DUF4238 - PFAM28P - GREMLIN Contacts

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DUF4238 - Protein of unknown function (DUF4238)

PFAM:	PF14022	Sequences: RQHYVPQFYLKRFADDKDGKIWVYDKKTGKIFRTSPKNVAYERDFYTIEDEDEGEDDDEIEKFLSKIEGKAAPALRKLLSKGDGGEPLTEEEREALARFIALQLLRTPAFREEYKEELKELLEEYLRELERLEELLDELLDELKKILDLKEDLEELLLLLMLELAEELAPLLLDMKWTLLRNPTGSPFITSDNPVVLYNPPDPGRGGGLGPGGAEIYFPLSPRLALVLTDPEVYKEPLDKDVRKLSEEEVREINRLIVANAERFVYSSDKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	271 (258)
Sequences:	6251 (5918)
Seq/√Len:	368.5
META:	0.823

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
1_R	41_Y	5.686	1.00
9_Y	190_T	4.211	1.00
77_K	92_E	4.169	1.00
8_F	72_A	3.568	1.00
40_A	266_Y	3.282	1.00
12_R	79_L	3.089	1.00
44_D	47_T	2.817	1.00
65_S	69_G	2.674	1.00
181_R	224_L	2.563	1.00
221_S	224_L	2.413	1.00
7_Q	36_P	2.374	1.00
7_Q	37_K	2.355	1.00
191_S	257_I	2.343	1.00
225_A	253_I	2.320	1.00
7_Q	11_K	2.284	1.00
182_N	188_F	2.254	1.00
42_E	108_P	2.244	1.00
103_Q	218_F	2.144	1.00
10_L	190_T	2.065	1.00
13_F	222_P	2.011	1.00
93_R	97_A	1.976	1.00
12_R	222_P	1.955	1.00
25_D	263_R	1.949	1.00
72_A	76_R	1.941	1.00
14_A	36_P	1.924	1.00
100_I	228_L	1.918	1.00
47_T	58_D	1.915	1.00
61_E	65_S	1.913	1.00
103_Q	107_T	1.905	1.00
8_F	71_A	1.899	1.00
70_K	95_A	1.895	1.00
45_F	111_R	1.864	1.00
177_W	228_L	1.857	1.00
97_A	177_W	1.795	1.00
4_Y	108_P	1.783	1.00
245_L	249_E	1.775	1.00
15_D	33_R	1.744	1.00
34_T	39_V	1.700	1.00
38_N	41_Y	1.689	1.00
12_R	76_R	1.670	1.00
76_R	80_S	1.659	1.00
71_A	75_L	1.620	1.00
89_T	92_E	1.604	1.00
246_S	249_E	1.572	1.00
21_I	36_P	1.561	1.00
20_K	33_R	1.560	1.00
1_R	37_K	1.527	1.00
175_M	230_D	1.521	1.00
35_S	38_N	1.520	1.00
2_Q	47_T	1.516	1.00
100_I	218_F	1.506	1.00
6_P	103_Q	1.499	1.00
2_Q	61_E	1.492	1.00
5_V	103_Q	1.492	1.00
2_Q	46_Y	1.485	1.00
23_V	32_F	1.485	1.00
182_N	250_V	1.480	1.00
222_P	268_S	1.479	1.00
21_I	266_Y	1.464	1.00
217_Y	225_A	1.439	1.00
19_G	36_P	1.435	1.00
182_N	187_P	1.434	1.00
34_T	38_N	1.431	1.00
107_T	193_N	1.403	1.00
23_V	34_T	1.395	1.00
188_F	245_L	1.372	1.00
39_V	266_Y	1.353	1.00
109_A	193_N	1.345	1.00
188_F	225_A	1.322	1.00
25_D	28_T	1.318	1.00
104_L	197_L	1.316	1.00
180_L	227_V	1.294	1.00
98_R	169_A	1.294	1.00
45_F	107_T	1.289	1.00
74_A	95_A	1.285	1.00
208_G	211_P	1.277	1.00
190_T	257_I	1.273	1.00
36_P	41_Y	1.270	1.00
79_L	224_L	1.269	1.00
141_D	144_K	1.266	1.00
211_P	214_A	1.259	1.00
217_Y	257_I	1.258	1.00
180_L	245_L	1.231	1.00
