DUF4252 - PFAM28P - GREMLIN Contacts

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DUF4252 - Domain of unknown function (DUF4252)

PFAM:	PF14060	Sequences: KKILLLLLLLLLSLPAFAQSAQKLSLDKLFDKYADADGVTSVTISGSMLKLAAKFDDDEDDDEAKELLKGLKGIRVLSFEDGEYSKADYKEVRKQLKSPGYEELMRVKDKGENVKIYVKEEGDKIKELLVLVAGPDEFVLVNIVGDIDLEKLSKLAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	157 (151)
Sequences:	10362 (8147)
Seq/√Len:	663.0
META:	0.923

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
148_D	151_K	3.922	1.00
78_S	139_V	3.288	1.00
19_Q	22_Q	3.203	1.00
114_V	132_V	2.898	1.00
12_L	15_P	2.717	1.00
85_S	88_D	2.594	1.00
66_E	151_K	2.570	1.00
46_G	72_K	2.406	1.00
103_E	106_R	2.400	1.00
108_K	113_N	2.241	1.00
70_G	151_K	2.218	1.00
64_A	68_L	2.216	1.00
124_K	146_D	2.131	1.00
103_E	115_K	2.127	1.00
9_L	12_L	2.033	1.00
29_L	33_Y	1.915	1.00
84_Y	87_A	1.915	1.00
116_I	130_V	1.856	1.00
132_V	139_V	1.759	1.00
47_S	102_E	1.745	1.00
121_E	126_K	1.738	1.00
118_V	125_I	1.738	1.00
70_G	146_D	1.690	1.00
119_K	126_K	1.680	1.00
10_L	13_S	1.673	1.00
85_S	89_Y	1.627	1.00
103_E	117_Y	1.604	1.00
14_L	17_F	1.601	1.00
40_T	78_S	1.572	1.00
107_V	114_V	1.571	1.00
81_D	136_D	1.560	1.00
20_S	23_K	1.525	1.00
84_Y	88_D	1.518	1.00
24_L	27_D	1.483	1.00
27_D	31_D	1.458	1.00
81_D	85_S	1.447	1.00
89_Y	133_A	1.436	1.00
30_F	33_Y	1.428	1.00
74_I	143_I	1.395	1.00
127_E	144_V	1.388	1.00
105_M	116_I	1.357	1.00
120_E	123_D	1.341	1.00
63_E	154_K	1.319	1.00
106_R	115_K	1.299	1.00
116_I	128_L	1.271	1.00
66_E	69_K	1.258	1.00
8_L	11_L	1.243	1.00
151_K	154_K	1.237	1.00
11_L	14_L	1.236	1.00
39_V	77_L	1.234	1.00
19_Q	23_K	1.229	1.00
127_E	142_N	1.202	1.00
76_V	141_V	1.141	1.00
33_Y	91_E	1.134	1.00
41_S	106_R	1.129	1.00
64_A	67_L	1.125	1.00
63_E	66_E	1.110	1.00
75_R	142_N	1.104	1.00
41_S	77_L	1.104	1.00
47_S	50_K	1.103	1.00
6_L	10_L	1.095	1.00
47_S	120_E	1.093	1.00
84_Y	89_Y	1.087	1.00
58_D	61_D	1.084	1.00
65_K	69_K	1.083	1.00
133_A	138_F	1.078	1.00
90_K	93_R	1.076	1.00
90_K	94_K	1.072	1.00
9_L	13_S	1.067	1.00
4_L	7_L	1.057	1.00
134_G	137_E	1.055	1.00
46_G	50_K	1.052	1.00
41_S	75_R	1.042	1.00
102_E	120_E	1.039	1.00
121_E	124_K	1.030	1.00
53_A	56_D	1.028	1.00
89_Y	93_R	1.022	1.00
97_K	100_G	1.016	1.00
150_E	153_S	1.015	1.00
15_P	18_A	1.012	1.00
92_V	95_Q	1.008	1.00
28_K	31_D	0.999	1.00
7_L	10_L	0.994	1.00
78_S	132_V	0.991	1.00
10_L	14_L	0.985	1.00
95_Q	99_P	0.980	1.00
86_K	90_K	0.967	1.00
81_D	89_Y	0.966	1.00
101_Y	127_E	0.947	1.00
49_L	52_A	0.946	1.00
45_S	48_M	0.945	1.00
13_S	17_F	0.941	1.00
88_D	92_V	0.934	1.00
32_K	91_E	0.927	1.00
11_L	15_P	0.925	1.00
20_S	24_L	0.919	1.00
126_K	146_D	0.912	1.00
25_S	28_K	0.888	1.00
24_L	28_K	0.885	1.00
73_G	144_V	0.879	1.00
96_L	129_L	0.869	1.00
8_L	12_L	0.863	1.00
91_E	95_Q	0.854	1.00
22_Q	25_S	0.854	1.00
45_S	102_E	0.852	1.00
72_K	144_V	0.846	1.00
130_V	141_V	0.846	1.00
81_D	84_Y	0.845	1.00
86_K	89_Y	0.842	1.00
17_F	20_S	0.837	1.00
112_E	134_G	0.836	1.00
16_A	19_Q	0.834	1.00
93_R	115_K	0.832	1.00
