DUF1614 - PFAM28P - GREMLIN Contacts

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DUF1614 - Protein of unknown function (DUF1614)

PFAM:	PF07758	Sequences: LLGSYINIPLARLPSERPVGEEVSFFGMRYVVPVVRERWPGTVIAVNVGGAVIPVLLSLYLLLRNPLSLLRALIATAIVAAVVYLLARPVPGVGIAVPVFIPPLVAALVALLLSREYAAPLAYISGTLGTLIGADLLNLGKIRGLGAPVASIGGAGTFDGIFLTGILAVLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	171 (170)
Sequences:	2994 (2151)
Seq/√Len:	165.0
META:	0.923

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
83_V	97_V	4.578	1.00
12_R	41_G	4.471	1.00
138_N	141_K	4.461	1.00
75_A	125_S	4.395	1.00
82_V	105_V	3.313	1.00
132_I	136_L	2.916	1.00
62_L	72_A	2.851	1.00
48_V	52_V	2.834	1.00
80_A	137_L	2.743	1.00
84_Y	138_N	2.572	1.00
78_I	109_V	2.415	1.00
11_A	44_I	2.293	1.00
46_V	51_A	2.284	1.00
13_L	42_T	2.255	1.00
46_V	55_V	2.253	1.00
97_V	102_P	2.251	1.00
13_L	44_I	2.219	1.00
90_V	96_A	2.095	1.00
81_A	85_L	2.057	1.00
141_K	144_G	1.994	1.00
142_I	150_A	1.835	1.00
79_V	109_V	1.828	1.00
76_T	80_A	1.822	1.00
128_L	132_I	1.815	1.00
84_Y	137_L	1.813	1.00
45_A	149_V	1.755	1.00
104_L	108_L	1.702	1.00
58_S	61_L	1.687	1.00
135_D	159_D	1.620	1.00
6_I	48_V	1.608	1.00
3_G	9_P	1.579	1.00
87_A	95_I	1.502	1.00
117_Y	120_P	1.496	1.00
80_A	132_I	1.489	1.00
86_L	97_V	1.487	1.00
24_S	29_R	1.478	1.00
52_V	56_L	1.437	1.00
86_L	101_I	1.434	1.00
58_S	123_Y	1.430	1.00
110_A	125_S	1.420	1.00
76_T	132_I	1.389	1.00
114_S	117_Y	1.346	1.00
87_A	138_N	1.323	1.00
75_A	110_A	1.306	1.00
42_T	150_A	1.304	1.00
58_S	127_T	1.304	1.00
89_P	95_I	1.300	1.00
81_A	137_L	1.294	1.00
62_L	124_I	1.278	1.00
103_P	163_L	1.262	1.00
10_L	44_I	1.251	1.00
22_E	29_R	1.240	1.00
135_D	138_N	1.238	1.00
10_L	46_V	1.222	1.00
23_V	27_G	1.221	1.00
51_A	161_I	1.217	1.00
83_V	130_T	1.201	1.00
159_D	165_G	1.194	1.00
80_A	84_Y	1.185	1.00
55_V	58_S	1.162	1.00
35_V	39_W	1.152	1.00
61_L	64_R	1.147	1.00
25_F	28_M	1.145	1.00
103_P	106_A	1.133	1.00
164_T	168_A	1.132	1.00
123_Y	127_T	1.113	1.00
44_I	150_A	1.097	1.00
126_G	164_T	1.090	1.00
87_A	134_A	1.089	1.00
23_V	29_R	1.085	1.00
107_A	118_A	1.085	1.00
110_A	114_S	1.082	1.00
106_A	110_A	1.082	1.00
17_R	21_E	1.081	1.00
82_V	101_I	1.060	0.99
72_A	76_T	1.047	0.99
76_T	128_L	1.036	0.99
