DUF4378 - PFAM28P - GREMLIN Contacts

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DUF4378 - Domain of unknown function (DUF4378)

PFAM:	PF14309	Sequences: DFSYVKDILSASGLLGEDSDSLLARWHSSDSPLDPSLFDELEKKYSLESRSDRKLLFDCVNEILLEILERYSFSYPPPWVSSVKPRIRPPVPSGEKLLEEVWKEISRWLLDELVDKDLSGGGGWLDLREEIEEIGLEIERLILDDLVEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	149 (148)
Sequences:	1214 (915)
Seq/√Len:	75.2
META:	0.086

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_Y	38_F	5.828	1.00
38_F	42_E	3.162	1.00
75_Y	78_P	2.930	1.00
2_F	5_V	2.886	1.00
38_F	54_K	2.727	1.00
4_Y	42_E	2.357	1.00
2_F	102_W	2.323	1.00
42_E	53_R	2.221	1.00
58_D	124_W	2.142	1.00
110_L	118_L	2.137	1.00
62_E	149_E	2.132	1.00
82_S	85_P	2.048	1.00
118_L	122_G	1.906	1.00
60_V	129_E	1.866	1.00
140_R	143_L	1.835	1.00
22_L	29_S	1.831	1.00
76_P	81_S	1.830	1.00
79_W	83_V	1.827	1.00
5_V	123_G	1.798	1.00
5_V	101_V	1.772	1.00
62_E	117_D	1.756	1.00
146_L	149_E	1.698	1.00
111_D	118_L	1.654	1.00
75_Y	79_W	1.599	0.99
37_L	41_L	1.557	0.99
73_F	77_P	1.550	0.99
79_W	84_K	1.537	0.99
79_W	82_S	1.532	0.99
111_D	114_V	1.528	0.99
55_L	117_D	1.488	0.99
56_L	105_I	1.480	0.99
8_I	60_V	1.456	0.99
4_Y	57_F	1.451	0.99
19_S	23_L	1.404	0.99
114_V	118_L	1.392	0.99
23_L	26_W	1.385	0.99
80_V	84_K	1.353	0.98
57_F	61_N	1.331	0.98
26_W	29_S	1.324	0.98
73_F	79_W	1.273	0.97
97_L	139_E	1.271	0.97
74_S	77_P	1.258	0.97
80_V	83_V	1.258	0.97
112_E	136_L	1.251	0.97
81_S	85_P	1.246	0.97
48_E	147_V	1.244	0.97
59_C	105_I	1.243	0.97
32_P	139_E	1.235	0.97
135_G	139_E	1.212	0.96
47_L	64_L	1.209	0.96
104_E	108_W	1.202	0.96
38_F	53_R	1.201	0.96
77_P	82_S	1.201	0.96
44_K	50_R	1.195	0.96
9_L	113_L	1.169	0.96
41_L	107_R	1.152	0.95
106_S	135_G	1.146	0.95
3_S	8_I	1.141	0.95
74_S	79_W	1.131	0.95
63_I	104_E	1.129	0.95
113_L	118_L	1.108	0.94
54_K	104_E	1.097	0.94
13_G	61_N	1.091	0.94
141_L	145_D	1.068	0.93
77_P	80_V	1.064	0.93
136_L	143_L	1.055	0.93
12_S	141_L	1.039	0.92
73_F	76_P	1.029	0.92
113_L	133_E	1.027	0.92
69_E	114_V	1.027	0.92
55_L	123_G	1.025	0.91
122_G	127_L	1.021	0.91
114_V	119_S	1.019	0.91
36_S	137_E	1.008	0.91
97_L	106_S	1.002	0.91
10_S	15_L	0.993	0.90
60_V	141_L	0.988	0.90
94_G	103_K	0.976	0.89
59_C	115_D	0.975	0.89
42_E	45_Y	0.971	0.89
50_R	53_R	0.966	0.89
26_W	105_I	0.961	0.89
60_V	115_D	0.959	0.89
121_G	142_I	0.958	0.88
99_E	103_K	0.958	0.88
119_S	122_G	0.946	0.88
96_K	125_L	0.944	0.88
6_K	59_C	0.944	0.88
50_R	57_F	0.944	0.88
5_V	11_A	0.930	0.87
45_Y	130_E	0.925	0.87
45_Y	56_L	0.923	0.87
116_K	135_G	0.914	0.86
6_K	53_R	0.913	0.86
80_V	85_P	0.912	0.86
42_E	57_F	0.911	0.86
53_R	109_L	0.909	0.86
144_D	149_E	0.908	0.86
16_G	138_I	0.898	0.85
138_I	147_V	0.897	0.85
86_R	89_P	0.896	0.85
90_P	114_V	0.896	0.85
94_G	97_L	0.890	0.84
113_L	117_D	0.879	0.84
131_I	135_G	0.874	0.83
55_L	66_E	0.873	0.83
11_A	58_D	0.856	0.82
13_G	32_P	0.856	0.82
61_N	65_L	0.851	0.82
42_E	54_K	0.847	0.81
36_S	130_E	0.836	0.81
48_E	106_S	0.833	0.80
