DUF1361 - PFAM28P - GREMLIN Contacts

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DUF1361 - Protein of unknown function (DUF1361)

PFAM:	PF07099	Sequences: WNLFLAWIPLLLALLLYRLSRRRRSRWLLLLLLLLWLLFFPNAPYILTDLIHLRERPSGLRDGVPLWYDLLLLLSFAWTGLLLGFLSLYLMQRIVRRRFGRRRLARGWLFVLAVLFLSSFGIYLGRFLRWNSWDVLTNPGGLLRDILDRLHPRAWGFTLLFGVFLLIV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	168 (161)
Sequences:	4820 (3740)
Seq/√Len:	294.8
META:	0.883

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_I	80_G	3.437	1.00
40_F	118_S	3.308	1.00
130_W	145_D	3.189	1.00
8_I	12_L	3.118	1.00
33_L	91_M	2.693	1.00
50_L	74_L	2.364	1.00
8_I	39_F	2.353	1.00
116_F	162_G	2.204	1.00
12_L	32_L	2.130	1.00
38_L	132_S	2.122	1.00
40_F	88_L	2.121	1.00
12_L	35_L	2.094	1.00
134_D	137_T	2.079	1.00
88_L	115_L	2.003	1.00
92_Q	107_G	1.973	1.00
13_A	90_L	1.961	1.00
138_N	141_G	1.945	1.00
120_F	124_L	1.944	1.00
34_L	38_L	1.935	1.00
51_I	70_L	1.901	1.00
16_L	91_M	1.862	1.00
37_L	114_V	1.843	1.00
46_I	73_L	1.834	1.00
7_W	83_L	1.753	1.00
38_L	135_V	1.702	1.00
92_Q	108_W	1.700	1.00
123_Y	128_L	1.665	1.00
100_G	107_G	1.662	1.00
111_V	115_L	1.645	1.00
119_S	162_G	1.608	1.00
47_L	74_L	1.593	1.00
16_L	94_I	1.539	1.00
130_W	142_L	1.536	1.00
40_F	84_G	1.516	1.00
17_Y	90_L	1.511	1.00
151_H	155_W	1.491	1.00
36_W	87_S	1.480	1.00
158_T	162_G	1.468	1.00
119_S	158_T	1.424	1.00
124_L	128_L	1.410	1.00
70_L	74_L	1.385	1.00
99_F	105_A	1.373	1.00
92_Q	111_V	1.369	1.00
154_A	158_T	1.359	1.00
96_R	107_G	1.358	1.00
149_R	154_A	1.352	1.00
151_H	154_A	1.341	1.00
77_A	80_G	1.338	1.00
131_N	134_D	1.327	1.00
1_W	4_F	1.318	1.00
153_R	156_G	1.310	1.00
72_L	76_F	1.296	1.00
95_V	110_F	1.278	1.00
107_G	111_V	1.277	1.00
124_L	146_I	1.269	1.00
10_L	83_L	1.255	1.00
68_Y	72_L	1.253	1.00
144_R	148_D	1.253	1.00
96_R	103_R	1.244	1.00
114_V	118_S	1.243	1.00
120_F	158_T	1.243	1.00
4_F	8_I	1.239	1.00
115_L	119_S	1.235	1.00
69_D	72_L	1.229	1.00
2_N	49_D	1.206	1.00
1_W	131_N	1.203	1.00
51_I	126_R	1.196	1.00
120_F	149_R	1.182	1.00
12_L	16_L	1.176	1.00
51_I	127_F	1.174	1.00
67_W	127_F	1.173	1.00
99_F	107_G	1.149	1.00
16_L	32_L	1.135	1.00
153_R	157_F	1.127	1.00
95_V	107_G	1.120	1.00
15_L	32_L	1.111	1.00
73_L	77_A	1.099	1.00
14_L	90_L	1.075	1.00
46_I	49_D	1.065	1.00
115_L	165_L	1.051	1.00
80_G	88_L	1.048	1.00
11_L	15_L	1.030	1.00
152_P	155_W	1.026	1.00
154_A	162_G	1.014	1.00
23_R	28_L	1.013	1.00
50_L	70_L	1.010	1.00
163_V	166_L	1.000	1.00
79_T	82_L	0.988	1.00
145_D	149_R	0.984	1.00
130_W	141_G	0.984	1.00
10_L	90_L	0.966	1.00
71_L	160_L	0.947	1.00
141_G	144_R	0.944	1.00
21_R	24_R	0.941	1.00
65_P	68_Y	0.934	1.00
49_D	52_H	0.934	1.00
100_G	103_R	0.933	1.00
46_I	77_A	0.928	1.00
79_T	83_L	0.927	1.00
120_F	146_I	0.917	1.00
19_L	32_L	0.912	1.00
127_F	157_F	0.907	1.00
115_L	162_G	0.906	1.00
44_P	118_S	0.890	1.00
109_L	113_A	0.876	1.00
15_L	18_R	0.868	1.00
158_T	161_F	0.858	1.00
162_G	166_L	0.857	1.00
55_E	58_S	0.856	1.00
143_L	147_L	0.853	1.00
40_F	44_P	0.851	1.00
93_R	96_R	0.843	1.00
100_G	105_A	0.833	1.00
30_L	34_L	0.827	1.00
20_S	23_R	0.821	1.00
38_L	136_L	0.821	1.00
154_A	157_F	0.820	1.00
152_P	157_F	0.818	1.00
20_S	97_R	0.817	1.00
16_L	33_L	0.808	1.00
37_L	117_L	0.794	0.99
