DUF4420 - PFAM28P - GREMLIN Contacts

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DUF4420 - Putative PD-(D/E)XK family member, (DUF4420)

PFAM:	PF14390	Sequences: IEEPWDELEAPSSGGGGLRARRVDPDHPLDLFAGVDSPGNRRLLLVSFSDPSLPPSLKPSLKGIELSRRSEEGGRYLVLTLLDPELRDIFAALCEDLIEALEDAPDEAEALRALLNRLERWQELFRKGRSGGLSEEEQRGLFGELLFLRRLLDPGLGPEEAVEAWTGPEGARQDFEFGDGAIEVKTTSSSSGRRVHISSLEQLDPPGGGPLFLASVRLEESGNGESLPDLVDEIRELLSSDPEALELFEEKLAAAGYLDLHEDLYDERRFTLREERLYEVDDDFPRITRSDLPPGVSDVRYSIDLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	306 (300)
Sequences:	2920 (2559)
Seq/√Len:	147.8
META:	0.791

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
149_R	233_E	6.378	1.00
143_G	186_T	6.228	1.00
235_R	249_E	4.990	1.00
147_F	182_I	3.940	1.00
59_P	63_G	3.637	1.00
169_E	251_K	3.625	1.00
298_D	302_S	3.181	1.00
149_R	237_L	3.050	1.00
96_D	117_R	2.910	1.00
247_L	251_K	2.885	1.00
232_D	262_E	2.650	1.00
238_L	248_F	2.576	1.00
148_L	161_A	2.560	1.00
164_A	177_F	2.515	1.00
229_D	269_R	2.436	1.00
195_V	215_S	2.435	1.00
234_I	238_L	2.425	1.00
225_E	233_E	2.405	1.00
147_F	184_V	2.374	1.00
153_D	237_L	2.369	1.00
145_L	234_I	2.322	1.00
61_L	64_I	2.216	1.00
36_D	40_N	2.213	1.00
196_H	300_R	2.203	1.00
123_E	126_R	2.195	1.00
135_E	270_F	2.183	1.00
226_S	269_R	2.129	1.00
200_L	299_V	2.091	1.00
166_T	171_A	2.036	1.00
142_F	230_L	1.997	1.00
200_L	287_I	1.986	1.00
133_L	265_Y	1.984	1.00
201_E	289_R	1.980	1.00
86_L	124_L	1.931	1.00
31_L	98_I	1.911	1.00
154_P	157_G	1.909	1.00
295_G	303_I	1.908	1.00
228_P	257_Y	1.908	1.00
22_R	30_D	1.901	1.00
139_R	186_T	1.897	1.00
196_H	302_S	1.825	1.00
214_A	277_L	1.814	1.00
235_R	259_D	1.801	1.00
278_Y	284_F	1.787	1.00
173_Q	181_A	1.787	1.00
231_V	257_Y	1.757	1.00
293_P	296_V	1.746	1.00
96_D	121_W	1.741	1.00
257_Y	265_Y	1.722	1.00
186_T	218_L	1.707	1.00
200_L	292_L	1.698	1.00
142_F	225_E	1.680	1.00
147_F	216_V	1.670	1.00
146_L	216_V	1.646	1.00
20_A	34_G	1.642	1.00
205_P	286_R	1.607	1.00
34_G	42_R	1.607	1.00
297_S	304_D	1.595	1.00
149_R	225_E	1.573	1.00
235_R	245_L	1.541	1.00
159_E	241_D	1.518	1.00
173_Q	211_L	1.499	1.00
228_P	266_D	1.497	1.00
133_L	137_E	1.482	1.00
22_R	32_F	1.473	1.00
29_L	110_A	1.470	1.00
227_L	265_Y	1.445	1.00
181_A	209_G	1.442	1.00
153_D	157_G	1.442	1.00
292_L	295_G	1.431	1.00
163_E	247_L	1.421	1.00
