DUF1415 - PFAM28P - GREMLIN Contacts

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DUF1415 - Protein of unknown function (DUF1415)

PFAM:	PF07209	Sequences: QVIAATRRWLERAVIGLNLCPFAKAVHVKGQIRYVVSEATDPEALLEDLLAELELLAAADPEEIETTLLIHPNVLQDFLDYNDFLDLADALLEELGLEGVLQIASFHPDYQFAGTEPDDIENYTNRSPYPMLHLLREASIERAVAAFPDPEAIPERNIETLRRLGLEGWQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	171 (169)
Sequences:	4758 (3377)
Seq/√Len:	259.7
META:	0.864

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_L	64_I	2.806	1.00
37_S	48_D	2.645	1.00
34_Y	70_I	2.574	1.00
93_E	98_E	2.569	1.00
65_E	139_S	2.523	1.00
57_A	101_L	2.494	1.00
24_K	28_V	2.446	1.00
15_I	27_H	2.344	1.00
45_L	71_H	2.285	1.00
144_V	150_P	2.211	1.00
11_E	27_H	2.206	1.00
115_T	121_E	2.049	1.00
6_T	131_M	2.034	1.00
88_A	103_I	2.021	1.00
99_G	137_E	1.934	1.00
33_R	52_E	1.929	1.00
85_L	105_S	1.870	1.00
121_E	158_I	1.812	1.00
33_R	64_I	1.801	1.00
166_L	170_Q	1.714	1.00
33_R	55_L	1.710	1.00
27_H	32_I	1.692	1.00
19_L	161_L	1.656	1.00
52_E	55_L	1.654	1.00
55_L	59_A	1.643	1.00
27_H	34_Y	1.619	1.00
8_R	12_R	1.609	1.00
160_T	164_L	1.588	1.00
10_L	27_H	1.581	1.00
159_E	163_R	1.511	1.00
50_L	95_L	1.475	1.00
50_L	91_L	1.449	1.00
52_E	67_T	1.444	1.00
115_T	122_N	1.443	1.00
121_E	162_R	1.440	1.00
140_I	144_V	1.436	1.00
152_A	155_E	1.434	1.00
59_A	63_E	1.421	1.00
71_H	74_V	1.403	1.00
41_D	44_A	1.400	1.00
135_L	140_I	1.398	1.00
111_Q	115_T	1.383	1.00
5_A	129_Y	1.365	1.00
141_E	145_A	1.363	1.00
120_I	166_L	1.363	1.00
81_Y	131_M	1.359	1.00
120_I	123_Y	1.357	1.00
105_S	110_Y	1.342	1.00
7_R	30_G	1.336	1.00
40_T	73_N	1.327	1.00
13_A	169_W	1.325	1.00
156_R	160_T	1.324	1.00
10_L	68_L	1.317	1.00
119_D	162_R	1.314	1.00
155_E	159_E	1.302	1.00
75_L	84_F	1.299	1.00
150_P	153_I	1.281	1.00
160_T	163_R	1.271	1.00
124_T	161_L	1.245	1.00
115_T	119_D	1.226	1.00
165_G	168_G	1.224	1.00
54_E	57_A	1.189	1.00
111_Q	117_P	1.185	1.00
31_Q	65_E	1.184	1.00
144_V	147_F	1.179	1.00
123_Y	166_L	1.171	1.00
26_V	65_E	1.171	1.00
81_Y	105_S	1.158	1.00
48_D	51_A	1.158	1.00
97_L	101_L	1.143	1.00
10_L	15_I	1.126	1.00
7_R	34_Y	1.119	1.00
79_L	83_D	1.114	1.00
147_F	154_P	1.112	1.00
35_V	52_E	1.112	1.00
47_E	51_A	1.111	1.00
147_F	152_A	1.105	1.00