258_V	265_V	1.224	1.00
179_L	224_L	1.223	1.00
187_P	223_R	1.219	1.00
79_L	221_S	1.196	1.00
4_Y	45_F	1.191	1.00
8_F	75_L	1.182	1.00
4_Y	40_A	1.182	1.00
71_A	99_F	1.181	1.00
151_E	154_E	1.177	1.00
69_G	73_P	1.174	1.00
71_A	74_A	1.171	1.00
100_I	195_V	1.170	1.00
61_E	64_L	1.169	1.00
15_D	18_D	1.149	1.00
2_Q	44_D	1.148	1.00
8_F	99_F	1.136	1.00
187_P	268_S	1.136	1.00
177_W	226_L	1.131	1.00
47_T	57_D	1.129	1.00
45_F	108_P	1.121	1.00
255_R	259_A	1.111	1.00
182_N	186_S	1.110	1.00
70_K	73_P	1.085	1.00
11_K	36_P	1.077	1.00
182_N	223_R	1.077	1.00
180_L	225_A	1.075	1.00
147_L	150_K	1.074	1.00
9_Y	218_F	1.064	1.00
182_N	185_G	1.062	1.00
117_E	121_L	1.059	1.00
94_E	173_L	1.056	1.00
10_L	40_A	1.055	1.00
134_E	137_D	1.055	1.00
209_L	212_G	1.054	1.00
191_S	194_P	1.053	1.00
183_P	244_K	1.053	1.00
149_L	153_L	1.046	1.00
8_F	68_E	1.040	1.00
96_L	226_L	1.035	1.00
74_A	92_E	1.034	1.00
1_R	38_N	1.033	1.00
64_L	102_L	1.028	1.00
6_P	46_Y	1.021	1.00
12_R	75_L	1.005	1.00
210_G	214_A	0.993	1.00
50_D	55_E	0.992	1.00
109_A	262_E	0.984	1.00
99_F	103_Q	0.984	1.00
68_E	71_A	0.983	1.00
252_E	255_R	0.979	1.00
149_L	152_D	0.979	1.00
2_Q	45_F	0.976	1.00
121_L	125_Y	0.967	1.00
5_V	40_A	0.956	1.00
188_F	250_V	0.955	1.00
208_G	213_G	0.951	1.00
200_P	203_P	0.943	1.00
6_P	106_R	0.942	1.00
9_Y	191_S	0.941	1.00
22_W	33_R	0.938	1.00
192_D	261_A	0.936	1.00
119_K	123_E	0.936	1.00
184_T	187_P	0.935	1.00
210_G	213_G	0.931	1.00
51_E	54_G	0.924	1.00
145_K	148_D	0.922	1.00
245_L	250_V	0.912	1.00
150_K	153_L	0.908	1.00
147_L	151_E	0.907	1.00
73_P	77_K	0.905	1.00
12_R	221_S	0.902	1.00
208_G	212_G	0.897	1.00
56_D	62_K	0.897	1.00
190_T	266_Y	0.894	1.00
120_E	124_E	0.894	1.00
21_I	26_K	0.881	1.00
189_I	258_V	0.880	1.00
101_A	105_L	0.879	1.00
88_L	92_E	0.876	1.00
208_G	214_A	0.872	1.00
158_L	161_M	0.869	1.00
139_L	143_L	0.869	1.00
141_D	145_K	0.867	1.00
148_D	151_E	0.866	1.00
146_I	149_L	0.858	1.00
178_T	227_V	0.856	1.00
75_L	220_L	0.851	1.00
181_R	223_R	0.847	1.00
65_S	68_E	0.846	1.00
147_L	153_L	0.845	1.00
166_E	170_P	0.844	1.00
10_L	36_P	0.843	1.00
186_S	247_E	0.843	1.00
97_A	173_L	0.842	1.00
144_K	147_L	0.841	1.00
23_V	39_V	0.839	1.00
118_L	122_L	0.838	1.00
209_L	213_G	0.833	1.00
63_F	66_K	0.830	1.00
140_L	149_L	0.829	1.00
131_R	135_L	0.827	1.00
10_L	266_Y	0.827	1.00
126_L	130_E	0.826	1.00
48_I	59_E	0.825	1.00
93_R	177_W	0.825	1.00
58_D	62_K	0.818	1.00
107_T	110_F	0.813	1.00
181_R	244_K	0.812	1.00
176_K	231_P	0.807	1.00
