DUF4132 - PFAM28P - GREMLIN Contacts

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DUF4132 - Domain of unknown function (DUF4132)

PFAM:	PF13569	Sequences: GKRLKSLPAPVKKDDAEAKELKALKKELKAVLSAQRARLERAMLTGRRWPAAEWRERLLDHPLVGPLARRLVWGFYDDGKALLGTFREDGSLVDADGEPVELPDDARVRLAHPLDLDAEEVAAWREHLADYEIVQPFKQLFREVYLLTDAERETRYSNRFAGHILRQHQLRALLKKRGW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	179 (178)
Sequences:	4733 (3912)
Seq/√Len:	293.2
META:	0.804

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
127_H	131_Y	3.384	1.00
149_D	152_R	3.257	1.00
55_R	60_D	3.130	1.00
94_D	98_E	3.019	1.00
117_D	120_E	2.960	1.00
48_R	109_R	2.954	1.00
151_E	159_R	2.895	1.00
74_G	109_R	2.678	1.00
50_P	53_E	2.581	1.00
58_L	68_A	2.531	1.00
48_R	107_R	2.513	1.00
35_Q	64_V	2.408	1.00
97_G	131_Y	2.359	1.00
65_G	69_R	2.244	1.00
72_V	140_L	2.223	1.00
103_P	106_A	2.167	1.00
166_R	169_Q	2.165	1.00
46_G	115_D	2.038	1.00
65_G	90_G	1.978	1.00
148_T	151_E	1.969	1.00
76_Y	109_R	1.883	1.00
158_N	161_A	1.866	1.00
138_K	143_E	1.833	1.00
51_A	102_L	1.805	1.00
171_R	175_K	1.774	1.00
42_A	49_W	1.756	1.00
35_Q	38_R	1.747	1.00
51_A	55_R	1.733	1.00
125_R	141_F	1.679	1.00
88_E	91_S	1.671	1.00
126_E	130_D	1.629	1.00
52_A	56_E	1.601	1.00
121_V	125_R	1.597	1.00
154_T	158_N	1.583	1.00
74_G	115_D	1.548	1.00
74_G	82_L	1.542	1.00
111_A	116_L	1.530	1.00
147_L	152_R	1.514	1.00
72_V	128_L	1.504	1.00
128_L	133_I	1.485	1.00
43_M	110_L	1.432	1.00
10_P	18_A	1.402	1.00
22_K	25_K	1.391	1.00
11_V	18_A	1.371	1.00
56_E	60_D	1.346	1.00
82_L	86_F	1.321	1.00
52_A	104_D	1.319	1.00
53_E	57_R	1.313	1.00
40_E	142_R	1.296	1.00
84_G	87_R	1.295	1.00
14_D	18_A	1.282	1.00
15_D	18_A	1.257	1.00
9_A	12_K	1.249	1.00
76_Y	82_L	1.245	1.00
129_A	141_F	1.245	1.00
71_L	110_L	1.242	1.00
48_R	76_Y	1.235	1.00
49_W	54_W	1.233	1.00
53_E	56_E	1.229	1.00
9_A	13_K	1.222	1.00
27_E	30_A	1.211	1.00
41_R	45_T	1.178	1.00
118_A	122_A	1.175	1.00
128_L	140_L	1.174	1.00
30_A	33_S	1.173	1.00
97_G	130_D	1.172	1.00
55_R	59_L	1.166	1.00
40_E	137_F	1.163	1.00
95_A	123_A	1.162	1.00
74_G	111_A	1.147	1.00
95_A	120_E	1.146	1.00
27_E	31_V	1.145	1.00
170_L	174_L	1.135	1.00
19_K	22_K	1.132	1.00
116_L	120_E	1.129	1.00
49_W	53_E	1.120	1.00
169_Q	173_L	1.109	1.00
118_A	121_V	1.101	1.00
75_F	108_V	1.097	1.00
10_P	14_D	1.086	1.00
93_V	131_Y	1.082	1.00
