DUF2169 - PFAM28P - GREMLIN Contacts

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DUF2169 - Uncharacterized protein conserved in bacteria (DUF2169)

PFAM:	PF09937	Sequences: DGRELLVVVVKATFDLPPGGELRLAEEQEPLVLADEYLGEPGLSSLRYESDLAPFKPRTDVLLVGHAYAPGGRPVTALDVGLRVGPLDKTLRVFGDRVWRRGGGGLRPSEPEPFTRMPLRYERAFGGDPDPAKHAAYPRNPVGRGFAARRSAAGGLPLPNIEDPDAPITSPGDRPRPAGFGPIGRHWPPRARLAGTYDEAWLKERFPLLPEDFDPRFFNAAPPDQQLPGYLRGGEPVELENLHPEHGRLRFRLPGLRPRVFVRRRDGGRFEEVPLRLDTVWIDPDAERVSLVWR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	294 (290)
Sequences:	3968 (3512)
Seq/√Len:	206.2
META:	0.782

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
96_D	160_N	3.501	1.00
89_K	224_D	3.225	1.00
66_H	285_D	2.959	1.00
79_D	92_R	2.924	1.00
239_L	242_L	2.870	1.00
234_G	255_G	2.809	1.00
75_V	78_L	2.688	1.00
91_L	161_I	2.650	1.00
199_E	203_K	2.620	1.00
78_L	241_N	2.617	1.00
200_A	204_E	2.536	1.00
237_V	251_F	2.536	1.00
66_H	116_R	2.522	1.00
81_G	90_T	2.490	1.00
114_F	117_M	2.385	1.00
96_D	112_E	2.299	1.00
83_R	88_D	2.278	1.00
205_R	211_E	2.275	1.00
81_G	88_D	2.263	1.00
63_L	82_L	2.261	1.00
69_A	75_V	2.261	1.00
117_M	160_N	2.237	1.00
83_R	238_E	2.233	1.00
45_S	122_E	2.222	1.00
238_E	250_R	2.186	1.00
188_P	192_R	2.150	1.00
123_R	144_R	2.108	1.00
78_L	114_F	2.085	1.00
68_Y	116_R	2.050	1.00
193_L	216_R	2.019	1.00
79_D	90_T	1.975	1.00
277_L	291_L	1.967	1.00
81_G	240_E	1.952	1.00
161_I	179_G	1.923	1.00
77_A	92_R	1.922	1.00
278_D	294_R	1.914	1.00
74_P	115_T	1.910	1.00
96_D	123_R	1.860	1.00
123_R	160_N	1.855	1.00
222_P	225_Q	1.824	1.00
260_V	275_L	1.793	1.00
59_T	231_L	1.788	1.00
38_L	47_R	1.780	1.00
108_P	158_L	1.775	1.00
144_R	157_P	1.751	1.00
56_K	279_T	1.745	1.00
15_D	25_A	1.740	1.00
58_R	226_Q	1.739	1.00
62_L	182_P	1.715	1.00
236_P	250_R	1.704	1.00
238_E	248_R	1.672	1.00
283_D	286_A	1.647	1.00
236_P	252_R	1.637	1.00
80_V	91_L	1.635	1.00
91_L	178_A	1.632	1.00
120_R	123_R	1.626	1.00
63_L	242_L	1.622	1.00
58_R	216_R	1.620	1.00
163_D	178_A	1.613	1.00
264_R	271_E	1.610	1.00
49_E	185_R	1.610	1.00
237_V	282_I	1.602	1.00
61_V	82_L	1.589	1.00
117_M	123_R	1.523	1.00
240_E	248_R	1.516	1.00
76_T	110_E	1.506	1.00
196_T	212_D	1.498	1.00
89_K	225_Q	1.497	1.00
94_F	167_P	1.482	1.00
166_A	176_R	1.464	1.00
188_P	191_A	1.458	1.00
139_R	176_R	1.430	1.00
283_D	288_R	1.399	1.00
230_Y	276_R	1.376	1.00
38_L	120_R	1.362	1.00
102_G	105_G	1.356	1.00
80_V	180_F	1.355	1.00
58_R	228_P	1.342	1.00
259_R	272_E	1.332	1.00
87_L	227_L	1.327	1.00
62_L	279_T	1.326	1.00
58_R	229_G	1.318	1.00
91_L	180_F	1.305	1.00
15_D	288_R	1.289	1.00
84_V	237_V	1.283	1.00
213_F	218_F	1.269	1.00
118_P	123_R	1.261	1.00
16_L	249_L	1.259	1.00
261_F	270_F	1.259	1.00
25_A	28_Q	1.256	1.00
36_E	47_R	1.252	1.00
67_A	78_L	1.250	1.00
41_P	44_S	1.241	1.00