62_L	69_L	1.036	0.99
67_L	121_L	1.032	0.99
57_L	103_P	1.014	0.99
72_A	124_I	1.000	0.99
71_R	114_S	0.997	0.99
6_I	57_L	0.993	0.99
2_L	5_Y	0.989	0.99
6_I	103_P	0.984	0.99
73_L	77_A	0.982	0.99
108_L	111_L	0.978	0.99
145_L	148_P	0.977	0.99
79_V	130_T	0.965	0.99
85_L	89_P	0.965	0.99
27_G	33_P	0.961	0.99
110_A	113_L	0.946	0.99
121_L	124_I	0.941	0.99
11_A	15_S	0.929	0.99
58_S	128_L	0.927	0.99
71_R	121_L	0.914	0.98
1_L	5_Y	0.914	0.98
55_V	131_L	0.911	0.98
79_V	83_V	0.884	0.98
106_A	168_A	0.880	0.98
82_V	86_L	0.879	0.98
61_L	65_N	0.873	0.98
27_G	32_V	0.871	0.98
130_T	161_I	0.849	0.97
14_P	41_G	0.848	0.97
93_V	96_A	0.844	0.97
123_Y	162_F	0.843	0.97
76_T	125_S	0.840	0.97
23_V	26_F	0.834	0.97
113_L	116_E	0.825	0.97
16_E	20_G	0.820	0.97
23_V	32_V	0.816	0.97
134_A	151_S	0.809	0.96
69_L	73_L	0.809	0.96
72_A	121_L	0.809	0.96
95_I	134_A	0.806	0.96
69_L	72_A	0.805	0.96
112_L	115_R	0.799	0.96
61_L	124_I	0.790	0.96
99_V	163_L	0.781	0.96
48_V	53_I	0.777	0.96
21_E	25_F	0.777	0.96
34_V	74_I	0.776	0.96
8_I	48_V	0.770	0.95
94_G	133_G	0.766	0.95
6_I	59_L	0.759	0.95
139_L	142_I	0.757	0.95
108_L	112_L	0.756	0.95
45_A	151_S	0.750	0.95
78_I	105_V	0.746	0.94
166_I	169_V	0.745	0.94
49_G	158_F	0.738	0.94
75_A	113_L	0.735	0.94
127_T	165_G	0.735	0.94
140_G	143_R	0.734	0.94
31_V	34_V	0.729	0.94
32_V	35_V	0.728	0.94
17_R	40_P	0.719	0.93
27_G	30_Y	0.716	0.93
2_L	13_L	0.708	0.93
104_L	107_A	0.698	0.92
44_I	60_Y	0.697	0.92
22_E	25_F	0.693	0.92
14_P	18_P	0.690	0.92
103_P	107_A	0.688	0.92
110_A	115_R	0.688	0.92
20_G	36_R	0.683	0.91
96_A	99_V	0.683	0.91
156_G	160_G	0.680	0.91
3_G	126_G	0.679	0.91
20_G	34_V	0.676	0.91
89_P	93_V	0.676	0.91
165_G	169_V	0.674	0.91
94_G	102_P	0.665	0.90
25_F	29_R	0.665	0.90
88_R	140_G	0.665	0.90
19_V	22_E	0.664	0.90
25_F	30_Y	0.662	0.90
60_Y	64_R	0.661	0.90
81_A	116_E	0.659	0.90
107_A	110_A	0.656	0.90
155_A	168_A	0.654	0.90
23_V	28_M	0.652	0.89
72_A	75_A	0.652	0.89
83_V	105_V	0.651	0.89
77_A	81_A	0.651	0.89
126_G	155_A	0.649	0.89
153_G	156_G	0.645	0.89
120_P	124_I	0.642	0.89
103_P	164_T	0.642	0.89
5_Y	127_T	0.641	0.89
97_V	160_G	0.640	0.89
23_V	31_V	0.640	0.89
162_F	166_I	0.638	0.88
87_A	97_V	0.637	0.88
84_Y	140_G	0.635	0.88
18_P	21_E	0.634	0.88
105_V	109_V	0.631	0.88