57_A	97_L	1.103	1.00
92_L	103_I	1.100	1.00
101_L	134_L	1.093	1.00
45_L	75_L	1.091	1.00
13_A	19_L	1.089	1.00
81_Y	110_Y	1.087	1.00
38_E	73_N	1.085	1.00
54_E	58_A	1.082	1.00
68_L	131_M	1.081	1.00
164_L	168_G	1.070	1.00
111_Q	122_N	1.066	1.00
147_F	156_R	1.066	1.00
2_V	36_V	1.061	1.00
46_L	91_L	1.060	1.00
156_R	159_E	1.059	1.00
149_D	152_A	1.055	1.00
26_V	29_K	1.054	1.00
46_L	87_L	1.041	1.00
26_V	31_Q	1.027	1.00
3_I	7_R	1.018	1.00
71_H	132_L	1.009	1.00
51_A	54_E	0.996	1.00
4_A	8_R	0.986	1.00
7_R	11_E	0.983	1.00
17_L	160_T	0.980	1.00
152_A	156_R	0.978	1.00
3_I	34_Y	0.976	1.00
123_Y	126_R	0.974	1.00
54_E	95_L	0.972	1.00
6_T	127_S	0.970	1.00
147_F	150_P	0.964	1.00
39_A	48_D	0.961	1.00
59_A	64_I	0.944	1.00
24_K	29_K	0.942	1.00
27_H	30_G	0.929	1.00
120_I	169_W	0.926	1.00
57_A	100_V	0.923	1.00
154_P	158_I	0.922	1.00
127_S	131_M	0.917	1.00
45_L	74_V	0.917	1.00
79_L	82_N	0.904	1.00
53_L	97_L	0.900	1.00
3_I	36_V	0.898	1.00
161_L	169_W	0.895	1.00
10_L	34_Y	0.893	1.00
43_E	47_E	0.889	1.00
39_A	44_A	0.888	1.00
167_E	170_Q	0.887	1.00
50_L	94_E	0.884	1.00
82_N	89_D	0.881	1.00
53_L	101_L	0.878	1.00
14_V	19_L	0.876	1.00
86_D	89_D	0.872	1.00
116_E	122_N	0.862	1.00
3_I	70_I	0.859	1.00
25_A	29_K	0.855	1.00
90_A	94_E	0.844	0.99
35_V	51_A	0.843	0.99
61_P	142_R	0.842	0.99
46_L	84_F	0.842	0.99
150_P	154_P	0.840	0.99
81_Y	104_A	0.839	0.99
50_L	54_E	0.838	0.99
161_L	164_L	0.827	0.99
33_R	67_T	0.823	0.99
74_V	84_F	0.818	0.99
5_A	8_R	0.814	0.99
116_E	121_E	0.813	0.99
123_Y	165_G	0.813	0.99
36_V	70_I	0.811	0.99
25_A	28_V	0.805	0.99
90_A	93_E	0.788	0.99
83_D	86_D	0.785	0.99
79_L	111_Q	0.782	0.99
48_D	69_L	0.781	0.99
49_L	134_L	0.780	0.99
49_L	69_L	0.776	0.99
70_I	131_M	0.776	0.99
18_N	24_K	0.774	0.99
15_I	24_K	0.771	0.99
50_L	53_L	0.767	0.99
120_I	165_G	0.761	0.99
77_D	80_D	0.744	0.99
142_R	146_A	0.740	0.99
151_E	154_P	0.737	0.99
104_A	110_Y	0.735	0.99
26_V	66_T	0.731	0.98
164_L	169_W	0.730	0.98
91_L	95_L	0.723	0.98
84_F	132_L	0.709	0.98
103_I	132_L	0.707	0.98
109_D	117_P	0.705	0.98
89_D	103_I	0.704	0.98
151_E	155_E	0.700	0.98
49_L	132_L	0.692	0.98
158_I	162_R	0.691	0.98
47_E	50_L	0.689	0.98
60_D	63_E	0.688	0.98
100_V	138_A	0.688	0.98
106_F	161_L	0.687	0.98