51_I	66_L	0.793	0.99
44_P	84_G	0.792	0.99
1_W	133_W	0.786	0.99
47_L	81_L	0.782	0.99
5_L	129_R	0.781	0.99
35_L	136_L	0.780	0.99
53_L	73_L	0.779	0.99
78_W	82_L	0.779	0.99
146_I	149_R	0.775	0.99
66_L	70_L	0.775	0.99
153_R	164_F	0.770	0.99
100_G	104_L	0.767	0.99
84_G	87_S	0.765	0.99
88_L	111_V	0.761	0.99
86_L	90_L	0.759	0.99
140_G	144_R	0.757	0.99
47_L	70_L	0.753	0.99
74_L	77_A	0.751	0.99
33_L	95_V	0.748	0.99
85_F	111_V	0.746	0.99
108_W	166_L	0.743	0.99
71_L	164_F	0.740	0.99
13_A	17_Y	0.739	0.99
2_N	5_L	0.738	0.99
157_F	161_F	0.736	0.99
2_N	6_A	0.736	0.99
19_L	22_R	0.728	0.99
67_W	70_L	0.728	0.99
155_W	162_G	0.726	0.99
65_P	69_D	0.722	0.99
15_L	19_L	0.720	0.99
137_T	142_L	0.720	0.99
73_L	76_F	0.719	0.99
128_L	145_D	0.715	0.99
155_W	159_L	0.711	0.99
19_L	24_R	0.702	0.99
81_L	85_F	0.686	0.98
34_L	135_V	0.684	0.98
157_F	166_L	0.674	0.98
54_R	66_L	0.669	0.98
119_S	161_F	0.667	0.98
75_S	115_L	0.660	0.98
142_L	146_I	0.658	0.98
3_L	76_F	0.658	0.98
138_N	142_L	0.653	0.98
20_S	26_R	0.649	0.98
135_V	142_L	0.648	0.98
110_F	114_V	0.644	0.98
94_I	97_R	0.639	0.98
120_F	142_L	0.635	0.97
9_P	43_A	0.630	0.97
3_L	7_W	0.628	0.97
20_S	94_I	0.628	0.97
64_V	69_D	0.626	0.97
50_L	53_L	0.622	0.97
91_M	110_F	0.621	0.97
99_F	103_R	0.616	0.97
91_M	95_V	0.608	0.97
26_R	98_R	0.603	0.97
13_A	91_M	0.603	0.97
29_L	94_I	0.602	0.97
157_F	164_F	0.600	0.96
10_L	13_A	0.600	0.96
112_L	116_F	0.599	0.96
92_Q	96_R	0.597	0.96
115_L	166_L	0.596	0.96
156_G	164_F	0.596	0.96
160_L	164_F	0.595	0.96
36_W	91_M	0.594	0.96
15_L	26_R	0.592	0.96
111_V	118_S	0.590	0.96
16_L	29_L	0.585	0.96
20_S	98_R	0.579	0.96
116_F	119_S	0.579	0.96
161_F	166_L	0.579	0.96
17_Y	93_R	0.577	0.96
42_N	125_G	0.576	0.96
40_F	165_L	0.575	0.96
21_R	26_R	0.575	0.96
8_I	35_L	0.574	0.95
64_V	68_Y	0.573	0.95
143_L	146_I	0.572	0.95
22_R	28_L	0.569	0.95
85_F	115_L	0.568	0.95
74_L	78_W	0.565	0.95
138_N	144_R	0.562	0.95
112_L	166_L	0.560	0.95
116_F	120_F	0.558	0.95
7_W	14_L	0.558	0.95
11_L	14_L	0.558	0.95
89_Y	92_Q	0.556	0.95
56_R	59_G	0.552	0.94
156_G	160_L	0.549	0.94
49_D	126_R	0.549	0.94
48_T	67_W	0.547	0.94
96_R	100_G	0.546	0.94
70_L	73_L	0.541	0.94
50_L	126_R	0.540	0.94
44_P	121_G	0.539	0.94
96_R	108_W	0.539	0.94
107_G	110_F	0.535	0.93
134_D	138_N	0.534	0.93
44_P	122_I	0.533	0.93
18_R	22_R	0.533	0.93
149_R	158_T	0.530	0.93
68_Y	76_F	0.529	0.93
19_L	23_R	0.529	0.93
9_P	13_A	0.527	0.93
40_F	65_P	0.524	0.93
24_R	27_W	0.522	0.93
154_A	164_F	0.515	0.92
104_L	109_L	0.515	0.92
20_S	24_R	0.514	0.92
22_R	33_L	0.514	0.92
76_F	143_L	0.513	0.92
89_Y	93_R	0.510	0.92
42_N	129_R	0.506	0.91
28_L	31_L	0.505	0.91
124_L	149_R	0.505	0.91
159_L	163_V	0.503	0.91
141_G	145_D	0.500	0.91

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
4or2A	2	0.4405	3.7	0.95	Contact Map
2fyuK	1	0.0952	3.5	0.951	Contact Map
2j5dA	2	0.25	2.7	0.953	Contact Map
3m73A	3	0.494	1.4	0.96	Contact Map
1fftB	1	0.2083	1.3	0.96	Contact Map
2vpzC	2	0.6012	1.3	0.961	Contact Map
4xp4A	1	0.9167	1.3	0.961	Contact Map
4yayA	1	0.5774	1.2	0.961	Contact Map
3j9pD	4	0.869	1.2	0.962	Contact Map
2lnlA	1	0.6071	1.1	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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