DUF3871 - PFAM28P - GREMLIN Contacts

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DUF3871 - Domain of unknown function, B. Theta Gene description (DUF3871)

PFAM:	PF12987	Sequences: YAEDAEIIEEEVIESSSKPFIEANTKEVTLEHLKNDCIIPVFSKDNELTISHQEFIETVQEAASDVFPGETILKPEIRVSHPIKGRIPEAIHKPAKELLEHEKTIYYERMAFVIEIPSITETINGNRLSLTIGGVRAYNLENLYSKKSAEKFKVFIGFKNKVCTNLCVSTDGYKSELRVMSTAELYQKILELFQNYNAEKHLHLMEQLSNYSLTEHQFAQLIGRMRLYQYLPKKEKKELPPLLLTDSQINTVAKDYYRDENFCRDEDGSINLWNLYNLFTGANKSSYIDTFLDRSVNATEFVEGINKALNGDSEYSWFL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	319 (310)
Sequences:	687 (488)
Seq/√Len:	27.7
META:	0.859

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
196_Y	201_H	8.088	1.00
147_K	150_E	5.765	1.00
59_V	189_I	4.299	1.00
133_G	155_F	4.270	1.00
156_I	193_F	4.249	1.00
170_T	174_K	4.119	1.00
136_R	141_E	3.712	1.00
227_L	253_A	3.629	1.00
67_F	156_I	3.581	1.00
93_K	102_E	3.158	1.00
120_T	127_R	3.095	1.00
154_V	189_I	2.914	1.00
154_V	177_L	2.913	1.00
32_H	107_Y	2.673	1.00
49_T	136_R	2.667	0.99
116_I	132_I	2.640	0.99
189_I	193_F	2.622	0.99
154_V	192_L	2.521	0.99
100_E	103_K	2.515	0.99
275_L	279_F	2.496	0.99
219_A	257_Y	2.413	0.99
126_N	160_N	2.393	0.99
214_T	217_Q	2.381	0.99
255_D	261_N	2.310	0.99
28_V	32_H	2.304	0.98
304_G	318_F	2.238	0.98
94_P	97_E	2.224	0.98
271_N	274_N	2.165	0.98
140_L	153_K	2.144	0.98
32_H	36_D	2.133	0.97
255_D	263_C	2.094	0.97
188_K	191_E	2.050	0.97
265_D	269_S	2.014	0.96
141_E	151_K	1.955	0.96
271_N	279_F	1.955	0.96
208_L	302_V	1.954	0.96
272_L	302_V	1.927	0.95
243_L	297_N	1.920	0.95
124_N	274_N	1.889	0.95
244_L	279_F	1.881	0.95
115_E	159_K	1.839	0.94
222_I	249_I	1.827	0.94
91_I	136_R	1.791	0.93
119_I	158_F	1.783	0.93
304_G	315_Y	1.732	0.92
82_P	105_I	1.721	0.92
37_C	151_K	1.701	0.91
37_C	91_I	1.696	0.91
243_L	279_F	1.640	0.89
283_N	295_S	1.636	0.89
160_N	164_T	1.605	0.88
175_S	293_D	1.583	0.88
217_Q	309_L	1.581	0.88
230_Y	250_N	1.554	0.87
244_L	248_Q	1.553	0.87
62_A	186_Y	1.536	0.86
221_L	275_L	1.526	0.86
311_G	315_Y	1.516	0.85
225_M	249_I	1.514	0.85
37_C	49_T	1.500	0.85
137_A	140_L	1.495	0.85
63_A	193_F	1.482	0.84
32_H	37_C	1.470	0.83
37_C	136_R	1.463	0.83
44_K	106_Y	1.462	0.83
41_V	46_N	1.457	0.83
122_T	127_R	1.452	0.83
168_V	224_R	1.430	0.82
247_S	250_N	1.427	0.82
199_E	203_H	1.419	0.81
63_A	132_I	1.404	0.81
120_T	129_S	1.359	0.78
34_K	57_E	1.346	0.78
