DUF4255 - PFAM28P - GREMLIN Contacts

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DUF4255 - Protein of unknown function (DUF4255)

PFAM:	PF14065	Sequences: DVTATLRDLLRDALPALVSGVDVSFDPPDDDWAASLTAPTLNLFLYRVRENAALRNAPLPRRRDGGTTRRRPPLALDLHYLLTAWGSDDEDDEEHRLLGRAMQVLHDHPVLPRDLLPGSDLADQIEPLRITLEPLSLEELSKLWSALGGPYRPSVAYVVRVVLIESDRPPRAAPPVLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	178 (174)
Sequences:	9735 (8003)
Seq/√Len:	606.7
META:	0.904

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_N	77_D	4.121	1.00
41_L	101_A	3.861	1.00
82_L	101_A	3.599	1.00
50_E	55_R	3.147	1.00
7_R	11_R	3.137	1.00
138_E	142_K	3.101	1.00
112_P	115_L	3.018	1.00
77_D	158_V	2.952	1.00
45_L	78_L	2.551	1.00
130_I	159_V	2.301	1.00
74_L	102_M	2.279	1.00
4_A	7_R	2.259	1.00
13_A	104_V	2.253	1.00
41_L	84_A	2.041	1.00
136_S	139_E	1.995	1.00
8_D	11_R	1.973	1.00
80_Y	95_H	1.914	1.00
43_L	82_L	1.888	1.00
46_Y	156_A	1.847	1.00
128_L	159_V	1.812	1.00
151_Y	154_S	1.768	1.00
108_H	115_L	1.758	1.00
8_D	12_D	1.720	1.00
3_T	95_H	1.705	1.00
79_H	158_V	1.704	1.00
42_N	83_T	1.661	1.00
102_M	155_V	1.631	1.00
63_R	67_T	1.582	1.00
105_L	157_Y	1.554	1.00
81_L	156_A	1.553	1.00
102_M	157_Y	1.550	1.00
2_V	78_L	1.512	1.00
11_R	15_P	1.496	1.00
51_N	54_L	1.483	1.00
47_R	79_H	1.483	1.00
49_R	79_H	1.483	1.00
79_H	133_E	1.481	1.00
107_D	166_S	1.473	1.00
101_A	155_V	1.458	1.00
75_A	163_L	1.450	1.00
9_L	13_A	1.439	1.00
133_E	158_V	1.427	1.00
172_A	175_P	1.423	1.00
139_E	142_K	1.362	1.00
62_R	70_R	1.352	1.00
84_A	101_A	1.348	1.00
3_T	25_F	1.338	1.00
98_L	153_P	1.327	1.00
100_R	103_Q	1.295	1.00
9_L	108_H	1.288	1.00
121_L	124_Q	1.285	1.00
83_T	154_S	1.283	1.00
103_Q	164_I	1.282	1.00
45_L	80_Y	1.276	1.00
141_S	145_S	1.267	1.00
44_F	151_Y	1.259	1.00
135_L	156_A	1.238	1.00
74_L	106_H	1.237	1.00
4_A	8_D	1.226	1.00
60_P	70_R	1.225	1.00
5_T	117_P	1.198	1.00
3_T	80_Y	1.178	1.00
26_D	30_D	1.177	1.00
12_D	15_P	1.172	1.00
12_D	115_L	1.167	1.00
100_R	104_V	1.160	1.00
90_E	93_E	1.159	1.00
25_F	28_P	1.157	1.00
119_S	122_A	1.135	1.00
132_L	155_V	1.135	1.00
9_L	104_V	1.122	1.00
24_S	42_N	1.116	1.00
30_D	33_A	1.115	1.00
80_Y	159_V	1.114	1.00
76_L	102_M	1.113	1.00
11_R	22_D	1.111	1.00
49_R	77_D	1.089	1.00
46_Y	79_H	1.081	1.00
18_V	21_V	1.080	1.00
