DUF998 - PFAM28P - GREMLIN Contacts

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DUF998 - Protein of unknown function (DUF998)

PFAM:	PF06197	Sequences: IAAPLLFVAAVLVAGLLRPGYSPVRQTISELGAIGGPTGWLFNAGFILLGLLLLAFAVGLRRARRGRAGRIGAALLALAGLGLILAGLFPMDPGGGFPTLHGTLHGVAALLAFLLLPLAALLLAARRRRRGWRLLSLLSGVALLLLLALLALFLAAANLPGPGVGLAERIAVLAILLWLAVLALH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	185 (181)
Sequences:	18164 (14789)
Seq/√Len:	1099.2
META:	0.874

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_L	108_A	4.282	1.00
138_L	142_A	3.385	1.00
135_L	139_S	3.020	1.00
27_T	30_E	2.974	1.00
42_F	46_F	2.899	1.00
165_G	169_R	2.741	1.00
100_L	104_L	2.677	1.00
26_Q	30_E	2.659	1.00
15_G	23_P	2.438	1.00
92_D	99_T	2.311	1.00
89_F	104_L	2.189	1.00
137_L	141_V	2.173	1.00
30_E	91_M	2.173	1.00
27_T	164_V	2.163	1.00
39_G	43_N	2.142	1.00
32_G	43_N	2.132	1.00
57_A	77_A	2.115	1.00
10_A	45_G	1.943	1.00
141_V	145_L	1.861	1.00
42_F	45_G	1.837	1.00
22_S	25_R	1.827	1.00
43_N	90_P	1.821	1.00
24_V	166_L	1.798	1.00
91_M	95_G	1.797	1.00
134_L	138_L	1.714	1.00
72_G	123_L	1.698	1.00
116_L	175_I	1.679	1.00
47_I	84_I	1.675	1.00
129_R	132_W	1.643	1.00
125_A	128_R	1.641	1.00
28_I	172_V	1.636	1.00
92_D	102_G	1.628	1.00
82_G	108_A	1.612	1.00
136_S	139_S	1.587	1.00
136_S	140_G	1.534	1.00
128_R	131_G	1.523	1.00
132_W	136_S	1.517	1.00
11_V	28_I	1.517	1.00
61_R	73_A	1.496	1.00
116_L	120_A	1.488	1.00
71_I	74_A	1.488	1.00
140_G	144_L	1.487	1.00
47_I	87_G	1.457	1.00
54_L	80_G	1.427	1.00
6_L	10_A	1.386	1.00
132_W	135_L	1.371	1.00
32_G	42_F	1.348	1.00
56_F	183_A	1.339	1.00
99_T	102_G	1.326	1.00
109_A	113_F	1.319	1.00
91_M	94_G	1.317	1.00
54_L	77_A	1.295	1.00
137_L	140_G	1.282	1.00
11_V	23_P	1.266	1.00
85_L	89_F	1.251	1.00
53_L	80_G	1.247	1.00
132_W	137_L	1.225	1.00
126_R	129_R	1.214	1.00
82_G	111_L	1.201	1.00
125_A	131_G	1.197	1.00
130_R	133_R	1.191	1.00
78_L	115_L	1.175	1.00
86_A	109_A	1.174	1.00
50_G	80_G	1.166	1.00
53_L	79_A	1.165	1.00
135_L	138_L	1.165	1.00
14_A	18_R	1.148	1.00
76_L	119_A	1.138	1.00
150_L	153_F	1.136	1.00
90_P	101_H	1.134	1.00
13_V	16_L	1.121	1.00
131_G	134_L	1.115	1.00
40_W	44_A	1.102	1.00
18_R	36_G	1.098	1.00
163_G	167_A	1.094	1.00
36_G	42_F	1.092	1.00
18_R	21_Y	1.092	1.00
111_L	115_L	1.086	1.00
143_L	147_L	1.072	1.00
133_R	137_L	1.071	1.00
44_A	48_L	1.069	1.00
52_L	56_F	1.067	1.00
140_G	143_L	1.065	1.00