303_E	306_N	1.341	0.77
222_I	264_R	1.338	0.77
47_E	160_N	1.337	0.77
39_I	87_I	1.330	0.77
255_D	281_G	1.329	0.77
206_E	210_N	1.299	0.75
63_A	114_I	1.298	0.75
100_E	147_K	1.282	0.74
48_L	92_H	1.267	0.73
216_H	220_Q	1.266	0.73
145_S	256_Y	1.263	0.73
44_K	108_E	1.257	0.73
296_V	300_E	1.239	0.71
149_A	180_M	1.239	0.71
227_L	257_Y	1.238	0.71
136_R	150_E	1.237	0.71
240_P	304_G	1.236	0.71
259_D	281_G	1.236	0.71
197_N	200_K	1.216	0.70
225_M	242_L	1.212	0.70
111_A	221_L	1.205	0.69
33_L	37_C	1.204	0.69
95_A	102_E	1.197	0.69
16_S	19_P	1.194	0.69
180_M	184_E	1.172	0.67
286_S	290_T	1.160	0.66
227_L	308_A	1.158	0.66
224_R	319_L	1.157	0.66
127_R	161_K	1.147	0.65
155_F	169_S	1.143	0.65
213_L	253_A	1.136	0.65
58_T	305_I	1.136	0.65
242_L	297_N	1.129	0.64
51_S	55_F	1.127	0.64
126_N	255_D	1.126	0.64
121_E	140_L	1.123	0.64
197_N	203_H	1.114	0.63
211_Y	306_N	1.099	0.62
37_C	141_E	1.095	0.62
213_L	309_L	1.082	0.61
58_T	224_R	1.080	0.61
87_I	102_E	1.076	0.60
240_P	250_N	1.074	0.60
139_N	150_E	1.070	0.60
70_E	118_S	1.065	0.60
121_E	206_E	1.065	0.60
174_K	177_L	1.057	0.59
59_V	193_F	1.050	0.58
67_F	193_F	1.035	0.57
140_L	224_R	1.022	0.56
193_F	247_S	1.021	0.56
110_M	236_K	1.019	0.56
304_G	308_A	1.017	0.56
151_K	176_E	1.013	0.56
221_L	301_F	1.007	0.55
150_E	247_S	1.003	0.55
136_R	151_K	0.999	0.55
62_A	66_V	0.999	0.55
132_I	200_K	0.999	0.55
290_T	293_D	0.992	0.54
66_V	69_G	0.992	0.54
128_L	170_T	0.989	0.54
97_E	101_H	0.988	0.54
115_E	131_T	0.986	0.54
244_L	298_A	0.985	0.54
84_K	106_Y	0.981	0.53
261_N	274_N	0.972	0.53
46_N	106_Y	0.971	0.52
103_K	154_V	0.970	0.52
92_H	136_R	0.959	0.52
316_S	319_L	0.958	0.51
89_E	102_E	0.956	0.51
263_C	271_N	0.952	0.51
181_S	184_E	0.951	0.51
226_R	250_N	0.947	0.51
300_E	303_E	0.945	0.50
224_R	239_L	0.945	0.50
307_K	311_G	0.941	0.50
242_L	301_F	0.936	0.50
128_L	160_N	0.934	0.50
32_H	105_I	0.932	0.49
55_F	134_G	0.924	0.49
66_V	193_F	0.923	0.49
49_T	150_E	0.917	0.48
55_F	152_F	0.912	0.48
48_L	54_E	0.911	0.48
28_V	79_V	0.903	0.47
164_T	174_K	0.899	0.47
42_F	45_D	0.894	0.47
39_I	48_L	0.894	0.47
173_Y	293_D	0.892	0.46
43_S	136_R	0.891	0.46
261_N	264_R	0.891	0.46
73_L	115_E	0.890	0.46
235_E	238_E	0.884	0.46
151_K	155_F	0.884	0.46
58_T	182_T	0.883	0.46
42_F	49_T	0.882	0.46
179_V	185_L	0.881	0.46
263_C	274_N	0.881	0.46
299_T	304_G	0.880	0.46
48_L	102_E	0.878	0.45
16_S	73_L	0.874	0.45
228_Y	240_P	0.874	0.45
