DUF554 - PFAM28P - GREMLIN Contacts

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DUF554 - Protein of unknown function (DUF554)

PFAM:	PF04474	Sequences: LGTIVNAAAILVGSLIGLLLGKRLPERIRETVMQALGLATLLIGISMALKTENILIVILSLVLGGLIGELLDIEDRLERLGEWLERRFGGGGRFAEGFVTASLLFCVGPMAILGSIQDGLTGDHSLLFTKSVLDGFASIAFASTLGIGVLFSAIPVLVYQGGITLLAGLLGPFLTPAMIAEMTAVGGLLILGIGLNLLEIKKIKVANLLPALLIAPLLVW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	220 (219)
Sequences:	6898 (4885)
Seq/√Len:	330.1
META:	0.825

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_D	75_D	4.403	1.00
67_I	214_I	3.351	1.00
65_G	208_L	3.314	1.00
5_V	128_F	3.288	1.00
14_S	150_L	2.941	1.00
118_D	124_H	2.759	1.00
76_R	79_R	2.643	1.00
117_Q	121_T	2.574	1.00
7_A	157_L	2.571	1.00
69_E	207_N	2.490	1.00
124_H	128_F	2.489	1.00
9_A	131_S	2.274	1.00
26_E	30_E	2.207	1.00
83_W	87_R	2.182	1.00
31_T	65_G	1.979	1.00
111_A	159_Y	1.954	1.00
117_Q	123_D	1.935	1.00
42_L	188_L	1.866	1.00
104_L	141_F	1.859	1.00
10_I	156_V	1.856	1.00
82_E	85_E	1.852	1.00
47_M	187_G	1.813	1.00
74_E	206_A	1.770	1.00
199_E	202_K	1.760	1.00
41_L	194_G	1.757	1.00
63_L	214_I	1.748	1.00
26_E	29_R	1.745	1.00
35_A	61_L	1.736	1.00
42_L	48_A	1.702	1.00
51_T	181_E	1.695	1.00
73_I	206_A	1.680	1.00
4_I	8_A	1.671	1.00
11_L	153_A	1.663	1.00
3_T	160_Q	1.662	1.00
82_E	95_A	1.655	1.00
30_E	34_Q	1.628	1.00
85_E	96_E	1.615	1.00
110_M	126_L	1.576	1.00
67_I	71_L	1.570	1.00
3_T	164_T	1.540	1.00
196_N	202_K	1.530	1.00
195_L	200_I	1.527	1.00
35_A	65_G	1.493	1.00
74_E	78_E	1.490	1.00
28_I	70_L	1.489	1.00
93_R	96_E	1.485	1.00
101_A	141_F	1.485	1.00
176_P	180_A	1.484	1.00
196_N	201_K	1.473	1.00
46_S	50_K	1.469	1.00
195_L	201_K	1.439	1.00
36_L	137_A	1.431	1.00
94_F	151_F	1.414	1.00
189_L	211_A	1.404	1.00
116_I	163_I	1.404	1.00
25_P	28_I	1.401	1.00
97_G	145_L	1.391	1.00
38_L	192_G	1.387	1.00
72_D	76_R	1.375	1.00
153_A	157_L	1.374	1.00
157_L	161_G	1.370	1.00
39_A	61_L	1.343	1.00
97_G	101_A	1.330	1.00
75_D	79_R	1.305	1.00
115_S	119_G	1.302	1.00
214_I	218_L	1.298	1.00
102_S	155_P	1.287	1.00
147_I	151_F	1.273	1.00
7_A	153_A	1.267	1.00
57_V	188_L	1.259	1.00
192_G	205_V	1.259	1.00
27_R	72_D	1.245	1.00
30_E	199_E	1.225	1.00
56_I	215_A	1.208	1.00
118_D	164_T	1.208	1.00
166_L	169_L	1.205	1.00
5_V	124_H	1.200	1.00
175_T	178_M	1.198	1.00
111_A	155_P	1.184	1.00
69_E	204_K	1.182	1.00
60_S	214_I	1.181	1.00
41_L	45_I	1.180	1.00
16_I	139_I	1.176	1.00
9_A	135_G	1.174	1.00
14_S	18_L	1.152	1.00
102_S	156_V	1.133	1.00
46_S	49_L	1.132	1.00
5_V	131_S	1.129	1.00
31_T	69_E	1.128	1.00
125_S	129_T	1.122	1.00
11_L	150_L	1.121	1.00
61_L	188_L	1.114	1.00
153_A	156_V	1.113	1.00
113_L	126_L	1.110	1.00
39_A	58_I	1.110	1.00
56_I	218_L	1.109	1.00
85_E	95_A	1.107	1.00
117_Q	126_L	1.106	1.00
18_L	147_I	1.102	1.00
181_E	219_V	1.102	1.00
83_W	86_R	1.096	1.00
