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

UHM lachnoNovelclade: 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 (17412 sequences in 9078 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 2026-10-14T21:58:06. Source tables: studies/bacteria/UHM_lachnoNovelclade/analysis/enrichment/outputs/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 (Ub71, Lsp1, Lsph, Easp, Cami), 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
Ub71	universe	2681	81.4%	66.0%	0.0%	0.0%	81.4%
Ub71	candidates	125	95.2%	84.8%	0.0%	0.0%	95.2%
Lsp1	universe	4274	87.8%	75.0%	0.0%	0.0%	87.8%
Lsp1	candidates	568	96.1%	80.3%	0.0%	0.0%	96.1%
Lsph	universe	4675	87.8%	75.0%	0.0%	0.0%	87.8%
Lsph	candidates	615	95.1%	80.5%	0.0%	0.0%	95.1%
Easp	universe	5589	85.3%	72.5%	0.0%	0.0%	85.3%
Easp	candidates	616	93.8%	80.4%	0.0%	0.0%	93.8%
Cami	universe	2547	87.4%	72.6%	0.0%	0.0%	87.4%
Cami	candidates	430	94.7%	77.7%	0.0%	0.0%	94.7%
ALL_IN	universe	19766	86.2%	72.8%	0.0%	0.0%	86.2%
ALL_IN	candidates	2354	94.9%	80.1%	0.0%	0.0%	94.9%

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	941	13 / 696	5 / 241	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
whole_set	protein	2354	159 / 1787	33 / 356	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Cami	family	419	0 / 156	0 / 106	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Cami	protein	430	0 / 187	0 / 112	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Easp	family	548	1 / 288	0 / 157	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Easp	protein	616	6 / 408	2 / 175	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Lsp1	family	518	0 / 271	1 / 140	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Lsp1	protein	568	5 / 329	4 / 149	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Lsph	family	550	2 / 270	0 / 142	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Lsph	protein	615	5 / 353	3 / 149	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Ub71	family	123	0 / 135	0 / 94	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
Ub71	protein	125	0 / 162	0 / 103	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; 13 have FDR < 0.05 (bold).

Term	Name	k / N cand.	n / M bg	Fold	FDR (BH)
PF06580	His_kinase: Histidine kinase	33 / 904	61 / 7844	4.694	3.46e-13
PF02518	HATPase_c: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	43 / 904	155 / 7844	2.407	6.88e-06
PF03466	LysR_substrate: LysR substrate binding domain	23 / 904	79 / 7844	2.526	0.004
PF00672	HAMP: HAMP domain	20 / 904	66 / 7844	2.629	0.005
PF00126	HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family	23 / 904	86 / 7844	2.321	0.010
PF00165	HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family	26 / 904	107 / 7844	2.108	0.017
PF19085	Choline_bind_2: Choline-binding repeat	10 / 904	24 / 7844	3.615	0.017
PF02311	AraC_binding: AraC-like ligand binding domain	16 / 904	53 / 7844	2.619	0.018
PF02378	PTS_EIIC: Phosphotransferase system, EIIC	10 / 904	26 / 7844	3.337	0.028
PF07729	FCD: FCD domain	11 / 904	31 / 7844	3.079	0.028
PF00367	PTS_EIIB: phosphotransferase system, EIIB	7 / 904	14 / 7844	4.338	0.028
PF00535	Glycos_transf_2: Glycosyl transferase family 2	14 / 904	47 / 7844	2.585	0.034
PF25137	ADH_Fe_C: Fe-containing alcohol dehydrogenase family, C-terminal	5 / 904	8 / 7844	5.423	0.045
PF13641	Glyco_tranf_2_3: Glycosyltransferase like family 2	11 / 904	34 / 7844	2.807	0.052
PF01228	Gly_radical: Glycine radical	5 / 904	9 / 7844	4.821	0.079
PF12833	HTH_18: Helix-turn-helix domain	28 / 904	138 / 7844	1.761	0.081
PF12733	Cadherin-like: Cadherin-like beta sandwich domain	4 / 904	6 / 7844	5.785	0.089
PF00392	GntR: Bacterial regulatory proteins, gntR family	16 / 904	65 / 7844	2.136	0.090
PF01479	S4: S4 domain	6 / 904	14 / 7844	3.719	0.107
PF00465	Fe-ADH: Iron-containing alcohol dehydrogenase	5 / 904	10 / 7844	4.338	0.107
PF01522	Polysacc_deac_1: Polysaccharide deacetylase	7 / 904	19 / 7844	3.197	0.120
PF13242	Hydrolase_like: HAD-hyrolase-like	7 / 904	19 / 7844	3.197	0.120
PF12821	ThrE_2: Threonine/Serine exporter, ThrE	4 / 904	7 / 7844	4.958	0.139
PF00358	PTS_EIIA_1: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1	5 / 904	11 / 7844	3.944	0.148
PF08239	SH3_3: Bacterial SH3 domain	6 / 904	16 / 7844	3.254	0.185

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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