HC2 - PFAM28P - GREMLIN Contacts

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HC2 - Histone H1-like nucleoprotein HC2

PFAM:	PF07382	Sequences: MATAAKKPAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAAKKPAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAAKKAAAKKAAAKKAAAKKAAAKKAAAKKAAAKAKKAAAKKAAPKKPAAAPAAAAAPAAKTALNPAAAWPQQLFPTGSR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	194 (169)
Sequences:	1150 (983)
Seq/√Len:	75.6
META:	0.702

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_K	61_A	4.102	1.00
174_A	177_A	3.211	1.00
167_A	173_A	2.756	1.00
53_A	56_A	2.720	1.00
173_A	176_T	2.429	1.00
84_A	94_A	2.428	1.00
99_A	109_A	2.428	1.00
144_K	147_A	2.229	1.00
109_A	112_K	2.218	1.00
71_A	101_A	2.176	1.00
75_A	95_A	2.031	1.00
175_K	179_N	1.943	1.00
176_T	179_N	1.942	1.00
94_A	104_A	1.936	1.00
151_K	156_K	1.899	1.00
100_A	110_A	1.880	1.00
38_A	69_A	1.848	1.00
69_A	99_A	1.816	1.00
56_A	61_A	1.798	1.00
150_K	155_K	1.767	1.00
79_A	89_A	1.762	1.00
168_A	173_A	1.687	1.00
115_A	125_A	1.686	1.00
79_A	109_A	1.662	1.00
65_A	95_A	1.652	1.00
120_A	130_A	1.622	1.00
71_A	86_A	1.602	1.00
160_K	165_A	1.597	0.99
173_A	177_A	1.590	0.99
32_K	47_K	1.584	0.99
95_A	105_A	1.559	0.99
87_K	97_K	1.557	0.99
79_A	99_A	1.524	0.99
64_A	74_A	1.524	0.99
79_A	82_K	1.511	0.99
94_A	109_A	1.498	0.99
125_A	135_A	1.476	0.99
28_A	89_A	1.476	0.99
89_A	109_A	1.458	0.99
53_A	74_A	1.449	0.99
28_A	38_A	1.448	0.99
80_A	100_A	1.443	0.99
138_K	143_K	1.423	0.99
107_K	112_K	1.423	0.99
26_K	46_K	1.398	0.99
168_A	172_P	1.383	0.99
155_K	160_K	1.366	0.98
43_A	84_A	1.337	0.98
48_A	79_A	1.320	0.98
69_A	89_A	1.304	0.98
91_A	101_A	1.304	0.98
36_K	46_K	1.302	0.98
116_A	120_A	1.274	0.97
64_A	94_A	1.271	0.97
87_K	92_K	1.267	0.97
81_A	96_A	1.257	0.97
96_A	106_A	1.255	0.97
88_K	98_K	1.255	0.97
73_K	93_K	1.241	0.97
58_K	63_K	1.241	0.97
51_K	56_A	1.230	0.97
35_A	45_A	1.228	0.97
71_A	91_A	1.224	0.97
156_K	161_K	1.197	0.96
77_K	87_K	1.195	0.96
13_A	23_A	1.190	0.96
70_A	100_A	1.187	0.96
72_K	82_K	1.163	0.96
77_K	97_K	1.159	0.96
89_A	104_A	1.147	0.95
127_A	137_A	1.142	0.95
20_A	23_A	1.137	0.95
11_K	16_K	1.132	0.95
100_A	105_A	1.116	0.95
24_A	34_A	1.108	0.94
83_K	93_K	1.098	0.94
174_A	179_N	1.091	0.94
37_K	47_K	1.087	0.94
26_K	41_K	1.076	0.93
101_A	111_A	1.075	0.93
123_K	133_K	1.061	0.93
121_A	131_A	1.060	0.93
133_K	138_K	1.054	0.93
85_A	116_A	1.045	0.92
165_A	177_A	1.044	0.92
22_K	27_K	1.038	0.92
86_A	101_A	1.024	0.92
33_A	43_A	1.017	0.91
41_K	72_K	1.012	0.91
74_A	94_A	0.999	0.91
12_K	22_K	0.998	0.90
86_A	117_A	0.994	0.90
70_A	90_A	0.990	0.90
60_A	64_A	0.983	0.90
44_A	75_A	0.981	0.90
43_A	53_A	0.975	0.89
82_K	102_K	0.975	0.89
105_A	110_A	0.975	0.89
84_A	104_A	0.960	0.89
131_A	141_A	0.959	0.89
30_A	40_A	0.955	0.88
92_K	102_K	0.955	0.88
169_A	178_L	0.954	0.88
26_K	31_K	0.953	0.88
63_K	66_A	0.952	0.88
116_A	121_A	0.950	0.88
175_K	178_L	0.947	0.88
89_A	99_A	0.939	0.88
41_K	92_K	0.934	0.87
104_A	115_A	0.925	0.87
168_A	176_T	0.925	0.87
17_K	32_K	0.909	0.86
74_A	84_A	0.906	0.86
26_K	36_K	0.903	0.85
38_A	48_A	0.901	0.85
161_K	166_P	0.893	0.85
73_K	88_K	0.889	0.85
35_A	66_A	0.888	0.85
161_K	165_A	0.880	0.84
156_K	159_P	0.877	0.84
98_K	108_K	0.874	0.84
102_K	123_K	0.874	0.84
94_A	115_A	0.871	0.83
94_A	125_A	0.865	0.83
70_A	74_A	0.859	0.83
82_K	92_K	0.851	0.82
78_K	108_K	0.850	0.82