170_L	173_F	1.089	1.00
171_G	175_T	1.085	1.00
3_T	7_A	1.080	1.00
126_L	129_T	1.075	1.00
10_I	111_A	1.071	1.00
215_A	219_V	1.065	1.00
56_I	60_S	1.060	1.00
105_F	138_S	1.057	1.00
59_L	63_L	1.056	1.00
31_T	34_Q	1.055	1.00
18_L	150_L	1.053	1.00
45_I	49_L	1.046	1.00
104_L	137_A	1.042	1.00
27_R	69_E	1.036	1.00
103_L	107_V	1.033	1.00
67_I	70_L	1.032	1.00
185_V	215_A	1.028	1.00
77_L	206_A	1.026	1.00
14_S	138_S	1.020	1.00
58_I	129_T	1.013	1.00
162_G	166_L	1.008	1.00
111_A	115_S	1.005	1.00
73_I	76_R	1.000	1.00
14_S	142_A	0.997	1.00
135_G	139_I	0.991	1.00
8_A	12_V	0.982	1.00
81_G	99_V	0.971	1.00
177_A	180_A	0.961	1.00
21_G	29_R	0.954	1.00
105_F	139_I	0.951	1.00
166_L	170_L	0.950	1.00
45_I	191_L	0.944	1.00
39_A	133_L	0.940	1.00
63_L	67_I	0.935	1.00
15_L	150_L	0.927	1.00
60_S	215_A	0.923	1.00
190_I	193_I	0.918	1.00
35_A	208_L	0.918	1.00
101_A	105_F	0.918	1.00
215_A	218_L	0.913	1.00
78_E	82_E	0.909	1.00
81_G	206_A	0.909	1.00
2_G	127_L	0.906	1.00
138_S	142_A	0.902	1.00
174_L	179_I	0.894	1.00
98_F	102_S	0.893	1.00
82_E	86_R	0.890	1.00
57_V	185_V	0.886	1.00
40_T	133_L	0.872	1.00
10_I	105_F	0.863	1.00
3_T	118_D	0.850	1.00
85_E	94_F	0.849	1.00
53_N	181_E	0.841	1.00
41_L	191_L	0.839	1.00
213_L	216_P	0.839	1.00
5_V	9_A	0.833	1.00
28_I	69_E	0.828	1.00
51_T	57_V	0.827	1.00
121_T	124_H	0.826	1.00
155_P	159_Y	0.825	1.00
51_T	184_A	0.821	1.00
20_L	23_R	0.818	1.00
32_V	136_F	0.818	1.00
42_L	191_L	0.814	1.00
138_S	149_V	0.812	1.00
52_E	181_E	0.807	1.00
84_L	151_F	0.805	1.00
59_L	136_F	0.805	1.00
162_G	165_L	0.805	1.00
11_L	15_L	0.803	1.00
100_T	104_L	0.802	1.00
102_S	111_A	0.801	1.00
48_A	191_L	0.792	1.00
15_L	19_L	0.791	1.00
72_D	207_N	0.790	1.00
94_F	148_G	0.788	1.00
62_V	136_F	0.786	1.00
28_I	66_L	0.784	1.00
55_L	59_L	0.783	1.00
115_S	163_I	0.783	1.00
101_A	104_L	0.782	1.00
31_T	35_A	0.781	1.00
1_L	5_V	0.780	1.00
79_R	83_W	0.775	1.00
36_L	62_V	0.775	1.00
37_G	197_L	0.772	1.00
61_L	189_L	0.771	1.00
131_S	135_G	0.770	1.00
181_E	184_A	0.767	1.00
168_G	171_G	0.766	1.00
163_I	167_A	0.760	1.00
4_I	7_A	0.756	1.00
123_D	126_L	0.746	0.99
30_E	204_K	0.741	0.99
150_L	154_I	0.741	0.99
156_V	162_G	0.739	0.99
18_L	142_A	0.734	0.99
115_S	118_D	0.732	0.99
132_V	135_G	0.730	0.99
59_L	140_A	0.726	0.99
115_S	160_Q	0.725	0.99
62_V	140_A	0.720	0.99
42_L	46_S	0.719	0.99
72_D	79_R	0.718	0.99
118_D	128_F	0.714	0.99
154_I	158_V	0.713	0.99
129_T	132_V	0.708	0.99
57_V	181_E	0.703	0.99
16_I	135_G	0.701	0.99
2_G	118_D	0.700	0.99
40_T	197_L	0.697	0.99
11_L	14_S	0.694	0.99
184_A	187_G	0.693	0.99
147_I	150_L	0.689	0.99
206_A	209_L	0.686	0.99
79_R	82_E	0.685	0.99
195_L	203_I	0.685	0.99
74_E	204_K	0.684	0.99
193_I	205_V	0.682	0.99
94_F	97_G	0.680	0.99
97_G	149_V	0.680	0.99
137_A	140_A	0.676	0.99
169_L	172_P	0.673	0.99
189_L	212_L	0.669	0.99
198_L	203_I	0.669	0.99
