DUF1007 - PFAM28P - GREMLIN Contacts

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DUF1007 - Protein of unknown function (DUF1007)

PFAM:	PF06226	Sequences: LAAALLLLAAAPAQAHPHVWVDARSEVVFDPDGRVTGVRHAWTFDEMFSAFALQGLDKNGDGKLTREELAPLAKVNVESLKEFDYFTFAKADGKKVKFGEPPVDYWLEYKDGRLTLHFTLPLKTPVKAKGKPLTLEVYDPTYFVDFSFAEKDPVKLVGAPAGCKLTVVRPDPDAAAAYAQSLSELPADQFFLPPPGSNLGAQFANKITVTC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	211 (203)
Sequences:	3198 (2225)
Seq/√Len:	156.1
META:	0.792

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_D	34_R	5.042	1.00
74_K	78_E	5.030	1.00
27_V	35_V	3.838	1.00
37_G	119_T	2.801	1.00
70_A	74_K	2.707	1.00
25_S	38_V	2.643	1.00
26_E	39_R	2.526	1.00
57_D	68_E	2.496	1.00
43_T	115_T	2.430	1.00
57_D	61_D	2.403	1.00
189_Q	193_P	2.335	1.00
53_L	64_L	2.279	1.00
59_N	68_E	2.277	1.00
66_R	70_A	2.250	1.00
89_A	133_L	2.246	1.00
66_R	106_W	2.239	1.00
41_A	117_H	2.206	1.00
97_K	123_K	2.187	1.00
104_D	119_T	2.108	1.00
76_N	116_L	2.101	1.00
22_D	113_R	1.998	1.00
28_V	39_R	1.989	1.00
60_G	63_K	1.970	1.00
59_N	65_T	1.962	1.00
43_T	113_R	1.953	1.00
193_P	197_S	1.943	1.00
91_A	96_V	1.939	1.00
61_D	65_T	1.930	1.00
200_G	203_F	1.875	1.00
28_V	37_G	1.859	1.00
53_L	109_Y	1.793	1.00
26_E	157_V	1.751	1.00
35_V	133_L	1.734	1.00
51_F	55_G	1.726	1.00
99_G	123_K	1.675	1.00
23_A	148_F	1.615	1.00
35_V	122_L	1.612	1.00
193_P	196_G	1.574	1.00
88_F	138_Y	1.572	1.00
28_V	119_T	1.528	1.00
73_A	77_V	1.519	1.00
173_D	177_A	1.519	1.00
39_R	117_H	1.502	1.00
77_V	116_L	1.499	1.00
24_R	155_K	1.494	1.00
26_E	155_K	1.428	1.00
156_L	159_A	1.425	1.00
73_A	105_Y	1.421	1.00
34_R	127_K	1.411	1.00
89_A	98_F	1.403	1.00
99_G	121_P	1.363	1.00
110_K	115_T	1.341	1.00
61_D	68_E	1.338	1.00
194_P	198_N	1.332	1.00
174_A	177_A	1.326	1.00
87_T	120_L	1.321	1.00
106_W	117_H	1.321	1.00
39_R	119_T	1.320	1.00
22_D	149_A	1.317	1.00
24_R	43_T	1.315	1.00
122_L	125_P	1.282	1.00
40_H	137_V	1.279	1.00
23_A	137_V	1.263	1.00
98_F	120_L	1.238	1.00
64_L	68_E	1.233	1.00
188_D	193_P	1.229	1.00
108_E	117_H	1.214	1.00
57_D	60_G	1.209	1.00
73_A	116_L	1.199	1.00
107_L	114_L	1.195	1.00
23_A	146_F	1.190	1.00
189_Q	194_P	1.172	1.00
84_D	88_F	1.170	1.00
176_A	181_S	1.167	1.00
192_L	195_P	1.159	1.00
192_L	196_G	1.154	1.00
122_L	126_V	1.152	1.00
52_A	114_L	1.151	1.00
184_E	189_Q	1.144	1.00
189_Q	192_L	1.137	1.00
179_A	183_S	1.133	1.00
84_D	95_K	1.126	1.00
177_A	180_Q	1.112	1.00
20_W	145_D	1.111	1.00
9_A	12_P	1.095	0.99
30_D	36_T	1.094	0.99
39_R	157_V	1.091	0.99
199_L	202_Q	1.090	0.99
180_Q	184_E	1.079	0.99
70_A	73_A	1.077	0.99
148_F	167_V	1.066	0.99
6_L	9_A	1.063	0.99
170_P	205_N	1.057	0.99
