DUF4131 - PFAM28P - GREMLIN Contacts

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DUF4131 - Domain of unknown function (DUF4131)

PFAM:	PF13567	Sequences: IAGILLAFLPALPPPLWLLAALLALLLLLLLLRRRRRRRRLLLLLLLLLLLGFLGAALRAARRLADDLPRLLEAGRPVTVEGVVVELPERREDGTRFVLRVESVLDGGRWRPVPGRVRLSVYGDPAPALRYGDRVRLTGRLRPPRGPRNPGGFDYRRYLARQGIYATGYVRSAEWV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	176 (168)
Sequences:	40700 (35524)
Seq/√Len:	2740.7
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
139_G	168_G	4.113	1.00
82_G	99_L	3.753	1.00
153_F	158_Y	3.051	1.00
85_V	100_R	2.999	1.00
155_Y	159_L	2.907	1.00
81_E	136_R	2.705	1.00
130_R	133_D	2.678	1.00
146_G	156_R	2.333	1.00
79_T	136_R	2.210	1.00
86_E	98_V	2.201	1.00
79_T	138_T	2.179	1.00
83_V	134_R	2.178	1.00
81_E	134_R	2.148	1.00
55_G	59_R	2.120	1.00
102_E	134_R	2.084	1.00
144_P	159_L	1.969	1.00
52_G	55_G	1.963	1.00
81_E	103_S	1.962	1.00
157_R	161_R	1.950	1.00
98_V	116_R	1.945	1.00
85_V	116_R	1.942	1.00
82_G	137_L	1.910	1.00
160_A	165_Y	1.759	1.00
57_A	61_A	1.750	1.00
53_F	56_A	1.746	1.00
105_L	110_W	1.696	1.00
158_Y	162_Q	1.671	1.00
144_P	167_T	1.612	1.00
4_I	7_A	1.592	1.00
83_V	102_E	1.575	1.00
98_V	164_I	1.541	1.00
146_G	154_D	1.519	1.00
100_R	116_R	1.502	1.00
67_D	70_R	1.500	1.00
58_L	62_R	1.487	1.00
80_V	139_G	1.467	1.00
154_D	157_R	1.450	1.00
147_P	152_G	1.420	1.00
103_S	110_W	1.397	1.00
87_L	131_Y	1.378	1.00
54_L	57_A	1.365	1.00
97_F	121_V	1.360	1.00
149_N	152_G	1.328	1.00
55_G	58_L	1.316	1.00
56_A	59_R	1.311	1.00
98_V	118_R	1.294	1.00
143_P	156_R	1.288	1.00
61_A	64_L	1.276	1.00
8_F	11_A	1.276	1.00
68_L	71_L	1.268	1.00
57_A	60_A	1.255	1.00
9_L	12_L	1.250	1.00
96_R	118_R	1.248	1.00
94_G	120_S	1.233	1.00
99_L	135_V	1.224	1.00
82_G	135_V	1.206	1.00
66_D	69_P	1.197	1.00
83_V	100_R	1.194	1.00
85_V	98_V	1.184	1.00
49_L	52_G	1.181	1.00
69_P	73_E	1.180	1.00
84_V	129_L	1.179	1.00
59_R	62_R	1.171	1.00
156_R	160_A	1.165	1.00
70_R	73_E	1.164	1.00
142_R	169_Y	1.128	1.00
56_A	60_A	1.122	1.00
90_R	95_T	1.090	1.00
117_V	141_L	1.078	1.00
91_R	94_G	1.077	1.00
64_L	67_D	1.070	1.00
145_R	148_R	1.067	1.00
58_L	61_A	1.065	1.00
59_R	63_R	1.064	1.00
117_V	166_A	1.058	1.00
68_L	72_L	1.057	1.00
91_R	96_R	1.054	1.00
68_L	73_E	1.052	1.00
77_P	138_T	1.052	1.00
148_R	152_G	1.048	1.00
77_P	140_R	1.046	1.00
53_F	57_A	1.035	1.00
145_R	156_R	1.032	1.00
67_D	71_L	1.015	1.00
65_A	68_L	1.006	1.00
45_L	48_L	1.000	1.00
88_P	91_R	0.997	1.00
60_A	63_R	0.996	1.00
106_D	109_R	0.993	1.00
54_L	58_L	0.984	1.00
81_E	102_E	0.976	1.00
85_V	88_P	0.975	1.00
8_F	12_L	0.969	1.00
141_L	168_G	0.967	1.00
112_P	115_G	0.966	1.00
96_R	120_S	0.964	1.00
10_P	13_P	0.958	1.00
99_L	119_L	0.958	1.00
157_R	160_A	0.951	1.00
137_L	168_G	0.946	1.00
12_L	16_L	0.944	1.00
61_A	65_A	0.938	1.00
159_L	164_I	0.938	1.00
137_L	170_V	0.931	1.00
147_P	154_D	0.930	1.00
60_A	64_L	0.927	1.00
51_L	54_L	0.925	1.00
52_G	56_A	0.922	1.00
42_L	45_L	0.919	1.00
147_P	156_R	0.919	1.00
69_P	72_L	0.914	1.00
98_V	162_Q	0.913	1.00
101_V	117_V	0.904	1.00
121_V	124_D	0.903	1.00
89_E	96_R	0.902	1.00
26_L	30_L	0.897	1.00
155_Y	167_T	0.895	1.00
43_L	46_L	0.880	1.00
143_P	166_A	0.872	1.00
159_L	167_T	0.865	1.00
121_V	129_L	0.860	1.00
14_P	17_W	0.854	1.00
47_L	50_L	0.851	1.00
8_F	13_P	0.851	1.00
41_L	44_L	0.847	1.00
144_P	156_R	0.845	1.00