43_I	54_I	0.666	0.99
1_L	128_F	0.665	0.99
105_F	135_G	0.663	0.99
111_A	163_I	0.662	0.99
109_P	113_L	0.659	0.99
191_L	195_L	0.657	0.99
39_A	43_I	0.656	0.99
23_R	140_A	0.653	0.99
42_L	45_I	0.653	0.99
101_A	152_S	0.649	0.98
45_I	48_A	0.648	0.98
3_T	115_S	0.648	0.98
155_P	158_V	0.647	0.98
116_I	120_L	0.644	0.98
178_M	216_P	0.638	0.98
115_S	127_L	0.638	0.98
78_E	202_K	0.637	0.98
48_A	188_L	0.637	0.98
33_M	137_A	0.633	0.98
201_K	204_K	0.631	0.98
192_G	203_I	0.629	0.98
1_L	124_H	0.627	0.98
28_I	31_T	0.626	0.98
128_F	132_V	0.625	0.98
165_L	169_L	0.624	0.98
53_N	56_I	0.622	0.98
24_L	28_I	0.622	0.98
51_T	54_I	0.621	0.98
39_A	54_I	0.621	0.98
16_I	20_L	0.620	0.98
47_M	183_T	0.619	0.98
44_G	194_G	0.619	0.98
195_L	199_E	0.617	0.98
168_G	172_P	0.616	0.98
133_L	137_A	0.615	0.98
142_A	150_L	0.613	0.98
178_M	215_A	0.613	0.98
52_E	177_A	0.606	0.98
139_I	143_S	0.605	0.98
196_N	205_V	0.604	0.98
20_L	24_L	0.603	0.98
115_S	164_T	0.602	0.98
10_I	106_C	0.596	0.97
80_L	83_W	0.595	0.97
57_V	184_A	0.593	0.97
34_Q	203_I	0.593	0.97
34_Q	201_K	0.593	0.97
44_G	48_A	0.592	0.97
71_L	76_R	0.589	0.97
196_N	203_I	0.589	0.97
2_G	124_H	0.588	0.97
190_I	194_G	0.588	0.97
47_M	126_L	0.587	0.97
39_A	190_I	0.587	0.97
161_G	165_L	0.584	0.97
180_A	184_A	0.584	0.97
85_E	89_G	0.582	0.97
128_F	131_S	0.582	0.97
116_I	167_A	0.579	0.97
159_Y	163_I	0.575	0.97
43_I	47_M	0.571	0.97
150_L	153_A	0.570	0.97
66_L	70_L	0.570	0.97
40_T	137_A	0.566	0.96
100_T	145_L	0.563	0.96
135_G	138_S	0.561	0.96
50_K	180_A	0.560	0.96
75_D	78_E	0.558	0.96
137_A	197_L	0.558	0.96
56_I	219_V	0.555	0.96
154_I	157_L	0.551	0.96
54_I	57_V	0.551	0.96
106_C	156_V	0.550	0.96
14_S	147_I	0.550	0.96
182_M	215_A	0.541	0.95
42_L	57_V	0.541	0.95
12_V	15_L	0.540	0.95
63_L	218_L	0.539	0.95
40_T	190_I	0.532	0.95
71_L	75_D	0.532	0.95
10_I	155_P	0.530	0.95
121_T	126_L	0.527	0.95
3_T	127_L	0.525	0.95
105_F	149_V	0.521	0.94
1_L	118_D	0.520	0.94
76_R	83_W	0.519	0.94
47_M	110_M	0.519	0.94
7_A	11_L	0.518	0.94
179_I	182_M	0.518	0.94
77_L	99_V	0.518	0.94
38_L	188_L	0.515	0.94
59_L	132_V	0.513	0.94
14_S	153_A	0.512	0.94
77_L	107_V	0.511	0.94
178_M	181_E	0.511	0.94
59_L	214_I	0.511	0.94
153_A	162_G	0.510	0.94
110_M	193_I	0.509	0.94
112_I	115_S	0.507	0.94
203_I	208_L	0.507	0.94
51_T	180_A	0.501	0.93
120_L	167_A	0.500	0.93

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
1lypA	1	0.1455	6.4	0.962	Contact Map
1t5jA	1	0.2318	6.3	0.962	Contact Map
3rqwA	4	0.4545	4.8	0.964	Contact Map
2llyA	1	0.4955	4.6	0.965	Contact Map
4us3A	1	1	3.6	0.966	Contact Map
2nwlA	3	0.6273	3.2	0.967	Contact Map
3l1lA	2	0.3773	3	0.968	Contact Map
4eneA	2	0.4091	3	0.968	Contact Map
4o93B	1	0.7864	2.9	0.968	Contact Map
2pcoA	1	0.1136	2.8	0.968	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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