DUF3990 - PFAM28P - GREMLIN Contacts

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DUF3990 - Protein of unknown function (DUF3990)

PFAM:	PF13151	Sequences: MILYHGSNVIIEKPDLSKSRPNKDFGKGFYTTTIKEQAERWAKRKARRRRGGKGIVNVYEFDEDALKDLKILRFDEYDEEWLDFVVANRKGKNPGHDYDIVIGPVANDDVFNTIQLYLDGIISKEEALERLKFKKLTNQICFKTEKALSYLKF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	153 (151)
Sequences:	7359 (4764)
Seq/√Len:	387.7
META:	0.934

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_K	39_E	3.957	1.00
83_D	124_K	3.186	1.00
145_E	149_S	2.879	1.00
33_T	138_N	2.702	1.00
126_E	130_R	2.646	1.00
28_G	141_C	2.427	1.00
123_S	126_E	2.393	1.00
3_L	31_T	2.378	1.00
79_E	124_K	2.312	1.00
21_P	27_K	2.310	1.00
2_I	58_V	2.270	1.00
11_I	57_N	2.196	1.00
7_S	57_N	2.166	1.00
116_L	121_I	2.030	1.00
61_F	66_L	1.992	1.00
102_I	140_I	1.885	1.00
15_D	18_K	1.866	1.00
70_K	97_D	1.848	1.00
31_T	142_F	1.846	1.00
7_S	11_I	1.819	1.00
109_D	134_K	1.783	1.00
2_I	60_E	1.756	1.00
142_F	147_A	1.709	1.00
72_L	80_E	1.653	1.00
34_I	137_T	1.651	1.00
146_K	149_S	1.637	1.00
82_L	127_A	1.621	1.00
86_V	118_L	1.620	1.00
87_A	92_K	1.620	1.00
126_E	129_E	1.611	1.00
113_T	127_A	1.580	1.00
36_E	39_E	1.563	1.00
35_K	56_V	1.548	1.00
39_E	43_K	1.547	1.00
10_I	57_N	1.534	1.00
144_T	147_A	1.480	1.00
102_I	138_N	1.480	1.00
73_R	102_I	1.472	1.00
8_N	52_G	1.467	1.00
79_E	125_E	1.450	1.00
71_I	100_I	1.439	1.00
84_F	88_N	1.381	1.00
60_E	152_K	1.379	1.00
116_L	122_I	1.365	1.00
93_N	96_H	1.351	1.00
3_L	140_I	1.332	1.00
133_F	137_T	1.324	1.00
69_L	147_A	1.315	1.00
65_A	150_Y	1.305	1.00
123_S	129_E	1.292	1.00
36_E	40_R	1.273	1.00
122_I	126_E	1.271	1.00
42_A	54_G	1.255	1.00
72_L	98_Y	1.242	1.00
17_S	27_K	1.242	1.00
39_E	56_V	1.237	1.00
101_V	143_K	1.224	1.00
46_A	54_G	1.210	1.00
96_H	143_K	1.209	1.00
113_T	130_R	1.202	1.00
125_E	129_E	1.193	1.00
142_F	151_L	1.181	1.00
46_A	52_G	1.140	1.00
67_K	73_R	1.097	1.00
35_K	58_V	1.091	1.00
122_I	127_A	1.089	1.00
114_I	118_L	1.079	1.00
71_I	102_I	1.065	1.00
62_D	65_A	1.061	1.00
86_V	114_I	1.058	1.00
16_L	148_L	1.051	1.00
64_D	68_D	1.044	1.00
110_V	114_I	1.044	1.00
1_M	60_E	1.030	1.00
20_R	23_K	1.017	1.00
129_E	132_K	1.013	1.00
70_K	98_Y	1.003	1.00
100_I	140_I	1.002	1.00
74_F	84_F	0.995	1.00
87_A	95_G	0.995	1.00
65_A	68_D	0.992	1.00
113_T	122_I	0.991	1.00
14_P	17_S	0.987	1.00
16_L	19_S	0.981	1.00
79_E	83_D	0.962	1.00
146_K	150_Y	0.961	1.00
112_N	116_L	0.959	1.00
32_T	38_A	0.956	1.00
10_I	55_I	0.944	1.00
113_T	116_L	0.941	1.00
83_D	87_A	0.937	1.00
33_T	140_I	0.931	1.00
91_G	94_P	0.925	1.00
77_Y	136_L	0.893	1.00
127_A	131_L	0.889	1.00
19_S	27_K	0.888	1.00
130_R	134_K	0.881	1.00
31_T	140_I	0.864	1.00
41_W	44_R	0.859	1.00
128_L	132_K	0.855	1.00
19_S	23_K	0.841	1.00
72_L	101_V	0.841	1.00
62_D	152_K	0.835	1.00
63_E	66_L	0.834	1.00
99_D	144_T	0.831	1.00
43_K	54_G	0.831	1.00
8_N	45_K	0.829	1.00
69_L	99_D	0.824	1.00
15_D	19_S	0.821	1.00
37_Q	105_V	0.820	1.00
33_T	102_I	0.807	1.00
9_V	12_E	0.804	1.00
45_K	48_R	0.783	1.00
64_D	67_K	0.779	1.00
