DUF418 - PFAM28P - GREMLIN Contacts

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DUF418 - Protein of unknown function (DUF418)

PFAM:	PF04235	Sequences: LGRSGVLTDGERHRRLYRRLALIGLGIGLPLNLLGALLLAAGFPPPLLGLLGLLLYYLGRLLLALGYAALIVLLYRRGAGRRLLRPLAAVGRMALTNYLLQSLICTLIFYGYGLGLFGRLGRAQLLLIALAIWALQLLFSRWWLRRFRFGPLEWLWRSLTYGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	163 (161)
Sequences:	14065 (10810)
Seq/√Len:	851.9
META:	0.809

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_N	140_S	3.678	1.00
99_L	152_L	3.358	1.00
9_D	12_R	3.162	1.00
86_P	89_A	2.770	1.00
106_T	112_Y	2.758	1.00
21_A	70_L	2.724	1.00
89_A	141_R	2.517	1.00
142_W	146_R	2.372	1.00
141_R	145_R	2.303	1.00
149_F	154_W	2.295	1.00
5_G	8_T	2.276	1.00
26_G	30_P	2.268	1.00
25_L	67_Y	2.120	1.00
108_I	116_L	2.061	1.00
101_Q	136_Q	2.004	1.00
15_R	19_R	1.917	1.00
14_R	76_R	1.910	1.00
137_L	141_R	1.891	1.00
90_V	97_N	1.887	1.00
107_L	114_L	1.875	1.00
105_C	132_I	1.866	1.00
93_M	144_L	1.858	1.00
92_R	144_L	1.807	1.00
104_I	132_I	1.737	1.00
14_R	18_R	1.725	1.00
96_T	100_L	1.717	1.00
154_W	158_S	1.713	1.00
12_R	16_L	1.651	1.00
86_P	141_R	1.596	1.00
100_L	139_F	1.572	1.00
6_V	16_L	1.516	1.00
100_L	136_Q	1.489	1.00
106_T	110_Y	1.473	1.00
95_L	152_L	1.453	1.00
121_G	124_Q	1.422	1.00
27_I	30_P	1.412	1.00
19_R	23_I	1.392	1.00
116_L	120_L	1.378	1.00
9_D	13_H	1.376	1.00
124_Q	127_L	1.362	1.00
21_A	66_G	1.351	1.00
90_V	137_L	1.341	1.00
20_L	69_A	1.334	1.00
120_L	124_Q	1.323	1.00
13_H	16_L	1.319	1.00
77_R	80_G	1.312	1.00
97_N	136_Q	1.296	1.00
21_A	69_A	1.287	1.00
90_V	133_W	1.286	1.00
80_G	83_L	1.280	1.00
16_L	20_L	1.272	1.00
138_L	141_R	1.266	1.00
10_G	13_H	1.257	1.00
71_I	75_Y	1.254	1.00
23_I	26_G	1.254	1.00
30_P	34_L	1.244	1.00
127_L	131_A	1.242	1.00
22_L	26_G	1.230	1.00
25_L	66_G	1.216	1.00
63_L	67_Y	1.214	1.00
120_L	128_I	1.200	1.00
107_L	112_Y	1.186	1.00
24_G	69_A	1.182	1.00
116_L	119_R	1.180	1.00
120_L	125_L	1.171	1.00
138_L	142_W	1.163	1.00
16_L	19_R	1.148	1.00
158_S	162_G	1.132	1.00
102_S	106_T	1.127	1.00
135_L	139_F	1.121	1.00
72_V	76_R	1.120	1.00
18_R	73_L	1.112	1.00
20_L	24_G	1.094	1.00
123_A	127_L	1.092	1.00
134_A	138_L	1.084	1.00
148_R	154_W	1.083	1.00
56_Y	60_R	1.074	1.00
30_P	33_L	1.057	1.00
85_R	88_A	1.057	1.00
18_R	22_L	1.054	1.00
62_L	66_G	1.042	1.00
142_W	145_R	1.042	1.00
149_F	158_S	1.040	1.00
149_F	157_R	1.033	1.00
81_R	85_R	1.019	1.00
32_N	59_G	1.017	1.00
93_M	143_W	1.007	1.00
78_G	81_R	1.004	1.00
82_R	86_P	1.004	1.00
93_M	140_S	0.997	1.00
40_A	43_F	0.991	1.00
14_R	73_L	0.989	1.00
21_A	25_L	0.985	1.00
28_G	32_N	0.985	1.00
111_G	115_G	0.973	1.00
74_L	84_L	0.972	1.00
13_H	17_Y	0.969	1.00
83_L	86_P	0.967	1.00
100_L	104_I	0.967	1.00
159_L	162_G	0.949	1.00
18_R	21_A	0.923	1.00
11_E	76_R	0.920	1.00
17_Y	69_A	0.903	1.00
149_F	161_Y	0.888	1.00
70_L	74_L	0.884	1.00
37_L	40_A	0.880	1.00
5_G	9_D	0.877	1.00
45_P	48_L	0.872	1.00
68_A	72_V	0.869	1.00
99_L	102_S	0.865	1.00
108_I	128_I	0.848	1.00
86_P	137_L	0.848	1.00
103_L	152_L	0.846	1.00
81_R	84_L	0.843	1.00
28_G	66_G	0.835	1.00
156_W	159_L	0.834	1.00
2_G	8_T	0.830	1.00
105_C	109_F	0.830	1.00
93_M	139_F	0.828	1.00
37_L	41_A	0.828	1.00
