Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation

Table 3 Member regions' statistics for PUA_UR50 MCs

MC (PUA)	Size	Average length	SDL	LC fraction	MC (PUA)	Size	Average length	SDL	LC fraction
1	1575	207.4	42.5	0.04	11	120	396.3	*61.8	0.04
2	862	623.1	*102.9	0.04	12	109	154.2	26.7	0.02
3	791	152.7	30.5	0.02	13	430	40.6	3.3	0.00
4	682	125.1	16.9	0.01	14	399	54.2	3.1	0.00
5	487	119.7	10.9	0.02	15	309	125.9	35.5	0.01
6	452	109.8	14.4	0.02	16	162	95.5	11.1	0.02
7	432	441.4	44.8	0.03	17	162	115.8	15.5	0.05
8	392	136.7	19.9	0.02	18	675	148.5	24.0	0.02
9	282	320.7	48.7	0.02	19	339	88.4	13.3	0.07
10	251	102.3	8.7	0.02

MC (A-PUA)	Size	Average length	SDL	LC fraction	MC (A-PUA)	Size	Average length	SDL	LC fraction
A1	69369	223.7	29.9	0.02	A28	1365	83.9	13.2	0.02
A2	8908	203.9	19.1	0.05	A29	615	84.5	8.4	0.04
A3	8324	49.1	5.6	0.00	A30	506	47.7	4.8	0.01
A4	4523	158.6	36.5	0.02	A31	464	99.5	10.8	0.01
A5	3559	210.2	28.7	0.03	A32	406	191.7	18.6	0.06
A6	3386	193.1	17.9	0.05	A33	340	183.3	33.4	0.02
A7	2934	102.7	12.1	0.02	A34	294	99.0	10.6	0.03
A8	2915	347.2	*76.5	0.04	A35	285	48.8	6.6	0.01
A9	2870	392.0	48.9	0.06	A36	248	59.6	7.5	0.03
A10	2735	257.3	12.6	0.02	A37	198	210.5	30.9	0.03
A11	2392	146.5	40.2	0.03	A38	1588	226.5	45.2	0.01
A12	1795	153.3	11.4	0.01	A39	691	86.7	19.7	0.00
A13	1751	235.9	25.9	0.03	A40	565	369.6	35.2	0.04
A14	986	289.8	*57.4	0.05	A41	430	339.6	36.9	0.01
A15	851	164.1	13.9	0.03	A42	359	328.7	*52.0	0.03
A16	839	193.3	26.1	0.01	A43	267	165.1	32.6	0.08
A17	700	259.4	29.3	0.03	A44	208	36.3	3.6	0.00
A18	556	46.8	5.0	0.02	A45	186	181.8	37.9	0.09
A19	452	173.0	17.0	0.02	A46	121	311.9	26.4	0.04
A20	384	189.3	32.3	0.01	A47	110	211.3	23.1	0.02
A21	193	293.9	36.0	0.02	A48	677	87.5	15.4	0.02
A22	190	114.7	13.7	0.02	A49	625	119.5	19.9	0.03
A23	172	43.0	4.2	0.00	A50	277	77.9	6.4	0.01
A24	162	60.4	4.8	0.01	A51	178	132.0	15.4	0.01
A25	146	86.6	16.1	0.04	A52	126	62.2	10.2	0.11
A26	135	216.7	12.3	0.02
A27	3181	196.9	21.1	0.02

Top section: MCs containing PUA domains; bottom section, MCs containing PUA-associated domains (A-PUA, with “A” prefix). For each MC, we report size (i.e., number of sequence members), average and standard deviation of members’ lengths and, the fraction of residues (of all members) that are found in low-complexity regions (LC fraction, using the segmask software of the NCBI-BLAST+ suite [30]). We flag MCs (*) for which the SDL is larger than 50 amino acids (about the size of a small domain)

ISSN: 1471-2105