DUF3035 - PFAM28P - GREMLIN Contacts

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DUF3035 - Protein of unknown function (DUF3035)

PFAM:	PF11233	Sequences: LALAGCGSSTRRALGLTKSAPDEFAVVTRAPLSMPPDYNLRPPPTPGAPRPQELTPRAQARAALGGNPAAAAPAAGGRSAGEQALLAKAGADGADPNIRQTVDAEDAALRRKDRSFTDRLLFWRDPYPPGQVLDAAAEAERLRENGALGPSAP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	153 (147)
Sequences:	2603 (1964)
Seq/√Len:	162.0
META:	0.882

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
138_E	141_R	4.626	1.00
101_T	105_E	3.658	1.00
37_D	40_L	3.560	1.00
45_T	48_A	3.062	1.00
139_A	143_R	2.852	1.00
134_D	137_A	2.841	1.00
34_M	38_Y	2.816	1.00
142_L	147_A	2.324	1.00
10_T	14_L	2.152	1.00
97_N	100_Q	2.140	1.00
137_A	140_E	2.081	1.00
12_R	17_T	2.080	1.00
55_T	58_A	2.043	1.00
140_E	144_E	2.032	1.00
140_E	143_R	2.018	1.00
97_N	101_T	1.923	1.00
138_E	142_L	1.905	1.00
95_D	101_T	1.903	1.00
50_R	53_E	1.828	1.00
84_A	88_K	1.821	1.00
145_N	150_P	1.817	1.00
79_S	82_E	1.784	1.00
144_E	148_L	1.779	1.00
11_R	17_T	1.747	1.00
38_Y	41_R	1.704	1.00
47_G	50_R	1.646	1.00
100_Q	104_A	1.617	1.00
54_L	59_Q	1.601	1.00
56_P	59_Q	1.548	1.00
15_G	18_K	1.514	1.00
106_D	109_L	1.512	1.00
11_R	16_L	1.510	1.00
80_A	84_A	1.508	1.00
9_S	12_R	1.504	1.00
142_L	146_G	1.503	1.00
56_P	60_A	1.485	1.00
29_R	33_S	1.457	1.00
2_A	5_G	1.429	1.00
33_S	51_P	1.412	1.00
46_P	50_R	1.408	1.00
81_G	85_L	1.391	1.00
141_R	145_N	1.388	1.00
13_A	18_K	1.377	1.00
145_N	148_L	1.375	1.00
103_D	106_D	1.371	1.00
80_A	83_Q	1.356	1.00
117_T	120_L	1.334	1.00
136_A	140_E	1.306	1.00
145_N	149_G	1.287	1.00
65_G	68_P	1.273	1.00
68_P	72_A	1.265	1.00
10_T	13_A	1.244	1.00
36_P	40_L	1.232	1.00
86_L	89_A	1.227	1.00
56_P	63_A	1.220	1.00
46_P	49_P	1.217	1.00
136_A	139_A	1.211	1.00
98_I	101_T	1.201	1.00
106_D	110_R	1.193	1.00
83_Q	87_A	1.179	1.00
109_L	113_D	1.165	1.00
11_R	14_L	1.146	1.00
132_V	135_A	1.140	1.00
27_V	82_E	1.108	1.00
86_L	91_A	1.101	1.00
37_D	41_R	1.086	1.00
142_L	145_N	1.082	0.99
104_A	108_A	1.079	0.99
10_T	16_L	1.058	0.99
109_L	112_K	1.055	0.99
108_A	111_R	1.052	0.99
61_R	65_G	1.052	0.99
114_R	118_D	1.037	0.99
60_A	63_A	1.032	0.99
61_R	71_A	1.018	0.99
11_R	15_G	0.995	0.99
5_G	13_A	0.993	0.99
90_G	99_R	0.969	0.99
116_F	120_L	0.968	0.99
55_T	59_Q	0.954	0.99
69_A	72_A	0.937	0.99
29_R	52_Q	0.932	0.98
113_D	117_T	0.914	0.98
10_T	15_G	0.898	0.98
140_E	148_L	0.896	0.98
67_N	70_A	0.890	0.98
82_E	89_A	0.889	0.98
46_P	52_Q	0.888	0.98
118_D	123_W	0.880	0.98
21_P	24_F	0.880	0.98
145_N	151_S	0.869	0.98
142_L	149_G	0.856	0.97
88_K	110_R	0.850	0.97
81_G	84_A	0.848	0.97
142_L	148_L	0.836	0.97
57_R	61_R	0.834	0.97
12_R	19_S	0.811	0.96
4_A	8_S	0.807	0.96
70_A	73_P	0.806	0.96
58_A	61_R	0.803	0.96
133_L	145_N	0.801	0.96
115_S	118_D	0.799	0.96
21_P	47_G	0.798	0.96
125_D	128_P	0.796	0.96
47_G	52_Q	0.790	0.96
13_A	16_L	0.785	0.96
124_R	129_P	0.785	0.96
119_R	126_P	0.780	0.95
16_L	19_S	0.778	0.95
135_A	138_E	0.768	0.95
85_L	88_K	0.768	0.95