92_R	167_P	1.228	1.00
57_P	219_N	1.220	1.00
94_F	111_P	1.218	1.00
64_V	281_W	1.201	1.00
138_P	191_A	1.198	1.00
261_F	272_E	1.197	1.00
68_Y	244_P	1.193	1.00
66_H	118_P	1.191	1.00
58_R	219_N	1.190	1.00
199_E	202_L	1.187	1.00
78_L	117_M	1.183	1.00
121_Y	187_W	1.180	1.00
253_L	280_V	1.161	1.00
68_Y	285_D	1.158	1.00
35_D	49_E	1.154	1.00
245_E	287_E	1.153	1.00
46_L	49_E	1.152	1.00
62_L	220_A	1.148	1.00
77_A	94_F	1.124	1.00
251_F	282_I	1.118	1.00
142_V	187_W	1.117	1.00
67_A	80_V	1.116	1.00
54_P	218_F	1.115	1.00
96_D	117_M	1.099	1.00
193_L	223_P	1.099	1.00
227_L	231_L	1.098	1.00
185_R	217_F	1.098	1.00
163_D	166_A	1.097	1.00
213_F	217_F	1.094	1.00
98_V	109_S	1.084	1.00
121_Y	222_P	1.079	1.00
239_L	282_I	1.068	1.00
243_H	247_G	1.068	1.00
13_T	28_Q	1.063	1.00
15_D	26_E	1.061	1.00
97_R	162_E	1.053	1.00
231_L	280_V	1.050	1.00
59_T	230_Y	1.049	1.00
64_V	182_P	1.045	1.00
281_W	292_V	1.045	1.00
60_D	226_Q	1.045	1.00
194_A	217_F	1.042	1.00
232_R	235_E	1.039	1.00
182_P	220_A	1.032	1.00
63_L	180_F	1.030	1.00
99_W	168_I	1.025	1.00
277_L	293_W	1.025	1.00
262_V	273_V	1.022	1.00
69_A	115_T	1.020	1.00
121_Y	179_G	1.020	1.00
12_A	293_W	1.015	1.00
169_T	173_D	1.015	1.00
95_G	111_P	1.006	1.00
11_K	51_D	1.004	1.00
162_E	168_I	1.000	1.00
241_N	247_G	1.000	1.00
62_L	221_A	0.999	1.00
234_G	253_L	0.997	1.00
138_P	188_P	0.993	1.00
197_Y	201_W	0.991	1.00
216_R	226_Q	0.989	1.00
40_E	44_S	0.988	1.00
45_S	120_R	0.981	1.00
193_L	226_Q	0.976	1.00
60_D	231_L	0.972	1.00
197_Y	212_D	0.972	1.00
67_A	93_V	0.972	1.00
51_D	292_V	0.969	1.00
166_A	173_D	0.968	1.00
13_T	25_A	0.966	1.00
39_G	44_S	0.964	1.00
249_L	287_E	0.962	1.00
137_Y	146_F	0.954	0.99
126_G	145_G	0.952	0.99
40_E	43_L	0.950	0.99
15_D	23_R	0.948	0.99
163_D	176_R	0.942	0.99
36_E	48_Y	0.931	0.99
98_V	112_E	0.930	0.99
119_L	161_I	0.925	0.99
71_G	74_P	0.922	0.99
46_L	184_G	0.922	0.99
193_L	214_D	0.921	0.99
55_F	230_Y	0.921	0.99
60_D	219_N	0.918	0.99
243_H	249_L	0.918	0.99
189_P	192_R	0.917	0.99
219_N	226_Q	0.915	0.99
243_H	287_E	0.915	0.99
61_V	87_L	0.913	0.99
109_S	158_L	0.910	0.99
282_I	289_V	0.910	0.99
139_R	189_P	0.909	0.99
83_R	236_P	0.909	0.99
280_V	289_V	0.907	0.99
198_D	201_W	0.906	0.99
131_P	134_H	0.901	0.99
14_F	256_L	0.900	0.99
48_Y	283_D	0.896	0.99
125_F	145_G	0.889	0.99
202_L	206_F	0.887	0.99
129_P	134_H	0.886	0.99
82_L	225_Q	0.886	0.99
119_L	242_L	0.885	0.99
13_T	30_P	0.883	0.99
8_V	260_V	0.883	0.99
92_R	162_E	0.877	0.99
128_D	134_H	0.875	0.99
93_V	161_I	0.874	0.99
38_L	45_S	0.871	0.99
195_G	212_D	0.862	0.99
82_L	180_F	0.861	0.99
55_F	215_P	0.859	0.99
183_I	187_W	0.858	0.99
61_V	227_L	0.848	0.99
16_L	251_F	0.844	0.99
119_L	180_F	0.844	0.99
65_G	285_D	0.843	0.99
201_W	207_P	0.842	0.99
201_W	212_D	0.836	0.99
62_L	281_W	0.835	0.99
