DUF3881 - PFAM28P - GREMLIN Contacts

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DUF3881 - Domain of unknown function, E. rectale Gene description (DUF3881)

PFAM:	PF12997	Sequences: LRAIGFSKIKKRKELEKLLTDVIENPDERKYTSNDEGTLLAEFSKEFAEGIGIAVCGEYDEDDKFHYEYYFPYLRGSGISSYEDVSVERHADKESYAGVCDDIRVGVSLIFYLQNVIEYLKEKNLGKLPIKGTSVTLSGLSLEGKILLPIEKDEEQKKKEKKESKNRNKLIAAARNGDEEAIESLTLEDMDTYSMISRRIQKEDVFSIVDTYFMPYGVECDQYSILGEILDVREVKNSLTGEEIYIMTLECNDLIFDVCINKKDLLGEPAVGRRFKGNIWLQG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	283 (283)
Sequences:	700 (534)
Seq/√Len:	31.7
META:	0.79

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
139_G	258_V	5.297	1.00
243_E	262_K	5.094	1.00
173_A	178_D	4.896	1.00
212_Y	226_L	4.827	1.00
46_E	73_Y	4.426	1.00
234_E	262_K	4.359	1.00
51_I	244_I	4.154	1.00
48_A	51_I	3.961	1.00
2_R	264_D	3.480	1.00
90_H	95_S	3.469	1.00
199_R	203_E	3.413	1.00
234_E	243_E	3.058	1.00
78_G	136_T	2.928	1.00
44_S	54_A	2.909	1.00
236_K	241_G	2.817	1.00
2_R	141_S	2.767	1.00
236_K	243_E	2.640	1.00
76_G	136_T	2.602	1.00
200_I	205_V	2.537	1.00
225_I	249_L	2.524	1.00
177_G	181_A	2.422	0.99
234_E	245_Y	2.341	0.99
8_K	263_K	2.235	0.99
260_I	265_L	2.214	0.99
174_A	181_A	2.147	0.98
232_V	271_V	2.122	0.98
91_A	222_Q	2.058	0.98
89_R	94_E	1.980	0.97
227_G	249_L	1.977	0.97
256_F	281_L	1.944	0.97
90_H	97_A	1.930	0.97
48_A	235_V	1.864	0.96
261_N	264_D	1.830	0.96
150_I	207_S	1.775	0.95
245_Y	262_K	1.759	0.95
38_T	58_E	1.750	0.95
19_L	23_I	1.749	0.95
46_E	50_G	1.729	0.94
174_A	177_G	1.727	0.94
21_D	25_N	1.718	0.94
235_V	246_I	1.708	0.94
99_V	108_S	1.704	0.94
94_E	123_K	1.662	0.93
7_S	242_E	1.611	0.92
74_L	246_I	1.563	0.90
140_L	282_Q	1.545	0.90
152_K	210_D	1.513	0.89
199_R	208_I	1.509	0.89
227_G	258_V	1.498	0.88
74_L	259_C	1.493	0.88
90_H	222_Q	1.490	0.88
18_L	49_E	1.489	0.88
141_S	277_G	1.488	0.88
1_L	53_I	1.474	0.88
113_L	119_Y	1.459	0.87
268_E	273_R	1.454	0.87
27_D	45_K	1.410	0.85
136_T	256_F	1.408	0.85
15_L	70_Y	1.401	0.85
51_I	235_V	1.401	0.85
77_S	257_D	1.382	0.84
212_Y	224_S	1.378	0.84
46_E	75_R	1.377	0.84
163_E	206_F	1.360	0.83
18_L	239_L	1.331	0.82
147_L	208_I	1.315	0.81
78_G	257_D	1.303	0.80
21_D	47_F	1.303	0.80
152_K	156_Q	1.295	0.80
230_L	255_I	1.288	0.79
23_I	41_A	1.280	0.79
19_L	67_Y	1.278	0.79
61_E	239_L	1.276	0.79
123_K	150_I	1.276	0.79
232_V	247_M	1.273	0.79
88_E	99_V	1.266	0.78
170_L	181_A	1.250	0.77
3_A	141_S	1.250	0.77
203_E	207_S	1.243	0.77
173_A	176_N	1.243	0.77
246_I	257_D	1.230	0.76
71_F	263_K	1.225	0.76
30_K	121_K	1.220	0.76
186_T	191_D	1.220	0.76
27_D	46_E	1.213	0.75
267_G	274_R	1.207	0.75
107_V	114_Q	1.204	0.75
216_Y	278_N	1.203	0.75
248_T	257_D	1.170	0.72
20_T	64_K	1.169	0.72