139_R	143_G	1.400	1.00
61_L	67_S	1.399	1.00
280_V	284_F	1.396	1.00
134_S	137_E	1.395	1.00
33_A	94_C	1.395	1.00
99_E	102_E	1.381	1.00
31_L	101_L	1.380	1.00
139_R	218_L	1.379	1.00
146_L	230_L	1.378	1.00
64_I	67_S	1.375	1.00
184_V	214_A	1.366	1.00
173_Q	176_E	1.365	1.00
149_R	234_I	1.361	1.00
138_Q	268_R	1.360	1.00
4_P	33_A	1.353	1.00
142_F	146_L	1.352	1.00
171_A	176_E	1.347	1.00
150_R	275_E	1.347	1.00
195_V	213_L	1.342	1.00
187_T	215_S	1.337	1.00
146_L	149_R	1.328	1.00
288_T	291_D	1.289	1.00
292_L	299_V	1.283	1.00
146_L	272_L	1.283	1.00
245_L	249_E	1.280	1.00
59_P	64_I	1.252	1.00
63_G	66_L	1.243	1.00
119_E	122_Q	1.241	1.00
83_D	86_L	1.234	1.00
135_E	139_R	1.219	1.00
172_R	201_E	1.218	1.00
214_A	275_E	1.218	1.00
241_D	244_A	1.208	1.00
162_V	244_A	1.200	1.00
74_G	77_L	1.193	1.00
259_D	262_E	1.190	1.00
166_T	176_E	1.189	1.00
41_R	87_R	1.188	1.00
147_F	214_A	1.188	1.00
100_A	117_R	1.180	1.00
159_E	244_A	1.173	1.00
63_G	67_S	1.166	1.00
149_R	230_L	1.164	1.00
231_V	252_L	1.160	1.00
224_G	229_D	1.148	1.00
151_L	154_P	1.137	0.99
234_I	248_F	1.136	0.99
60_S	63_G	1.135	0.99
95_E	99_E	1.130	0.99
142_F	218_L	1.129	0.99
176_E	181_A	1.126	0.99
36_D	39_G	1.120	0.99
257_Y	262_E	1.099	0.99
117_R	120_R	1.093	0.99
138_Q	265_Y	1.088	0.99
229_D	232_D	1.085	0.99
252_L	257_Y	1.079	0.99
206_P	209_G	1.072	0.99
204_D	289_R	1.069	0.99
27_H	101_L	1.064	0.99
138_Q	227_L	1.063	0.99
204_D	290_S	1.061	0.99
166_T	251_K	1.052	0.99
194_R	302_S	1.052	0.99
75_R	78_V	1.028	0.99
141_L	175_F	1.015	0.99
73_G	76_Y	1.008	0.99
115_L	119_E	1.004	0.99
157_G	160_E	0.999	0.99
216_V	275_E	0.999	0.99
287_I	291_D	0.997	0.99
133_L	227_L	0.995	0.99
4_P	21_R	0.976	0.98
91_A	95_E	0.972	0.98
187_T	217_R	0.965	0.98
142_F	272_L	0.963	0.98
194_R	297_S	0.961	0.98
36_D	80_T	0.953	0.98
158_P	238_L	0.945	0.98
148_L	175_F	0.937	0.98
42_R	78_V	0.935	0.98
106_D	109_E	0.930	0.98
146_L	225_E	0.929	0.98
203_L	211_L	0.927	0.98
6_D	10_A	0.922	0.98
193_R	215_S	0.915	0.98
20_A	32_F	0.912	0.98
152_L	161_A	0.910	0.98
36_D	42_R	0.907	0.98
143_G	216_V	0.902	0.97
93_L	125_F	0.902	0.97
35_V	39_G	0.900	0.97
71_E	77_L	0.900	0.97
261_H	265_Y	0.895	0.97
287_I	293_P	0.891	0.97
180_G	212_F	0.886	0.97
137_E	255_A	0.885	0.97
141_L	257_Y	0.880	0.97
169_E	254_A	0.873	0.97
33_A	42_R	0.868	0.97
91_A	94_C	0.867	0.97
