DUF2083 - PFAM28P - GREMLIN Contacts

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DUF2083 - Predicted transcriptional regulator (DUF2083)

PFAM:	PF09856	Sequences: TLQRPGARGVPFFFVRVDRAGNISKRFSATGFPFARFGGACPLWNVHEAFATPGRILTQLAEMPDGARYFCIARTVSKPGGGFGAPRRRFAIGLGCEIRHADRLVYADGLDLDDPAAATPIGVSCRLCERPDCPQRAFPPLGRPLRVDENRRGVSPY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	157 (157)
Sequences:	3807 (1927)
Seq/√Len:	153.8
META:	0.785

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_E	68_R	5.818	1.00
60_L	98_I	4.557	1.00
52_T	55_R	3.858	1.00
11_P	100_H	3.483	1.00
10_V	104_L	3.472	1.00
16_R	24_S	2.709	1.00
12_F	104_L	2.640	1.00
19_R	51_A	2.633	1.00
148_D	151_R	2.561	1.00
97_E	100_H	2.365	1.00
3_Q	8_R	2.219	1.00
72_I	94_L	2.181	1.00
62_E	118_A	2.163	1.00
16_R	25_K	2.135	1.00
61_A	71_C	2.036	1.00
58_T	70_F	1.905	1.00
68_R	118_A	1.854	1.00
71_C	93_G	1.847	1.00
111_D	114_D	1.810	1.00
52_T	57_L	1.795	1.00
100_H	103_R	1.762	1.00
54_G	75_T	1.712	1.00
78_K	90_F	1.687	1.00
124_S	127_L	1.639	1.00
13_F	30_T	1.625	1.00
64_P	129_E	1.622	1.00
79_P	87_R	1.619	1.00
68_R	98_I	1.584	1.00
70_F	107_A	1.582	1.00
22_N	137_A	1.577	1.00
48_E	51_A	1.572	1.00
1_T	4_R	1.522	1.00
63_M	123_V	1.514	1.00
70_F	110_L	1.502	1.00
50_F	75_T	1.490	1.00
17_V	91_A	1.476	1.00
64_P	130_R	1.469	1.00
146_R	151_R	1.459	1.00
125_C	128_C	1.382	1.00
13_F	19_R	1.338	1.00
67_A	97_E	1.330	1.00
60_L	110_L	1.303	1.00
24_S	27_F	1.303	1.00
13_F	93_G	1.277	1.00
17_V	46_V	1.262	1.00
50_F	91_A	1.237	1.00
15_V	46_V	1.237	1.00
83_F	105_V	1.236	1.00
77_S	89_R	1.228	1.00
13_F	95_G	1.200	1.00
48_E	119_T	1.199	1.00
30_T	34_F	1.191	1.00
61_A	121_I	1.177	1.00
62_E	130_R	1.177	1.00
48_E	55_R	1.162	1.00
84_G	108_D	1.159	1.00
45_N	71_C	1.144	1.00
43_L	135_Q	1.142	1.00
120_P	132_D	1.134	1.00
70_F	96_C	1.132	1.00
142_G	156_P	1.126	1.00
131_P	140_P	1.122	1.00
53_P	75_T	1.108	0.99
131_P	143_R	1.098	0.99
35_A	124_S	1.081	0.99
90_F	135_Q	1.071	0.99
35_A	91_A	1.056	0.99
108_D	114_D	1.055	0.99
150_N	153_G	1.047	0.99
32_F	38_G	1.039	0.99
32_F	35_A	1.039	0.99
120_P	130_R	1.024	0.99
146_R	149_E	1.010	0.99
101_A	104_L	1.010	0.99
23_I	34_F	1.008	0.99
10_V	96_C	0.998	0.99
32_F	61_A	0.985	0.99
58_T	83_F	0.983	0.99
50_F	54_G	0.964	0.99
13_F	31_G	0.961	0.99
40_A	47_H	0.958	0.98
133_C	136_R	0.947	0.98
45_N	73_A	0.934	0.98
29_A	47_H	0.930	0.98
56_I	75_T	0.917	0.98
98_I	118_A	0.910	0.98
102_D	113_D	0.904	0.98
63_M	121_I	0.902	0.98
54_G	77_S	0.901	0.98
43_L	51_A	0.900	0.98
129_E	141_L	0.897	0.98
43_L	71_C	0.892	0.98
19_R	48_E	0.891	0.98
14_F	25_K	0.890	0.98
123_V	127_L	0.888	0.98
142_G	147_V	0.882	0.97
60_L	118_A	0.881	0.97
14_F	24_S	0.874	0.97
38_G	156_P	0.870	0.97
124_S	135_Q	0.866	0.97
62_E	115_P	0.865	0.97
51_A	89_R	0.863	0.97
18_D	22_N	0.861	0.97
14_F	27_F	0.854	0.97
15_V	93_G	0.854	0.97
39_G	96_C	0.854	0.97
151_R	154_V	0.852	0.97
54_G	89_R	0.848	0.97
35_A	40_A	0.846	0.97
26_R	34_F	0.845	0.97
37_F	40_A	0.843	0.97
45_N	93_G	0.829	0.96
73_A	93_G	0.827	0.96
60_L	112_L	0.804	0.96
27_F	127_L	0.802	0.95
147_V	150_N	0.801	0.95
60_L	68_R	0.800	0.95
56_I	106_Y	0.798	0.95
150_N	154_V	0.797	0.95
