YHYH - PFAM28P - GREMLIN Contacts

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YHYH - YHYH protein

PFAM:	PF14240	Sequences: TFRIPLNPTLATGTTTLTGLGAIGVALNGVPFDPGDAESWNNDRGSGWNYEALGGAENLGLDCNNAHVQPTGAYHYHGNPTALLESLDSTQHHSPLIGWAADGFPIYGPYGYSNATDATSGIRRMKSSYRLKSGTGGPGGAYYPDGTFTEDYEYVAGSGDLDECNGRFGVTPEYPNGTYAYFVTDDFPYIPRCFKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	196 (192)
Sequences:	3396 (2412)
Seq/√Len:	174.1
META:	0.942

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
169_G	182_F	3.653	1.00
123_R	160_D	3.623	1.00
130_R	155_V	3.584	1.00
10_L	104_F	3.113	1.00
130_R	158_S	2.965	1.00
99_W	174_Y	2.801	1.00
113_S	123_R	2.794	1.00
166_G	179_Y	2.734	1.00
67_H	77_H	2.710	1.00
111_G	125_M	2.662	1.00
162_D	166_G	2.637	1.00
50_Y	148_F	2.590	1.00
67_H	75_H	2.574	1.00
134_G	137_G	2.532	1.00
162_D	179_Y	2.507	1.00
169_G	180_A	2.492	1.00
64_N	82_A	2.488	1.00
128_S	154_Y	2.480	1.00
164_C	193_C	2.430	1.00
113_S	121_G	2.418	1.00
130_R	153_E	2.312	1.00
128_S	158_S	2.277	1.00
43_D	47_G	2.190	1.00
26_A	32_F	2.132	1.00
97_I	183_V	2.099	1.00
124_R	185_D	2.091	1.00
132_K	153_E	1.968	1.00
115_A	120_S	1.953	1.00
96_L	99_W	1.687	1.00
49_N	150_E	1.684	1.00
125_M	182_F	1.667	1.00
31_P	73_A	1.645	1.00
22_A	31_P	1.637	1.00
125_M	160_D	1.636	1.00
24_G	32_F	1.613	1.00
44_R	47_G	1.582	1.00
36_D	49_N	1.574	1.00
54_G	147_T	1.534	1.00
128_S	159_G	1.527	1.00
33_D	69_Q	1.526	1.00
167_R	180_A	1.508	1.00
167_R	182_F	1.492	1.00
98_G	106_I	1.482	1.00
128_S	156_A	1.465	1.00
104_F	166_G	1.454	1.00
174_Y	177_G	1.451	1.00
26_A	76_Y	1.421	1.00
126_K	160_D	1.414	1.00
25_V	31_P	1.398	1.00
39_S	42_N	1.383	1.00
56_A	147_T	1.376	1.00
51_E	152_Y	1.354	1.00
100_A	106_I	1.335	1.00
66_A	76_Y	1.327	1.00
43_D	46_S	1.325	1.00
48_W	52_A	1.296	1.00
146_G	151_D	1.289	1.00
155_V	158_S	1.275	1.00
140_G	144_P	1.236	1.00
69_Q	72_G	1.231	1.00
27_L	96_L	1.224	1.00
2_F	31_P	1.210	1.00
53_L	78_G	1.197	1.00
36_D	39_S	1.189	1.00
116_T	120_S	1.184	1.00
66_A	74_Y	1.176	1.00
88_D	92_H	1.175	1.00
89_S	92_H	1.174	1.00
191_P	194_F	1.173	1.00
32_F	69_Q	1.154	1.00
139_G	144_P	1.138	1.00
183_V	190_I	1.125	1.00
183_V	191_P	1.123	1.00
115_A	118_A	1.108	1.00
24_G	29_G	1.100	1.00
175_P	178_T	1.098	1.00
117_D	120_S	1.098	1.00
140_G	145_D	1.087	1.00
11_A	15_T	1.086	1.00
92_H	95_P	1.077	1.00
87_L	90_T	1.053	1.00
9_T	104_F	1.052	1.00
94_S	122_I	1.048	1.00
111_G	180_A	1.046	0.99
114_N	120_S	1.041	0.99
128_S	155_V	1.037	0.99
60_G	68_V	1.036	0.99
169_G	172_P	1.026	0.99
