DUF1995 - PFAM28P - GREMLIN Contacts

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DUF1995 - Domain of unknown function (DUF1995)

PFAM:	PF09353	Sequences: PKSLEEAIAQAAEATQAALADGKTRLEVELLFPELMDDYDGEALRLLPLALQFLRLLAELGSGARLKVLFPDAGAAALARREDDLFLFVAPSAVELEDVEKLCEAAGDRPVVLLNPRLEDVASVGIGYAARGKQLRERFLSTFEPVYYLRPLSEGGISGALFRCYPGPWQVWLETDDGGYELVAEFPQRPSGEELEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	197 (192)
Sequences:	927 (698)
Seq/√Len:	50.4
META:	0.544

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_L	146_V	4.527	1.00
10_Q	147_Y	4.453	1.00
21_D	165_Y	4.447	1.00
100_E	138_R	4.058	1.00
163_R	166_P	3.469	1.00
25_R	142_T	3.443	1.00
86_F	109_R	3.212	1.00
161_L	171_V	3.016	1.00
191_S	194_E	2.908	1.00
91_P	116_P	2.647	1.00
103_C	111_V	2.514	1.00
67_K	83_D	2.494	1.00
87_L	112_V	2.418	1.00
19_L	110_P	2.294	1.00
168_P	187_P	2.286	1.00
88_F	102_L	2.284	1.00
171_V	195_L	2.212	1.00
88_F	99_V	2.205	1.00
115_N	149_L	2.201	1.00
70_F	79_A	2.161	1.00
152_L	159_G	2.058	1.00
162_F	170_Q	2.055	1.00
25_R	143_F	2.025	1.00
14_A	164_C	2.014	1.00
41_G	45_R	1.899	0.99
175_T	181_E	1.889	0.99
186_F	194_E	1.829	0.99
27_E	116_P	1.715	0.99
182_L	185_E	1.683	0.98
3_S	6_E	1.650	0.98
74_G	77_A	1.624	0.98
42_E	45_R	1.594	0.98
170_Q	185_E	1.582	0.98
21_D	25_R	1.539	0.97
50_A	114_L	1.516	0.97
42_E	46_L	1.504	0.97
83_D	109_R	1.464	0.96
28_V	82_E	1.460	0.96
88_F	113_L	1.456	0.96
168_P	185_E	1.429	0.96
140_L	145_P	1.385	0.95
191_S	195_L	1.378	0.95
74_G	136_R	1.369	0.94
46_L	50_A	1.354	0.94
109_R	147_Y	1.344	0.94
10_Q	164_C	1.343	0.94
99_V	113_L	1.318	0.93
145_P	163_R	1.311	0.93
51_L	55_R	1.309	0.93
161_L	181_E	1.308	0.93
127_G	131_R	1.285	0.92
63_G	182_L	1.281	0.92
36_M	39_Y	1.276	0.92
3_S	62_S	1.273	0.92
128_Y	134_Q	1.268	0.92
106_A	111_V	1.255	0.91
66_L	87_L	1.245	0.91
2_K	6_E	1.232	0.91
14_A	18_A	1.225	0.90
106_A	109_R	1.221	0.90
18_A	21_D	1.215	0.90
74_G	78_L	1.215	0.90
15_T	146_V	1.203	0.89
84_D	194_E	1.198	0.89
113_L	116_P	1.188	0.89
50_A	89_V	1.186	0.89
51_L	179_G	1.176	0.88
190_P	195_L	1.171	0.88
144_E	165_Y	1.168	0.88
117_R	161_L	1.153	0.87
70_F	76_A	1.134	0.86
84_D	105_A	1.128	0.86
134_Q	137_E	1.128	0.86
46_L	49_L	1.127	0.86
167_G	170_Q	1.120	0.86
188_Q	194_E	1.089	0.84
45_R	48_P	1.075	0.83
124_V	130_A	1.067	0.83
100_E	104_E	1.062	0.83
147_Y	162_F	1.057	0.82
27_E	30_L	1.055	0.82
17_A	21_D	1.053	0.82
126_I	129_A	1.049	0.82
19_L	183_V	1.049	0.82
14_A	21_D	1.043	0.81
24_T	146_V	1.035	0.81
142_T	152_L	1.027	0.80
