DUF4254 - PFAM28P - GREMLIN Contacts

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DUF4254 - Protein of unknown function (DUF4254)

PFAM:	PF14063	Sequences: EHLLYRKHWIDTVQWHLEDIIRDPDIDPVEALALKRRIDRSNQDRTDLVERIDSYFLEKLKDVKPKPDARINTESPAWAIDRLSILALKIYHMREEAERTDASEEHRAKCQAKLAVLLEQRADLSTAIDQLLDDIAAGRKYMKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	144 (142)
Sequences:	4087 (2127)
Seq/√Len:	178.5
META:	0.899

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_R	98_E	3.654	1.00
73_T	79_A	3.066	1.00
30_E	33_A	2.726	1.00
104_E	108_A	2.575	1.00
102_A	106_H	2.455	1.00
66_K	139_R	2.434	1.00
94_R	118_L	2.302	1.00
9_W	13_V	2.229	1.00
134_D	139_R	2.198	1.00
111_Q	115_A	2.125	1.00
79_A	128_I	2.124	1.00
126_T	130_Q	2.072	1.00
70_R	130_Q	2.069	1.00
17_L	37_R	2.019	1.00
40_R	44_D	1.975	1.00
51_R	54_S	1.947	1.00
10_I	44_D	1.857	1.00
97_A	107_R	1.850	1.00
119_E	143_K	1.833	1.00
73_T	127_A	1.810	1.00
58_E	61_K	1.795	1.00
87_A	121_R	1.748	1.00
108_A	112_A	1.715	1.00
20_I	34_L	1.687	1.00
13_V	41_S	1.663	1.00
3_L	51_R	1.573	1.00
17_L	20_I	1.553	1.00
134_D	140_K	1.552	1.00
107_R	111_Q	1.537	1.00
112_A	115_A	1.526	1.00
13_V	17_L	1.521	1.00
109_K	112_A	1.488	1.00
17_L	34_L	1.484	1.00
93_M	117_L	1.442	1.00
104_E	107_R	1.421	1.00
133_D	137_A	1.402	1.00
123_D	143_K	1.362	1.00
27_D	30_E	1.351	1.00
133_D	136_A	1.344	1.00
96_E	99_R	1.341	1.00
100_T	107_R	1.340	1.00
70_R	140_K	1.317	1.00
94_R	97_A	1.297	1.00
21_I	31_A	1.252	1.00
17_L	41_S	1.246	1.00
8_H	84_S	1.245	1.00
33_A	37_R	1.211	1.00
43_Q	47_D	1.182	1.00
29_V	33_A	1.168	1.00
79_A	127_A	1.159	1.00
129_D	133_D	1.155	1.00
90_I	117_L	1.141	1.00
106_H	110_C	1.116	1.00
30_E	34_L	1.113	1.00
130_Q	134_D	1.106	1.00
90_I	118_L	1.104	1.00
109_K	113_K	1.093	1.00
93_M	113_K	1.092	1.00
49_V	78_W	1.090	1.00
16_H	92_H	1.090	1.00
10_I	48_L	1.089	1.00
105_E	109_K	1.087	1.00
12_T	16_H	1.078	1.00
23_D	30_E	1.075	1.00
28_P	32_L	1.069	1.00
16_H	95_E	1.068	1.00
3_L	6_R	1.047	1.00
60_L	135_I	1.044	1.00
91_Y	95_E	1.036	1.00
20_I	23_D	1.033	1.00
35_K	39_D	1.010	0.99
12_T	88_L	1.003	0.99
4_L	7_K	0.999	0.99
105_E	108_A	0.998	0.99
103_S	107_R	0.995	0.99
71_I	141_Y	0.983	0.99
108_A	111_Q	0.980	0.99
55_Y	59_K	0.977	0.99
26_I	31_A	0.976	0.99
76_P	142_M	0.974	0.99
48_L	51_R	0.973	0.99
122_A	126_T	0.972	0.99
93_M	110_C	0.969	0.99
27_D	32_L	0.965	0.99
11_D	14_Q	0.964	0.99
90_I	114_L	0.954	0.99
76_P	132_L	0.947	0.99
10_I	41_S	0.945	0.99
119_E	122_A	0.943	0.99
44_D	48_L	0.942	0.99
35_K	42_N	0.928	0.99
7_K	11_D	0.925	0.99
23_D	26_I	0.922	0.99
54_S	58_E	0.906	0.99
8_H	11_D	0.902	0.99
96_E	106_H	0.902	0.99
49_V	75_S	0.899	0.99
51_R	57_L	0.895	0.99
18_E	22_R	0.894	0.99
59_K	136_A	0.893	0.99
115_A	118_L	0.891	0.99
56_F	60_L	0.883	0.98
31_A	34_L	0.874	0.98
71_I	127_A	0.869	0.98
56_F	76_P	0.866	0.98
70_R	139_R	0.865	0.98
28_P	31_A	0.860	0.98