173_D	203_F	1.055	0.99
191_F	194_P	1.050	0.99
91_A	126_V	1.047	0.99
65_T	68_E	1.045	0.99
27_V	209_V	1.045	0.99
188_D	192_L	1.033	0.99
52_A	72_L	1.033	0.99
188_D	191_F	1.025	0.99
40_H	87_T	1.017	0.99
25_S	40_H	1.015	0.99
193_P	198_N	1.014	0.99
180_Q	183_S	1.002	0.99
5_L	9_A	1.000	0.99
173_D	176_A	0.997	0.99
30_D	33_G	0.997	0.99
86_F	121_P	0.996	0.99
196_G	199_L	0.994	0.99
86_F	146_F	0.988	0.99
49_S	109_Y	0.988	0.99
52_A	76_N	0.986	0.99
24_R	41_A	0.984	0.99
172_P	183_S	0.974	0.99
168_V	208_T	0.967	0.99
46_E	113_R	0.942	0.98
127_K	130_G	0.938	0.98
57_D	65_T	0.929	0.98
179_A	199_L	0.923	0.98
35_V	128_A	0.916	0.98
200_G	204_A	0.914	0.98
29_F	128_A	0.906	0.98
4_A	10_A	0.902	0.98
39_R	104_D	0.901	0.98
41_A	115_T	0.898	0.98
181_S	184_E	0.891	0.98
166_T	210_T	0.886	0.98
40_H	120_L	0.880	0.97
24_R	115_T	0.876	0.97
154_V	165_L	0.871	0.97
34_R	124_T	0.865	0.97
29_F	160_P	0.857	0.97
134_T	206_K	0.847	0.97
199_L	206_K	0.846	0.97
37_G	121_P	0.840	0.97
195_P	199_L	0.837	0.97
152_D	155_K	0.833	0.96
28_V	157_V	0.826	0.96
48_F	76_N	0.825	0.96
194_P	197_S	0.818	0.96
4_A	11_A	0.813	0.96
109_Y	115_T	0.813	0.96
67_E	70_A	0.810	0.96
150_E	153_P	0.810	0.96
125_P	128_A	0.810	0.96
197_S	203_F	0.807	0.96
188_D	195_P	0.801	0.96
75_V	79_S	0.799	0.96
108_E	115_T	0.797	0.95
183_S	188_D	0.790	0.95
77_V	105_Y	0.787	0.95
26_E	41_A	0.783	0.95
89_A	122_L	0.776	0.95
197_S	202_Q	0.774	0.95
38_V	135_L	0.774	0.95
198_N	201_A	0.773	0.95
90_K	95_K	0.771	0.95
37_G	122_L	0.771	0.95
43_T	110_K	0.769	0.95
57_D	63_K	0.767	0.94
183_S	191_F	0.760	0.94
154_V	207_I	0.759	0.94
27_V	135_L	0.755	0.94
72_L	76_N	0.753	0.94
57_D	62_G	0.752	0.94
21_V	144_V	0.747	0.94
179_A	184_E	0.746	0.94
73_A	107_L	0.745	0.94
11_A	14_Q	0.742	0.93
48_F	80_L	0.741	0.93
191_F	195_P	0.740	0.93
10_A	13_A	0.723	0.93
19_V	48_F	0.722	0.92
80_L	139_D	0.720	0.92
76_N	107_L	0.711	0.92
60_G	68_E	0.705	0.92
4_A	167_V	0.705	0.92
200_G	205_N	0.696	0.91
96_V	126_V	0.694	0.91
24_R	149_A	0.687	0.91
80_L	137_V	0.686	0.90
89_A	135_L	0.685	0.90
2_A	8_L	0.684	0.90
79_S	82_E	0.682	0.90
21_V	146_F	0.681	0.90
184_E	188_D	0.681	0.90
88_F	95_K	0.679	0.90
196_G	202_Q	0.678	0.90
55_G	116_L	0.676	0.90
195_P	198_N	0.676	0.90
148_F	170_P	0.675	0.90
52_A	55_G	0.674	0.90
48_F	136_E	0.672	0.90
77_V	107_L	0.666	0.89
176_A	180_Q	0.662	0.89
6_L	11_A	0.660	0.89
51_F	54_Q	0.655	0.88
50_A	53_L	0.654	0.88
101_P	120_L	0.650	0.88
142_Y	145_D	0.648	0.88
20_W	47_M	0.647	0.88
58_K	65_T	0.644	0.87
183_S	193_P	0.644	0.87
38_V	41_A	0.643	0.87
66_R	108_E	0.642	0.87
171_D	177_A	0.641	0.87
6_L	94_K	0.635	0.87
176_A	195_P	0.633	0.87
165_L	207_I	0.633	0.87
100_E	103_V	0.630	0.86
