DUF3427 - PFAM28P - GREMLIN Contacts

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DUF3427 - Domain of unknown function (DUF3427)

PFAM:	PF11907	Sequences: FLSKELLNGKRPHELLILKLLLENGSISIEELKKELKKKYGYEVSEETIESALNVLNLEFFTESEKKKYGDCPLIEYDQKEGGDYSLSESFKELLKNPEFKEELLDLIEYGLERYEKYYSEELYGDTPFKLYQKYSRKDVCRLLNWEKNEVSSNIGGYKYDKDTTCPIFVTYHKEEDISESTKYEDYFISPSLFHWQSKSNRTLDSPEVQRIINHKENGIRIHLFVRKNKDDGEGKDFYYLGEVDPVSHSAEETTMPNTNGKKPVEITWKLETPVPEDLYDYLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	284 (279)
Sequences:	1799 (1507)
Seq/√Len:	90.2
META:	0.633

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
190_S	193_L	4.900	1.00
12_P	112_L	4.349	1.00
15_L	111_G	4.075	1.00
245_D	272_E	3.987	1.00
179_S	182_T	3.720	1.00
221_R	243_E	3.472	1.00
223_H	240_Y	3.391	1.00
243_E	272_E	3.318	1.00
2_L	104_L	3.217	1.00
153_S	156_G	3.083	1.00
170_V	244_V	2.886	1.00
187_Y	195_H	2.799	1.00
19_K	112_L	2.782	1.00
256_M	264_P	2.734	1.00
210_Q	214_N	2.693	1.00
214_N	217_E	2.607	1.00
199_K	208_E	2.519	1.00
224_L	244_V	2.463	1.00
170_V	194_F	2.328	1.00
101_K	105_L	2.320	1.00
17_I	32_L	2.251	1.00
33_K	46_E	2.169	1.00
149_N	152_S	2.114	1.00
197_Q	266_E	2.072	1.00
45_S	48_T	2.004	1.00
88_S	91_F	1.986	1.00
216_K	245_D	1.947	1.00
194_F	224_L	1.932	1.00
2_L	6_L	1.890	1.00
17_I	52_A	1.835	1.00
195_H	266_E	1.833	1.00
244_V	269_W	1.829	1.00
226_V	241_L	1.814	1.00
188_F	275_V	1.814	1.00
246_P	249_H	1.790	1.00
178_I	182_T	1.775	1.00
200_S	256_M	1.763	1.00
19_K	109_E	1.760	1.00
213_I	251_A	1.748	1.00
15_L	112_L	1.741	1.00
93_E	96_K	1.731	1.00
54_N	59_E	1.694	1.00
192_S	270_K	1.687	1.00
160_Y	220_I	1.684	1.00
247_V	270_K	1.675	1.00
141_C	155_I	1.664	1.00
180_E	183_K	1.645	1.00
198_S	209_V	1.616	1.00
202_R	209_V	1.604	1.00
178_I	183_K	1.601	1.00
248_S	268_T	1.597	1.00
150_E	159_K	1.593	1.00
202_R	208_E	1.580	1.00
144_L	167_P	1.559	1.00
224_L	271_L	1.558	1.00
20_L	35_E	1.555	1.00
192_S	274_P	1.536	1.00
178_I	181_S	1.525	1.00
209_V	265_V	1.523	1.00
156_G	199_K	1.500	1.00
70_G	73_P	1.480	1.00
158_Y	199_K	1.479	1.00
134_K	239_Y	1.476	1.00
152_S	156_G	1.460	0.99
203_T	263_K	1.454	0.99
161_D	164_T	1.453	0.99
19_K	23_E	1.452	0.99
20_L	24_N	1.446	0.99
32_L	52_A	1.443	0.99
241_L	275_V	1.429	0.99
198_S	202_R	1.401	0.99
276_P	279_L	1.393	0.99
182_T	200_S	1.353	0.99
6_L	55_V	1.312	0.99
5_E	138_K	1.306	0.99
22_L	105_L	1.291	0.99
19_K	105_L	1.289	0.99
193_L	268_T	1.281	0.99
31_E	34_K	1.277	0.99
130_K	133_Q	1.263	0.99
227_R	235_G	1.252	0.98
7_L	15_L	1.243	0.98
72_C	76_E	1.241	0.98
212_I	222_I	1.241	0.98
202_R	206_S	1.230	0.98
39_K	116_E	1.223	0.98
166_C	212_I	1.222	0.98
256_M	259_T	1.210	0.98
205_D	253_E	1.201	0.98