108_G	111_R	0.833	1.00
48_L	51_L	0.827	1.00
36_R	39_R	0.823	1.00
12_L	15_P	0.820	1.00
44_L	48_L	0.816	1.00
119_L	168_G	0.811	1.00
81_E	85_V	0.808	1.00
62_R	65_A	0.807	1.00
115_G	119_L	0.796	1.00
37_R	41_L	0.795	1.00
86_E	131_Y	0.791	1.00
141_L	166_A	0.779	1.00
46_L	49_L	0.775	1.00
142_R	167_T	0.774	1.00
29_L	32_L	0.772	1.00
99_L	137_L	0.771	1.00
114_P	165_Y	0.761	1.00
161_R	165_Y	0.759	1.00
38_R	41_L	0.758	1.00
134_R	138_T	0.749	1.00
80_V	137_L	0.743	1.00
50_L	53_F	0.739	1.00
44_L	55_G	0.738	1.00
63_R	66_D	0.734	1.00
155_Y	158_Y	0.724	1.00
84_V	97_F	0.721	1.00
99_L	117_V	0.718	1.00
144_P	166_A	0.710	1.00
129_L	133_D	0.709	1.00
51_L	55_G	0.706	1.00
36_R	40_R	0.696	1.00
16_L	19_L	0.695	1.00
13_P	17_W	0.693	1.00
88_P	95_T	0.693	1.00
42_L	46_L	0.683	1.00
19_L	22_L	0.683	1.00
72_L	166_A	0.683	1.00
55_G	61_A	0.678	1.00
28_L	32_L	0.676	1.00
9_L	15_P	0.672	1.00
11_A	15_P	0.672	1.00
44_L	47_L	0.665	1.00
49_L	53_F	0.665	1.00
88_P	97_F	0.665	1.00
27_L	31_L	0.665	1.00
122_Y	169_Y	0.664	1.00
105_L	109_R	0.658	1.00
105_L	108_G	0.657	1.00
120_S	167_T	0.657	1.00
80_V	141_L	0.654	1.00
43_L	47_L	0.653	1.00
41_L	45_L	0.651	1.00
131_Y	134_R	0.651	1.00
80_V	101_V	0.649	1.00
40_R	44_L	0.648	1.00
39_R	42_L	0.648	1.00
77_P	81_E	0.638	1.00
115_G	118_R	0.636	1.00
86_E	97_F	0.633	1.00
9_L	14_P	0.630	1.00
50_L	54_L	0.627	1.00
45_L	49_L	0.626	1.00
90_R	93_D	0.623	1.00
15_P	19_L	0.620	1.00
119_L	137_L	0.619	1.00
158_Y	161_R	0.617	1.00
10_P	14_P	0.616	1.00
19_L	23_L	0.615	1.00
118_R	155_Y	0.615	1.00
115_G	122_Y	0.615	1.00
23_L	27_L	0.613	1.00
118_R	122_Y	0.609	1.00
129_L	135_V	0.609	1.00
17_W	20_A	0.606	1.00
29_L	33_R	0.606	1.00
20_A	23_L	0.604	1.00
37_R	40_R	0.601	1.00
10_P	15_P	0.599	1.00
14_P	18_L	0.598	1.00
83_V	87_L	0.597	1.00
48_L	52_G	0.597	1.00
64_L	70_R	0.592	1.00
120_S	169_Y	0.589	1.00
25_L	28_L	0.588	1.00
30_L	33_R	0.587	1.00
78_V	82_G	0.584	1.00
92_E	95_T	0.582	1.00
67_D	73_E	0.581	1.00
63_R	67_D	0.577	1.00
46_L	57_A	0.577	1.00
116_R	120_S	0.576	1.00
11_A	17_W	0.573	1.00
43_L	50_L	0.569	1.00
110_W	113_V	0.566	1.00
62_R	66_D	0.566	1.00
121_V	170_V	0.564	1.00
27_L	30_L	0.562	1.00
119_L	139_G	0.555	1.00
95_T	129_L	0.553	1.00
82_G	102_E	0.552	1.00
124_D	127_P	0.549	1.00
11_A	14_P	0.547	1.00
147_P	151_G	0.543	1.00
2_A	5_L	0.542	1.00
25_L	29_L	0.538	1.00
95_T	123_G	0.538	1.00
81_E	110_W	0.537	1.00
104_V	113_V	0.536	1.00
52_G	57_A	0.535	1.00
97_F	129_L	0.534	1.00
12_L	17_W	0.532	1.00
118_R	159_L	0.531	1.00
54_L	59_R	0.527	1.00
80_V	168_G	0.526	1.00
53_F	60_A	0.525	1.00
97_F	101_V	0.524	1.00
90_R	94_G	0.521	1.00
75_G	78_V	0.517	1.00
66_D	71_L	0.517	1.00
90_R	123_G	0.516	1.00
55_G	60_A	0.513	1.00
17_W	21_A	0.508	1.00
77_P	171_R	0.503	1.00
40_R	43_L	0.501	1.00
42_L	52_G	0.501	1.00
24_A	28_L	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
1n9wA	2	0.483	32.1	0.875	Contact Map
3ja87	1	0.8239	25.1	0.881	Contact Map
3nemA	2	0.5057	23.2	0.883	Contact Map
4gn4B	1	0.5398	22.6	0.884	Contact Map
1l0wA	2	0.5341	22.6	0.884	Contact Map
1wydA	2	0.5057	21.7	0.885	Contact Map
3f2bA	1	0.5682	21.1	0.886	Contact Map
1c0aA	1	0.5398	19.3	0.888	Contact Map
4me3A	1	0.7386	18.9	0.888	Contact Map
2jwaA	2	0.1761	17.9	0.889	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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