167_C	276_Y	0.872	0.45
31_E	35_N	0.871	0.45
146_K	205_M	0.870	0.45
51_S	115_E	0.868	0.45
203_H	206_E	0.867	0.45
300_E	318_F	0.866	0.44
37_C	48_L	0.862	0.44
142_N	160_N	0.862	0.44
59_V	63_A	0.860	0.44
137_A	308_A	0.858	0.44
42_F	253_A	0.857	0.44
220_Q	227_L	0.856	0.44
47_E	52_H	0.856	0.44
113_V	131_T	0.854	0.44
102_E	248_Q	0.853	0.43
19_P	159_K	0.852	0.43
83_I	137_A	0.851	0.43
92_H	168_V	0.851	0.43
233_K	237_K	0.849	0.43
39_I	224_R	0.847	0.43
276_Y	280_T	0.846	0.43
82_P	91_I	0.845	0.43
48_L	51_S	0.844	0.43
153_K	166_L	0.844	0.43
164_T	281_G	0.844	0.43
243_L	271_N	0.842	0.43
113_V	166_L	0.840	0.43
63_A	118_S	0.837	0.42
71_T	118_S	0.832	0.42
97_E	188_K	0.831	0.42
33_L	53_Q	0.830	0.42
89_E	93_K	0.830	0.42
48_L	136_R	0.829	0.42
295_S	301_F	0.826	0.41
69_G	205_M	0.826	0.41
62_A	190_L	0.824	0.41
247_S	252_V	0.824	0.41
110_M	220_Q	0.818	0.41
264_R	268_G	0.811	0.40
15_S	132_I	0.807	0.40
161_K	169_S	0.807	0.40
51_S	70_E	0.806	0.40
65_D	197_N	0.805	0.40
31_E	43_S	0.800	0.40
280_T	283_N	0.797	0.39
32_H	82_P	0.794	0.39
76_E	136_R	0.794	0.39
272_L	279_F	0.792	0.39
37_C	82_P	0.789	0.39
113_V	159_K	0.785	0.38
191_E	197_N	0.784	0.38
31_E	36_D	0.783	0.38
302_V	308_A	0.783	0.38
225_M	244_L	0.779	0.38
75_P	117_P	0.777	0.38
189_I	221_L	0.777	0.38
69_G	224_R	0.777	0.38
227_L	275_L	0.775	0.38
279_F	302_V	0.772	0.38
204_L	299_T	0.767	0.37
133_G	169_S	0.765	0.37
222_I	253_A	0.764	0.37
123_I	151_K	0.763	0.37
240_P	297_N	0.763	0.37
240_P	315_Y	0.760	0.37
177_L	187_Q	0.760	0.37
134_G	152_F	0.760	0.37
261_N	269_S	0.759	0.37
270_I	278_L	0.759	0.37
88_P	107_Y	0.758	0.37
100_E	120_T	0.756	0.36
208_L	291_F	0.755	0.36
261_N	300_E	0.753	0.36
168_V	293_D	0.750	0.36
49_T	138_Y	0.744	0.36
96_K	203_H	0.743	0.35
275_L	302_V	0.742	0.35
66_V	77_I	0.741	0.35
307_K	314_E	0.739	0.35
224_R	290_T	0.738	0.35
117_P	205_M	0.738	0.35
42_F	138_Y	0.735	0.35
248_Q	285_S	0.735	0.35
56_I	114_I	0.734	0.35
139_N	144_Y	0.733	0.35
129_S	132_I	0.731	0.35
227_L	318_F	0.730	0.35
113_V	155_F	0.730	0.35
192_L	195_N	0.729	0.35
170_T	226_R	0.727	0.34
304_G	316_S	0.726	0.34
41_V	106_Y	0.723	0.34
20_F	24_N	0.722	0.34
106_Y	159_K	0.721	0.34
87_I	101_H	0.721	0.34
283_N	286_S	0.720	0.34
148_S	179_V	0.719	0.34
257_Y	264_R	0.718	0.34
52_H	136_R	0.718	0.34
191_E	200_K	0.712	0.33
16_S	31_E	0.710	0.33
181_S	296_V	0.709	0.33
16_S	76_E	0.706	0.33
168_V	174_K	0.704	0.33