15_W	18_E	0.857	0.98
110_C	113_K	0.852	0.98
92_H	95_E	0.838	0.98
20_I	30_E	0.833	0.98
6_R	10_I	0.832	0.98
70_R	134_D	0.824	0.98
76_P	128_I	0.824	0.98
35_K	38_I	0.823	0.98
118_L	121_R	0.817	0.97
14_Q	21_I	0.807	0.97
102_A	110_C	0.802	0.97
134_D	137_A	0.795	0.97
93_M	97_A	0.789	0.97
104_E	111_Q	0.775	0.96
6_R	44_D	0.774	0.96
14_Q	46_T	0.767	0.96
54_S	57_L	0.761	0.96
133_D	139_R	0.755	0.96
12_T	92_H	0.754	0.96
102_A	107_R	0.748	0.96
132_L	136_A	0.745	0.96
85_I	89_K	0.745	0.96
96_E	101_D	0.741	0.95
69_A	141_Y	0.736	0.95
87_A	91_Y	0.733	0.95
135_I	141_Y	0.731	0.95
86_L	116_V	0.728	0.95
34_L	37_R	0.721	0.95
12_T	91_Y	0.718	0.95
97_A	114_L	0.717	0.95
6_R	48_L	0.715	0.94
56_F	142_M	0.709	0.94
80_I	128_I	0.708	0.94
38_I	42_N	0.707	0.94
128_I	132_L	0.706	0.94
121_R	125_S	0.696	0.94
5_Y	12_T	0.695	0.94
40_R	51_R	0.682	0.93
46_T	49_V	0.681	0.93
115_A	119_E	0.676	0.93
89_K	117_L	0.673	0.92
65_P	69_A	0.670	0.92
16_H	91_Y	0.668	0.92
101_D	107_R	0.664	0.92
72_N	78_W	0.662	0.92
111_Q	118_L	0.662	0.92
70_R	133_D	0.661	0.92
135_I	140_K	0.652	0.91
39_D	42_N	0.652	0.91
26_I	32_L	0.650	0.91
7_K	10_I	0.648	0.91
96_E	102_A	0.647	0.91
90_I	121_R	0.644	0.91
56_F	77_A	0.636	0.90
97_A	110_C	0.635	0.90
18_E	42_N	0.623	0.89
22_R	42_N	0.620	0.89
97_A	102_A	0.616	0.89
43_Q	46_T	0.611	0.88
15_W	22_R	0.610	0.88
96_E	128_I	0.606	0.88
52_I	80_I	0.605	0.88
83_L	125_S	0.605	0.88
57_L	142_M	0.602	0.88
15_W	19_D	0.596	0.87
71_I	76_P	0.589	0.86
22_R	39_D	0.586	0.86
4_L	11_D	0.580	0.86
86_L	114_L	0.573	0.85
3_L	48_L	0.573	0.85
20_I	37_R	0.571	0.85
21_I	34_L	0.570	0.85
3_L	55_Y	0.568	0.84
135_I	142_M	0.567	0.84
4_L	52_I	0.565	0.84
48_L	97_A	0.561	0.84
112_A	119_E	0.560	0.84
33_A	40_R	0.560	0.84
71_I	126_T	0.558	0.83
18_E	35_K	0.557	0.83
29_V	32_L	0.555	0.83
17_L	75_S	0.554	0.83
79_A	83_L	0.539	0.81
7_K	48_L	0.538	0.81
130_Q	139_R	0.538	0.81
11_D	21_I	0.537	0.81
106_H	109_K	0.536	0.81
10_I	13_V	0.531	0.80
99_R	106_H	0.531	0.80
17_L	30_E	0.529	0.80
130_Q	140_K	0.528	0.80
43_Q	85_I	0.528	0.80
78_W	86_L	0.527	0.80
131_L	134_D	0.520	0.79
92_H	99_R	0.519	0.79
27_D	34_L	0.519	0.79
89_K	110_C	0.517	0.79
42_N	85_I	0.517	0.79
10_I	14_Q	0.514	0.78
19_D	22_R	0.512	0.78
64_K	68_D	0.508	0.77
72_N	140_K	0.506	0.77
109_K	136_A	0.504	0.77
22_R	35_K	0.503	0.77
119_E	123_D	0.501	0.76
63_V	69_A	0.500	0.76

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
4q4gX	1	0	64.3	0.916	Contact Map
4cgkA	3	0.9792	31.8	0.931	Contact Map
3swyA	3	0.2569	16.6	0.939	Contact Map
3swfA	3	0.2639	15	0.941	Contact Map
1flkA	3	0.4097	8.6	0.947	Contact Map
3pp5A	2	0.3889	2.9	0.958	Contact Map
4n78D	1	0.3472	2.8	0.958	Contact Map
3csxA	2	0.3264	2.7	0.958	Contact Map
3tweA	2	0.1806	2.6	0.958	Contact Map
1b9pA	1	0.2361	2.6	0.958	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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