31_D	35_S	1.079	1.00
33_A	36_L	1.064	1.00
48_V	78_L	1.054	1.00
42_N	85_W	1.052	1.00
143_L	147_L	1.044	1.00
83_T	152_R	1.036	1.00
66_G	69_R	1.031	1.00
71_R	168_R	1.024	1.00
10_L	43_L	1.021	1.00
23_V	28_P	1.004	1.00
7_R	43_L	1.002	1.00
5_T	9_L	0.997	1.00
63_R	68_T	0.997	1.00
77_D	160_R	0.992	1.00
55_R	58_P	0.984	1.00
131_T	158_V	0.980	1.00
41_L	97_L	0.976	1.00
45_L	48_V	0.973	1.00
6_L	43_L	0.971	1.00
10_L	101_A	0.964	1.00
44_F	83_T	0.958	1.00
122_A	125_I	0.957	1.00
129_R	160_R	0.955	1.00
141_S	146_A	0.953	1.00
70_R	165_E	0.951	1.00
93_E	96_R	0.929	1.00
29_D	33_A	0.928	1.00
103_Q	107_D	0.926	1.00
46_Y	143_L	0.919	1.00
27_P	30_D	0.918	1.00
114_D	117_P	0.908	1.00
45_L	95_H	0.908	1.00
137_L	141_S	0.908	1.00
48_V	98_L	0.889	1.00
25_F	31_D	0.885	1.00
112_P	127_P	0.867	1.00
19_S	22_D	0.859	1.00
22_D	40_T	0.855	1.00
113_R	126_E	0.853	1.00
32_W	37_T	0.848	1.00
113_R	127_P	0.846	1.00
79_H	156_A	0.845	1.00
50_E	132_L	0.842	1.00
12_D	16_A	0.837	1.00
120_D	125_I	0.835	1.00
88_D	91_D	0.832	1.00
54_L	57_A	0.826	1.00
21_V	25_F	0.817	1.00
8_D	117_P	0.800	1.00
41_L	82_L	0.798	1.00
133_E	156_A	0.795	1.00
113_R	116_L	0.794	1.00
32_W	36_L	0.794	1.00
28_P	31_D	0.792	1.00
120_D	123_D	0.788	1.00
94_E	152_R	0.785	1.00
142_K	145_S	0.777	1.00
21_V	24_S	0.775	1.00
98_L	155_V	0.769	1.00
46_Y	154_S	0.759	1.00
64_D	68_T	0.753	1.00
20_G	24_S	0.752	1.00
81_L	154_S	0.751	1.00
110_V	129_R	0.747	1.00
171_R	174_P	0.742	1.00
84_A	153_P	0.740	1.00
104_V	108_H	0.738	1.00
173_A	176_V	0.737	1.00
64_D	67_T	0.736	1.00
124_Q	128_L	0.735	1.00
135_L	139_E	0.735	1.00
31_D	36_L	0.734	1.00
31_D	34_A	0.729	1.00
47_R	140_L	0.725	1.00
15_P	21_V	0.724	1.00
81_L	147_L	0.724	1.00
5_T	116_L	0.722	1.00
114_D	118_G	0.720	1.00
110_V	127_P	0.719	1.00
10_L	23_V	0.717	1.00
85_W	152_R	0.717	1.00
27_P	31_D	0.715	1.00
59_L	63_R	0.710	1.00
30_D	34_A	0.710	1.00
170_P	173_A	0.709	1.00
117_P	122_A	0.704	1.00
137_L	140_L	0.690	1.00
120_D	124_Q	0.686	1.00
7_R	23_V	0.684	1.00
86_G	94_E	0.677	1.00
124_Q	129_R	0.674	1.00
24_S	28_P	0.670	1.00
34_A	37_T	0.667	1.00
47_R	133_E	0.666	1.00
84_A	98_L	0.666	1.00
169_P	172_A	0.665	1.00
146_A	151_Y	0.664	1.00
63_R	66_G	0.663	1.00
21_V	26_D	0.658	1.00
23_V	27_P	0.652	1.00
24_S	40_T	0.649	1.00
62_R	65_G	0.649	1.00
20_G	28_P	0.649	1.00