304_G	310_N	0.701	0.33
226_R	230_Y	0.700	0.33
279_F	282_A	0.699	0.32
136_R	144_Y	0.699	0.32
60_Q	64_S	0.697	0.32
131_T	159_K	0.695	0.32
46_N	51_S	0.693	0.32
126_N	274_N	0.690	0.32
159_K	164_T	0.687	0.32
49_T	91_I	0.683	0.31
212_S	225_M	0.682	0.31
183_A	241_P	0.681	0.31
113_V	133_G	0.679	0.31
252_V	283_N	0.675	0.31
222_I	290_T	0.672	0.31
17_S	22_E	0.665	0.30
250_N	281_G	0.664	0.30
30_L	222_I	0.662	0.30
159_K	170_T	0.659	0.30
235_E	271_N	0.655	0.30
76_E	250_N	0.654	0.30
136_R	169_S	0.654	0.30
129_S	193_F	0.653	0.29
43_S	282_A	0.651	0.29
190_L	194_Q	0.651	0.29
83_I	100_E	0.648	0.29
124_N	184_E	0.647	0.29
282_A	286_S	0.645	0.29
140_L	293_D	0.645	0.29
91_I	151_K	0.643	0.29
94_P	100_E	0.643	0.29
20_F	25_T	0.643	0.29
198_A	203_H	0.642	0.29
49_T	147_K	0.642	0.29
141_E	164_T	0.638	0.29
137_A	166_L	0.635	0.28
58_T	186_Y	0.634	0.28
312_D	315_Y	0.634	0.28
155_F	168_V	0.633	0.28
91_I	141_E	0.632	0.28
177_L	188_K	0.632	0.28
41_V	44_K	0.630	0.28
19_P	113_V	0.628	0.28
120_T	205_M	0.628	0.28
94_P	226_R	0.627	0.28
133_G	153_K	0.627	0.28
204_L	236_K	0.625	0.28
63_A	83_I	0.624	0.28
161_K	164_T	0.623	0.28
220_Q	308_A	0.623	0.28
87_I	120_T	0.623	0.28
306_N	319_L	0.621	0.27
49_T	169_S	0.620	0.27
52_H	160_N	0.619	0.27
123_I	128_L	0.619	0.27
245_T	272_L	0.619	0.27
44_K	147_K	0.618	0.27
123_I	166_L	0.616	0.27
115_E	129_S	0.614	0.27
54_E	102_E	0.612	0.27
267_D	319_L	0.612	0.27
149_A	179_V	0.610	0.27
170_T	192_L	0.609	0.27
69_G	164_T	0.609	0.27
307_K	310_N	0.609	0.27
140_L	144_Y	0.607	0.27
195_N	266_E	0.607	0.27
154_V	193_F	0.604	0.26
213_L	275_L	0.604	0.26
79_V	168_V	0.602	0.26
100_E	173_Y	0.601	0.26
214_T	228_Y	0.600	0.26
239_L	318_F	0.600	0.26
205_M	275_L	0.600	0.26
59_V	62_A	0.597	0.26
48_L	91_I	0.597	0.26
311_G	316_S	0.597	0.26
47_E	150_E	0.597	0.26
70_E	295_S	0.596	0.26
160_N	255_D	0.594	0.26
224_R	244_L	0.592	0.26
207_Q	210_N	0.592	0.26
66_V	189_I	0.590	0.26
160_N	196_Y	0.589	0.26
82_P	245_T	0.589	0.26
198_A	290_T	0.588	0.26
188_K	251_T	0.586	0.25
102_E	230_Y	0.584	0.25
150_E	229_Q	0.583	0.25
136_R	147_K	0.582	0.25
33_L	36_D	0.582	0.25
84_K	108_E	0.579	0.25
221_L	244_L	0.578	0.25
90_A	104_T	0.577	0.25
255_D	271_N	0.576	0.25
46_N	167_C	0.575	0.25
15_S	76_E	0.574	0.25
257_Y	275_L	0.574	0.25
289_D	294_R	0.573	0.25
308_A	315_Y	0.572	0.25
169_S	200_K	0.572	0.25
19_P	27_E	0.567	0.24
191_E	195_N	0.565	0.24
49_T	141_E	0.565	0.24
