DUF4233 - PFAM28P - GREMLIN Contacts

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DUF4233 - Protein of unknown function (DUF4233)

PFAM:	PF14017	Sequences: RGLCAAVLILEAIVVLLAILVAIGLGDVSPGTALGVGGGLAVLLVLLAGLLRRPWGYALGWVLQVALIAAGFVVPAMFVLGVIFAALWVYALVLGRRIDRRRAR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	104 (102)
Sequences:	3157 (2019)
Seq/√Len:	199.9
META:	0.768

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_L	59_L	3.319	1.00
31_G	35_G	3.182	1.00
72_F	78_F	3.156	1.00
71_G	78_F	2.673	1.00
11_E	67_L	2.563	1.00
82_V	86_A	2.368	1.00
89_V	93_V	2.224	1.00
68_I	85_A	2.196	1.00
47_L	56_G	2.143	1.00
12_A	45_V	2.089	1.00
35_G	39_G	2.003	1.00
58_A	62_V	1.971	1.00
55_W	59_L	1.906	1.00
94_L	97_R	1.864	1.00
58_A	61_W	1.782	1.00
5_A	48_A	1.772	1.00
90_Y	94_L	1.759	1.00
4_C	57_Y	1.674	1.00
13_I	17_L	1.673	1.00
2_G	6_A	1.643	1.00
95_G	99_D	1.635	1.00
68_I	81_G	1.595	1.00
34_L	38_G	1.585	1.00
81_G	85_A	1.529	1.00
32_T	35_G	1.516	1.00
20_L	24_G	1.509	1.00
55_W	58_A	1.500	1.00
98_I	101_R	1.436	1.00
17_L	20_L	1.408	1.00
44_L	63_L	1.403	1.00
78_F	82_V	1.384	1.00
68_I	78_F	1.380	1.00
9_I	48_A	1.374	1.00
61_W	89_V	1.363	1.00
51_L	57_Y	1.359	1.00
50_L	53_R	1.350	1.00
19_I	37_G	1.332	1.00
86_A	90_Y	1.324	1.00
50_L	55_W	1.308	1.00
35_G	38_G	1.272	1.00
15_V	44_L	1.219	1.00
56_G	59_L	1.164	1.00
34_L	37_G	1.152	1.00
23_I	26_G	1.126	1.00
98_I	102_R	1.108	1.00
85_A	89_V	1.106	1.00
61_W	65_V	1.095	1.00
43_L	47_L	1.091	1.00
48_A	51_L	1.064	1.00
6_A	10_L	1.056	1.00
94_L	98_I	1.056	1.00
32_T	36_V	1.036	1.00
47_L	50_L	1.022	1.00
99_D	102_R	1.022	1.00
20_L	23_I	0.980	1.00
70_A	77_M	0.970	0.99
71_G	81_G	0.967	0.99
43_L	63_L	0.956	0.99
38_G	42_V	0.932	0.99
19_I	41_A	0.924	0.99
4_C	51_L	0.919	0.99
91_A	98_I	0.909	0.99
22_A	74_V	0.886	0.99
62_V	66_A	0.865	0.99
54_P	58_A	0.855	0.99
47_L	63_L	0.848	0.99
21_V	74_V	0.847	0.99
15_V	67_L	0.839	0.98
79_V	83_I	0.828	0.98
90_Y	93_V	0.809	0.98
62_V	65_V	0.805	0.98
4_C	92_L	0.780	0.98
96_R	100_R	0.774	0.97
49_G	52_R	0.753	0.97
43_L	59_L	0.752	0.97
72_F	75_P	0.750	0.97
22_A	25_L	0.749	0.97
46_L	50_L	0.747	0.97
19_I	34_L	0.745	0.97
16_L	20_L	0.742	0.97
18_A	80_L	0.729	0.96
71_G	75_P	0.727	0.96
29_S	32_T	0.725	0.96
9_I	45_V	0.722	0.96
91_A	95_G	0.722	0.96
37_G	73_V	0.720	0.96
24_G	27_D	0.717	0.96
75_P	78_F	0.713	0.96
46_L	49_G	0.711	0.96
30_P	36_V	0.708	0.96
3_L	6_A	0.700	0.95
1_R	5_A	0.695	0.95
23_I	30_P	0.677	0.95
33_A	36_V	0.676	0.94
23_I	27_D	0.672	0.94
3_L	91_A	0.670	0.94
30_P	34_L	0.670	0.94
6_A	91_A	0.659	0.94
6_A	9_I	0.651	0.93
56_G	60_G	0.645	0.93
7_V	91_A	0.645	0.93
93_V	96_R	0.633	0.92
28_V	33_A	0.624	0.92
59_L	62_V	0.616	0.91
10_L	13_I	0.598	0.90
67_L	77_M	0.594	0.90
77_M	80_L	0.592	0.90
40_L	67_L	0.592	0.90
92_L	95_G	0.586	0.89
14_V	18_A	0.585	0.89
7_V	87_L	0.584	0.89
57_Y	92_L	0.584	0.89
15_V	18_A	0.583	0.89
9_I	13_I	0.583	0.89
68_I	71_G	0.582	0.89
13_I	16_L	0.581	0.89
18_A	77_M	0.577	0.88
97_R	100_R	0.577	0.88
92_L	96_R	0.574	0.88
4_C	60_G	0.560	0.87
41_A	48_A	0.557	0.87
90_Y	95_G	0.557	0.87
77_M	81_G	0.557	0.87
44_L	67_L	0.556	0.87
82_V	85_A	0.556	0.87
84_F	87_L	0.553	0.86
93_V	97_R	0.552	0.86
33_A	37_G	0.548	0.86
86_A	89_V	0.547	0.86
15_V	70_A	0.545	0.85
69_A	75_P	0.544	0.85
66_A	69_A	0.544	0.85
38_G	45_V	0.543	0.85
51_L	60_G	0.539	0.85
33_A	38_G	0.535	0.84
4_C	91_A	0.531	0.84
9_I	18_A	0.527	0.83
61_W	95_G	0.526	0.83
94_L	101_R	0.525	0.83
31_G	38_G	0.524	0.83
76_A	80_L	0.524	0.83
11_E	64_Q	0.524	0.83
36_V	40_L	0.520	0.83
94_L	102_R	0.515	0.82
69_A	72_F	0.508	0.81
31_G	36_V	0.506	0.81
29_S	37_G	0.505	0.81
18_A	70_A	0.504	0.81
41_A	44_L	0.503	0.81
97_R	101_R	0.502	0.80
90_Y	102_R	0.501	0.80
31_G	34_L	0.501	0.80
42_V	49_G	0.500	0.80

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
2m20A	2	0.3654	15.4	0.899	Contact Map
2kluA	1	0.4135	8.6	0.91	Contact Map
2l2tA	2	0.4231	5.8	0.916	Contact Map
4httA	1	0.6923	3.3	0.926	Contact Map
4b4aA	1	0.6923	2.5	0.931	Contact Map
2kncB	1	0.4615	2	0.934	Contact Map
1fftB	1	0.4615	1.9	0.935	Contact Map
2b2hA	3	0.9904	1.8	0.935	Contact Map
3pcvA	3	0.8846	1.8	0.936	Contact Map
4m5bA	1	0.375	1.5	0.939	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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