173_A	179_N	0.840	0.81
147_A	150_K	0.837	0.81
170_A	179_N	0.834	0.81
22_K	37_K	0.828	0.80
43_A	64_A	0.828	0.80
89_A	120_A	0.823	0.80
45_A	96_A	0.818	0.79
43_A	74_A	0.808	0.78
47_K	52_K	0.807	0.78
169_A	173_A	0.805	0.78
77_K	92_K	0.803	0.78
43_A	69_A	0.801	0.78
141_A	158_A	0.799	0.78
37_K	78_K	0.798	0.78
68_K	98_K	0.794	0.77
81_A	111_A	0.793	0.77
92_K	107_K	0.793	0.77
42_K	73_K	0.774	0.75
105_A	116_A	0.774	0.75
45_A	55_A	0.770	0.75
85_A	105_A	0.764	0.75
85_A	95_A	0.764	0.75
97_K	107_K	0.763	0.74
77_K	107_K	0.762	0.74
165_A	169_A	0.760	0.74
63_K	83_K	0.758	0.74
14_A	24_A	0.755	0.74
65_A	85_A	0.753	0.73
128_K	138_K	0.746	0.73
75_A	85_A	0.743	0.72
170_A	173_A	0.741	0.72
31_K	67_K	0.741	0.72
167_A	172_P	0.730	0.71
19_A	29_A	0.730	0.71
71_A	81_A	0.728	0.71
104_A	125_A	0.720	0.70
69_A	84_A	0.719	0.70
31_K	41_K	0.711	0.69
108_K	113_K	0.705	0.68
110_A	121_A	0.704	0.68
82_K	97_K	0.696	0.67
12_K	27_K	0.688	0.67
67_K	72_K	0.687	0.66
134_K	137_A	0.685	0.66
165_A	168_A	0.684	0.66
73_K	83_K	0.681	0.66
172_P	177_A	0.678	0.65
53_A	64_A	0.677	0.65
95_A	126_A	0.676	0.65
46_K	97_K	0.674	0.65
41_K	102_K	0.671	0.65
32_K	93_K	0.669	0.64
168_A	174_A	0.668	0.64
84_A	99_A	0.668	0.64
69_A	79_A	0.666	0.64
76_A	96_A	0.666	0.64
22_K	32_K	0.660	0.63
21_K	46_K	0.659	0.63
81_A	101_A	0.657	0.63
90_A	110_A	0.657	0.63
94_A	99_A	0.656	0.63
48_A	51_K	0.656	0.63
124_K	134_K	0.654	0.63
83_K	103_K	0.654	0.63
22_K	83_K	0.654	0.63
117_A	137_A	0.650	0.62
68_K	119_K	0.648	0.62
47_K	78_K	0.644	0.61
104_A	109_A	0.644	0.61
34_A	38_A	0.640	0.61
75_A	105_A	0.639	0.61
89_A	140_A	0.638	0.61
72_K	97_K	0.634	0.60
52_K	57_K	0.628	0.60
78_K	83_K	0.625	0.59
119_K	129_K	0.623	0.59
22_K	129_K	0.616	0.58
36_K	77_K	0.615	0.58
40_A	76_A	0.613	0.58
155_K	159_P	0.611	0.57
68_K	78_K	0.609	0.57
80_A	90_A	0.606	0.57
124_K	129_K	0.604	0.57
42_K	98_K	0.602	0.56
162_P	172_P	0.602	0.56
63_K	68_K	0.601	0.56
40_A	71_A	0.595	0.55
83_K	98_K	0.589	0.55
41_K	51_K	0.585	0.54
99_A	120_A	0.585	0.54
159_P	162_P	0.575	0.53
128_K	133_K	0.570	0.52
65_A	75_A	0.570	0.52
159_P	163_A	0.567	0.52
54_A	65_A	0.559	0.51
84_A	115_A	0.558	0.51
66_A	91_A	0.552	0.50
43_A	104_A	0.551	0.50
119_K	124_K	0.550	0.50
35_A	50_A	0.550	0.50
45_A	86_A	0.549	0.50
46_K	72_K	0.546	0.49
75_A	79_A	0.544	0.49
16_K	21_K	0.544	0.49
29_A	80_A	0.540	0.49
118_K	138_K	0.538	0.48
74_A	104_A	0.535	0.48
53_A	58_K	0.535	0.48
63_K	73_K	0.535	0.48
131_A	135_A	0.532	0.48
104_A	140_A	0.528	0.47
91_A	122_A	0.526	0.47
90_A	94_A	0.524	0.47
171_A	174_A	0.524	0.47
78_K	88_K	0.523	0.46
46_K	51_K	0.520	0.46
166_P	171_A	0.514	0.45
117_A	120_A	0.514	0.45
14_A	29_A	0.513	0.45
32_K	42_K	0.512	0.45
21_K	82_K	0.512	0.45
141_A	153_A	0.511	0.45
172_P	175_K	0.508	0.45
44_A	85_A	0.507	0.44
72_K	102_K	0.504	0.44
154_A	159_P	0.502	0.44
96_A	111_A	0.500	0.44

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1tjlA	2	0.2629	10.1	0.919	Contact Map
1useA	3	0.1031	9.2	0.92	Contact Map
1x4tA	1	0.201	8.4	0.922	Contact Map
4tq1B	1	0.0773	3.4	0.935	Contact Map
2jm6A	1	0.1392	2.6	0.939	Contact Map
4g35B	1	0.0876	2.5	0.939	Contact Map
2dgzA	1	0.2113	1.5	0.947	Contact Map
1ydiB	1	0.0619	1.4	0.947	Contact Map
1wudA	3	0.1186	1.4	0.947	Contact Map
4w20M	1	0.134	1.1	0.95	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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