3_A	142_L	1.165	0.72
164_S	168_N	1.161	0.72
76_G	257_D	1.158	0.72
146_I	249_L	1.155	0.71
99_V	218_V	1.152	0.71
34_N	38_T	1.148	0.71
2_R	47_F	1.135	0.70
90_H	93_K	1.134	0.70
109_L	211_T	1.123	0.69
22_V	141_S	1.119	0.69
56_C	92_D	1.111	0.68
203_E	208_I	1.098	0.68
146_I	277_G	1.095	0.67
273_R	279_I	1.094	0.67
208_I	226_L	1.092	0.67
146_I	275_F	1.091	0.67
97_A	218_V	1.091	0.67
4_I	140_L	1.089	0.67
147_L	206_F	1.088	0.67
179_E	183_E	1.087	0.67
74_L	257_D	1.085	0.67
104_R	224_S	1.083	0.66
36_E	190_M	1.080	0.66
90_H	198_R	1.076	0.66
81_S	105_V	1.072	0.66
218_V	222_Q	1.071	0.66
121_K	226_L	1.067	0.65
113_L	210_D	1.055	0.64
46_E	245_Y	1.053	0.64
259_C	282_Q	1.044	0.64
23_I	63_D	1.036	0.63
31_Y	39_L	1.032	0.63
179_E	188_E	1.030	0.63
234_E	244_I	1.024	0.62
95_S	112_Y	1.021	0.62
9_I	15_L	1.019	0.62
276_K	280_W	1.019	0.62
80_S	104_R	1.019	0.62
213_F	251_C	1.008	0.61
90_H	112_Y	1.007	0.61
38_T	120_L	1.003	0.60
57_G	65_F	1.001	0.60
23_I	67_Y	1.001	0.60
80_S	254_L	0.996	0.60
78_G	256_F	0.993	0.60
60_D	102_D	0.991	0.59
28_E	75_R	0.981	0.59
84_D	135_V	0.980	0.59
49_E	233_R	0.978	0.58
260_I	264_D	0.978	0.58
214_M	228_E	0.973	0.58
43_F	208_I	0.972	0.58
18_L	62_D	0.971	0.58
103_I	171_I	0.971	0.58
249_L	258_V	0.961	0.57
274_R	283_G	0.959	0.57
15_L	19_L	0.950	0.56
55_V	175_R	0.947	0.56
101_D	188_E	0.942	0.56
217_G	221_D	0.942	0.56
107_V	184_S	0.939	0.55
92_D	95_S	0.938	0.55
55_V	67_Y	0.934	0.55
52_G	57_G	0.934	0.55
104_R	139_G	0.931	0.55
167_R	276_K	0.926	0.54
69_Y	93_K	0.924	0.54
106_G	109_L	0.922	0.54
154_E	158_K	0.920	0.54
36_E	250_E	0.920	0.54
41_A	59_Y	0.919	0.54
97_A	222_Q	0.917	0.54
244_I	249_L	0.912	0.53
48_A	238_S	0.907	0.53
143_E	211_T	0.907	0.53
152_K	228_E	0.901	0.52
186_T	189_D	0.901	0.52
170_L	184_S	0.900	0.52
97_A	214_M	0.899	0.52
144_G	275_F	0.899	0.52
178_D	212_Y	0.893	0.52
170_L	174_A	0.892	0.52
23_I	55_V	0.892	0.52
167_R	193_Y	0.881	0.51
91_A	146_I	0.878	0.50
61_E	93_K	0.866	0.49
40_L	120_L	0.864	0.49
145_K	208_I	0.859	0.49
8_K	164_S	0.851	0.48
262_K	268_E	0.851	0.48
269_P	274_R	0.847	0.48
260_I	275_F	0.846	0.48
178_D	181_A	0.842	0.47
54_A	102_D	0.841	0.47
170_L	276_K	0.840	0.47
244_I	259_C	0.837	0.47
70_Y	186_T	0.837	0.47
12_R	66_H	0.834	0.47
250_E	255_I	0.829	0.46
45_K	73_Y	0.821	0.46
277_G	283_G	0.812	0.45
231_D	248_T	0.809	0.45
181_A	185_L	0.808	0.45
246_I	259_C	0.806	0.44
19_L	70_Y	0.804	0.44
85_V	133_T	0.796	0.44
40_L	116_V	0.793	0.43
168_N	207_S	0.790	0.43
35_D	41_A	0.790	0.43
267_G	272_G	0.788	0.43
29_R	99_V	0.786	0.43
209_V	226_L	0.786	0.43
242_E	261_N	0.783	0.43
125_L	139_G	0.781	0.42
170_L	185_L	0.775	0.42
46_E	249_L	0.774	0.42
147_L	153_D	0.772	0.42
56_C	116_V	0.771	0.42
187_L	191_D	0.771	0.42