69_A	73_L	0.826	1.00
136_Q	139_F	0.826	1.00
128_I	132_I	0.821	1.00
66_G	70_L	0.812	1.00
66_G	69_A	0.809	1.00
135_L	138_L	0.808	1.00
94_A	97_N	0.808	1.00
32_N	35_G	0.800	1.00
27_I	62_L	0.799	1.00
70_L	73_L	0.798	1.00
20_L	23_I	0.797	1.00
79_A	82_R	0.796	1.00
122_R	125_L	0.794	1.00
21_A	73_L	0.789	1.00
4_S	7_L	0.787	1.00
39_L	43_F	0.785	1.00
15_R	18_R	0.785	1.00
41_A	44_P	0.782	1.00
143_W	147_F	0.767	1.00
104_I	135_L	0.755	1.00
133_W	137_L	0.740	1.00
31_L	59_G	0.731	1.00
57_Y	60_R	0.729	1.00
39_L	44_P	0.719	1.00
129_A	133_W	0.718	1.00
64_A	68_A	0.716	1.00
87_L	137_L	0.709	1.00
104_I	107_L	0.706	1.00
26_G	66_G	0.700	1.00
29_L	32_N	0.695	1.00
46_P	50_L	0.692	1.00
125_L	129_A	0.685	1.00
54_L	58_L	0.684	1.00
148_R	158_S	0.683	1.00
130_L	134_A	0.683	1.00
6_V	17_Y	0.681	1.00
63_L	66_G	0.675	1.00
6_V	12_R	0.671	1.00
141_R	144_L	0.667	1.00
109_F	117_F	0.663	1.00
15_R	22_L	0.657	1.00
90_V	93_M	0.657	1.00
10_G	76_R	0.656	1.00
110_Y	113_G	0.656	1.00
144_L	148_R	0.648	1.00
40_A	44_P	0.646	1.00
4_S	8_T	0.644	1.00
44_P	47_L	0.644	1.00
67_Y	71_I	0.643	1.00
29_L	33_L	0.640	1.00
75_Y	78_G	0.639	1.00
74_L	80_G	0.638	1.00
38_L	41_A	0.631	1.00
80_G	84_L	0.628	1.00
97_N	139_F	0.628	1.00
85_R	89_A	0.623	1.00
93_M	96_T	0.621	1.00
132_I	136_Q	0.619	1.00
97_N	100_L	0.617	1.00
24_G	66_G	0.613	1.00
82_R	85_R	0.610	1.00
31_L	35_G	0.610	1.00
47_L	50_L	0.608	1.00
119_R	122_R	0.606	1.00
8_T	12_R	0.605	1.00
65_L	69_A	0.604	1.00
21_A	24_G	0.604	1.00
73_L	77_R	0.604	1.00
25_L	30_P	0.600	1.00
104_I	108_I	0.597	1.00
24_G	62_L	0.593	1.00
147_F	154_W	0.593	1.00
76_R	80_G	0.593	1.00
131_A	134_A	0.592	1.00
6_V	20_L	0.588	1.00
60_R	64_A	0.583	1.00
32_N	56_Y	0.579	1.00
44_P	48_L	0.579	1.00
56_Y	59_G	0.579	1.00
38_L	43_F	0.579	1.00
10_G	72_V	0.578	1.00
43_F	48_L	0.576	1.00
28_G	63_L	0.571	1.00
45_P	50_L	0.571	1.00
2_G	7_L	0.565	1.00
155_L	158_S	0.565	1.00
57_Y	61_L	0.563	1.00
21_A	26_G	0.561	1.00
17_Y	21_A	0.560	1.00
47_L	51_L	0.558	1.00
26_G	29_L	0.556	1.00
81_R	86_P	0.555	1.00
17_Y	20_L	0.549	1.00
38_L	42_G	0.547	1.00
58_L	61_L	0.545	1.00
108_I	114_L	0.544	1.00
126_L	129_A	0.543	1.00
11_E	14_R	0.542	1.00
39_L	42_G	0.542	1.00
144_L	147_F	0.540	1.00
22_L	25_L	0.540	1.00
2_G	5_G	0.539	1.00
53_L	56_Y	0.538	1.00
33_L	36_A	0.537	1.00
86_P	138_L	0.537	1.00
101_Q	132_I	0.535	1.00
28_G	31_L	0.534	1.00
155_L	159_L	0.529	1.00
86_P	90_V	0.529	1.00
107_L	110_Y	0.523	1.00
49_G	52_G	0.521	1.00
31_L	62_L	0.518	1.00
78_G	84_L	0.517	1.00
112_Y	117_F	0.517	1.00
42_G	45_P	0.517	1.00
64_A	67_Y	0.510	1.00
96_T	139_F	0.505	1.00
23_I	27_I	0.502	1.00
40_A	45_P	0.501	1.00
43_F	47_L	0.501	1.00
58_L	62_L	0.501	1.00
85_R	141_R	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
3mktA	1	0.9202	7.1	0.923	Contact Map
3l1lA	2	0.8037	6.8	0.924	Contact Map
4lz6A	1	0.8773	4.8	0.929	Contact Map
4i0uA	4	0.4417	4.4	0.931	Contact Map
4humA	1	0.9141	3.9	0.932	Contact Map
4ev6A	3	0.454	3.9	0.932	Contact Map
3giaA	1	0.8221	2.7	0.937	Contact Map
2a65A	2	0.5092	2.5	0.939	Contact Map
4ryoA	1	0.816	2.3	0.94	Contact Map
4uc1A	3	0.8221	2.2	0.94	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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