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

UHM Koxytoca: 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 (89506 sequences in 7838 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 2026-10-14T22:00:34. Source tables: studies/bacteria/UHM_Koxytoca/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 (KoxO_050916275, KoxO_017310465, KoxO_929608445, KoxO_040561445, KoxO_900083795, KoxO_024918735, KoxO_902162875, KoxO_053276915, KoxO_030343105, KoxO_030343375, KoxO_016734995, KoxO_030343565, KoxO_900083995, KoxO_004360035, KoxO_030344075, KoxO_051951865), 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
KoxO_050916275	universe	5234	94.8%	78.2%	0.0%	0.0%	94.8%
KoxO_050916275	candidates	81	75.3%	23.5%	0.0%	0.0%	75.3%
KoxO_017310465	universe	5794	89.8%	73.4%	0.0%	0.0%	89.8%
KoxO_017310465	candidates	83	73.5%	22.9%	0.0%	0.0%	73.5%
KoxO_929608445	universe	5789	91.5%	75.1%	0.0%	0.0%	91.5%
KoxO_929608445	candidates	77	75.3%	23.4%	0.0%	0.0%	75.3%
KoxO_040561445	universe	5446	93.0%	76.3%	0.0%	0.0%	93.0%
KoxO_040561445	candidates	80	76.2%	23.8%	0.0%	0.0%	76.2%
KoxO_900083795	universe	5482	93.8%	77.0%	0.0%	0.0%	93.8%
KoxO_900083795	candidates	80	76.2%	22.5%	0.0%	0.0%	76.2%
KoxO_024918735	universe	5886	90.3%	73.6%	0.0%	0.0%	90.3%
KoxO_024918735	candidates	85	72.9%	23.5%	0.0%	0.0%	72.9%
KoxO_902162875	universe	5883	92.2%	75.3%	0.0%	0.0%	92.2%
KoxO_902162875	candidates	85	75.3%	24.7%	0.0%	0.0%	75.3%
KoxO_053276915	universe	5373	93.8%	77.1%	0.0%	0.0%	93.8%
KoxO_053276915	candidates	81	72.8%	21.0%	0.0%	0.0%	72.8%
KoxO_030343105	universe	5974	90.5%	73.5%	0.0%	0.0%	90.5%
KoxO_030343105	candidates	89	75.3%	23.6%	0.0%	0.0%	75.3%
KoxO_030343375	universe	5998	90.5%	73.5%	0.0%	0.0%	90.5%
KoxO_030343375	candidates	88	75.0%	23.9%	0.0%	0.0%	75.0%
KoxO_016734995	universe	4956	95.0%	78.3%	0.0%	0.0%	95.0%
KoxO_016734995	candidates	75	76.0%	21.3%	0.0%	0.0%	76.0%
KoxO_030343565	universe	6048	90.4%	73.4%	0.0%	0.0%	90.4%
KoxO_030343565	candidates	88	75.0%	23.9%	0.0%	0.0%	75.0%
KoxO_900083995	universe	5998	90.8%	73.6%	0.0%	0.0%	90.8%
KoxO_900083995	candidates	86	74.4%	24.4%	0.0%	0.0%	74.4%
KoxO_004360035	universe	5426	94.2%	77.1%	0.0%	0.0%	94.2%
KoxO_004360035	candidates	79	74.7%	21.5%	0.0%	0.0%	74.7%
KoxO_030344075	universe	5994	90.5%	73.5%	0.0%	0.0%	90.5%
KoxO_030344075	candidates	87	74.7%	23.0%	0.0%	0.0%	74.7%
KoxO_051951865	universe	5545	93.2%	76.4%	0.0%	0.0%	93.2%
KoxO_051951865	candidates	76	75.0%	22.4%	0.0%	0.0%	75.0%
ALL_OUT	universe	90826	92.0%	75.2%	0.0%	0.0%	92.0%
ALL_OUT	candidates	1320	74.9%	23.1%	0.0%	0.0%	74.9%

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	100	0 / 480	0 / 227	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
whole_set	protein	1320	80 / 3657	19 / 451	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_004360035	family	79	0 / 326	0 / 178	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_004360035	protein	79	1 / 417	0 / 191	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_016734995	family	75	0 / 288	0 / 168	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_016734995	protein	75	1 / 390	0 / 183	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_017310465	family	83	0 / 311	0 / 188	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_017310465	protein	83	1 / 424	0 / 203	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_024918735	family	85	0 / 313	0 / 183	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_024918735	protein	85	1 / 426	0 / 198	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_030343105	family	88	0 / 320	0 / 192	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_030343105	protein	89	1 / 439	0 / 208	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_030343375	family	88	0 / 323	0 / 193	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_030343375	protein	88	1 / 442	0 / 208	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_030343565	family	87	0 / 