DUF2867 - PFAM28P - GREMLIN Contacts

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DUF2867 - Protein of unknown function (DUF2867)

PFAM:	PF11066	Sequences: WAGGARLVDVRAVPVPGDAPPETVFRVIERMIGGEPGWYYALWRLRDRLVGGVGLRRGRAGLGSRDPDELRVGDALDFWRVEALEPDEMKLPIGDAWLEFRVSPVGGGGGTRLRQTALFRPRGLLGRLYWYAILPFHRLIFRGM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	144 (132)
Sequences:	13638 (8185)
Seq/√Len:	712.4
META:	0.872

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_A	112_R	3.163	1.00
14_P	112_R	2.640	1.00
10_V	114_R	2.592	1.00
14_P	110_G	2.487	1.00
133_I	136_F	2.320	1.00
14_P	105_V	2.284	1.00
40_Y	143_G	2.272	1.00
95_D	120_R	2.237	1.00
23_T	26_R	2.130	1.00
20_P	23_T	2.113	1.00
10_V	116_T	2.057	1.00
103_S	114_R	1.991	1.00
138_R	142_R	1.954	1.00
66_D	69_E	1.949	1.00
12_A	114_R	1.917	1.00
134_L	138_R	1.903	1.00
105_V	112_R	1.891	1.00
25_F	84_L	1.848	1.00
25_F	29_E	1.843	1.00
72_V	83_A	1.828	1.00
30_R	68_D	1.683	1.00
131_Y	134_L	1.662	1.00
102_V	111_T	1.647	1.00
32_I	39_Y	1.642	1.00
22_E	87_D	1.639	1.00
103_S	112_R	1.633	1.00
104_P	111_T	1.616	1.00
26_R	29_E	1.595	1.00
80_R	88_E	1.590	1.00
24_V	27_V	1.514	1.00
48_R	51_G	1.513	1.00
40_Y	139_L	1.510	1.00
30_R	36_P	1.433	1.00
70_L	76_L	1.432	1.00
121_P	130_W	1.409	1.00
100_F	113_L	1.399	1.00
16_P	19_A	1.378	1.00
133_I	140_I	1.375	1.00
101_R	114_R	1.368	1.00
65_R	69_E	1.336	1.00
105_V	110_G	1.333	1.00
25_F	28_I	1.329	1.00
72_V	84_L	1.320	1.00
11_R	142_R	1.307	1.00
29_E	84_L	1.266	1.00
27_V	30_R	1.256	1.00
23_T	27_V	1.246	1.00
136_F	140_I	1.242	1.00
127_R	131_Y	1.238	1.00
6_R	120_R	1.237	1.00
28_I	102_V	1.219	1.00
48_R	52_G	1.207	1.00
47_D	52_G	1.173	1.00
106_G	109_G	1.154	1.00
16_P	20_P	1.107	1.00
65_R	71_R	1.088	1.00
88_E	103_S	1.084	1.00
24_V	113_L	1.050	1.00
15_V	24_V	1.040	1.00
27_V	36_P	1.039	1.00
100_F	115_Q	1.037	1.00
106_G	110_G	1.030	1.00
29_E	68_D	1.026	1.00
104_P	110_G	1.020	1.00
101_R	116_T	1.018	1.00
11_R	138_R	1.005	1.00
8_V	118_L	1.000	1.00
39_Y	43_W	0.996	1.00
124_L	128_L	0.990	1.00
6_R	121_P	0.987	1.00
42_L	136_F	0.981	1.00
47_D	58_G	0.980	1.00
47_D	57_R	0.977	1.00
36_P	39_Y	0.976	1.00
15_V	113_L	0.964	1.00
47_D	51_G	0.964	1.00
24_V	28_I	0.962	1.00
50_V	55_L	0.957	1.00
67_P	71_R	0.951	1.00
82_E	97_W	0.950	1.00
21_P	104_P	0.949	1.00
94_G	101_R	0.940	1.00
70_L	73_G	0.938	1.00
7_L	130_W	0.928	1.00
91_L	96_A	0.904	1.00
4_G	120_R	0.904	1.00
75_A	80_R	0.894	1.00
23_T	28_I	0.894	1.00
84_L	89_M	0.885	1.00
26_R	68_D	0.872	1.00
29_E	69_E	0.863	1.00
70_L	84_L	0.857	1.00
130_W	134_L	0.850	1.00
50_V	53_V	0.844	1.00
35_E	67_P	0.840	1.00
77_D	81_V	0.839	1.00
125_L	128_L	0.837	1.00
21_P	25_F	0.832	1.00
99_E	118_L	0.828	1.00