5_V	65_L	0.833	0.80
26_W	30_D	0.832	0.80
22_L	27_H	0.827	0.80
78_P	84_K	0.819	0.79
38_F	41_L	0.819	0.79
40_E	61_N	0.818	0.79
52_D	98_L	0.807	0.78
6_K	12_S	0.806	0.78
72_S	77_P	0.798	0.77
74_S	84_K	0.794	0.77
128_R	145_D	0.792	0.77
82_S	86_R	0.792	0.77
8_I	40_E	0.787	0.76
109_L	137_E	0.773	0.75
7_D	52_D	0.772	0.75
27_H	30_D	0.770	0.75
102_W	106_S	0.765	0.74
84_K	87_I	0.763	0.74
97_L	111_D	0.763	0.74
110_L	113_L	0.761	0.74
67_I	104_E	0.748	0.73
67_I	144_D	0.745	0.72
73_F	81_S	0.743	0.72
25_R	29_S	0.741	0.72
140_R	149_E	0.740	0.72
63_I	108_W	0.739	0.72
83_V	86_R	0.734	0.71
74_S	78_P	0.733	0.71
115_D	118_L	0.730	0.71
52_D	130_E	0.730	0.71
6_K	10_S	0.729	0.71
117_D	132_E	0.729	0.71
33_L	61_N	0.725	0.70
26_W	31_S	0.724	0.70
58_D	61_N	0.719	0.70
54_K	137_E	0.711	0.69
21_S	134_I	0.703	0.68
74_S	136_L	0.688	0.66
4_Y	112_E	0.687	0.66
35_P	66_E	0.683	0.66
6_K	11_A	0.682	0.66
37_L	98_L	0.681	0.66
124_W	136_L	0.680	0.65
72_S	82_S	0.679	0.65
143_L	146_L	0.668	0.64
39_D	113_L	0.663	0.63
7_D	60_V	0.662	0.63
59_C	108_W	0.662	0.63
31_S	37_L	0.657	0.63
59_C	102_W	0.643	0.61
101_V	109_L	0.643	0.61
114_V	121_G	0.642	0.61
54_K	122_G	0.637	0.60
12_S	143_L	0.637	0.60
13_G	94_G	0.631	0.60
94_G	98_L	0.622	0.59
11_A	23_L	0.617	0.58
24_A	27_H	0.616	0.58
60_V	90_P	0.616	0.58
8_I	52_D	0.615	0.58
18_D	29_S	0.613	0.57
50_R	54_K	0.613	0.57
41_L	50_R	0.613	0.57
13_G	97_L	0.612	0.57
66_E	120_G	0.611	0.57
136_L	144_D	0.608	0.57
25_R	31_S	0.604	0.56
33_L	40_E	0.600	0.56
59_C	116_K	0.595	0.55
32_P	55_L	0.594	0.55
37_L	129_E	0.594	0.55
34_D	51_S	0.583	0.54
32_P	59_C	0.582	0.54
116_K	130_E	0.581	0.54
79_W	85_P	0.578	0.53
34_D	66_E	0.572	0.52
12_S	64_L	0.567	0.52
109_L	148_E	0.567	0.52
120_G	143_L	0.564	0.51
78_P	81_S	0.564	0.51
122_G	132_E	0.561	0.51
93_S	105_I	0.561	0.51
103_K	142_I	0.561	0.51
54_K	89_P	0.555	0.50
43_K	48_E	0.552	0.50
46_S	99_E	0.549	0.49
10_S	143_L	0.546	0.49
23_L	146_L	0.546	0.49
84_K	88_R	0.539	0.48
65_L	68_L	0.539	0.48
8_I	15_L	0.536	0.48
89_P	93_S	0.536	0.48
55_L	128_R	0.532	0.47
128_R	132_E	0.531	0.47
72_S	78_P	0.531	0.47
81_S	84_K	0.531	0.47
57_F	140_R	0.525	0.46
93_S	99_E	0.525	0.46
27_H	149_E	0.524	0.46
84_K	141_L	0.518	0.46
30_D	96_K	0.514	0.45
3_S	103_K	0.511	0.45
140_R	144_D	0.511	0.45
22_L	68_L	0.509	0.44
37_L	137_E	0.509	0.44
46_S	148_E	0.507	0.44
50_R	83_V	0.506	0.44
53_R	139_E	0.505	0.44
7_D	14_L	0.502	0.44
102_W	120_G	0.500	0.43

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
2lseA	1	0.5101	7.5	0.928	Contact Map
2dmeA	1	0.3893	5.1	0.933	Contact Map
4kk0A	2	0.8591	4.5	0.935	Contact Map
1ldjA	1	0.3423	3.3	0.939	Contact Map
1q1vA	1	0.3557	3.1	0.94	Contact Map
2vxoA	2	0.4564	3.1	0.94	Contact Map
2btmA	2	0.9128	2.9	0.941	Contact Map
3upsA	2	0.3624	2.6	0.942	Contact Map
3p9aA	4	0.5302	2.4	0.944	Contact Map
1fc6A	1	0.3624	2.3	0.944	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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