214_N	218_N	1.201	0.98
211_R	218_N	1.187	0.98
255_T	258_N	1.187	0.98
229_N	238_F	1.182	0.98
174_K	186_D	1.179	0.98
73_P	76_E	1.163	0.97
185_E	197_Q	1.150	0.97
246_P	251_A	1.150	0.97
215_H	246_P	1.146	0.97
48_T	52_A	1.144	0.97
196_W	212_I	1.138	0.97
76_E	86_S	1.138	0.97
168_I	222_I	1.133	0.97
91_F	94_L	1.127	0.97
81_E	86_S	1.121	0.97
204_L	265_V	1.119	0.97
166_C	222_I	1.119	0.97
6_L	15_L	1.118	0.97
241_L	244_V	1.117	0.97
72_C	75_I	1.113	0.97
140_V	169_F	1.106	0.97
118_Y	133_Q	1.097	0.96
141_C	150_E	1.095	0.96
213_I	267_I	1.094	0.96
87_L	92_K	1.092	0.96
223_H	243_E	1.085	0.96
51_S	56_L	1.082	0.96
49_I	52_A	1.076	0.96
166_C	220_I	1.075	0.96
95_L	105_L	1.064	0.96
46_E	50_E	1.058	0.96
193_L	270_K	1.056	0.95
36_L	42_Y	1.033	0.95
160_Y	166_C	1.029	0.95
26_S	84_D	1.027	0.95
141_C	172_Y	1.026	0.95
180_E	259_T	1.019	0.95
89_E	93_E	1.016	0.94
168_I	244_V	1.015	0.94
70_G	76_E	1.013	0.94
181_S	200_S	1.011	0.94
137_R	171_T	1.010	0.94
108_I	112_L	1.008	0.94
210_Q	213_I	1.002	0.94
245_D	270_K	1.000	0.94
87_L	91_F	0.998	0.94
167_P	172_Y	0.995	0.94
141_C	146_W	0.983	0.93
204_L	253_E	0.980	0.93
150_E	153_S	0.980	0.93
201_N	263_K	0.977	0.93
44_V	52_A	0.968	0.93
205_D	210_Q	0.964	0.93
207_P	210_Q	0.962	0.93
147_E	163_D	0.960	0.93
13_H	36_L	0.958	0.92
19_K	39_K	0.958	0.92
114_R	118_Y	0.955	0.92
20_L	23_E	0.947	0.92
91_F	104_L	0.945	0.92
171_T	232_D	0.943	0.92
20_L	27_I	0.942	0.92
7_L	107_L	0.939	0.92
198_S	208_E	0.938	0.92
233_G	237_D	0.935	0.92
44_V	49_I	0.929	0.91
211_R	220_I	0.922	0.91
244_V	271_L	0.920	0.91
88_S	94_L	0.916	0.91
212_I	269_W	0.915	0.91
16_L	19_K	0.912	0.91
13_H	48_T	0.912	0.91
129_F	143_L	0.912	0.91
258_N	262_K	0.909	0.90
255_T	263_K	0.909	0.90
209_V	267_I	0.905	0.90
215_H	219_G	0.901	0.90
37_K	43_E	0.892	0.90
11_R	14_E	0.891	0.89
154_N	199_K	0.885	0.89
2_L	7_L	0.884	0.89
52_A	56_L	0.879	0.89
119_Y	130_K	0.877	0.89
195_H	268_T	0.877	0.89
114_R	224_L	0.876	0.89
35_E	39_K	0.874	0.89
253_E	256_M	0.871	0.88
60_F	141_C	0.868	0.88
158_Y	167_P	0.865	0.88
30_E	33_K	0.864	0.88
105_L	109_E	0.862	0.88
52_A	61_F	0.858	0.88
48_T	51_S	0.857	0.88
55_V	60_F	0.854	0.87
209_V	213_I	0.852	0.87
7_L	110_Y	0.850	0.87
106_D	109_E	0.850	0.87
199_K	202_R	0.848	0.87
136_S	233_G	0.847	0.87
137_R	229_N	0.847	0.87
141_C	154_N	0.844	0.87
63_E	68_K	0.841	0.87
132_Y	279_L	0.839	0.86
188_F	194_F	0.836	0.86
159_K	199_K	0.836	0.86
34_K	37_K	0.835	0.86
206_S	210_Q	0.835	0.86
2_L	107_L	0.833	0.86
277_E	281_D	0.832	0.86
196_W	199_K	0.827	0.86
151_V	154_N	0.825	0.86
203_T	207_P	0.822	0.85
53_L	85_Y	0.815	0.85
34_K	38_K	0.813	0.85
21_L	87_L	0.812	0.85
24_N	31_E	0.811	0.85
194_F	244_V	0.810	0.84
28_S	84_D	0.807	0.84