50_G	87_G	1.052	1.00
70_R	73_A	1.052	1.00
57_A	73_A	1.052	1.00
104_L	108_A	1.040	1.00
7_F	10_A	1.030	1.00
49_L	52_L	1.029	1.00
57_A	80_G	1.028	1.00
139_S	143_L	1.023	1.00
117_P	120_A	1.012	1.00
173_L	177_L	0.999	1.00
127_R	131_G	0.996	1.00
125_A	129_R	0.991	1.00
37_P	42_F	0.990	1.00
8_V	11_V	0.982	1.00
133_R	136_S	0.977	1.00
153_F	156_A	0.976	1.00
142_A	146_L	0.973	1.00
139_S	142_A	0.970	1.00
163_G	166_L	0.964	1.00
29_S	105_H	0.957	1.00
69_G	72_G	0.952	1.00
146_L	150_L	0.947	1.00
135_L	142_A	0.944	1.00
151_A	155_A	0.943	1.00
126_R	132_W	0.941	1.00
70_R	74_A	0.933	1.00
85_L	104_L	0.930	1.00
13_V	17_L	0.928	1.00
21_Y	26_Q	0.925	1.00
130_R	135_L	0.920	1.00
152_L	156_A	0.918	1.00
21_Y	31_L	0.917	1.00
125_A	132_W	0.910	1.00
132_W	140_G	0.907	1.00
34_I	92_D	0.903	1.00
4_P	8_V	0.899	1.00
5_L	9_A	0.892	1.00
38_T	41_L	0.885	1.00
72_G	119_A	0.877	1.00
131_G	135_L	0.875	1.00
12_L	16_L	0.872	1.00
66_G	69_G	0.857	1.00
178_W	182_L	0.856	1.00
106_G	110_L	0.856	1.00
100_L	103_T	0.847	1.00
14_A	41_L	0.846	1.00
7_F	11_V	0.839	1.00
103_T	107_V	0.834	1.00
145_L	149_L	0.833	1.00
160_P	163_G	0.827	1.00
14_A	42_F	0.827	1.00
59_G	62_R	0.826	1.00
38_T	42_F	0.824	1.00
149_L	152_L	0.814	1.00
57_A	76_L	0.814	1.00
128_R	134_L	0.811	1.00
118_L	122_L	0.811	1.00
85_L	88_L	0.810	1.00
140_G	154_L	0.806	1.00
127_R	130_R	0.805	1.00
24_V	163_G	0.800	1.00
83_L	86_A	0.792	1.00
86_A	108_A	0.791	1.00
135_L	141_V	0.790	1.00
15_G	21_Y	0.783	1.00
143_L	150_L	0.777	1.00
67_R	71_I	0.776	1.00
79_A	116_L	0.773	1.00
147_L	151_A	0.764	1.00
27_T	91_M	0.763	1.00
146_L	149_L	0.759	1.00
10_A	46_F	0.751	1.00
152_L	155_A	0.748	1.00
22_S	26_Q	0.747	1.00
15_G	18_R	0.744	1.00
104_L	107_V	0.743	1.00
126_R	131_G	0.743	1.00
171_A	174_A	0.743	1.00
136_S	146_L	0.737	1.00
131_G	139_S	0.736	1.00
50_G	84_I	0.730	1.00
128_R	132_W	0.726	1.00
39_G	42_F	0.725	1.00
106_G	109_A	0.722	1.00
68_A	72_G	0.721	1.00
58_V	62_R	0.721	1.00
132_W	138_L	0.719	1.00
129_R	133_R	0.717	1.00
172_V	176_L	0.716	1.00
75_L	115_L	0.711	1.00
35_G	39_G	0.707	1.00
79_A	112_A	0.706	1.00
125_A	133_R	0.706	1.00
36_G	39_G	0.706	1.00
138_L	141_V	0.704	1.00
140_G	147_L	0.704	1.00
168_E	172_V	0.703	1.00
14_A	38_T	0.699	1.00
158_N	161_G	0.698	1.00
53_L	83_L	0.698	1.00
127_R	132_W	0.697	1.00
129_R	135_L	0.694	1.00
134_L	139_S	0.691	1.00
150_L	156_A	0.688	1.00
135_L	140_G	0.681	1.00
134_L	137_L	0.678	1.00