250_E	254_A	0.866	0.97
153_D	156_L	0.865	0.97
184_V	216_V	0.863	0.97
63_G	76_Y	0.854	0.96
187_T	190_S	0.854	0.96
172_R	199_S	0.853	0.96
73_G	77_L	0.851	0.96
286_R	295_G	0.847	0.96
166_T	169_E	0.845	0.96
97_L	118_L	0.844	0.96
198_S	300_R	0.843	0.96
59_P	62_K	0.839	0.96
135_E	268_R	0.835	0.96
139_R	187_T	0.833	0.96
61_L	66_L	0.832	0.96
220_E	224_G	0.828	0.96
200_L	301_Y	0.826	0.96
284_F	303_I	0.826	0.96
204_D	288_T	0.825	0.96
34_G	43_L	0.824	0.96
167_G	255_A	0.824	0.96
90_F	121_W	0.820	0.95
4_P	7_E	0.819	0.95
11_P	19_R	0.816	0.95
24_D	27_H	0.812	0.95
146_L	150_R	0.809	0.95
181_A	211_L	0.808	0.95
287_I	299_V	0.802	0.95
248_F	251_K	0.798	0.95
133_L	257_Y	0.796	0.95
236_E	239_S	0.794	0.95
140_G	175_F	0.793	0.95
43_L	46_V	0.791	0.95
92_A	96_D	0.791	0.95
187_T	192_G	0.791	0.95
225_E	230_L	0.786	0.94
230_L	233_E	0.785	0.94
81_L	87_R	0.780	0.94
90_F	94_C	0.776	0.94
139_R	270_F	0.776	0.94
19_R	22_R	0.774	0.94
147_F	151_L	0.773	0.94
162_V	238_L	0.770	0.94
297_S	302_S	0.769	0.94
42_R	47_S	0.769	0.94
139_R	200_L	0.763	0.93
251_K	255_A	0.761	0.93
213_L	218_L	0.761	0.93
117_R	125_F	0.756	0.93
200_L	297_S	0.755	0.93
195_V	305_L	0.755	0.93
18_L	22_R	0.755	0.93
160_E	163_E	0.754	0.93
228_P	231_V	0.753	0.93
221_S	225_E	0.751	0.93
60_S	64_I	0.747	0.93
61_L	65_E	0.747	0.93
227_L	231_V	0.746	0.93
132_G	265_Y	0.741	0.92
136_E	139_R	0.741	0.92
252_L	265_Y	0.740	0.92
281_D	286_R	0.739	0.92
24_D	102_E	0.737	0.92
153_D	158_P	0.735	0.92
150_R	154_P	0.732	0.92
261_H	266_D	0.729	0.92
17_G	20_A	0.728	0.92
232_D	236_E	0.727	0.92
177_F	180_G	0.727	0.92
71_E	75_R	0.725	0.92
152_L	156_L	0.725	0.92
88_D	117_R	0.725	0.92
282_D	286_R	0.723	0.91
63_G	69_R	0.723	0.91
211_L	280_V	0.723	0.91
20_A	24_D	0.723	0.91
192_G	304_D	0.723	0.91
152_L	157_G	0.720	0.91
232_D	235_R	0.717	0.91
68_R	77_L	0.717	0.91
43_L	48_F	0.713	0.91
100_A	120_R	0.709	0.91
217_R	274_E	0.709	0.91
168_P	255_A	0.708	0.91
141_L	227_L	0.707	0.91
143_G	187_T	0.707	0.91
210_P	279_E	0.707	0.91
255_A	261_H	0.707	0.91
142_F	186_T	0.707	0.91
64_I	68_R	0.704	0.90
59_P	66_L	0.703	0.90
197_I	213_L	0.702	0.90
20_A	25_P	0.701	0.90
167_G	170_G	0.699	0.90
242_P	245_L	0.697	0.90
138_Q	228_P	0.696	0.90
138_Q	261_H	0.692	0.90
71_E	76_Y	0.691	0.90
133_L	256_G	0.689	0.89
7_E	12_S	0.687	0.89
198_S	213_L	0.686	0.89