17_I	20_L	0.805	0.84
238_F	241_L	0.804	0.84
222_I	269_W	0.803	0.84
258_N	261_G	0.802	0.84
22_L	108_I	0.801	0.84
115_Y	119_Y	0.798	0.84
253_E	263_K	0.798	0.84
141_C	156_G	0.796	0.83
29_I	85_Y	0.795	0.83
15_L	108_I	0.792	0.83
71_D	76_E	0.790	0.83
150_E	154_N	0.789	0.83
280_Y	283_L	0.785	0.83
147_E	162_K	0.783	0.82
226_V	275_V	0.782	0.82
22_L	25_G	0.782	0.82
222_I	244_V	0.781	0.82
189_I	195_H	0.781	0.82
29_I	33_K	0.779	0.82
129_F	244_V	0.777	0.82
62_T	74_L	0.771	0.81
71_D	74_L	0.770	0.81
171_T	199_K	0.769	0.81
81_E	84_D	0.765	0.81
27_I	32_L	0.764	0.81
254_T	266_E	0.763	0.81
171_T	227_R	0.762	0.81
30_E	34_K	0.759	0.80
169_F	238_F	0.759	0.80
171_T	230_K	0.757	0.80
9_G	15_L	0.756	0.80
154_N	159_K	0.752	0.80
146_W	159_K	0.750	0.80
110_Y	114_R	0.746	0.79
115_Y	118_Y	0.737	0.78
209_V	251_A	0.737	0.78
227_R	232_D	0.730	0.78
122_E	125_G	0.729	0.78
173_H	231_D	0.729	0.78
57_N	61_F	0.726	0.77
12_P	15_L	0.724	0.77
188_F	224_L	0.722	0.77
181_S	198_S	0.719	0.77
186_D	197_Q	0.715	0.76
99_E	103_E	0.714	0.76
113_E	116_E	0.706	0.75
35_E	38_K	0.705	0.75
153_S	159_K	0.705	0.75
137_R	141_C	0.700	0.75
142_R	158_Y	0.700	0.75
207_P	211_R	0.700	0.75
173_H	212_I	0.699	0.75
25_G	34_K	0.694	0.74
71_D	75_I	0.693	0.74
166_C	211_R	0.693	0.74
9_G	172_Y	0.692	0.74
64_S	68_K	0.691	0.74
155_I	158_Y	0.690	0.74
178_I	238_F	0.689	0.74
179_S	183_K	0.682	0.73
141_C	153_S	0.676	0.72
27_I	31_E	0.671	0.72
182_T	186_D	0.669	0.71
153_S	199_K	0.669	0.71
91_F	131_L	0.668	0.71
46_E	56_L	0.663	0.71
45_S	51_S	0.659	0.70
273_T	276_P	0.657	0.70
156_G	202_R	0.656	0.70
239_Y	279_L	0.655	0.70
99_E	102_E	0.655	0.70
175_E	178_I	0.654	0.70
191_P	277_E	0.650	0.69
241_L	271_L	0.650	0.69
28_S	31_E	0.649	0.69
37_K	47_E	0.646	0.69
13_H	115_Y	0.645	0.69
30_E	38_K	0.641	0.68
203_T	221_R	0.640	0.68
145_N	149_N	0.633	0.67
63_E	66_K	0.630	0.67
137_R	227_R	0.629	0.67
215_H	218_N	0.628	0.67
47_E	52_A	0.625	0.66
146_W	161_D	0.625	0.66
57_N	75_I	0.624	0.66
81_E	92_K	0.624	0.66
252_E	257_P	0.622	0.66
33_K	89_E	0.622	0.66
198_S	212_I	0.620	0.66
28_S	33_K	0.616	0.65
254_T	258_N	0.615	0.65
61_F	70_G	0.615	0.65
67_K	70_G	0.614	0.65
29_I	34_K	0.613	0.65
98_P	102_E	0.612	0.65
194_F	226_V	0.607	0.64
137_R	235_G	0.607	0.64
47_E	50_E	0.606	0.64
189_I	193_L	0.606	0.64
170_V	196_W	0.604	0.64
194_F	197_Q	0.604	0.64
46_E	49_I	0.600	0.63
139_D	142_R	0.600	0.63
34_K	43_E	0.598	0.63
67_K	74_L	0.598	0.63
252_E	266_E	0.597	0.63
146_W	208_E	0.596	0.63
234_E	282_Y	0.596	0.63
51_S	55_V	0.596	0.63
16_L	39_K	0.595	0.62
30_E	83_G	0.591	0.62
76_E	89_E	0.590	0.62
20_L	39_K	0.589	0.62
186_D	189_I	0.588	0.62
178_I	185_E	0.584	0.61
70_G	74_L	0.584	0.61