253_D	281_L	0.768	0.41
18_L	29_R	0.765	0.41
126_G	241_G	0.764	0.41
173_A	214_M	0.763	0.41
77_S	233_R	0.755	0.40
118_E	132_G	0.754	0.40
126_G	281_L	0.752	0.40
32_T	117_I	0.751	0.40
188_E	245_Y	0.745	0.40
90_H	218_V	0.744	0.40
270_A	273_R	0.743	0.39
247_M	260_I	0.741	0.39
20_T	23_I	0.740	0.39
247_M	272_G	0.738	0.39
248_T	255_I	0.737	0.39
111_F	240_T	0.737	0.39
108_S	196_I	0.734	0.39
50_G	235_V	0.733	0.39
97_A	108_S	0.730	0.38
10_K	168_N	0.723	0.38
118_E	122_E	0.721	0.38
91_A	97_A	0.719	0.38
43_F	59_Y	0.719	0.38
192_T	195_M	0.717	0.37
118_E	201_Q	0.717	0.37
23_I	101_D	0.716	0.37
274_R	277_G	0.716	0.37
103_I	196_I	0.713	0.37
161_K	253_D	0.713	0.37
90_H	183_E	0.705	0.37
53_I	241_G	0.703	0.36
129_P	132_G	0.700	0.36
99_V	187_L	0.696	0.36
129_P	133_T	0.695	0.36
50_G	246_I	0.694	0.36
158_K	161_K	0.693	0.36
183_E	218_V	0.693	0.36
8_K	14_E	0.691	0.36
265_L	275_F	0.690	0.35
265_L	269_P	0.689	0.35
107_V	194_S	0.688	0.35
74_L	102_D	0.687	0.35
146_I	163_E	0.687	0.35
275_F	283_G	0.686	0.35
141_S	275_F	0.683	0.35
147_L	199_R	0.680	0.35
88_E	214_M	0.679	0.35
167_R	171_I	0.679	0.35
7_S	165_K	0.678	0.35
13_K	245_Y	0.678	0.35
154_E	157_K	0.678	0.35
45_K	212_Y	0.678	0.35
95_S	99_V	0.675	0.34
86_S	206_F	0.674	0.34
96_Y	170_L	0.672	0.34
116_V	120_L	0.671	0.34
146_I	271_V	0.670	0.34
233_R	253_D	0.669	0.34
193_Y	273_R	0.669	0.34
232_V	245_Y	0.662	0.33
214_M	218_V	0.660	0.33
43_F	205_V	0.658	0.33
113_L	175_R	0.657	0.33
50_G	60_D	0.656	0.33
229_I	237_N	0.653	0.33
221_D	276_K	0.650	0.33
221_D	280_W	0.649	0.32
1_L	5_G	0.645	0.32
14_E	17_K	0.645	0.32
42_E	56_C	0.643	0.32
269_P	283_G	0.642	0.32
2_R	142_L	0.642	0.32
82_Y	107_V	0.641	0.32
151_E	247_M	0.641	0.32
230_L	236_K	0.640	0.32
222_Q	278_N	0.640	0.32
189_D	197_S	0.639	0.32
4_I	10_K	0.636	0.32
37_G	165_K	0.635	0.31
205_V	276_K	0.632	0.31
189_D	219_E	0.631	0.31
59_Y	65_F	0.630	0.31
42_E	259_C	0.628	0.31
88_E	97_A	0.628	0.31
40_L	117_I	0.628	0.31
30_K	33_S	0.626	0.31
189_D	213_F	0.626	0.31
141_S	261_N	0.624	0.31
267_G	283_G	0.623	0.31
108_S	143_E	0.623	0.31
273_R	276_K	0.621	0.30
28_E	37_G	0.621	0.30
214_M	220_C	0.621	0.30
10_K	207_S	0.620	0.30
86_S	102_D	0.616	0.30
55_V	75_R	0.615	0.30
119_Y	171_I	0.615	0.30
43_F	211_T	0.614	0.30
87_V	132_G	0.613	0.30
45_K	238_S	0.613	0.30
153_D	156_Q	0.612	0.30
168_N	172_A	0.611	0.30
141_S	260_I	0.611	0.30
155_E	192_T	0.607	0.29
141_S	264_D	0.602	0.29
85_V	136_T	0.601	0.29
8_K	62_D	0.601	0.29
94_E	163_E	0.600	0.29
236_K	262_K	0.600	0.29
220_C	228_E	0.600	0.29
38_T	66_H	0.600	0.29
39_L	208_I	0.598	0.29
166_N	169_K	0.596	0.29
79_I	134_S	0.596	0.29
56_C	71_F	0.595	0.29
139_G	171_I	0.591	0.28
80_S	98_G	0.591	0.28
82_Y	184_S	0.588	0.28
159_K	247_M	0.587	0.28