149_L	153_S	0.830	1.00
26_L	29_L	0.827	1.00
29_L	32_K	0.822	1.00
116_I	141_V	0.813	1.00
54_K	150_E	0.812	1.00
100_G	119_K	0.809	1.00
104_L	118_V	0.805	1.00
108_K	115_K	0.799	1.00
80_E	112_E	0.789	1.00
27_D	30_F	0.783	1.00
87_A	91_E	0.780	1.00
57_D	62_D	0.767	1.00
92_V	96_L	0.765	1.00
82_G	85_S	0.760	1.00
101_Y	142_N	0.757	1.00
147_I	151_K	0.746	1.00
62_D	66_E	0.743	1.00
42_V	76_V	0.738	1.00
112_E	137_E	0.737	1.00
49_L	71_L	0.736	1.00
70_G	147_I	0.735	1.00
81_D	86_K	0.726	1.00
36_A	39_V	0.721	1.00
93_R	97_K	0.715	1.00
128_L	143_I	0.714	1.00
50_K	53_A	0.713	1.00
52_A	55_F	0.709	1.00
52_A	56_D	0.706	1.00
39_V	84_Y	0.703	1.00
29_L	138_F	0.702	1.00
83_E	87_A	0.700	1.00
107_V	132_V	0.696	1.00
24_L	32_K	0.693	1.00
129_L	142_N	0.689	1.00
95_Q	100_G	0.684	1.00
27_D	140_L	0.680	1.00
95_Q	98_S	0.678	1.00
94_K	97_K	0.672	1.00
88_D	91_E	0.671	1.00
23_K	28_K	0.669	1.00
107_V	139_V	0.666	1.00
73_G	79_F	0.664	1.00
15_P	19_Q	0.657	1.00
26_L	30_F	0.657	1.00
125_I	128_L	0.656	1.00
96_L	99_P	0.654	1.00
23_K	27_D	0.653	1.00
103_E	107_V	0.648	1.00
97_K	103_E	0.648	1.00
13_S	19_Q	0.645	1.00
70_G	148_D	0.642	1.00
74_I	141_V	0.636	1.00
4_L	12_L	0.632	1.00
148_D	153_S	0.627	1.00
97_K	117_Y	0.627	1.00
4_L	10_L	0.623	1.00
56_D	59_E	0.620	1.00
88_D	138_F	0.605	1.00
147_I	153_S	0.604	1.00
13_S	16_A	0.602	1.00
39_V	79_F	0.602	1.00
149_L	152_L	0.602	1.00
6_L	9_L	0.592	1.00
106_R	113_N	0.589	1.00
33_Y	39_V	0.588	1.00
81_D	88_D	0.587	1.00
79_F	85_S	0.585	1.00
62_D	65_K	0.582	1.00
42_V	107_V	0.581	1.00
43_T	77_L	0.579	1.00
59_E	62_D	0.578	1.00
102_E	118_V	0.578	1.00
53_A	62_D	0.577	1.00
36_A	79_F	0.577	1.00
6_L	12_L	0.576	1.00
105_M	130_V	0.576	1.00
30_F	77_L	0.575	1.00
110_K	113_N	0.574	1.00
35_D	40_T	0.568	1.00
22_Q	28_K	0.568	1.00
33_Y	77_L	0.566	1.00
93_R	98_S	0.561	1.00
58_D	65_K	0.558	1.00
83_E	88_D	0.557	1.00
43_T	73_G	0.555	1.00
64_A	69_K	0.555	1.00
45_S	52_A	0.548	1.00
33_Y	36_A	0.548	1.00
91_E	94_K	0.547	1.00
6_L	11_L	0.547	1.00
37_D	110_K	0.544	1.00
119_K	122_G	0.544	1.00
35_D	108_K	0.537	1.00
43_T	75_R	0.532	1.00
40_T	107_V	0.530	1.00
42_V	78_S	0.528	0.99
20_S	25_S	0.528	0.99
120_E	125_I	0.526	0.99
56_D	65_K	0.524	0.99
45_S	73_G	0.522	0.99
4_L	13_S	0.522	0.99
128_L	153_S	0.521	0.99
87_A	90_K	0.518	0.99
115_K	118_V	0.514	0.99
71_L	143_I	0.513	0.99
94_K	98_S	0.513	0.99
26_L	33_Y	0.510	0.99
12_L	17_F	0.507	0.99
82_G	89_Y	0.506	0.99
63_E	151_K	0.505	0.99
109_D	137_E	0.505	0.99
9_L	15_P	0.505	0.99
93_R	131_L	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
2q22A	1	0.7707	20.6	0.887	Contact Map
3razA	1	0.7134	7	0.908	Contact Map
4k3bA	1	0.586	6.8	0.908	Contact Map
2p5qA	3	0.8344	5.8	0.911	Contact Map
2qtfA	1	0.4777	5.3	0.913	Contact Map
2v1mA	1	0.8344	5.2	0.913	Contact Map
2hyxA	2	0.7261	4.9	0.915	Contact Map
3dwvA	1	0.8344	4.8	0.915	Contact Map
2vupA	1	0.8344	4.6	0.916	Contact Map
2cvbA	1	0.7325	4.5	0.916	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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