114_F	160_N	0.827	0.99
277_L	280_V	0.827	0.99
96_D	157_P	0.824	0.98
230_Y	235_E	0.823	0.98
230_Y	233_G	0.816	0.98
95_G	109_S	0.816	0.98
222_P	226_Q	0.815	0.98
29_E	288_R	0.809	0.98
184_G	187_W	0.808	0.98
98_V	157_P	0.808	0.98
46_L	182_P	0.797	0.98
144_R	160_N	0.796	0.98
263_R	270_F	0.795	0.98
99_W	108_P	0.793	0.98
17_P	23_R	0.791	0.98
49_E	220_A	0.790	0.98
168_I	175_P	0.788	0.98
14_F	289_V	0.787	0.98
59_T	280_V	0.787	0.98
183_I	189_P	0.785	0.98
96_D	114_F	0.783	0.98
251_F	289_V	0.778	0.98
200_A	211_E	0.777	0.98
158_L	167_P	0.777	0.98
87_L	225_Q	0.777	0.98
84_V	280_V	0.776	0.98
125_F	146_F	0.774	0.98
38_L	122_E	0.773	0.98
283_D	290_S	0.772	0.98
10_V	258_P	0.772	0.98
35_D	50_S	0.772	0.98
128_D	133_K	0.771	0.98
33_L	36_E	0.770	0.98
281_W	290_S	0.766	0.98
162_E	167_P	0.765	0.98
94_F	158_L	0.760	0.97
265_R	268_G	0.758	0.97
17_P	20_G	0.757	0.97
7_V	278_D	0.757	0.97
239_L	280_V	0.757	0.97
167_P	175_P	0.755	0.97
168_I	173_D	0.749	0.97
69_A	78_L	0.744	0.97
209_L	218_F	0.744	0.97
235_E	253_L	0.736	0.97
33_L	52_L	0.736	0.97
32_V	36_E	0.735	0.97
125_F	137_Y	0.733	0.97
116_R	285_D	0.731	0.97
196_T	201_W	0.730	0.97
81_G	238_E	0.728	0.97
17_P	21_E	0.723	0.97
141_P	187_W	0.722	0.96
49_E	182_P	0.719	0.96
233_G	255_G	0.718	0.96
121_Y	181_G	0.715	0.96
221_A	226_Q	0.715	0.96
147_A	156_L	0.715	0.96
101_R	106_L	0.714	0.96
201_W	205_R	0.709	0.96
75_V	114_F	0.706	0.96
130_D	134_H	0.706	0.96
31_L	52_L	0.706	0.96
68_Y	242_L	0.703	0.96
82_L	282_I	0.696	0.96
200_A	205_R	0.696	0.96
65_G	82_L	0.693	0.96
69_A	74_P	0.693	0.96
89_K	222_P	0.690	0.95
64_V	283_D	0.686	0.95
59_T	227_L	0.686	0.95
205_R	208_L	0.686	0.95
280_V	291_L	0.684	0.95
94_F	97_R	0.683	0.95
59_T	277_L	0.682	0.95
257_R	274_P	0.682	0.95
100_R	103_G	0.682	0.95
170_S	173_D	0.681	0.95
61_V	282_I	0.680	0.95
89_K	178_A	0.680	0.95
67_A	114_F	0.679	0.95
63_L	284_P	0.678	0.95
256_L	293_W	0.674	0.95
201_W	210_P	0.673	0.95
245_E	249_L	0.673	0.95
68_Y	78_L	0.672	0.95
235_E	255_G	0.671	0.95
92_R	164_P	0.667	0.95
210_P	213_F	0.665	0.94
94_F	168_I	0.665	0.94
76_T	113_P	0.663	0.94
216_R	223_P	0.663	0.94
57_P	215_P	0.661	0.94
92_R	165_D	0.657	0.94
64_V	181_G	0.654	0.94
77_A	167_P	0.654	0.94
80_V	93_V	0.651	0.94
65_G	239_L	0.649	0.94
258_P	273_V	0.647	0.94
197_Y	210_P	0.646	0.94
39_G	43_L	0.643	0.93
48_Y	64_V	0.642	0.93
130_D	133_K	0.642	0.93
54_P	215_P	0.642	0.93
139_R	188_P	0.642	0.93
17_P	22_L	0.641	0.93
37_Y	46_L	0.641	0.93
16_L	287_E	0.641	0.93
59_T	229_G	0.640	0.93
258_P	262_V	0.637	0.93
163_D	167_P	0.637	0.93
91_L	164_P	0.637	0.93
136_A	146_F	0.636	0.93
183_I	226_Q	0.635	0.93
266_D	269_R	0.635	0.93
32_V	35_D	0.632	0.93
127_G	145_G	0.630	0.93
58_R	230_Y	0.628	0.93
89_K	163_D	0.627	0.93
37_Y	41_P	0.624	0.92
147_A	153_A	0.624	0.92
194_A	197_Y	0.624	0.92