230_L	250_E	0.587	0.28
70_Y	110_I	0.587	0.28
182_I	233_R	0.587	0.28
112_Y	200_I	0.587	0.28
212_Y	281_L	0.584	0.28
131_K	271_V	0.581	0.28
165_K	243_E	0.581	0.28
176_N	206_F	0.581	0.28
74_L	139_G	0.580	0.28
10_K	36_E	0.580	0.28
252_N	273_R	0.580	0.28
13_K	244_I	0.580	0.28
33_S	37_G	0.578	0.28
69_Y	221_D	0.575	0.27
159_K	233_R	0.573	0.27
40_L	56_C	0.573	0.27
236_K	249_L	0.572	0.27
57_G	113_L	0.569	0.27
87_V	123_K	0.569	0.27
231_D	247_M	0.567	0.27
189_D	193_Y	0.566	0.27
181_A	191_D	0.566	0.27
9_I	24_E	0.564	0.27
96_Y	207_S	0.557	0.26
101_D	148_L	0.556	0.26
56_C	107_V	0.555	0.26
234_E	241_G	0.555	0.26
27_D	235_V	0.554	0.26
258_V	263_K	0.553	0.26
61_E	127_K	0.553	0.26
227_G	237_N	0.553	0.26
83_E	261_N	0.552	0.26
268_E	279_I	0.551	0.26
159_K	190_M	0.551	0.26
191_D	194_S	0.550	0.26
73_Y	184_S	0.549	0.26
76_G	193_Y	0.548	0.26
30_K	40_L	0.545	0.25
171_I	251_C	0.543	0.25
128_L	138_S	0.543	0.25
110_I	209_V	0.542	0.25
110_I	252_N	0.541	0.25
52_G	73_Y	0.540	0.25
167_R	189_D	0.539	0.25
56_C	69_Y	0.538	0.25
146_I	224_S	0.538	0.25
34_N	37_G	0.538	0.25
11_K	20_T	0.534	0.25
4_I	53_I	0.534	0.25
99_V	200_I	0.533	0.25
162_K	202_K	0.533	0.25
16_E	116_V	0.532	0.25
174_A	185_L	0.531	0.25
81_S	256_F	0.529	0.24
96_Y	116_V	0.528	0.24
186_T	190_M	0.528	0.24
88_E	93_K	0.526	0.24
175_R	214_M	0.526	0.24
41_A	65_F	0.525	0.24
16_E	19_L	0.524	0.24
49_E	271_V	0.524	0.24
186_T	193_Y	0.523	0.24
81_S	168_N	0.523	0.24
135_V	148_L	0.521	0.24
44_S	139_G	0.521	0.24
85_V	111_F	0.520	0.24
150_I	208_I	0.520	0.24
15_L	250_E	0.518	0.24
115_N	118_E	0.517	0.24
95_S	220_C	0.516	0.24
89_R	152_K	0.516	0.24
86_S	180_E	0.516	0.24
56_C	259_C	0.516	0.24
101_D	212_Y	0.515	0.24
217_G	280_W	0.515	0.24
232_V	239_L	0.514	0.24
26_P	67_Y	0.513	0.24
108_S	217_G	0.513	0.24
12_R	58_E	0.513	0.24
98_G	138_S	0.512	0.23
76_G	156_Q	0.512	0.23
50_G	255_I	0.512	0.23
11_K	142_L	0.511	0.23
240_T	244_I	0.510	0.23
24_E	240_T	0.510	0.23
4_I	77_S	0.509	0.23
60_D	66_H	0.509	0.23
144_G	258_V	0.508	0.23
2_R	98_G	0.507	0.23
82_Y	187_L	0.507	0.23
217_G	276_K	0.505	0.23
128_L	133_T	0.504	0.23
117_I	133_T	0.502	0.23
107_V	252_N	0.502	0.23
111_F	114_Q	0.501	0.23
51_I	114_Q	0.500	0.23

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
1zmbA	2	0.3746	25.5	0.969	Contact Map
4upyB	1	0.5053	9.9	0.974	Contact Map
1us0A	1	0.5512	9	0.974	Contact Map
4gieA	1	0.5159	8.7	0.974	Contact Map
4wevX	1	0.5406	7.9	0.975	Contact Map
1vbjA	1	0.4982	7.4	0.975	Contact Map
4gacA	1	0.5618	5.5	0.977	Contact Map
2o3fA	1	0.0883	5.5	0.977	Contact Map
4hbkA	1	0.5194	5.3	0.977	Contact Map
3o0kA	1	0.4452	5.3	0.977	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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