DUF2058 - PFAM28P - GREMLIN Contacts

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DUF2058 - Uncharacterized protein conserved in bacteria (DUF2058)

PFAM:	PF09831	Sequences: SLQDQLLKAGLVDKKKAKKAKKEKRKQRKQKRKKEVDEAKAAAQRAQAEKAERDRELNRQRQEAAERKAIAAQIKQLIEQNRLPRDDGDIAYNFTDGGKIKRIYVTAEQRKQLSAGRLAIVRLDGRYELVPAEVAEKIRERDPSAVVLLNDAAEEAPDEDDPYADYQVPDDLMW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	174 (174)
Sequences:	3340 (2216)
Seq/√Len:	168.0
META:	0.83

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_E	59_R	2.989	1.00
96_D	122_R	2.852	1.00
82_R	128_E	2.707	1.00
62_Q	66_E	2.582	1.00
96_D	127_Y	2.569	1.00
91_A	102_R	2.484	1.00
59_R	63_E	2.383	1.00
111_K	115_A	2.343	1.00
45_R	49_E	2.300	1.00
85_R	128_E	2.118	1.00
91_A	104_Y	2.048	1.00
44_Q	47_Q	2.025	1.00
13_D	16_K	2.021	1.00
105_V	113_L	1.973	1.00
52_E	56_E	1.943	1.00
65_A	69_A	1.893	1.00
132_A	136_E	1.877	1.00
109_Q	129_L	1.822	1.00
94_F	127_Y	1.792	1.00
83_L	118_L	1.789	1.00
66_E	69_A	1.772	1.00
56_E	60_Q	1.761	1.00
60_Q	63_E	1.760	1.00
90_I	110_R	1.730	1.00
50_K	54_D	1.724	1.00
44_Q	48_A	1.717	1.00
136_E	140_E	1.678	1.00
112_Q	117_R	1.666	1.00
48_A	52_E	1.653	1.00
22_K	25_R	1.638	1.00
107_A	111_K	1.632	1.00
47_Q	51_A	1.593	1.00
52_E	55_R	1.589	1.00
37_D	40_K	1.550	1.00
121_V	130_V	1.543	1.00
118_L	129_L	1.542	1.00
136_E	139_R	1.522	1.00
63_E	67_R	1.470	1.00
62_Q	65_A	1.466	1.00
106_T	109_Q	1.458	1.00
93_N	102_R	1.455	1.00
121_V	146_V	1.453	1.00
66_E	70_I	1.450	1.00
73_Q	141_R	1.442	1.00
41_A	44_Q	1.431	1.00
59_R	62_Q	1.428	1.00
92_Y	148_L	1.426	1.00
119_A	135_A	1.424	1.00
14_K	18_K	1.416	1.00
69_A	73_Q	1.411	1.00
77_L	134_V	1.401	1.00
53_R	57_L	1.385	1.00
12_V	16_K	1.379	1.00
108_E	112_Q	1.377	1.00
48_A	51_A	1.362	1.00
75_K	124_D	1.345	1.00
39_A	43_A	1.338	1.00
110_R	114_S	1.308	1.00
63_E	66_E	1.298	1.00
130_V	134_V	1.294	1.00
159_E	162_P	1.288	1.00
41_A	45_R	1.281	1.00
109_Q	118_L	1.277	1.00
164_A	167_Q	1.270	1.00
28_R	32_R	1.263	1.00
3_Q	21_K	1.254	1.00
74_I	142_D	1.229	1.00
16_K	20_A	1.225	1.00
81_N	134_V	1.221	1.00
1_S	4_D	1.221	1.00
46_A	50_K	1.219	1.00
55_R	59_R	1.216	1.00
40_K	44_Q	1.198	1.00
12_V	17_A	1.182	1.00
15_K	22_K	1.179	1.00
42_A	45_R	1.169	1.00
60_Q	64_A	1.166	1.00
74_I	145_A	1.162	1.00
95_T	98_G	1.148	1.00
