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

UHM lachnoNovelclade: 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 (7068 sequences in 3256 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 2026-10-14T21:58:21. Source tables: studies/bacteria/UHM_lachnoNovelclade/analysis/enrichment/outputs/loss/proteome_clustered. Full record: PROVENANCE. Run report: report.html.

Caveats

Annotation: Pfam-A HMM search (hmmsearch, Pfam gathering thresholds) for every species; no UniProt annotation. Each annotation file has a provenance sidecar (domain table, HMMER version, Pfam release); PROVENANCE.yaml lists the files and their checksums.
GO: not available for this study (no GO annotation in any species).
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.
GO and InterPro: not available for this study. No species has GO and InterPro annotation (Ub56, Ub85, Ub22, Ub119), so no GO and InterPro test was run.

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
Ub56	universe	2116	84.5%	66.5%	0.0%	0.0%	84.5%
Ub56	candidates	378	73.8%	49.5%	0.0%	0.0%	73.8%
Ub85	universe	2051	85.9%	67.4%	0.0%	0.0%	85.9%
Ub85	candidates	388	73.7%	47.9%	0.0%	0.0%	73.7%
Ub22	universe	2249	86.0%	69.4%	0.0%	0.0%	86.0%
Ub22	candidates	372	75.5%	52.4%	0.0%	0.0%	75.5%
Ub119	universe	2175	84.8%	67.2%	0.0%	0.0%	84.8%
Ub119	candidates	385	73.8%	50.1%	0.0%	0.0%	73.8%
ALL_OUT	universe	8591	85.3%	67.6%	0.0%	0.0%	85.3%
ALL_OUT	candidates	1523	74.2%	50.0%	0.0%	0.0%	74.2%

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	603	0 / 275	0 / 140	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
whole_set	protein	1523	51 / 786	16 / 244	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Ub119	family	378	0 / 104	0 / 78	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Ub119	protein	385	0 / 125	0 / 85	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Ub22	family	365	0 / 130	0 / 90	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Ub22	protein	372	0 / 142	0 / 93	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Ub56	family	371	0 / 104	0 / 79	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Ub56	protein	378	0 / 125	0 / 83	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Ub85	family	381	0 / 95	0 / 79	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Ub85	protein	388	0 / 112	0 / 84	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)

Top 25 Pfam terms (whole set, family level)

25 rows shown, ordered by FDR then p-value; 0 have FDR < 0.05 (bold).

Term	Name	k / N cand.	n / M bg	Fold	FDR (BH)
PF12673	SipL: SipL, SPOCS domain	5 / 454	7 / 3011	4.737	0.339
PF13181	TPR_8: Tetratricopeptide repeat	3 / 454	5 / 3011	3.979	1.000
PF01077	NIR_SIR: Nitrite and sulphite reductase 4Fe-4S domain	3 / 454	6 / 3011	3.316	1.000
PF02899	Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain	3 / 454	6 / 3011	3.316	1.000
PF12800	Fer4_4: 4Fe-4S binding domain	3 / 454	6 / 3011	3.316	1.000
PF12838	Fer4_7: 4Fe-4S dicluster domain	7 / 454	24 / 3011	1.934	1.000
PF07715	Plug: TonB-dependent Receptor Plug Domain	6 / 454	20 / 3011	1.99	1.000
PF00037	Fer4: 4Fe-4S binding domain	8 / 454	30 / 3011	1.769	1.000
PF00580	UvrD-helicase: UvrD/REP helicase N-terminal domain	3 / 454	7 / 3011	2.842	1.000
PF01656	CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain	5 / 454	16 / 3011	2.073	1.000
PF13237	Fer4_10: 4Fe-4S dicluster domain	6 / 454	21 / 3011	1.895	1.000
PF00083	Sugar_tr: Sugar (and other) transporter	3 / 454	9 / 3011	2.211	1.000
PF00149	Metallophos: Calcineurin-like phosphoesterase	3 / 454	9 / 3011	2.211	1.000
PF00593	TonB_dep_Rec_b-barrel: TonB dependent receptor-like, beta-barrel	5 / 454	19 / 3011	1.745	1.000
PF13187	Fer4_9: 4Fe-4S dicluster domain	5 / 454	19 / 3011	1.745	1.000
PF00142	Fer4_NifH: 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family	2 / 454	5 / 3011	2.653	1.000
PF02080	TrkA_C: TrkA-C domain	2 / 454	5 / 3011	2.653	1.000
PF02254	TrkA_N: TrkA-N domain	2 / 454	5 / 3011	2.653	1.000
PF02514	CobN-Mg_chel: CobN/Magnesium Chelatase	2 / 454	5 / 3011	2.653	1.000
PF03460	NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain	2 / 454	5 / 3011	2.653	1.000
PF04932	Wzy_C: O-Antigen ligase	2 / 454	5 / 3011	2.653	1.000
PF07195	FliD_C: Flagellar hook-associated protein 2 C-terminus	2 / 454	5 / 3011	2.653	1.000
PF13524	Glyco_trans_1_2: Glycosyl transferase-like	2 / 454	5 / 3011	2.653	1.000
PF02811	PHP: PHP domain	3 / 454	10 / 3011	1.99	1.000
PF13614	AAA_31: AAA domain	3 / 454	10 / 3011	1.99	1.000

Top 25 InterPro terms (whole set, family level)

Not available: no protein of the candidate source group has a InterPro annotation in this study (for example Pfam-only HMM annotation). No InterPro test was run.

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

Not available: no protein of the candidate source group has a GO annotation in this study (for example Pfam-only HMM annotation). No GO test was run.

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

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