121_W	256_G	0.685	0.89
172_R	206_P	0.685	0.89
233_E	236_E	0.683	0.89
64_I	70_S	0.683	0.89
79_L	118_L	0.682	0.89
182_I	212_F	0.678	0.89
9_E	12_S	0.673	0.88
162_V	247_L	0.670	0.88
142_F	270_F	0.664	0.88
238_L	243_E	0.662	0.87
21_R	40_N	0.661	0.87
145_L	231_V	0.661	0.87
132_G	264_L	0.660	0.87
7_E	10_A	0.659	0.87
41_R	91_A	0.658	0.87
223_N	271_T	0.655	0.87
201_E	298_D	0.653	0.87
213_L	303_I	0.653	0.87
123_E	246_E	0.649	0.86
36_D	41_R	0.649	0.86
64_I	78_V	0.648	0.86
226_S	266_D	0.648	0.86
24_D	28_P	0.647	0.86
170_G	255_A	0.646	0.86
67_S	73_G	0.646	0.86
31_L	43_L	0.644	0.86
89_I	120_R	0.644	0.86
262_E	265_Y	0.643	0.86
20_A	27_H	0.642	0.86
79_L	180_G	0.641	0.86
7_E	22_R	0.636	0.85
16_G	24_D	0.636	0.85
228_P	265_Y	0.635	0.85
180_G	210_P	0.635	0.85
4_P	8_L	0.634	0.85
65_E	68_R	0.633	0.85
268_R	305_L	0.629	0.85
36_D	43_L	0.628	0.85
168_P	251_K	0.627	0.84
122_Q	126_R	0.627	0.84
117_R	121_W	0.627	0.84
227_L	257_Y	0.625	0.84
89_I	138_Q	0.623	0.84
186_T	216_V	0.622	0.84
101_L	113_A	0.622	0.84
42_R	48_F	0.619	0.84
238_L	244_A	0.617	0.84
122_Q	127_K	0.617	0.84
63_G	68_R	0.617	0.84
17_G	26_D	0.616	0.83
228_P	259_D	0.616	0.83
156_L	161_A	0.614	0.83
138_Q	270_F	0.614	0.83
116_N	283_D	0.613	0.83
6_D	11_P	0.612	0.83
189_S	192_G	0.612	0.83
167_G	197_I	0.612	0.83
38_P	52_S	0.612	0.83
41_R	44_L	0.611	0.83
23_V	27_H	0.611	0.83
5_W	173_Q	0.609	0.83
94_C	124_L	0.609	0.83
183_E	301_Y	0.605	0.82
215_S	278_Y	0.605	0.82
86_L	89_I	0.604	0.82
117_R	253_A	0.604	0.82
11_P	35_V	0.602	0.82
124_L	128_G	0.601	0.82
197_I	284_F	0.600	0.82
148_L	151_L	0.598	0.82
125_F	195_V	0.596	0.81
19_R	24_D	0.591	0.81
157_G	161_A	0.590	0.81
6_D	9_E	0.588	0.81
97_L	252_L	0.587	0.80
9_E	87_R	0.587	0.80
39_G	43_L	0.587	0.80
182_I	214_A	0.586	0.80
133_L	252_L	0.586	0.80
42_R	46_V	0.585	0.80
138_Q	142_F	0.584	0.80
123_E	249_E	0.583	0.80
107_E	282_D	0.583	0.80
81_L	93_L	0.583	0.80
87_R	91_A	0.582	0.80
283_D	291_D	0.582	0.80
7_E	13_S	0.581	0.80
43_L	94_C	0.580	0.80
79_L	93_L	0.579	0.80
30_D	45_L	0.576	0.79
154_P	207_G	0.576	0.79
172_R	191_S	0.574	0.79
93_L	124_L	0.573	0.79
133_L	138_Q	0.572	0.79
192_G	201_E	0.572	0.79
63_G	77_L	0.572	0.79
147_F	277_L	0.570	0.78
60_S	67_S	0.570	0.78
146_L	218_L	0.570	0.78
186_T	235_R	0.570	0.78
203_L	284_F	0.570	0.78
270_F	273_R	0.568	0.78
172_R	181_A	0.567	0.78