93_V	127_H	1.077	1.00
82_L	85_T	1.063	1.00
59_L	92_L	1.062	1.00
109_R	115_D	1.060	1.00
23_A	27_E	1.055	1.00
169_Q	172_A	1.053	1.00
42_A	58_L	1.053	1.00
50_P	107_R	1.035	1.00
72_V	124_W	1.032	1.00
148_T	159_R	1.030	1.00
26_K	30_A	1.030	1.00
54_W	73_W	1.028	1.00
25_K	29_K	1.023	1.00
167_Q	171_R	1.018	1.00
171_R	176_K	1.016	1.00
74_G	116_L	0.999	1.00
55_R	92_L	0.998	1.00
93_V	97_G	0.994	1.00
46_G	109_R	0.988	1.00
127_H	133_I	0.970	1.00
94_D	100_V	0.964	1.00
151_E	154_T	0.961	1.00
83_L	86_F	0.958	1.00
55_R	104_D	0.957	1.00
59_L	68_A	0.938	1.00
112_H	142_R	0.925	1.00
29_K	33_S	0.920	1.00
97_G	127_H	0.912	1.00
138_K	141_F	0.910	1.00
168_H	171_R	0.908	1.00
32_L	36_R	0.905	1.00
89_D	131_Y	0.900	1.00
77_D	80_K	0.897	1.00
75_F	105_D	0.892	1.00
20_E	24_L	0.872	1.00
120_E	123_A	0.863	1.00
88_E	93_V	0.856	1.00
87_R	127_H	0.855	1.00
173_L	177_R	0.852	1.00
38_R	47_R	0.851	1.00
37_A	40_E	0.850	1.00
77_D	105_D	0.841	1.00
72_V	111_A	0.836	1.00
165_L	170_L	0.836	1.00
158_N	162_G	0.822	1.00
91_S	99_P	0.816	1.00
73_W	110_L	0.811	1.00
24_L	28_L	0.808	1.00
70_R	133_I	0.807	1.00
172_A	176_K	0.805	1.00
85_T	124_W	0.802	1.00
22_K	26_K	0.799	0.99
52_A	105_D	0.798	0.99
151_E	157_S	0.797	0.99
113_P	121_V	0.790	0.99
75_F	100_V	0.787	0.99
39_L	42_A	0.783	0.99
171_R	174_L	0.783	0.99
126_E	129_A	0.777	0.99
54_W	108_V	0.773	0.99
79_G	82_L	0.771	0.99
68_A	73_W	0.768	0.99
75_F	106_A	0.763	0.99
7_L	10_P	0.758	0.99
135_Q	138_K	0.758	0.99
33_S	37_A	0.756	0.99
149_D	153_E	0.752	0.99
122_A	126_E	0.751	0.99
152_R	157_S	0.749	0.99
119_E	122_A	0.746	0.99
39_L	64_V	0.741	0.99
113_P	142_R	0.732	0.99
76_Y	79_G	0.729	0.99
75_F	86_F	0.718	0.99
7_L	18_A	0.717	0.99
168_H	173_L	0.715	0.99
148_T	153_E	0.713	0.99
14_D	17_E	0.710	0.99
39_L	58_L	0.706	0.99
114_L	144_V	0.701	0.99
148_T	154_T	0.700	0.99
4_L	7_L	0.697	0.99
30_A	34_A	0.690	0.98
142_R	179_W	0.688	0.98
87_R	131_Y	0.685	0.98
11_V	14_D	0.685	0.98
31_V	34_A	0.684	0.98
88_E	130_D	0.681	0.98
168_H	172_A	0.681	0.98
116_L	140_L	0.681	0.98
38_R	61_H	0.679	0.98
150_A	154_T	0.677	0.98
135_Q	143_E	0.676	0.98
145_Y	151_E	0.671	0.98
156_Y	161_A	0.670	0.98
167_Q	170_L	0.662	0.98
88_E	131_Y	0.662	0.98
70_R	136_P	0.661	0.98
163_H	169_Q	0.660	0.98
111_A	140_L	0.657	0.98
39_L	67_L	0.657	0.98
58_L	64_V	0.656	0.98
165_L	173_L	0.656	0.98
157_S	163_H	0.654	0.98