114_N	117_D	1.023	0.99
139_G	142_Y	1.022	0.99
131_L	145_D	1.016	0.99
39_S	49_N	1.008	0.99
69_Q	73_A	1.006	0.99
109_P	124_R	1.005	0.99
51_E	149_T	1.003	0.99
11_A	14_T	0.978	0.99
95_P	108_G	0.973	0.99
15_T	19_G	0.968	0.99
94_S	180_A	0.963	0.99
35_G	149_T	0.961	0.99
118_A	121_G	0.956	0.99
19_G	36_D	0.928	0.99
148_F	151_D	0.924	0.99
140_G	143_Y	0.908	0.99
88_D	91_Q	0.905	0.99
62_D	74_Y	0.894	0.98
110_Y	122_I	0.887	0.98
2_F	22_A	0.886	0.98
15_T	164_C	0.877	0.98
52_A	61_L	0.872	0.98
153_E	158_S	0.869	0.98
36_D	52_A	0.868	0.98
54_G	57_E	0.863	0.98
79_N	183_V	0.845	0.98
21_G	194_F	0.844	0.98
10_L	15_T	0.840	0.98
125_M	167_R	0.838	0.98
112_Y	121_G	0.835	0.98
185_D	188_P	0.835	0.98
139_G	143_Y	0.833	0.97
2_F	25_V	0.832	0.97
173_E	177_G	0.830	0.97
109_P	185_D	0.830	0.97
62_D	66_A	0.827	0.97
32_F	73_A	0.825	0.97
171_T	175_P	0.823	0.97
110_Y	124_R	0.820	0.97
174_Y	178_T	0.816	0.97
161_L	165_N	0.816	0.97
79_N	84_L	0.814	0.97
134_G	139_G	0.812	0.97
49_N	149_T	0.810	0.97
49_N	52_A	0.803	0.97
182_F	191_P	0.800	0.97
16_T	19_G	0.800	0.97
171_T	174_Y	0.798	0.97
22_A	101_A	0.796	0.97
38_E	68_V	0.789	0.97
22_A	73_A	0.789	0.97
80_P	83_L	0.788	0.97
92_H	122_I	0.780	0.96
54_G	144_P	0.777	0.96
50_Y	54_G	0.776	0.96
38_E	59_L	0.775	0.96
171_T	177_G	0.774	0.96
162_D	184_T	0.772	0.96
33_D	38_E	0.771	0.96
114_N	133_S	0.771	0.96
114_N	170_V	0.769	0.96
65_N	81_T	0.767	0.96
40_W	137_G	0.761	0.96
142_Y	145_D	0.757	0.96
54_G	152_Y	0.756	0.96
104_F	179_Y	0.753	0.95
146_G	152_Y	0.753	0.95
132_K	145_D	0.752	0.95
94_S	169_G	0.746	0.95
154_Y	163_E	0.743	0.95
108_G	182_F	0.742	0.95
50_Y	53_L	0.741	0.95
156_A	163_E	0.736	0.95
22_A	33_D	0.736	0.95
152_Y	187_F	0.734	0.95
146_G	150_E	0.733	0.95
161_L	166_G	0.725	0.94
107_Y	173_E	0.724	0.94
62_D	75_H	0.719	0.94
17_L	35_G	0.717	0.94
62_D	67_H	0.714	0.94
48_W	138_P	0.708	0.94
41_N	47_G	0.705	0.94
87_L	91_Q	0.704	0.94
10_L	14_T	0.704	0.94
132_K	142_Y	0.703	0.94
30_V	76_Y	0.702	0.93
55_G	61_L	0.694	0.93
78_G	81_T	0.690	0.93
49_N	53_L	0.689	0.93
38_E	70_P	0.683	0.93
128_S	160_D	0.681	0.92
23_I	194_F	0.681	0.92
168_F	178_T	0.681	0.92
87_L	92_H	0.677	0.92
104_F	178_T	0.673	0.92
154_Y	159_G	0.673	0.92
166_G	184_T	0.669	0.92
114_N	121_G	0.669	0.92
146_G	153_E	0.666	0.92
9_T	13_G	0.664	0.91
123_R	126_K	0.662	0.91
127_S	186_D	0.661	0.91
133_S	142_Y	0.658	0.91
135_T	139_G	0.657	0.91
141_A	144_P	0.653	0.91
41_N	46_S	0.652	0.91
35_G	51_E	0.650	0.91
114_N	118_A	0.649	0.90
97_I	109_P	0.643	0.90
25_V	101_A	0.638	0.90
