DUF4340 - PFAM28P - GREMLIN Contacts

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DUF4340 - Domain of unknown function (DUF4340)

PFAM:	PF14238	Sequences: WRITEPVDYPADQSAVESLLSALADLKAERFVTEDPADLARYGLDKPAATVTLTDGDLATLLIGKKTPGDGGGVYARLAGEPRVYLVSGSLLDSLDKSPDDWRDKRLLDFDPDDVTRIEVITAGGGTLTLERDGDGWWWLLTKPAGAKADSAKVESLLSALSDLRADDFVDDDPADLAKYGLDKP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	185 (167)
Sequences:	25409 (20662)
Seq/√Len:	1598.9
META:	0.965

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_L	77_R	3.066	1.00
38_D	41_R	2.764	1.00
117_R	129_T	2.751	1.00
52_T	60_T	2.478	1.00
60_T	79_A	2.423	1.00
119_E	129_T	2.344	1.00
76_A	87_V	2.325	1.00
50_T	60_T	2.284	1.00
39_L	77_R	2.211	1.00
141_L	144_P	2.109	1.00
78_L	81_E	2.085	1.00
111_D	114_D	2.083	1.00
98_S	101_D	2.071	1.00
134_G	137_W	2.052	1.00
117_R	131_E	1.924	1.00
13_Q	17_E	1.915	1.00
166_A	169_F	1.876	1.00
50_T	62_L	1.873	1.00
62_L	79_A	1.840	1.00
2_R	8_D	1.828	1.00
40_A	45_D	1.795	1.00
89_G	93_D	1.786	1.00
11_A	16_V	1.752	1.00
122_T	127_T	1.711	1.00
106_R	165_R	1.704	1.00
29_E	88_S	1.687	1.00
19_L	102_W	1.683	1.00
39_L	84_V	1.671	1.00
16_V	20_L	1.653	1.00
103_R	169_F	1.618	1.00
133_D	138_W	1.579	1.00
123_A	126_G	1.578	1.00
119_E	127_T	1.577	1.00
3_I	11_A	1.558	1.00
121_I	126_G	1.499	1.00
151_S	155_E	1.483	1.00
63_I	74_V	1.473	1.00
39_L	44_L	1.442	1.00
44_L	62_L	1.437	1.00
97_K	101_D	1.425	1.00
73_G	86_L	1.420	1.00
149_A	154_V	1.413	1.00
100_D	168_D	1.413	1.00
155_E	159_S	1.390	1.00
31_F	34_E	1.363	1.00
150_D	153_K	1.362	1.00
12_D	15_A	1.337	1.00
112_P	162_S	1.321	1.00
18_S	22_A	1.316	1.00
54_T	57_D	1.303	1.00
17_E	21_S	1.301	1.00
39_L	82_P	1.291	1.00
21_S	25_D	1.235	1.00
52_T	58_L	1.233	1.00
153_K	156_S	1.226	1.00
28_A	85_Y	1.225	1.00
34_E	83_R	1.221	1.00
10_P	104_D	1.204	1.00
106_R	109_D	1.199	1.00
42_Y	84_V	1.193	1.00
12_D	105_K	1.172	1.00
112_P	159_S	1.164	1.00
154_V	158_L	1.164	1.00
76_A	85_Y	1.160	1.00
29_E	73_G	1.144	1.00
43_G	65_K	1.140	1.00
4_T	8_D	1.137	1.00
30_R	86_L	1.133	1.00
36_P	39_L	1.123	1.00
54_T	58_L	1.117	1.00
22_A	94_S	1.114	1.00
67_T	70_D	1.110	1.00
92_L	96_D	1.109	1.00
74_V	92_L	1.108	1.00
130_L	154_V	1.105	1.00
3_I	6_P	1.104	1.00
121_I	127_T	1.101	1.00
47_P	50_T	1.098	1.00
67_T	86_L	1.091	1.00
131_E	142_T	1.088	1.00
63_I	76_A	1.071	1.00
156_S	159_S	1.071	1.00
143_K	146_G	1.067	1.00
100_D	105_K	1.066	1.00
12_D	104_D	1.064	1.00
152_A	156_S	1.058	1.00
97_K	102_W	1.051	1.00
3_I	99_P	1.032	1.00
133_D	136_G	1.027	1.00
127_T	143_K	1.018	1.00
121_I	124_G	1.014	1.00
59_A	78_L	1.014	1.00
18_S	94_S	1.013	1.00
133_D	137_W	1.006	1.00
61_L	76_A	1.005	1.00
18_S	21_S	1.002	1.00
121_I	125_G	0.997	1.00
112_P	155_E	0.996	1.00
31_F	83_R	0.993	1.00
93_D	96_D	0.987	1.00
19_L	95_L	0.983	1.00
66_K	74_V	0.975	1.00
42_Y	75_Y	0.974	1.00
14_S	18_S	0.960	1.00
77_R	82_P	0.953	1.00
126_G	130_L	0.949	1.00
15_A	97_K	0.947	1.00
15_A	18_S	0.945	1.00
55_D	58_L	0.940	1.00
142_T	146_G	0.924	1.00
141_L	145_A	0.917	1.00
110_F	162_S	0.915	1.00
67_T	73_G	0.912	1.00
144_P	147_A	0.911	1.00
74_V	78_L	0.911	1.00
105_K	166_A	0.910	1.00
23_L	53_L	0.897	1.00
48_A	74_V	0.896	1.00
141_L	146_G	0.893	1.00
12_D	165_R	0.892	1.00
110_F	115_V	0.886	1.00
66_K	89_G	0.886	1.00
66_K	71_G	0.882	1.00
143_K	147_A	0.879	1.00
141_L	147_A	0.871	1.00