113_R	122_A	0.644	1.00
74_L	109_P	0.644	1.00
136_S	142_K	0.643	1.00
133_E	139_E	0.642	1.00
53_A	57_A	0.640	1.00
63_R	69_R	0.640	1.00
23_V	26_D	0.639	1.00
34_A	39_P	0.636	1.00
105_L	130_I	0.635	1.00
91_D	95_H	0.635	1.00
5_T	8_D	0.634	1.00
17_L	100_R	0.634	1.00
7_R	25_F	0.633	1.00
107_D	168_R	0.633	1.00
65_G	68_T	0.631	1.00
147_L	151_Y	0.629	1.00
18_V	22_D	0.628	1.00
65_G	69_R	0.626	1.00
22_D	38_A	0.626	1.00
7_R	16_A	0.624	1.00
126_E	130_I	0.618	1.00
50_E	75_A	0.617	1.00
84_A	94_E	0.610	1.00
13_A	16_A	0.610	1.00
138_E	151_Y	0.609	1.00
44_F	152_R	0.606	1.00
28_P	33_A	0.604	1.00
29_D	32_W	0.604	1.00
108_H	112_P	0.600	1.00
86_G	97_L	0.599	1.00
24_S	29_D	0.583	1.00
54_L	73_P	0.577	1.00
11_R	20_G	0.568	1.00
26_D	34_A	0.568	1.00
39_P	91_D	0.566	1.00
48_V	76_L	0.564	1.00
134_P	158_V	0.562	1.00
24_S	27_P	0.559	1.00
15_P	19_S	0.559	1.00
20_G	25_F	0.558	1.00
73_P	165_E	0.557	1.00
121_L	126_E	0.556	1.00
76_L	164_I	0.556	1.00
11_R	14_L	0.556	1.00
36_L	39_P	0.553	0.99
53_A	56_N	0.547	0.99
22_D	25_F	0.547	0.99
99_G	103_Q	0.546	0.99
125_I	128_L	0.546	0.99
25_F	29_D	0.541	0.99
11_R	23_V	0.539	0.99
80_Y	130_I	0.537	0.99
21_V	28_P	0.536	0.99
96_R	100_R	0.531	0.99
88_D	93_E	0.529	0.99
60_P	65_G	0.526	0.99
123_D	128_L	0.522	0.99
78_L	162_V	0.520	0.99
35_S	38_A	0.519	0.99
21_V	27_P	0.519	0.99
6_L	9_L	0.517	0.99
146_A	152_R	0.517	0.99
10_L	13_A	0.516	0.99
14_L	17_L	0.516	0.99
132_L	135_L	0.516	0.99
71_R	109_P	0.515	0.99
103_Q	166_S	0.514	0.99
30_D	150_P	0.513	0.99
62_R	67_T	0.512	0.99
58_P	61_R	0.507	0.99
9_L	115_L	0.506	0.99
169_P	174_P	0.505	0.99
113_R	123_D	0.505	0.99
97_L	100_R	0.505	0.99
34_A	38_A	0.504	0.99
74_L	155_V	0.504	0.99
76_L	162_V	0.501	0.99
32_W	40_T	0.500	0.99
16_A	21_V	0.500	0.99

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
4hudA	3	0.8371	52.1	0.895	Contact Map
4e17B	1	0.0843	5.3	0.936	Contact Map
1dp3A	1	0.2584	4.5	0.938	Contact Map
3fz2A	5	0.7022	3.8	0.94	Contact Map
1wyqA	1	0.6573	3	0.943	Contact Map
4qpoA	4	0.2472	2.2	0.947	Contact Map
4lkbF	4	0.236	2.2	0.947	Contact Map
2jnsA	1	0.4831	1.9	0.949	Contact Map
3nw0A	1	0.4438	1.8	0.949	Contact Map
3zuzA	1	0.2921	1.6	0.951	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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