155_G	158_S	1.022	0.80
180_Y	194_E	1.021	0.80
29_E	70_F	1.021	0.80
74_G	79_A	1.017	0.80
185_E	188_Q	1.011	0.79
177_D	191_S	1.008	0.79
112_V	196_E	1.003	0.79
8_I	162_F	1.002	0.79
17_A	20_A	0.999	0.79
15_T	25_R	0.996	0.78
25_R	116_P	0.989	0.78
134_Q	138_R	0.983	0.77
99_V	140_L	0.978	0.77
53_F	72_D	0.966	0.76
116_P	120_D	0.965	0.76
32_F	149_L	0.948	0.75
20_A	104_E	0.948	0.75
1_P	6_E	0.948	0.75
171_V	186_F	0.945	0.75
101_K	104_E	0.939	0.74
91_P	190_P	0.928	0.73
172_W	182_L	0.922	0.73
51_L	54_L	0.921	0.73
160_A	180_Y	0.919	0.72
23_K	146_V	0.907	0.71
77_A	127_G	0.895	0.70
178_G	181_E	0.887	0.70
127_G	130_A	0.885	0.70
10_Q	162_F	0.878	0.69
72_D	138_R	0.878	0.69
16_Q	20_A	0.877	0.69
147_Y	190_P	0.875	0.69
120_D	136_R	0.869	0.68
24_T	110_P	0.867	0.68
46_L	90_A	0.862	0.68
42_E	52_Q	0.861	0.67
69_L	76_A	0.857	0.67
76_A	80_R	0.849	0.66
153_S	156_G	0.840	0.66
11_A	117_R	0.829	0.64
11_A	30_L	0.826	0.64
112_V	184_A	0.824	0.64
11_A	163_R	0.823	0.64
120_D	123_S	0.819	0.64
125_G	136_R	0.818	0.63
61_G	110_P	0.811	0.63
56_L	59_E	0.808	0.62
162_F	173_L	0.808	0.62
73_A	77_A	0.808	0.62
9_A	12_A	0.805	0.62
48_P	52_Q	0.801	0.62
151_P	169_W	0.800	0.62
84_D	188_Q	0.798	0.62
149_L	162_F	0.793	0.61
16_Q	62_S	0.792	0.61
95_E	118_L	0.783	0.60
45_R	52_Q	0.780	0.60
15_T	53_F	0.769	0.59
20_A	49_L	0.768	0.59
13_E	20_A	0.758	0.58
136_R	157_I	0.755	0.57
40_D	43_A	0.753	0.57
152_L	161_L	0.751	0.57
65_R	84_D	0.743	0.56
187_P	194_E	0.743	0.56
15_T	29_E	0.725	0.54
13_E	101_K	0.720	0.54
118_L	139_F	0.714	0.53
61_G	64_A	0.713	0.53
75_A	78_L	0.710	0.53
131_R	136_R	0.708	0.52
107_G	112_V	0.708	0.52
3_S	52_Q	0.705	0.52
21_D	104_E	0.703	0.52
67_K	70_F	0.702	0.52
5_E	52_Q	0.698	0.51
92_S	141_S	0.695	0.51
187_P	195_L	0.695	0.51
25_R	103_C	0.695	0.51
41_G	44_L	0.694	0.51
10_Q	14_A	0.692	0.51
66_L	71_P	0.690	0.51
27_E	154_E	0.688	0.50
13_E	17_A	0.687	0.50
69_L	161_L	0.686	0.50
16_Q	21_D	0.685	0.50
71_P	75_A	0.681	0.50
100_E	141_S	0.680	0.50
145_P	148_Y	0.678	0.49
54_L	88_F	0.677	0.49
29_E	148_Y	0.669	0.48
138_R	148_Y	0.669	0.48
148_Y	169_W	0.669	0.48
49_L	87_L	0.666	0.48
43_A	47_L	0.665	0.48
59_E	84_D	0.658	0.47
135_L	171_V	0.655	0.47
91_P	113_L	0.655	0.47
92_S	160_A	0.654	0.47
41_G	46_L	0.651	0.47
69_L	88_F	0.651	0.47
72_D	95_E	0.649	0.46
20_A	107_G	0.643	0.46
151_P	158_S	0.642	0.46
128_Y	131_R	0.641	0.46
42_E	48_P	0.639	0.45
120_D	124_V	0.638	0.45
17_A	23_K	0.637	0.45
144_E	163_R	0.632	0.45
2_K	183_V	0.631	0.45
42_E	54_L	0.629	0.44
13_E	191_S	0.626	0.44