7_R	27_H	0.685	0.98
42_P	87_L	0.674	0.97
85_L	132_L	0.674	0.97
166_L	169_W	0.672	0.97
46_L	50_L	0.669	0.97
49_L	88_A	0.665	0.97
86_D	90_A	0.659	0.97
17_L	164_L	0.655	0.97
44_A	47_E	0.654	0.97
12_R	16_G	0.648	0.97
53_L	57_A	0.646	0.97
10_L	135_L	0.637	0.96
64_I	136_R	0.636	0.96
110_Y	125_N	0.636	0.96
160_T	168_G	0.633	0.96
87_L	94_E	0.630	0.96
36_V	129_Y	0.628	0.96
71_H	84_F	0.626	0.96
121_E	161_L	0.626	0.96
102_Q	112_F	0.623	0.96
82_N	86_D	0.616	0.96
161_L	168_G	0.614	0.96
71_H	76_Q	0.614	0.96
110_Y	124_T	0.612	0.95
143_A	146_A	0.610	0.95
26_V	32_I	0.604	0.95
11_E	16_G	0.603	0.95
56_L	134_L	0.597	0.95
42_P	83_D	0.593	0.95
146_A	150_P	0.590	0.94
138_A	141_E	0.590	0.94
32_I	66_T	0.585	0.94
93_E	96_G	0.585	0.94
26_V	30_G	0.582	0.94
6_T	70_I	0.581	0.94
141_E	144_V	0.580	0.94
13_A	16_G	0.577	0.94
82_N	85_L	0.574	0.94
55_L	58_A	0.569	0.93
97_L	165_G	0.567	0.93
42_P	84_F	0.566	0.93
37_S	45_L	0.564	0.93
8_R	11_E	0.564	0.93
36_V	72_P	0.560	0.93
43_E	87_L	0.559	0.93
66_T	139_S	0.558	0.93
49_L	103_I	0.557	0.93
13_A	161_L	0.556	0.93
35_V	55_L	0.556	0.93
85_L	110_Y	0.553	0.92
45_L	84_F	0.552	0.92
56_L	67_T	0.551	0.92
66_T	135_L	0.550	0.92
35_V	69_L	0.549	0.92
51_A	55_L	0.549	0.92
49_L	53_L	0.549	0.92
120_I	162_R	0.545	0.92
50_L	87_L	0.537	0.91
56_L	101_L	0.533	0.91
11_E	28_V	0.531	0.91
76_Q	109_D	0.528	0.91
58_A	63_E	0.528	0.91
143_A	147_F	0.527	0.90
81_Y	85_L	0.526	0.90
120_I	168_G	0.520	0.90
90_A	96_G	0.520	0.90
61_P	65_E	0.520	0.90
4_A	7_R	0.518	0.90
7_R	32_I	0.517	0.90
42_P	74_V	0.515	0.89
120_I	124_T	0.514	0.89
26_V	135_L	0.512	0.89
43_E	90_A	0.512	0.89
19_L	124_T	0.510	0.89
88_A	91_L	0.507	0.89
31_Q	142_R	0.502	0.88
25_A	140_I	0.500	0.88

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
1go9A	1	0.2281	7.2	0.951	Contact Map
2rm9A	1	0.1754	7.1	0.951	Contact Map
3iclA	1	0.5848	6.7	0.952	Contact Map
3hvaA	1	0.5673	6.5	0.952	Contact Map
4n9gC	1	0.0877	6.3	0.953	Contact Map
1k3kA	1	0.2398	5.3	0.954	Contact Map
3mtkA	2	0.5848	4.4	0.956	Contact Map
3kt7A	2	0.4211	3.7	0.958	Contact Map
4i4tA	1	0.924	3.5	0.958	Contact Map
3optA	1	0.5556	3.4	0.958	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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