosin 2 tail (Myosin_tail_1)	PF01576		2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	2
Myosin head (all myosins)	PF00063		146	146	146	0	0	0	17	19	14	16	18	11	16	13	8	9	5	7	8	9	9	7	6	9	13	7	14	12

Page written by bin/generate_enrichment_page.py.