86_S	89_S	0.636	0.90
7_N	12_T	0.635	0.90
112_Y	120_S	0.635	0.90
18_T	21_G	0.630	0.89
14_T	164_C	0.630	0.89
48_W	53_L	0.626	0.89
27_L	99_W	0.618	0.88
80_P	84_L	0.616	0.88
84_L	108_G	0.613	0.88
113_S	120_S	0.611	0.88
28_N	74_Y	0.611	0.88
3_R	6_L	0.608	0.87
65_N	78_G	0.607	0.87
53_L	61_L	0.604	0.87
23_I	190_I	0.602	0.87
35_G	49_N	0.601	0.87
22_A	25_V	0.597	0.86
53_L	56_A	0.595	0.86
40_W	48_W	0.595	0.86
37_A	72_G	0.593	0.86
53_L	65_N	0.589	0.86
179_Y	184_T	0.588	0.86
118_A	170_V	0.585	0.85
187_F	192_R	0.585	0.85
7_N	121_G	0.584	0.85
14_T	17_L	0.583	0.85
94_S	182_F	0.583	0.85
154_Y	158_S	0.582	0.85
34_P	149_T	0.580	0.85
128_S	157_G	0.580	0.85
100_A	184_T	0.579	0.85
160_D	167_R	0.578	0.85
48_W	51_E	0.577	0.85
37_A	75_H	0.575	0.84
51_E	192_R	0.568	0.84
13_G	18_T	0.565	0.83
168_F	180_A	0.565	0.83
7_N	10_L	0.558	0.83
127_S	152_Y	0.558	0.83
111_G	120_S	0.555	0.82
64_N	76_Y	0.555	0.82
189_Y	193_C	0.555	0.82
172_P	175_P	0.554	0.82
146_G	154_Y	0.554	0.82
79_N	109_P	0.553	0.82
84_L	89_S	0.548	0.81
15_T	18_T	0.547	0.81
144_P	152_Y	0.544	0.81
4_I	25_V	0.544	0.81
157_G	160_D	0.542	0.81
181_Y	184_T	0.541	0.81
113_S	126_K	0.540	0.81
162_D	165_N	0.538	0.80
82_A	85_E	0.533	0.80
139_G	145_D	0.531	0.79
78_G	83_L	0.529	0.79
131_L	140_G	0.526	0.79
64_N	81_T	0.525	0.79
107_Y	177_G	0.525	0.79
37_A	52_A	0.524	0.79
143_Y	148_F	0.524	0.79
95_P	109_P	0.523	0.78
149_T	152_Y	0.521	0.78
18_T	35_G	0.520	0.78
32_F	190_I	0.519	0.78
88_D	95_P	0.519	0.78
94_S	172_P	0.519	0.78
111_G	121_G	0.518	0.78
116_T	119_T	0.518	0.78
23_I	26_A	0.517	0.78
115_A	121_G	0.517	0.78
86_S	90_T	0.516	0.77
37_A	67_H	0.516	0.77
170_V	176_N	0.515	0.77
167_R	175_P	0.515	0.77
55_G	58_N	0.514	0.77
29_G	66_A	0.514	0.77
5_P	8_P	0.513	0.77
167_R	170_V	0.512	0.77
84_L	88_D	0.511	0.77
12_T	116_T	0.511	0.77
105_P	175_P	0.509	0.77
112_Y	171_T	0.508	0.76
8_P	100_A	0.507	0.76
89_S	95_P	0.506	0.76
9_T	12_T	0.504	0.76
117_D	121_G	0.501	0.75
48_W	54_G	0.500	0.75
66_A	169_G	0.500	0.75

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
2w91A	1	0.2398	3.8	0.966	Contact Map
4jmqA	1	0.352	2.2	0.97	Contact Map
4aeqA	2	0.1633	1.8	0.971	Contact Map
2m83A	1	0.2398	1.8	0.971	Contact Map
1m5hA	5	0.3673	1.5	0.973	Contact Map
1m5sA	4	0.3673	1.4	0.973	Contact Map
2r5oA	3	0.3061	1.4	0.973	Contact Map
2dk1A	1	0.1071	1.2	0.974	Contact Map
4tmaI	1	0.0816	1.1	0.974	Contact Map
1ftrA	4	0.3673	1.1	0.975	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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