73_G	88_S	0.859	1.00
137_W	140_L	0.851	1.00
28_A	31_F	0.850	1.00
135_D	138_W	0.850	1.00
22_A	90_S	0.844	1.00
134_G	138_W	0.843	1.00
88_S	91_L	0.835	1.00
70_D	73_G	0.833	1.00
159_S	163_D	0.830	1.00
5_E	8_D	0.823	1.00
156_S	160_A	0.821	1.00
2_R	10_P	0.818	1.00
28_A	78_L	0.803	1.00
122_T	126_G	0.800	1.00
75_Y	86_L	0.794	1.00
39_L	42_Y	0.793	1.00
132_R	135_D	0.792	1.00
65_K	75_Y	0.791	1.00
59_A	79_A	0.790	1.00
37_A	41_R	0.783	1.00
15_A	105_K	0.781	1.00
129_T	143_K	0.781	1.00
122_T	125_G	0.780	1.00
129_T	142_T	0.779	1.00
103_R	166_A	0.779	1.00
77_R	80_G	0.772	1.00
20_L	24_A	0.768	1.00
66_K	92_L	0.766	1.00
67_T	71_G	0.762	1.00
6_P	168_D	0.762	1.00
141_L	149_A	0.761	1.00
33_T	36_P	0.752	1.00
103_R	107_L	0.751	1.00
152_A	155_E	0.749	1.00
26_L	91_L	0.749	1.00
55_D	59_A	0.743	1.00
7_V	99_P	0.725	1.00
121_I	128_L	0.722	1.00
72_G	89_G	0.722	1.00
140_L	143_K	0.718	1.00
107_L	166_A	0.712	1.00
44_L	77_R	0.705	1.00
132_R	137_W	0.704	1.00
14_S	17_E	0.694	1.00
98_S	102_W	0.689	1.00
36_P	82_P	0.689	1.00
49_A	92_L	0.688	1.00
35_D	82_P	0.681	1.00
15_A	101_D	0.680	1.00
104_D	109_D	0.677	1.00
30_R	33_T	0.676	1.00
118_I	157_L	0.663	1.00
74_V	87_V	0.652	1.00
90_S	93_D	0.651	1.00
22_A	25_D	0.650	1.00
142_T	145_A	0.648	1.00
68_P	72_G	0.647	1.00
21_S	24_A	0.645	1.00
3_I	9_Y	0.645	1.00
31_F	85_Y	0.643	1.00
140_L	146_G	0.642	1.00
94_S	97_K	0.635	1.00
2_R	6_P	0.633	1.00
100_D	103_R	0.632	1.00
111_D	162_S	0.629	1.00
145_A	149_A	0.628	1.00
158_L	162_S	0.628	1.00
3_I	7_V	0.627	1.00
132_R	136_G	0.622	1.00
112_P	116_T	0.618	1.00
28_A	87_V	0.617	1.00
49_A	96_D	0.615	1.00
67_T	72_G	0.614	1.00
36_P	41_R	0.613	1.00
99_P	103_R	0.612	1.00
118_I	130_L	0.610	1.00
32_V	75_Y	0.603	1.00
6_P	9_Y	0.602	1.00
33_T	39_L	0.599	1.00
107_L	164_L	0.588	1.00
35_D	38_D	0.586	1.00
33_T	37_A	0.584	1.00
74_V	89_G	0.581	1.00
132_R	138_W	0.580	1.00
29_E	32_V	0.578	1.00
48_A	62_L	0.575	1.00
81_E	85_Y	0.566	1.00
123_A	128_L	0.564	1.00
159_S	162_S	0.561	1.00
38_D	42_Y	0.559	1.00
39_L	45_D	0.557	1.00
77_R	81_E	0.555	1.00
65_K	68_P	0.555	1.00
6_P	103_R	0.555	1.00
87_V	91_L	0.554	1.00
123_A	127_T	0.553	1.00
115_V	158_L	0.553	1.00
116_T	131_E	0.551	1.00
124_G	127_T	0.546	1.00
50_T	79_A	0.542	1.00
26_L	87_V	0.539	1.00
53_L	59_A	0.537	1.00
44_L	47_P	0.536	1.00
30_R	73_G	0.535	1.00
68_P	71_G	0.533	1.00
118_I	158_L	0.533	1.00
40_A	46_K	0.530	1.00
129_T	132_R	0.529	1.00
136_G	151_S	0.528	1.00
27_K	88_S	0.523	1.00
44_L	84_V	0.522	1.00
112_P	158_L	0.521	1.00
37_A	42_Y	0.521	1.00
89_G	92_L	0.515	1.00
38_D	43_G	0.515	1.00
44_L	64_G	0.514	1.00
101_D	105_K	0.513	1.00
43_G	47_P	0.510	1.00
48_A	65_K	0.509	1.00
66_K	72_G	0.508	1.00
62_L	80_G	0.506	1.00
105_K	165_R	0.506	1.00
140_L	144_P	0.504	1.00
77_R	84_V	0.503	1.00
155_E	158_L	0.500	1.00

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
2l5yA	1	0.3351	2.7	0.936	Contact Map
2k60A	1	0.3351	2.1	0.94	Contact Map
3m4aA	1	0.8649	2.1	0.94	Contact Map
2fd4A	1	0.5189	2	0.94	Contact Map
1dd4C	7	0.2162	1.9	0.941	Contact Map
1zavU	5	0.1622	1.7	0.943	Contact Map
2jmcA	1	0.3784	1.7	0.943	Contact Map
1wjxA	1	0.6	1.5	0.944	Contact Map
3nfgB	2	0.4595	1.3	0.946	Contact Map
4bjjB	1	0.1838	1.3	0.947	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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