45_G	49_L	0.678	1.00
28_I	169_R	0.671	1.00
133_R	140_G	0.670	1.00
167_A	170_I	0.669	1.00
128_R	135_L	0.669	1.00
126_R	139_S	0.669	1.00
130_R	134_L	0.668	1.00
168_E	176_L	0.665	1.00
90_P	93_P	0.664	1.00
132_W	139_S	0.662	1.00
129_R	134_L	0.662	1.00
14_A	17_L	0.660	1.00
113_F	116_L	0.653	1.00
83_L	112_A	0.650	1.00
82_G	115_L	0.649	1.00
43_N	47_I	0.645	1.00
74_A	78_L	0.634	1.00
24_V	27_T	0.632	1.00
136_S	142_A	0.632	1.00
10_A	14_A	0.629	1.00
128_R	136_S	0.626	1.00
149_L	153_F	0.619	1.00
18_R	38_T	0.616	1.00
167_A	171_A	0.615	1.00
144_L	148_A	0.612	1.00
139_S	146_L	0.612	1.00
79_A	115_L	0.609	1.00
33_A	36_G	0.608	1.00
7_F	49_L	0.603	1.00
17_L	38_T	0.601	1.00
30_E	33_A	0.598	1.00
127_R	134_L	0.596	1.00
14_A	31_L	0.594	1.00
126_R	133_R	0.593	1.00
78_L	82_G	0.587	1.00
130_R	136_S	0.583	1.00
25_R	163_G	0.579	1.00
147_L	150_L	0.579	1.00
33_A	91_M	0.576	1.00
138_L	152_L	0.575	1.00
176_L	180_A	0.573	1.00
159_L	163_G	0.573	1.00
89_F	108_A	0.571	1.00
49_L	53_L	0.567	1.00
136_S	143_L	0.567	1.00
69_G	73_A	0.564	1.00
127_R	133_R	0.562	1.00
108_A	111_L	0.562	1.00
132_W	149_L	0.561	1.00
53_L	179_L	0.560	1.00
58_V	61_R	0.555	1.00
112_A	117_P	0.552	1.00
9_A	13_V	0.550	1.00
6_L	45_G	0.550	1.00
11_V	15_G	0.548	1.00
126_R	134_L	0.546	1.00
45_G	48_L	0.545	1.00
23_P	169_R	0.544	1.00
126_R	130_R	0.544	1.00
13_V	18_R	0.543	1.00
170_I	174_A	0.541	1.00
165_G	168_E	0.533	1.00
113_F	117_P	0.531	1.00
47_I	51_L	0.530	1.00
159_L	162_P	0.530	1.00
51_L	55_A	0.525	1.00
61_R	74_A	0.524	1.00
148_A	152_L	0.524	1.00
32_G	87_G	0.524	1.00
136_S	147_L	0.523	1.00
174_A	177_L	0.522	1.00
11_V	14_A	0.522	1.00
21_Y	169_R	0.522	1.00
132_W	150_L	0.521	1.00
142_A	149_L	0.517	1.00
108_A	112_A	0.514	1.00
173_L	176_L	0.510	1.00
138_L	153_F	0.507	1.00
113_F	172_V	0.505	1.00
32_G	91_M	0.505	1.00
148_A	155_A	0.503	1.00
115_L	119_A	0.502	1.00
95_G	98_P	0.500	1.00

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
2ks1B	1	0.2378	6.7	0.914	Contact Map
4o6yA	2	0.9459	4.9	0.919	Contact Map
2o9gA	3	0.3459	3.7	0.924	Contact Map
3m73A	3	0.5784	3.2	0.926	Contact Map
4nv5A	1	0.9405	3.1	0.926	Contact Map
4k5yA	1	0.4757	2.9	0.928	Contact Map
3llqA	3	0.3459	2.7	0.929	Contact Map
2f2bA	4	0.3351	2.7	0.929	Contact Map
4wfeA	2	0.6757	2.6	0.93	Contact Map
4nefA	4	0.4216	2.5	0.93	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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