70_E	180_M	0.564	0.24
99_L	256_Y	0.564	0.24
120_T	260_E	0.564	0.24
87_I	176_E	0.563	0.24
233_K	236_K	0.562	0.24
153_K	169_S	0.560	0.24
211_Y	310_N	0.560	0.24
284_K	287_Y	0.560	0.24
58_T	314_E	0.559	0.24
53_Q	240_P	0.558	0.24
226_R	246_D	0.558	0.24
187_Q	194_Q	0.557	0.24
92_H	253_A	0.557	0.24
281_G	295_S	0.555	0.24
235_E	239_L	0.555	0.24
33_L	306_N	0.554	0.24
195_N	270_I	0.552	0.23
59_V	116_I	0.552	0.23
94_P	175_S	0.552	0.23
105_I	177_L	0.551	0.23
245_T	271_N	0.549	0.23
156_I	271_N	0.549	0.23
226_R	241_P	0.548	0.23
256_Y	264_R	0.547	0.23
34_K	285_S	0.547	0.23
251_T	254_K	0.546	0.23
141_E	178_R	0.546	0.23
257_Y	280_T	0.545	0.23
304_G	312_D	0.543	0.23
48_L	52_H	0.541	0.23
141_E	150_E	0.540	0.23
156_I	252_V	0.537	0.23
251_T	301_F	0.535	0.23
263_C	281_G	0.535	0.23
79_V	111_A	0.534	0.23
34_K	129_S	0.533	0.22
22_E	276_Y	0.533	0.22
213_L	217_Q	0.533	0.22
110_M	160_N	0.531	0.22
203_H	209_S	0.530	0.22
30_L	208_L	0.529	0.22
260_E	281_G	0.528	0.22
23_A	47_E	0.528	0.22
222_I	263_C	0.527	0.22
38_I	139_N	0.527	0.22
204_L	207_Q	0.526	0.22
187_Q	191_E	0.525	0.22
249_I	265_D	0.525	0.22
248_Q	290_T	0.524	0.22
118_S	295_S	0.524	0.22
105_I	131_T	0.523	0.22
160_N	281_G	0.523	0.22
110_M	159_K	0.523	0.22
101_H	247_S	0.522	0.22
46_N	88_P	0.521	0.22
36_D	42_F	0.521	0.22
77_I	302_V	0.520	0.22
146_K	168_V	0.519	0.22
177_L	242_L	0.519	0.22
30_L	180_M	0.518	0.22
111_A	173_Y	0.517	0.22
249_I	276_Y	0.517	0.22
168_V	229_Q	0.515	0.22
26_K	161_K	0.514	0.21
236_K	276_Y	0.513	0.21
260_E	263_C	0.511	0.21
200_K	203_H	0.508	0.21
310_N	316_S	0.508	0.21
49_T	139_N	0.508	0.21
30_L	53_Q	0.507	0.21
301_F	306_N	0.507	0.21
93_K	112_F	0.507	0.21
82_P	151_K	0.505	0.21
232_P	265_D	0.504	0.21
263_C	269_S	0.503	0.21
37_C	52_H	0.503	0.21
89_E	108_E	0.502	0.21
87_I	93_K	0.501	0.21
22_E	76_E	0.501	0.21
99_L	254_K	0.500	0.21

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
2l4hA	1	0.5266	32.3	0.979	Contact Map
2huoA	1	0.232	30.9	0.979	Contact Map
1lm7A	2	0.163	22.5	0.98	Contact Map
2b1uA	1	0.2226	19.7	0.981	Contact Map
1exrA	1	0.4545	18.6	0.981	Contact Map
2m8uA	1	0.2414	17.3	0.981	Contact Map
2jnfA	1	0.4639	15.1	0.982	Contact Map
4mzjA	1	0.3793	13.9	0.982	Contact Map
1y1xA	2	0.5486	11.9	0.982	Contact Map
1cb1A	1	0.2445	11.6	0.983	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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