185_G	247_E	0.806	1.00
9_Y	194_P	0.806	1.00
155_E	159_L	0.802	1.00
25_D	264_F	0.798	1.00
8_F	12_R	0.798	1.00
91_E	95_A	0.796	1.00
206_G	209_L	0.796	1.00
1_R	43_R	0.795	1.00
97_A	101_A	0.790	1.00
217_Y	256_L	0.785	1.00
191_S	261_A	0.783	1.00
198_Y	215_E	0.782	1.00
97_A	169_A	0.780	1.00
54_G	57_D	0.775	1.00
26_K	261_A	0.775	1.00
156_L	159_L	0.775	1.00
144_K	150_K	0.775	1.00
24_Y	29_G	0.774	1.00
44_D	58_D	0.774	1.00
117_E	123_E	0.769	1.00
118_L	121_L	0.769	1.00
97_A	172_L	0.767	1.00
47_T	56_D	0.767	1.00
67_I	70_K	0.767	1.00
120_E	123_E	0.765	1.00
215_E	256_L	0.763	1.00
46_Y	106_R	0.762	1.00
253_I	257_I	0.762	1.00
131_R	134_E	0.757	1.00
66_K	70_K	0.755	1.00
181_R	242_V	0.754	1.00
38_N	43_R	0.752	1.00
178_T	229_T	0.752	1.00
24_Y	28_T	0.751	1.00
129_L	132_L	0.748	1.00
249_E	253_I	0.746	1.00
27_K	30_K	0.745	1.00
105_L	110_F	0.745	1.00
189_I	254_N	0.739	1.00
70_K	98_R	0.739	1.00
25_D	32_F	0.738	1.00
220_L	226_L	0.737	1.00
129_L	133_E	0.733	1.00
140_L	143_L	0.732	1.00
14_A	18_D	0.731	1.00
123_E	126_L	0.730	1.00
21_I	25_D	0.730	1.00
22_W	25_D	0.727	1.00
42_E	263_R	0.726	1.00
21_I	39_V	0.723	1.00
139_L	145_K	0.722	1.00
121_L	127_R	0.720	1.00
11_K	19_G	0.719	1.00
14_A	21_I	0.715	1.00
126_L	129_L	0.713	0.99
251_R	255_R	0.711	0.99
40_A	264_F	0.709	0.99
24_Y	31_I	0.708	0.99
74_A	96_L	0.707	0.99
122_L	125_Y	0.703	0.99
183_P	250_V	0.702	0.99
196_V	257_I	0.701	0.99
27_K	263_R	0.700	0.99
116_E	119_K	0.699	0.99
207_G	213_G	0.699	0.99
25_D	30_K	0.698	0.99
98_R	102_L	0.697	0.99
73_P	76_R	0.697	0.99
133_E	137_D	0.696	0.99
172_L	228_L	0.695	0.99
140_L	144_K	0.694	0.99
142_E	145_K	0.693	0.99
9_Y	99_F	0.691	0.99
140_L	146_I	0.689	0.99
6_P	99_F	0.689	0.99
171_L	174_D	0.687	0.99
46_Y	64_L	0.687	0.99
130_E	133_E	0.686	0.99
62_K	66_K	0.684	0.99
250_V	254_N	0.679	0.99
146_I	150_K	0.679	0.99
249_E	252_E	0.677	0.99
4_Y	41_Y	0.676	0.99
15_D	19_G	0.676	0.99
20_K	35_S	0.674	0.99
209_L	214_A	0.672	0.99
117_E	120_E	0.667	0.99
67_I	95_A	0.666	0.99
119_K	122_L	0.663	0.99
207_G	210_G	0.661	0.99
201_P	205_R	0.654	0.99
205_R	208_G	0.650	0.99
48_I	51_E	0.647	0.99
189_I	267_S	0.645	0.99
146_I	151_E	0.643	0.99
183_P	186_S	0.642	0.99
148_D	152_D	0.638	0.99
122_L	126_L	0.635	0.99
172_L	216_I	0.633	0.99
78_L	96_L	0.629	0.99
22_W	26_K	0.629	0.99
5_V	190_T	0.628	0.99
145_K	149_L	0.627	0.99
149_L	154_E	0.626	0.99
37_K	41_Y	0.623	0.99
8_F	11_K	0.622	0.99
139_L	142_E	0.620	0.99
175_M	228_L	0.620	0.99
215_E	229_T	0.618	0.99