47_Q	50_K	1.143	1.00
136_E	149_L	1.137	1.00
157_P	162_P	1.131	1.00
43_A	46_A	1.121	1.00
76_Q	79_E	1.116	1.00
58_N	62_Q	1.104	1.00
3_Q	7_L	1.094	1.00
162_P	165_D	1.089	1.00
119_A	149_L	1.079	1.00
7_L	14_K	1.075	1.00
75_K	79_E	1.070	1.00
58_N	61_R	1.070	1.00
2_L	6_L	1.068	1.00
17_A	20_A	1.050	0.99
45_R	48_A	1.039	0.99
90_I	107_A	1.035	0.99
158_D	162_P	1.034	0.99
107_A	110_R	1.027	0.99
139_R	149_L	1.021	0.99
88_G	106_T	1.019	0.99
16_K	19_K	1.016	0.99
156_A	159_E	1.012	0.99
122_R	127_Y	0.990	0.99
54_D	57_L	0.978	0.99
35_E	38_E	0.960	0.99
74_I	138_I	0.948	0.99
64_A	67_R	0.937	0.99
78_I	123_L	0.934	0.99
57_L	61_R	0.925	0.99
130_V	138_I	0.925	0.99
139_R	143_P	0.924	0.99
21_K	25_R	0.922	0.99
78_I	121_V	0.922	0.99
171_D	174_W	0.910	0.98
51_A	55_R	0.901	0.98
39_A	42_A	0.897	0.98
157_P	167_Q	0.897	0.98
38_E	41_A	0.893	0.98
38_E	42_A	0.890	0.98
77_L	80_Q	0.879	0.98
30_Q	33_K	0.871	0.98
29_K	32_R	0.868	0.98
92_Y	114_S	0.865	0.98
72_A	141_R	0.864	0.98
36_V	41_A	0.859	0.98
71_A	75_K	0.859	0.98
79_E	123_L	0.852	0.98
22_K	26_K	0.840	0.97
155_E	160_D	0.838	0.97
89_D	107_A	0.837	0.97
151_D	154_E	0.833	0.97
66_E	73_Q	0.831	0.97
14_K	17_A	0.826	0.97
137_K	140_E	0.826	0.97
12_V	20_A	0.818	0.97
25_R	32_R	0.812	0.97
103_I	109_Q	0.812	0.97
61_R	64_A	0.809	0.97
73_Q	77_L	0.807	0.97
51_A	54_D	0.802	0.96
121_V	128_E	0.801	0.96
131_P	134_V	0.800	0.96
108_E	111_K	0.800	0.96
58_N	69_A	0.798	0.96
123_L	126_R	0.790	0.96
37_D	41_A	0.768	0.96
162_P	166_Y	0.751	0.95
133_E	136_E	0.745	0.95
155_E	158_D	0.743	0.95
78_I	138_I	0.742	0.95
95_T	100_I	0.739	0.94
18_K	21_K	0.736	0.94
122_R	147_V	0.735	0.94
78_I	122_R	0.732	0.94
163_Y	166_Y	0.731	0.94
23_E	26_K	0.728	0.94
31_K	34_K	0.727	0.94
73_Q	137_K	0.722	0.94
49_E	52_E	0.719	0.94
71_A	142_D	0.719	0.94
132_A	149_L	0.719	0.94
119_A	130_V	0.711	0.93
85_R	109_Q	0.707	0.93
46_A	49_E	0.702	0.93
134_V	141_R	0.700	0.93
29_K	33_K	0.697	0.93
169_P	174_W	0.695	0.92
86_D	109_Q	0.689	0.92
71_A	124_D	0.688	0.92
15_K	19_K	0.687	0.92
119_A	132_A	0.687	0.92
18_K	22_K	0.686	0.92
161_D	164_A	0.684	0.92
25_R	29_K	0.683	0.92
153_A	156_A	0.682	0.92
103_I	129_L	0.680	0.92
19_K	29_K	0.677	0.91
84_P	87_D	0.677	0.91
158_D	161_D	0.674	0.91
170_D	174_W	0.674	0.91
109_Q	112_Q	0.672	0.91
105_V	109_Q	0.671	0.91