70_L	74_D	0.824	1.00
94_G	99_E	0.812	1.00
7_L	133_I	0.804	1.00
71_R	74_D	0.803	1.00
47_D	50_V	0.801	1.00
124_L	127_R	0.797	1.00
65_R	74_D	0.796	1.00
15_V	19_A	0.789	1.00
35_E	39_Y	0.786	1.00
91_L	119_F	0.780	1.00
49_L	52_G	0.775	1.00
132_A	135_P	0.772	1.00
24_V	29_E	0.771	1.00
51_G	59_R	0.766	1.00
9_D	133_I	0.762	1.00
44_R	48_R	0.759	1.00
16_P	110_G	0.753	1.00
92_P	119_F	0.752	1.00
21_P	24_V	0.750	1.00
22_E	26_R	0.749	1.00
43_W	47_D	0.742	1.00
15_V	111_T	0.741	1.00
100_F	117_A	0.740	1.00
37_G	40_Y	0.732	1.00
97_W	118_L	0.730	1.00
69_E	74_D	0.728	1.00
20_P	24_V	0.722	1.00
99_E	122_R	0.709	1.00
24_V	111_T	0.708	1.00
41_A	139_L	0.697	1.00
27_V	39_Y	0.688	1.00
75_A	78_F	0.686	1.00
95_D	118_L	0.686	1.00
17_G	20_P	0.683	1.00
96_A	117_A	0.681	1.00
46_R	129_Y	0.675	1.00
105_V	108_G	0.673	1.00
7_L	121_P	0.673	1.00
82_E	92_P	0.672	1.00
119_F	130_W	0.665	1.00
47_D	59_R	0.660	1.00
19_A	23_T	0.658	1.00
42_L	133_I	0.658	1.00
36_P	68_D	0.654	1.00
78_F	91_L	0.653	1.00
94_G	122_R	0.653	1.00
26_R	30_R	0.651	1.00
76_L	81_V	0.645	1.00
54_G	58_G	0.640	1.00
96_A	130_W	0.640	1.00
133_I	142_R	0.639	1.00
34_G	37_G	0.637	1.00
95_D	122_R	0.631	1.00
117_A	137_H	0.625	1.00
65_R	70_L	0.623	1.00
97_W	115_Q	0.621	1.00
125_L	132_A	0.620	1.00
88_E	105_V	0.609	1.00
123_G	126_G	0.607	1.00
133_I	138_R	0.603	1.00
104_P	113_L	0.600	1.00
11_R	117_A	0.599	1.00
19_A	27_V	0.599	1.00
83_A	86_P	0.599	1.00
32_I	89_M	0.595	1.00
40_Y	140_I	0.590	1.00
7_L	131_Y	0.587	1.00
17_G	111_T	0.584	1.00
106_G	111_T	0.584	1.00
135_P	139_L	0.583	1.00
76_L	80_R	0.580	1.00
50_V	95_D	0.573	1.00
49_L	53_V	0.572	1.00
69_E	72_V	0.571	1.00
58_G	78_F	0.566	1.00
97_W	127_R	0.561	1.00
12_A	16_P	0.559	1.00
115_Q	141_F	0.555	1.00
37_G	41_A	0.552	1.00
44_R	55_L	0.549	1.00
66_D	71_R	0.547	1.00
7_L	127_R	0.544	1.00
14_P	111_T	0.538	1.00
104_P	109_G	0.536	1.00
47_D	56_R	0.533	1.00
38_W	140_I	0.530	1.00
95_D	98_L	0.528	1.00
94_G	100_F	0.526	1.00
10_V	103_S	0.521	1.00
90_K	99_E	0.518	1.00
51_G	57_R	0.512	1.00
58_G	75_A	0.511	1.00
54_G	96_A	0.511	1.00
68_D	72_V	0.511	1.00
34_G	43_W	0.508	0.99
66_D	70_L	0.507	0.99
56_R	88_E	0.503	0.99
29_E	86_P	0.502	0.99
25_F	87_D	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
2pcsA	1	0.8611	14.8	0.92	Contact Map
2ns9A	2	0.9097	8.3	0.929	Contact Map
3ggnA	2	0.7778	7.5	0.93	Contact Map
3ossC	1	0.4375	5.7	0.934	Contact Map
3p9vA	2	0.9028	5.5	0.934	Contact Map
1t17A	1	0.8889	4.6	0.937	Contact Map
1vjkA	1	0.5069	4.5	0.937	Contact Map
2m19A	1	0.5556	3.5	0.94	Contact Map
2qjlA	1	0.5694	3.1	0.942	Contact Map
3f59A	1	0.3403	2.7	0.943	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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