102_D	108_D	0.797	0.95
96_C	106_Y	0.795	0.95
13_F	71_C	0.782	0.95
78_K	130_R	0.771	0.94
62_E	66_G	0.762	0.94
144_P	153_G	0.760	0.94
46_V	93_G	0.757	0.94
41_C	136_R	0.756	0.94
34_F	93_G	0.749	0.93
31_G	126_R	0.747	0.93
124_S	152_R	0.746	0.93
143_R	146_R	0.738	0.93
45_N	59_Q	0.737	0.93
153_G	156_P	0.729	0.93
4_R	9_G	0.724	0.92
146_R	154_V	0.722	0.92
49_A	91_A	0.715	0.92
51_A	57_L	0.711	0.92
60_L	70_F	0.710	0.92
72_I	106_Y	0.703	0.91
70_F	104_L	0.697	0.91
34_F	157_Y	0.694	0.91
146_R	157_Y	0.687	0.90
17_V	50_F	0.684	0.90
128_C	133_C	0.677	0.90
16_R	90_F	0.677	0.90
44_W	71_C	0.676	0.89
128_C	136_R	0.671	0.89
32_F	71_C	0.670	0.89
142_G	151_R	0.669	0.89
38_G	96_C	0.666	0.89
153_G	157_Y	0.664	0.89
52_T	75_T	0.663	0.89
51_A	58_T	0.663	0.89
45_N	119_T	0.662	0.88
144_P	150_N	0.659	0.88
124_S	142_G	0.658	0.88
81_G	85_A	0.657	0.88
4_R	7_A	0.656	0.88
62_E	120_P	0.656	0.88
88_R	135_Q	0.652	0.88
76_V	92_I	0.651	0.88
114_D	117_A	0.645	0.87
138_F	156_P	0.642	0.87
3_Q	11_P	0.641	0.87
36_R	49_A	0.640	0.87
22_N	39_G	0.638	0.87
77_S	87_R	0.638	0.87
46_V	69_Y	0.637	0.87
104_L	108_D	0.632	0.86
22_N	106_Y	0.630	0.86
61_A	119_T	0.626	0.86
29_A	95_G	0.625	0.85
125_C	136_R	0.618	0.85
43_L	143_R	0.618	0.85
89_R	92_I	0.617	0.85
122_G	125_C	0.611	0.84
122_G	133_C	0.606	0.84
144_P	147_V	0.605	0.84
23_I	28_S	0.599	0.83
38_G	97_E	0.599	0.83
29_A	35_A	0.599	0.83
152_R	157_Y	0.597	0.83
27_F	30_T	0.595	0.83
14_F	92_I	0.595	0.83
111_D	115_P	0.593	0.82
46_V	126_R	0.592	0.82
115_P	118_A	0.591	0.82
29_A	99_R	0.587	0.82
39_G	74_R	0.583	0.81
74_R	92_I	0.582	0.81
18_D	23_I	0.582	0.81
60_L	111_D	0.582	0.81
154_V	157_Y	0.579	0.81
144_P	154_V	0.577	0.81
127_L	141_L	0.577	0.81
41_C	122_G	0.576	0.81
109_G	112_L	0.575	0.80
38_G	124_S	0.572	0.80
101_A	112_L	0.570	0.80
56_I	74_R	0.567	0.80
142_G	145_L	0.562	0.79
151_R	155_S	0.557	0.78
75_T	92_I	0.554	0.78
139_P	156_P	0.554	0.78
39_G	130_R	0.553	0.78
35_A	93_G	0.540	0.76
63_M	119_T	0.539	0.76
134_P	144_P	0.537	0.76
17_V	45_N	0.532	0.75
33_P	124_S	0.527	0.74
138_F	152_R	0.527	0.74
22_N	96_C	0.525	0.74
45_N	57_L	0.525	0.74
83_F	153_G	0.524	0.74
5_P	10_V	0.522	0.74
61_A	70_F	0.521	0.74
125_C	133_C	0.521	0.74
98_I	112_L	0.517	0.73
140_P	146_R	0.516	0.73
147_V	155_S	0.516	0.73
17_V	93_G	0.513	0.72
146_R	153_G	0.513	0.72
101_A	107_A	0.511	0.72
3_Q	6_G	0.510	0.72
10_V	103_R	0.510	0.72
149_E	154_V	0.509	0.72
36_R	126_R	0.508	0.72
74_R	94_L	0.508	0.72
145_L	155_S	0.507	0.72
147_V	152_R	0.507	0.72
5_P	8_R	0.506	0.71
149_E	156_P	0.505	0.71
146_R	150_N	0.505	0.71
58_T	110_L	0.502	0.71
112_L	117_A	0.501	0.71
26_R	37_F	0.500	0.71

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
2mhgA	2	0.2611	12.6	0.947	Contact Map
3kxtA	1	0.2166	7.7	0.952	Contact Map
4o0cA	2	0.3439	6.7	0.953	Contact Map
3ph9A	1	0.4713	3.7	0.959	Contact Map
4k9zA	3	0.2739	2.9	0.961	Contact Map
1r4wA	2	0.3121	2.8	0.961	Contact Map
3fk8A	1	0.4204	2.5	0.962	Contact Map
3l9vA	1	0.3057	2.3	0.963	Contact Map
3kcmA	1	0.4331	2.2	0.963	Contact Map
3kh7A	1	0.4395	2	0.964	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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