82_L	113_T	0.779	1.00
84_F	143_K	0.776	1.00
8_N	46_A	0.775	1.00
22_N	91_G	0.771	1.00
4_Y	35_K	0.771	1.00
109_D	112_N	0.770	1.00
86_V	117_Y	0.770	1.00
127_A	130_R	0.767	1.00
52_G	55_I	0.767	1.00
61_F	142_F	0.767	1.00
43_K	46_A	0.765	1.00
99_D	146_K	0.765	1.00
92_K	95_G	0.765	1.00
115_Q	119_D	0.758	1.00
116_L	119_D	0.757	1.00
114_I	127_A	0.753	1.00
111_F	118_L	0.747	1.00
117_Y	124_K	0.736	1.00
148_L	151_L	0.735	1.00
15_D	20_R	0.734	1.00
63_E	73_R	0.734	1.00
80_E	83_D	0.719	1.00
88_N	95_G	0.719	1.00
122_I	130_R	0.707	1.00
15_D	27_K	0.706	1.00
38_A	56_V	0.704	1.00
77_Y	133_F	0.704	1.00
69_L	144_T	0.702	1.00
149_S	152_K	0.697	1.00
112_N	121_I	0.694	0.99
75_D	78_D	0.690	0.99
110_V	141_C	0.683	0.99
41_W	45_K	0.680	0.99
83_D	117_Y	0.679	0.99
69_L	150_Y	0.678	0.99
32_T	105_V	0.672	0.99
49_R	52_G	0.671	0.99
81_W	106_A	0.664	0.99
116_L	130_R	0.662	0.99
6_G	56_V	0.657	0.99
84_F	95_G	0.651	0.99
111_F	117_Y	0.647	0.99
100_I	147_A	0.647	0.99
48_R	51_G	0.644	0.99
82_L	86_V	0.642	0.99
44_R	109_D	0.638	0.99
9_V	13_K	0.637	0.99
87_A	93_N	0.634	0.99
78_D	131_L	0.632	0.99
87_A	94_P	0.631	0.99
66_L	71_I	0.631	0.99
111_F	134_K	0.631	0.99
82_L	124_K	0.612	0.99
62_D	66_L	0.611	0.99
7_S	10_I	0.604	0.99
70_K	96_H	0.602	0.99
86_V	121_I	0.602	0.99
142_F	148_L	0.600	0.99
77_Y	128_L	0.599	0.99
18_K	27_K	0.598	0.98
88_N	94_P	0.598	0.98
69_L	98_Y	0.591	0.98
77_Y	80_E	0.590	0.98
13_K	149_S	0.589	0.98
94_P	97_D	0.586	0.98
10_I	14_P	0.584	0.98
132_K	135_K	0.582	0.98
40_R	43_K	0.582	0.98
103_G	108_D	0.581	0.98
107_N	113_T	0.581	0.98
14_P	57_N	0.580	0.98
110_V	133_F	0.573	0.98
68_D	71_I	0.570	0.98
70_K	99_D	0.564	0.98
61_F	100_I	0.561	0.98
111_F	130_R	0.558	0.98
108_D	117_Y	0.558	0.98
87_A	91_G	0.556	0.98
31_T	141_C	0.555	0.98
112_N	115_Q	0.555	0.98
111_F	115_Q	0.551	0.97
145_E	148_L	0.551	0.97
11_I	14_P	0.547	0.97
105_V	137_T	0.547	0.97
114_I	131_L	0.546	0.97
61_F	64_D	0.542	0.97
85_V	114_I	0.541	0.97
106_A	136_L	0.541	0.97
110_V	134_K	0.539	0.97
108_D	113_T	0.539	0.97
42_A	56_V	0.538	0.97
37_Q	138_N	0.537	0.97
124_K	127_A	0.535	0.97
68_D	150_Y	0.533	0.97
112_N	130_R	0.531	0.97
6_G	41_W	0.530	0.97
34_I	138_N	0.530	0.97
107_N	111_F	0.528	0.97
6_G	57_N	0.527	0.97
128_L	131_L	0.522	0.96
23_K	111_F	0.522	0.96
61_F	150_Y	0.518	0.96
14_P	148_L	0.517	0.96
12_E	59_Y	0.516	0.96
77_Y	104_P	0.516	0.96
84_F	101_V	0.514	0.96
49_R	53_K	0.514	0.96
13_K	17_S	0.510	0.96
95_G	143_K	0.508	0.96
40_R	109_D	0.507	0.96
109_D	116_L	0.504	0.96
16_L	144_T	0.500	0.96

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
2x5yA	1	0.6993	88.1	0.884	Contact Map
2pqfA	2	0.732	87.9	0.884	Contact Map
3smjA	2	0.7451	85.2	0.889	Contact Map
3bljA	1	0.7451	84.7	0.889	Contact Map
4pnlA	1	0.7778	82.1	0.893	Contact Map
4bueA	1	0.6928	78.1	0.897	Contact Map
4f0dA	1	0.549	76.1	0.899	Contact Map
3kjdA	1	0.7582	68.7	0.904	Contact Map
1efyA	1	0.7712	67.3	0.905	Contact Map
3hkvA	2	0.7582	61.7	0.908	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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