20_A	63_G	0.625	0.44
91_P	143_F	0.625	0.44
2_K	194_E	0.623	0.44
50_A	130_A	0.621	0.44
32_F	71_P	0.621	0.44
119_E	122_A	0.619	0.43
13_E	22_G	0.616	0.43
42_E	57_L	0.615	0.43
66_L	194_E	0.613	0.43
104_E	107_G	0.610	0.42
63_G	113_L	0.604	0.42
147_Y	186_F	0.603	0.42
67_K	71_P	0.602	0.42
60_L	63_G	0.600	0.41
32_F	93_A	0.600	0.41
78_L	81_R	0.598	0.41
33_P	95_E	0.598	0.41
35_L	160_A	0.597	0.41
11_A	28_V	0.593	0.41
173_L	177_D	0.592	0.41
173_L	186_F	0.589	0.40
86_F	110_P	0.589	0.40
75_A	79_A	0.588	0.40
60_L	101_K	0.587	0.40
45_R	51_L	0.586	0.40
188_Q	195_L	0.585	0.40
135_L	138_R	0.585	0.40
82_E	181_E	0.585	0.40
2_K	13_E	0.582	0.40
5_E	143_F	0.578	0.39
39_Y	43_A	0.577	0.39
43_A	78_L	0.574	0.39
75_A	131_R	0.573	0.39
95_E	100_E	0.572	0.39
170_Q	182_L	0.571	0.39
130_A	135_L	0.569	0.38
51_L	57_L	0.568	0.38
16_Q	88_F	0.567	0.38
44_L	48_P	0.566	0.38
84_D	115_N	0.566	0.38
50_A	138_R	0.565	0.38
5_E	11_A	0.565	0.38
43_A	46_L	0.562	0.38
16_Q	19_L	0.561	0.38
153_S	159_G	0.561	0.38
183_V	186_F	0.560	0.38
115_N	167_G	0.558	0.37
24_T	115_N	0.558	0.37
35_L	39_Y	0.554	0.37
51_L	101_K	0.553	0.37
126_I	189_R	0.550	0.37
94_V	163_R	0.549	0.36
127_G	136_R	0.546	0.36
147_Y	166_P	0.546	0.36
15_T	19_L	0.544	0.36
10_Q	15_T	0.542	0.36
4_L	149_L	0.541	0.36
16_Q	113_L	0.541	0.36
60_L	88_F	0.540	0.36
92_S	95_E	0.540	0.36
3_S	96_L	0.537	0.35
22_G	165_Y	0.536	0.35
42_E	49_L	0.532	0.35
89_V	114_L	0.532	0.35
45_R	49_L	0.529	0.35
45_R	58_A	0.529	0.35
162_F	172_W	0.529	0.35
128_Y	135_L	0.528	0.34
13_E	164_C	0.528	0.34
183_V	188_Q	0.527	0.34
70_F	118_L	0.526	0.34
31_L	159_G	0.526	0.34
71_P	80_R	0.526	0.34
5_E	96_L	0.525	0.34
125_G	137_E	0.525	0.34
88_F	111_V	0.524	0.34
96_L	179_G	0.522	0.34
5_E	177_D	0.521	0.34
28_V	144_E	0.519	0.34
69_L	188_Q	0.519	0.34
53_F	95_E	0.518	0.34
39_Y	42_E	0.513	0.33
145_P	183_V	0.512	0.33
26_L	110_P	0.504	0.32
115_N	143_F	0.504	0.32
93_A	149_L	0.503	0.32
79_A	100_E	0.502	0.32
77_A	97_E	0.500	0.32
13_E	16_Q	0.500	0.32

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
1x7fA	1	0.8782	6.6	0.947	Contact Map
3me7A	1	0.6802	6	0.948	Contact Map
3ia1A	2	0.665	5.8	0.948	Contact Map
4txoD	1	0.6396	5.2	0.949	Contact Map
2xz3A	3	0.5381	5.2	0.949	Contact Map
3txvA	2	0.934	4.7	0.95	Contact Map
3hhlA	3	0.5482	4.5	0.951	Contact Map
4bpyA	1	0.6954	4.4	0.951	Contact Map
2vtwA	3	0.3452	4.3	0.951	Contact Map
2k6vA	1	0.7208	3.3	0.954	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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