37_K	42_Y	0.583	0.61
154_N	186_D	0.583	0.61
156_G	161_D	0.582	0.61
156_G	186_D	0.582	0.61
128_P	155_I	0.582	0.61
66_K	74_L	0.581	0.61
35_E	89_E	0.580	0.61
255_T	260_N	0.580	0.61
165_T	221_R	0.578	0.60
62_T	66_K	0.576	0.60
146_W	167_P	0.574	0.60
254_T	257_P	0.573	0.60
28_S	35_E	0.572	0.59
26_S	96_K	0.572	0.59
11_R	51_S	0.572	0.59
254_T	259_T	0.571	0.59
146_W	165_T	0.570	0.59
20_L	25_G	0.570	0.59
16_L	35_E	0.567	0.59
57_N	60_F	0.566	0.59
158_Y	208_E	0.564	0.58
74_L	77_Y	0.563	0.58
188_F	271_L	0.563	0.58
26_S	35_E	0.562	0.58
151_V	156_G	0.560	0.58
150_E	155_I	0.559	0.58
32_L	36_L	0.559	0.58
21_L	26_S	0.558	0.58
208_E	265_V	0.558	0.58
65_E	68_K	0.557	0.57
136_S	236_K	0.557	0.57
230_K	235_G	0.556	0.57
7_L	269_W	0.556	0.57
24_N	27_I	0.556	0.57
55_V	58_L	0.556	0.57
132_Y	241_L	0.553	0.57
197_Q	267_I	0.552	0.57
134_K	237_D	0.550	0.57
152_S	199_K	0.549	0.56
56_L	60_F	0.548	0.56
197_Q	264_P	0.546	0.56
137_R	160_Y	0.545	0.56
59_E	66_K	0.544	0.56
161_D	165_T	0.541	0.55
29_I	50_E	0.539	0.55
195_H	281_D	0.538	0.55
172_Y	279_L	0.537	0.55
141_C	199_K	0.537	0.55
63_E	67_K	0.536	0.55
220_I	241_L	0.535	0.54
227_R	264_P	0.535	0.54
180_E	258_N	0.535	0.54
83_G	273_T	0.535	0.54
160_Y	208_E	0.534	0.54
208_E	212_I	0.533	0.54
132_Y	271_L	0.533	0.54
92_K	122_E	0.532	0.54
66_K	71_D	0.531	0.54
146_W	158_Y	0.531	0.54
119_Y	127_T	0.529	0.54
137_R	154_N	0.528	0.54
247_V	283_L	0.528	0.54
12_P	26_S	0.527	0.53
252_E	255_T	0.527	0.53
83_G	86_S	0.525	0.53
191_P	280_Y	0.521	0.53
252_E	258_N	0.521	0.53
150_E	161_D	0.520	0.52
21_L	28_S	0.519	0.52
187_Y	266_E	0.519	0.52
26_S	205_D	0.517	0.52
50_E	54_N	0.516	0.52
197_Q	269_W	0.514	0.52
61_F	65_E	0.514	0.52
140_V	144_L	0.513	0.51
118_Y	130_K	0.511	0.51
141_C	167_P	0.510	0.51
15_L	107_L	0.509	0.51
229_N	237_D	0.509	0.51
175_E	180_E	0.507	0.51
16_L	26_S	0.507	0.51
155_I	199_K	0.507	0.51
149_N	153_S	0.507	0.51
95_L	134_K	0.506	0.51
143_L	146_W	0.505	0.50
56_L	61_F	0.505	0.50
10_K	237_D	0.504	0.50
23_E	105_L	0.504	0.50
51_S	58_L	0.503	0.50
24_N	30_E	0.503	0.50
160_Y	246_P	0.502	0.50
16_L	112_L	0.502	0.50
151_V	155_I	0.500	0.50
197_Q	254_T	0.500	0.50

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
1bjaA	1	0.3063	21.5	0.962	Contact Map
2mh2A	1	0.2218	16.8	0.964	Contact Map
2k4jA	1	0.2817	16.8	0.964	Contact Map
1gxqA	1	0.2852	15.3	0.964	Contact Map
3rjpA	1	0.2817	14.2	0.965	Contact Map
1opcA	1	0.2852	13.7	0.965	Contact Map
2m87A	1	0.2817	11.6	0.966	Contact Map
1hsjA	2	0.3275	11.2	0.966	Contact Map
4nhjA	2	0.2852	10.5	0.967	Contact Map
2hwvA	1	0.2887	9.9	0.967	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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