22_E	31_V	0.630	0.88
89_P	169_V	0.629	0.88
115_R	118_A	0.621	0.87
84_Y	141_K	0.619	0.87
165_G	168_A	0.616	0.87
155_A	159_D	0.613	0.86
126_G	160_G	0.613	0.86
111_L	115_R	0.612	0.86
58_S	124_I	0.610	0.86
34_V	37_E	0.605	0.86
75_A	126_G	0.604	0.86
95_I	131_L	0.600	0.85
80_A	83_V	0.599	0.85
70_L	74_I	0.599	0.85
125_S	129_G	0.597	0.85
11_A	14_P	0.595	0.85
109_V	125_S	0.590	0.84
127_T	164_T	0.587	0.84
65_N	117_Y	0.586	0.84
12_R	15_S	0.583	0.84
24_S	27_G	0.583	0.84
77_A	132_I	0.582	0.83
89_P	158_F	0.579	0.83
149_V	167_L	0.578	0.83
84_Y	88_R	0.576	0.83
53_I	57_L	0.573	0.83
150_A	168_A	0.568	0.82
75_A	160_G	0.567	0.82
111_L	118_A	0.567	0.82
98_P	160_G	0.562	0.81
9_P	60_Y	0.562	0.81
106_A	164_T	0.560	0.81
83_V	137_L	0.560	0.81
133_G	139_L	0.559	0.81
36_R	40_P	0.558	0.81
39_W	81_A	0.555	0.80
2_L	6_I	0.555	0.80
88_R	103_P	0.554	0.80
24_S	34_V	0.554	0.80
12_R	116_E	0.554	0.80
157_T	167_L	0.553	0.80
114_S	118_A	0.553	0.80
18_P	36_R	0.551	0.80
148_P	164_T	0.550	0.80
63_L	69_L	0.549	0.80
5_Y	20_G	0.548	0.80
66_P	88_R	0.547	0.80
85_L	105_V	0.543	0.79
12_R	16_E	0.542	0.79
29_R	32_V	0.541	0.79
42_T	157_T	0.539	0.79
100_F	115_R	0.538	0.78
71_R	74_I	0.537	0.78
94_G	152_I	0.534	0.78
13_L	17_R	0.531	0.78
122_A	125_S	0.530	0.77
13_L	16_E	0.528	0.77
14_P	17_R	0.524	0.77
83_V	87_A	0.523	0.76
15_S	42_T	0.522	0.76
94_G	131_L	0.518	0.76
51_A	152_I	0.518	0.76
79_V	129_G	0.517	0.76
12_R	25_F	0.517	0.76
86_L	102_P	0.516	0.76
33_P	147_A	0.515	0.75
32_V	36_R	0.515	0.75
16_E	143_R	0.514	0.75
167_L	170_L	0.511	0.75
37_E	41_G	0.511	0.75
123_Y	148_P	0.510	0.75
24_S	31_V	0.510	0.75
29_R	34_V	0.510	0.75
113_L	118_A	0.509	0.75
20_G	23_V	0.503	0.74
35_V	40_P	0.502	0.74
162_F	169_V	0.500	0.73

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
4uzzA	1	0.2047	2	0.956	Contact Map
1y32A	1	0.0819	1.8	0.957	Contact Map
1rq8A	1	0.2339	1.5	0.959	Contact Map
2ksfA	1	0.5614	1.1	0.962	Contact Map
2nnuB	2	0.0936	0.9	0.964	Contact Map
3p5nA	2	0.5088	0.8	0.965	Contact Map
2k1kA	2	0.2222	0.8	0.965	Contact Map
2kncB	1	0.1813	0.8	0.965	Contact Map
4hzuS	1	0.5497	0.8	0.965	Contact Map
2k3cA	1	0.1287	0.8	0.965	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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