12_K	15_D	0.651	0.98
97_G	132_E	0.650	0.98
83_L	87_R	0.649	0.98
169_Q	175_K	0.643	0.98
159_R	163_H	0.642	0.98
19_K	23_A	0.640	0.98
80_K	83_L	0.635	0.97
118_A	146_L	0.635	0.97
168_H	174_L	0.634	0.97
164_I	167_Q	0.634	0.97
163_H	177_R	0.631	0.97
57_R	64_V	0.630	0.97
21_L	25_K	0.628	0.97
6_S	9_A	0.627	0.97
91_S	130_D	0.626	0.97
84_G	100_V	0.623	0.97
167_Q	174_L	0.621	0.97
38_R	49_W	0.619	0.97
35_Q	42_A	0.619	0.97
89_D	130_D	0.613	0.97
95_A	131_Y	0.608	0.97
113_P	138_K	0.603	0.97
127_H	130_D	0.602	0.96
11_V	15_D	0.600	0.96
101_E	105_D	0.593	0.96
148_T	152_R	0.592	0.96
157_S	160_F	0.591	0.96
89_D	97_G	0.591	0.96
166_R	170_L	0.583	0.96
167_Q	172_A	0.581	0.96
172_A	175_K	0.581	0.96
93_V	99_P	0.576	0.95
2_K	6_S	0.571	0.95
87_R	97_G	0.570	0.95
37_A	41_R	0.569	0.95
35_Q	67_L	0.569	0.95
41_R	47_R	0.568	0.95
12_K	16_A	0.568	0.95
79_G	105_D	0.567	0.95
43_M	137_F	0.567	0.95
35_Q	49_W	0.567	0.95
75_F	84_G	0.564	0.95
59_L	65_G	0.563	0.95
157_S	161_A	0.561	0.95
119_E	123_A	0.559	0.95
76_Y	107_R	0.559	0.95
51_A	104_D	0.556	0.95
110_L	116_L	0.556	0.95
145_Y	160_F	0.556	0.95
100_V	103_P	0.554	0.94
40_E	136_P	0.553	0.94
41_R	44_L	0.551	0.94
142_R	145_Y	0.544	0.94
85_T	120_E	0.542	0.94
61_H	65_G	0.537	0.93
42_A	45_T	0.536	0.93
49_W	63_L	0.535	0.93
168_H	176_K	0.534	0.93
75_F	103_P	0.534	0.93
4_L	10_P	0.528	0.93
76_Y	80_K	0.528	0.93
116_L	121_V	0.525	0.93
160_F	163_H	0.525	0.93
173_L	176_K	0.524	0.93
163_H	173_L	0.521	0.92
86_F	92_L	0.519	0.92
138_K	148_T	0.518	0.92
13_K	18_A	0.518	0.92
93_V	100_V	0.517	0.92
166_R	173_L	0.516	0.92
166_R	176_K	0.516	0.92
141_F	145_Y	0.515	0.92
63_L	70_R	0.514	0.92
63_L	66_P	0.513	0.92
72_V	95_A	0.512	0.92
34_A	37_A	0.511	0.92
91_S	98_E	0.510	0.92
29_K	32_L	0.509	0.92
125_R	129_A	0.508	0.91
54_W	92_L	0.508	0.91
157_S	179_W	0.501	0.91
4_L	11_V	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
3cr8A	4	0.8045	11.6	0.94	Contact Map
3cuqB	1	0.4246	5.8	0.947	Contact Map
4c26A	1	0.1229	4.5	0.95	Contact Map
4gehA	1	0.4804	4.4	0.951	Contact Map
2wdcA	1	0.9218	4.1	0.951	Contact Map
4onqA	1	0.3799	3.7	0.952	Contact Map
1xmbA	1	0.2682	3.7	0.952	Contact Map
3k6tA	2	0.3017	3.5	0.953	Contact Map
1n08A	1	0.3017	3.4	0.953	Contact Map
4dq1A	2	0.8603	3.3	0.953	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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