37_Y	285_D	0.621	0.92
39_G	42_G	0.618	0.92
71_G	115_T	0.616	0.92
151_S	154_G	0.612	0.92
80_V	242_L	0.610	0.92
37_Y	44_S	0.610	0.92
82_L	239_L	0.609	0.91
231_L	235_E	0.605	0.91
89_K	180_F	0.604	0.91
137_Y	177_P	0.601	0.91
122_E	142_V	0.599	0.91
9_V	292_V	0.599	0.91
16_L	22_L	0.597	0.91
62_L	222_P	0.591	0.90
197_Y	209_L	0.591	0.90
32_V	50_S	0.590	0.90
16_L	289_V	0.587	0.90
121_Y	177_P	0.587	0.90
35_D	185_R	0.587	0.90
11_K	31_L	0.584	0.90
56_K	60_D	0.578	0.89
223_P	226_Q	0.574	0.89
10_V	275_L	0.572	0.89
49_E	53_A	0.571	0.89
163_D	224_D	0.565	0.88
140_N	143_G	0.564	0.88
99_W	171_P	0.564	0.88
149_R	153_A	0.564	0.88
22_L	289_V	0.563	0.88
9_V	294_R	0.562	0.88
234_G	252_R	0.561	0.88
197_Y	213_F	0.560	0.88
129_P	132_A	0.559	0.88
81_G	248_R	0.557	0.87
99_W	158_L	0.554	0.87
135_A	146_F	0.553	0.87
78_L	93_V	0.551	0.87
65_G	119_L	0.550	0.87
10_V	293_W	0.550	0.87
215_P	219_N	0.549	0.87
125_F	173_D	0.548	0.87
162_E	175_P	0.548	0.87
149_R	154_G	0.546	0.86
68_Y	241_N	0.543	0.86
90_T	165_D	0.542	0.86
53_A	294_R	0.541	0.86
47_R	120_R	0.541	0.86
216_R	219_N	0.541	0.86
258_P	275_L	0.540	0.86
100_R	104_G	0.540	0.86
117_M	161_I	0.539	0.86
91_L	242_L	0.537	0.85
97_R	111_P	0.537	0.85
186_H	191_A	0.537	0.85
63_L	119_L	0.537	0.85
63_L	84_V	0.535	0.85
24_L	28_Q	0.534	0.85
11_K	28_Q	0.533	0.85
45_S	142_V	0.532	0.85
62_L	219_N	0.530	0.85
48_Y	281_W	0.530	0.85
91_L	119_L	0.529	0.85
187_W	190_R	0.529	0.85
6_L	262_V	0.528	0.85
192_R	223_P	0.527	0.84
51_D	56_K	0.526	0.84
202_L	205_R	0.524	0.84
139_R	177_P	0.523	0.84
242_L	248_R	0.522	0.84
60_D	225_Q	0.522	0.84
191_A	194_A	0.521	0.84
278_D	292_V	0.521	0.84
189_P	223_P	0.520	0.84
142_V	184_G	0.519	0.84
284_P	288_R	0.518	0.83
89_K	223_P	0.517	0.83
128_D	135_A	0.517	0.83
57_P	230_Y	0.516	0.83
96_D	144_R	0.516	0.83
158_L	162_E	0.515	0.83
150_R	154_G	0.515	0.83
60_D	227_L	0.514	0.83
125_F	175_P	0.513	0.83
85_G	236_P	0.512	0.83
90_T	240_E	0.510	0.82
76_T	112_E	0.509	0.82
69_A	114_F	0.508	0.82
197_Y	207_P	0.508	0.82
85_G	237_V	0.506	0.82
67_A	241_N	0.505	0.82
10_V	260_V	0.505	0.82
144_R	158_L	0.504	0.82
196_T	199_E	0.503	0.82
196_T	210_P	0.502	0.81
231_L	277_L	0.502	0.81
63_L	239_L	0.502	0.81
73_R	115_T	0.501	0.81
116_R	244_P	0.500	0.81
90_T	164_P	0.500	0.81

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
2blfA	1	0.5	7.8	0.968	Contact Map
1ogpA	4	0.5034	5.9	0.97	Contact Map
2a9dA	2	0.517	3.9	0.972	Contact Map
1soxA	2	0.517	3.6	0.973	Contact Map
4f7uQ	1	0.1939	3.1	0.974	Contact Map
4hhrA	1	0.534	2.9	0.974	Contact Map
4b2hA	5	0.0544	2.7	0.974	Contact Map
2miiA	1	0.3333	2.5	0.975	Contact Map
3vzaE	1	0.1054	2.5	0.975	Contact Map
3lzqA	2	0.4354	2	0.976	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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