325	0 / 192	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_030343565	protein	88	1 / 443	0 / 208	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_030344075	family	87	0 / 321	0 / 193	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_030344075	protein	87	1 / 439	0 / 208	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_040561445	family	80	0 / 308	0 / 177	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_040561445	protein	80	1 / 412	0 / 195	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_050916275	family	81	0 / 308	0 / 176	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_050916275	protein	81	1 / 411	0 / 194	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_051951865	family	76	0 / 322	0 / 178	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_051951865	protein	76	1 / 416	0 / 192	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_053276915	family	81	0 / 313	0 / 179	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_053276915	protein	81	1 / 407	0 / 192	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_900083795	family	79	0 / 322	0 / 181	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_900083795	protein	80	1 / 421	0 / 196	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_900083995	family	85	0 / 324	0 / 190	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_900083995	protein	86	1 / 434	0 / 205	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_902162875	family	85	0 / 325	0 / 191	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_902162875	protein	85	1 / 446	0 / 205	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_929608445	family	76	0 / 326	0 / 188	0 / 0 (not_available_no_annotated_units)	0 / 0 (not_available_no_annotated_units)
KoxO_929608445	protein	77	1 / 437	0 / 202	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)
PF04860	Phage_portal: Phage portal protein	3 / 75	11 / 6007	21.844	0.138
PF03354	TerL_ATPase: Terminase large subunit, ATPase domain	2 / 75	5 / 6007	32.037	0.298
PF20441	TerL_nuclease: Terminase large subunit, endonuclease domain	2 / 75	6 / 6007	26.698	0.298
PF05119	Terminase_4: Phage terminase, small subunit	2 / 75	7 / 6007	22.884	0.298
PF16083	Phage_holin_3_3: LydA holin phage, holin superfamily III	2 / 75	7 / 6007	22.884	0.298
PF20155	TMP_3: Tape measure protein	1 / 75	5 / 6007	16.019	1.000
PF09718	Tape_meas_lam_C: Lambda phage tail tape-measure protein (Tape_meas_lam_C)	1 / 75	6 / 6007	13.349	1.000
PF11745	DUF3304: Protein of unknown function (DUF3304)	1 / 75	7 / 6007	11.442	1.000
PF00004	AAA: ATPase family associated with various cellular activities (AAA)	0 / 75	24 / 6007	0.0	1.000
PF00005	ABC_tran: ABC transporter	0 / 75	52 / 6007	0.0	1.000
PF00009	GTP_EFTU: Elongation factor Tu GTP binding domain	0 / 75	16 / 6007	0.0	1.000
PF00012	HSP70: Hsp70 protein	0 / 75	5 / 6007	0.0	1.000
PF00027	cNMP_binding: Cyclic nucleotide-binding domain	0 / 75	6 / 6007	0.0	1.000
PF00037	Fer4: 4Fe-4S binding domain	0 / 75	11 / 6007	0.0	1.000
PF00043	GST_C: Glutathione S-transferase, C-terminal domain	0 / 75	9 / 6007	0.0	1.000
PF00070	Pyr_redox: Pyridine nucleotide-disulphide oxidoreductase	0 / 75	16 / 6007	0.0	1.000
PF00072	Response_reg: Response regulator receiver domain	0 / 75	17 / 6007	0.0	1.000
PF00078	RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase)	0 / 75	5 / 6007	0.0	1.000
PF00083	Sugar_tr: Sugar (and other) transporter	0 / 75	35 / 6007	0.0	1.000
PF00085	Thioredoxin: Thioredoxin	0 / 75	7 / 6007	0.0	1.000
PF00089	Trypsin: Trypsin	0 / 75	5 / 6007	0.0	1.000
PF00092	VWA: von Willebrand factor type A domain	0 / 75	5 / 6007	0.0	1.000
PF00106	adh_short: short chain dehydrogenase	0 / 75	19 / 6007	0.0	1.000
PF00107	ADH_zinc_N: Zinc-binding dehydrogenase	0 / 75	12 / 6007	0.0	1.000
PF00108	Thiolase_N: Thiolase, N-terminal domain	0 / 75	5 / 6007	0.0	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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