19_G	23_V	0.617	0.99
7_Q	41_Y	0.615	0.99
18_D	33_R	0.614	0.98
129_L	135_L	0.612	0.98
143_L	147_L	0.612	0.98
134_E	138_E	0.612	0.98
217_Y	253_I	0.611	0.98
22_W	267_S	0.605	0.98
123_E	127_R	0.604	0.98
247_E	251_R	0.603	0.98
141_D	152_D	0.598	0.98
144_K	148_D	0.596	0.98
195_V	216_I	0.595	0.98
184_T	247_E	0.594	0.98
69_G	72_A	0.594	0.98
9_Y	12_R	0.591	0.98
169_A	173_L	0.591	0.98
50_D	54_G	0.589	0.98
170_P	174_D	0.586	0.98
97_A	228_L	0.586	0.98
216_I	228_L	0.584	0.98
71_A	95_A	0.582	0.98
108_P	111_R	0.581	0.98
94_E	169_A	0.577	0.98
21_I	24_Y	0.577	0.98
167_E	170_P	0.576	0.98
182_N	245_L	0.575	0.98
40_A	47_T	0.574	0.98
2_Q	58_D	0.573	0.98
117_E	124_E	0.572	0.98
4_Y	107_T	0.571	0.98
99_F	218_F	0.570	0.98
28_T	32_F	0.569	0.98
143_L	146_I	0.568	0.98
105_L	165_A	0.567	0.97
225_A	257_I	0.567	0.97
126_L	135_L	0.566	0.97
188_F	253_I	0.565	0.97
183_P	223_R	0.565	0.97
28_T	31_I	0.564	0.97
14_A	19_G	0.563	0.97
157_L	161_M	0.557	0.97
9_Y	75_L	0.551	0.97
67_I	102_L	0.551	0.97
139_L	153_L	0.549	0.97
75_L	79_L	0.548	0.97
138_E	142_E	0.547	0.97
40_A	190_T	0.547	0.97
15_D	36_P	0.545	0.97
143_L	150_K	0.544	0.97
20_K	34_T	0.543	0.97
248_E	252_E	0.542	0.97
146_I	153_L	0.538	0.97
170_P	173_L	0.536	0.96
261_A	265_V	0.535	0.96
198_Y	252_E	0.533	0.96
119_K	125_Y	0.533	0.96
136_L	139_L	0.531	0.96
108_P	263_R	0.530	0.96
162_L	165_A	0.528	0.96
159_L	163_E	0.528	0.96
6_P	72_A	0.528	0.96
133_E	136_L	0.526	0.96
124_E	128_E	0.526	0.96
142_E	146_I	0.526	0.96
103_Q	106_R	0.525	0.96
118_L	123_E	0.524	0.96
145_K	150_K	0.524	0.96
39_V	264_F	0.524	0.96
148_D	153_L	0.516	0.96
143_L	148_D	0.512	0.95
132_L	135_L	0.510	0.95
5_V	9_Y	0.510	0.95
172_L	175_M	0.509	0.95
84_G	88_L	0.509	0.95
256_L	260_N	0.508	0.95
39_V	42_E	0.507	0.95
75_L	96_L	0.506	0.95
98_R	165_A	0.506	0.95
190_T	194_P	0.505	0.95
42_E	45_F	0.505	0.95
252_E	256_L	0.504	0.95
146_I	152_D	0.504	0.95
243_R	249_E	0.503	0.95
140_L	148_D	0.502	0.95
93_R	173_L	0.500	0.95

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
2b5uA	1	0.2362	9.6	0.942	Contact Map
1y66A	3	0.1845	7.7	0.945	Contact Map
4u6uA	1	0.2103	7.6	0.945	Contact Map
2krkA	1	0.2657	4	0.952	Contact Map
5aj3h	1	0	2.8	0.955	Contact Map
3bgvA	1	0.3026	2.7	0.956	Contact Map
2mkbA	1	0.0812	2.3	0.958	Contact Map
3i24A	2	0.2768	2	0.959	Contact Map
4jpoC	1	0.2435	2	0.959	Contact Map
1dzfA	1	0.2583	1.9	0.959	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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