103_V	121_P	0.629	0.86
189_Q	196_G	0.628	0.86
189_Q	195_P	0.628	0.86
29_F	156_L	0.628	0.86
173_D	183_S	0.626	0.86
75_V	107_L	0.625	0.86
199_L	203_F	0.617	0.85
183_S	196_G	0.616	0.85
18_H	143_F	0.614	0.85
175_A	196_G	0.612	0.85
6_L	10_A	0.611	0.85
30_D	125_P	0.610	0.85
115_T	144_V	0.606	0.84
193_P	202_Q	0.604	0.84
86_F	116_L	0.603	0.84
191_F	196_G	0.603	0.84
140_P	143_F	0.602	0.84
201_A	206_K	0.602	0.84
48_F	83_F	0.602	0.84
55_G	144_V	0.600	0.84
203_F	206_K	0.598	0.83
49_S	114_L	0.596	0.83
91_A	128_A	0.596	0.83
135_L	148_F	0.595	0.83
10_A	14_Q	0.594	0.83
136_E	206_K	0.592	0.83
189_Q	199_L	0.592	0.83
5_L	11_A	0.591	0.83
71_P	75_V	0.588	0.82
189_Q	197_S	0.586	0.82
29_F	33_G	0.585	0.82
138_Y	204_A	0.585	0.82
168_V	171_D	0.584	0.82
3_A	6_L	0.580	0.81
96_V	99_G	0.580	0.81
52_A	75_V	0.579	0.81
86_F	118_F	0.577	0.81
57_D	64_L	0.577	0.81
44_F	137_V	0.576	0.81
92_D	127_K	0.574	0.81
8_L	11_A	0.574	0.81
156_L	160_P	0.567	0.80
183_S	189_Q	0.566	0.80
59_N	67_E	0.565	0.80
101_P	105_Y	0.565	0.80
44_F	48_F	0.563	0.80
134_T	208_T	0.562	0.79
194_P	203_F	0.561	0.79
196_G	203_F	0.559	0.79
196_G	200_G	0.557	0.79
180_Q	189_Q	0.557	0.79
90_K	136_E	0.555	0.79
136_E	146_F	0.554	0.78
52_A	64_L	0.554	0.78
167_V	207_I	0.552	0.78
188_D	194_P	0.551	0.78
171_D	174_A	0.551	0.78
156_L	165_L	0.550	0.78
177_A	182_L	0.548	0.78
81_K	100_E	0.546	0.77
136_E	205_N	0.542	0.77
3_A	9_A	0.540	0.77
22_D	43_T	0.540	0.77
184_E	199_L	0.539	0.77
3_A	7_L	0.538	0.76
166_T	208_T	0.536	0.76
98_F	101_P	0.535	0.76
142_Y	192_L	0.535	0.76
36_T	125_P	0.530	0.75
149_A	153_P	0.530	0.75
163_C	211_C	0.530	0.75
28_V	35_V	0.529	0.75
189_Q	202_Q	0.527	0.75
191_F	199_L	0.526	0.75
193_P	199_L	0.526	0.75
44_F	50_A	0.526	0.75
173_D	196_G	0.526	0.75
192_L	203_F	0.523	0.74
6_L	12_P	0.522	0.74
80_L	86_F	0.520	0.74
192_L	199_L	0.518	0.74
20_W	120_L	0.516	0.73
200_G	211_C	0.516	0.73
141_T	144_V	0.513	0.73
147_S	150_E	0.512	0.73
8_L	12_P	0.511	0.73
45_D	49_S	0.508	0.72
189_Q	198_N	0.507	0.72
203_F	208_T	0.504	0.72
154_V	157_V	0.502	0.71
61_D	145_D	0.501	0.71
188_D	198_N	0.501	0.71
61_D	64_L	0.500	0.71

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
2julA	1	0.564	29	0.944	Contact Map
1nubA	1	0.4929	28.9	0.944	Contact Map
2l2eA	1	0.564	24.3	0.946	Contact Map
3nyvA	1	0.4976	24.2	0.946	Contact Map
1fpwA	1	0.5592	21.9	0.947	Contact Map
2kz2A	1	0.4408	20.8	0.948	Contact Map
2ma2A	1	0.3697	18.6	0.949	Contact Map
1yx7A	1	0.3318	18.3	0.949	Contact Map
2be4A	1	0.3744	18.1	0.949	Contact Map
4qoxA	1	0.5118	17.6	0.95	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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