103_D	111_R	0.761	0.95
144_E	150_P	0.760	0.95
11_R	28_T	0.756	0.95
77_G	80_A	0.756	0.95
68_P	73_P	0.749	0.94
36_P	41_R	0.746	0.94
3_L	6_C	0.738	0.94
128_P	132_V	0.736	0.94
30_A	59_Q	0.735	0.94
78_R	83_Q	0.734	0.94
29_R	112_K	0.732	0.94
133_L	138_E	0.725	0.93
82_E	86_L	0.717	0.93
56_P	64_L	0.717	0.93
124_R	127_Y	0.714	0.93
4_A	128_P	0.713	0.93
133_L	149_G	0.708	0.92
146_G	149_G	0.708	0.92
30_A	36_P	0.699	0.92
22_D	26_V	0.698	0.92
32_L	35_P	0.688	0.91
91_A	95_D	0.687	0.91
12_R	116_F	0.687	0.91
133_L	146_G	0.671	0.90
34_M	37_D	0.669	0.90
60_A	64_L	0.665	0.90
12_R	15_G	0.659	0.90
25_A	28_T	0.656	0.89
62_A	67_N	0.656	0.89
133_L	150_P	0.655	0.89
13_A	19_S	0.653	0.89
99_R	102_V	0.649	0.89
55_T	71_A	0.647	0.89
28_T	78_R	0.643	0.88
134_D	138_E	0.643	0.88
130_G	140_E	0.641	0.88
26_V	29_R	0.640	0.88
90_G	94_A	0.640	0.88
143_R	148_L	0.637	0.88
135_A	139_A	0.637	0.88
75_A	78_R	0.635	0.88
30_A	135_A	0.635	0.88
92_D	97_N	0.635	0.88
96_P	105_E	0.634	0.88
70_A	77_G	0.626	0.87
71_A	76_G	0.622	0.87
11_R	92_D	0.622	0.87
102_V	106_D	0.617	0.86
86_L	111_R	0.615	0.86
73_P	100_Q	0.612	0.86
86_L	90_G	0.606	0.85
64_L	67_N	0.604	0.85
13_A	20_A	0.599	0.85
113_D	116_F	0.596	0.84
118_D	121_L	0.590	0.84
30_A	34_M	0.590	0.84
6_C	35_P	0.590	0.84
148_L	151_S	0.586	0.83
62_A	65_G	0.580	0.83
93_G	110_R	0.577	0.82
100_Q	111_R	0.576	0.82
55_T	67_N	0.576	0.82
116_F	122_F	0.574	0.82
113_D	119_R	0.572	0.82
116_F	119_R	0.568	0.81
77_G	110_R	0.567	0.81
21_P	44_P	0.566	0.81
143_R	149_G	0.566	0.81
137_A	150_P	0.565	0.81
29_R	34_M	0.565	0.81
25_A	137_A	0.565	0.81
15_G	19_S	0.563	0.81
88_K	92_D	0.559	0.80
113_D	135_A	0.553	0.80
132_V	145_N	0.551	0.79
69_A	73_P	0.549	0.79
11_R	98_I	0.544	0.79
26_V	139_A	0.544	0.79
104_A	110_R	0.542	0.78
46_P	53_E	0.541	0.78
104_A	107_A	0.538	0.78
115_S	126_P	0.538	0.78
44_P	47_G	0.537	0.78
9_S	13_A	0.535	0.77
47_G	60_A	0.534	0.77
34_M	53_E	0.529	0.77
86_L	142_L	0.529	0.77
46_P	51_P	0.529	0.77
22_D	25_A	0.528	0.76
39_N	84_A	0.527	0.76
51_P	103_D	0.524	0.76
114_R	119_R	0.521	0.76
4_A	73_P	0.521	0.76
109_L	131_Q	0.520	0.75
95_D	134_D	0.519	0.75
15_G	123_W	0.517	0.75
63_A	67_N	0.515	0.75
82_E	142_L	0.513	0.74
72_A	82_E	0.513	0.74
118_D	122_F	0.511	0.74
12_R	16_L	0.511	0.74
139_A	147_A	0.510	0.74
13_A	17_T	0.506	0.73
87_A	129_P	0.505	0.73
100_Q	107_A	0.504	0.73
107_A	110_R	0.502	0.73
78_R	110_R	0.502	0.73
46_P	63_A	0.500	0.73
79_S	90_G	0.500	0.73

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
3tgoC	2	0.8235	56	0.903	Contact Map
3zbiC	1	0.183	10.3	0.933	Contact Map
3df0C	1	0.2288	7.8	0.937	Contact Map
4cbhA	1	0.5294	5.2	0.942	Contact Map
4p5wA	2	0.1765	5.2	0.942	Contact Map
2cmeA	2	0.1961	3.9	0.945	Contact Map
3tu5B	1	0	2.2	0.952	Contact Map
2gtvX	1	0.4052	1.7	0.955	Contact Map
1j8bA	2	0.1765	1.7	0.955	Contact Map
1th8B	1	0.2549	1.6	0.955	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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