71_E	74_G	0.567	0.78
194_R	298_D	0.566	0.78
4_P	125_F	0.564	0.78
60_S	66_L	0.563	0.78
189_S	201_E	0.562	0.77
22_R	26_D	0.562	0.77
163_E	271_T	0.562	0.77
17_G	38_P	0.561	0.77
74_G	78_V	0.560	0.77
35_V	41_R	0.556	0.77
195_V	303_I	0.555	0.77
245_L	248_F	0.555	0.77
233_E	237_L	0.555	0.77
89_I	117_R	0.555	0.77
139_R	215_S	0.553	0.76
6_D	12_S	0.553	0.76
153_D	161_A	0.552	0.76
212_F	277_L	0.552	0.76
26_D	29_L	0.552	0.76
295_G	304_D	0.551	0.76
48_F	107_E	0.551	0.76
150_R	153_D	0.550	0.76
213_L	278_Y	0.548	0.76
38_P	48_F	0.547	0.76
81_L	125_F	0.547	0.76
47_S	111_L	0.546	0.75
239_S	242_P	0.546	0.75
197_I	203_L	0.545	0.75
124_L	191_S	0.543	0.75
78_V	81_L	0.543	0.75
7_E	21_R	0.541	0.75
166_T	252_L	0.537	0.74
62_K	153_D	0.537	0.74
163_E	300_R	0.536	0.74
159_E	247_L	0.535	0.74
268_R	273_R	0.535	0.74
121_W	265_Y	0.530	0.73
252_L	266_D	0.529	0.73
193_R	217_R	0.528	0.73
44_L	91_A	0.527	0.73
96_D	204_D	0.526	0.73
70_S	73_G	0.525	0.73
281_D	303_I	0.523	0.72
4_P	10_A	0.523	0.72
195_V	302_S	0.521	0.72
151_L	277_L	0.521	0.72
240_S	252_L	0.520	0.72
23_V	188_S	0.520	0.72
16_G	19_R	0.519	0.72
153_D	234_I	0.519	0.72
19_R	25_P	0.519	0.72
215_S	218_L	0.517	0.71
157_G	162_V	0.515	0.71
161_A	175_F	0.515	0.71
220_E	293_P	0.514	0.71
19_R	27_H	0.512	0.71
5_W	8_L	0.512	0.71
33_A	43_L	0.511	0.71
12_S	16_G	0.511	0.71
10_A	16_G	0.511	0.71
123_E	250_E	0.509	0.70
67_S	76_Y	0.509	0.70
158_P	163_E	0.508	0.70
81_L	195_V	0.507	0.70
10_A	35_V	0.507	0.70
293_P	297_S	0.506	0.70
217_R	273_R	0.505	0.70
12_S	28_P	0.505	0.70
20_A	23_V	0.503	0.69
218_L	272_L	0.503	0.69
43_L	47_S	0.502	0.69
50_D	73_G	0.501	0.69
143_G	181_A	0.501	0.69
44_L	182_I	0.500	0.69

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
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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
1ob8A	1	0.3235	74.6	0.931	Contact Map
1hh1A	2	0.3137	69.9	0.933	Contact Map
2wcwA	2	0.3072	58.9	0.938	Contact Map
2eo0A	2	0.3137	47.2	0.942	Contact Map
1gefA	2	0.3137	30.1	0.948	Contact Map
3fovA	2	0.3105	21.2	0.952	Contact Map
1y0kA	1	0.4902	15.7	0.955	Contact Map
2oa5A	4	0.2614	14.2	0.955	Contact Map
2ostA	4	0.3693	7.5	0.961	Contact Map
2g30A	1	0.3072	5.7	0.963	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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