120_I	147_V	0.669	0.91
79_E	82_R	0.668	0.91
146_V	149_L	0.662	0.91
105_V	110_R	0.658	0.90
100_I	150_N	0.653	0.90
3_Q	17_A	0.652	0.90
130_V	135_A	0.651	0.90
152_A	157_P	0.651	0.90
30_Q	34_K	0.649	0.90
59_R	82_R	0.645	0.89
153_A	160_D	0.644	0.89
42_A	46_A	0.644	0.89
162_P	167_Q	0.643	0.89
67_R	71_A	0.641	0.89
130_V	146_V	0.640	0.89
7_L	12_V	0.639	0.89
88_G	113_L	0.639	0.89
119_A	148_L	0.638	0.89
24_K	32_R	0.635	0.89
26_K	30_Q	0.634	0.89
133_E	137_K	0.634	0.89
24_K	29_K	0.630	0.88
71_A	78_I	0.625	0.88
15_K	25_R	0.616	0.87
13_D	20_A	0.613	0.87
86_D	106_T	0.612	0.87
27_Q	31_K	0.610	0.87
77_L	138_I	0.608	0.86
57_L	74_I	0.602	0.86
138_I	141_R	0.601	0.86
113_L	148_L	0.594	0.85
12_V	92_Y	0.591	0.85
9_A	13_D	0.586	0.84
102_R	110_R	0.579	0.84
99_K	125_G	0.574	0.83
154_E	157_P	0.572	0.83
8_K	12_V	0.569	0.83
90_I	105_V	0.566	0.82
88_G	109_Q	0.565	0.82
51_A	141_R	0.560	0.82
3_Q	24_K	0.558	0.81
142_D	145_A	0.556	0.81
100_I	110_R	0.554	0.81
83_L	129_L	0.552	0.81
9_A	51_A	0.551	0.81
157_P	160_D	0.548	0.80
76_Q	81_N	0.547	0.80
21_K	27_Q	0.547	0.80
4_D	28_R	0.546	0.80
23_E	27_Q	0.545	0.80
152_A	155_E	0.543	0.80
9_A	17_A	0.543	0.80
169_P	172_L	0.542	0.80
70_I	74_I	0.542	0.80
25_R	93_N	0.541	0.79
111_K	114_S	0.538	0.79
19_K	26_K	0.537	0.79
95_T	148_L	0.533	0.78
70_I	73_Q	0.529	0.78
21_K	32_R	0.524	0.77
49_E	90_I	0.523	0.77
49_E	53_R	0.522	0.77
1_S	17_A	0.521	0.77
64_A	68_K	0.518	0.76
43_A	47_Q	0.517	0.76
11_L	14_K	0.513	0.76
3_Q	9_A	0.513	0.76
20_A	23_E	0.512	0.76
25_R	28_R	0.512	0.76
83_L	109_Q	0.512	0.76
165_D	173_M	0.511	0.76
77_L	140_E	0.511	0.76
15_K	29_K	0.510	0.75
81_N	135_A	0.508	0.75
54_D	58_N	0.508	0.75
1_S	5_Q	0.504	0.75
162_P	173_M	0.504	0.75
161_D	165_D	0.503	0.74
61_R	65_A	0.501	0.74
85_R	88_G	0.500	0.74

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
1pkhA	5	0.3851	12.1	0.948	Contact Map
4xk8G	1	0.3391	8.2	0.952	Contact Map
4rb5B	1	0.5805	5.4	0.956	Contact Map
1kcaA	6	0.3621	4.8	0.957	Contact Map
4relA	1	0.3621	4.8	0.957	Contact Map
1w85A	2	0.4023	4.3	0.958	Contact Map
2v3sA	1	0.5	4	0.958	Contact Map
3t5xB	1	0	3.5	0.959	Contact Map
3ojaB	1	0.4713	3.2	0.96	Contact Map
1vi6A	2	0.6207	3.1	0.96	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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