DUF3619 - PFAM28P - GREMLIN Contacts

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DUF3619 - Protein of unknown function (DUF3619)

PFAM:	PF12279	Sequences: NEDRFARRIAARLDEGAADLPADTAERLRAAREQALARRRPEAPARAPAPALALAGAGGALTLGGGGGGSWWRRLRSLLPLLALVAGLVGIQYWQQDQRAAELAEIDAALLTDDLPPDAYLDPGFQAWLKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	131 (125)
Sequences:	3153 (2416)
Seq/√Len:	216.1
META:	0.926

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_A	10_A	4.171	1.00
26_E	29_R	3.305	1.00
34_Q	37_A	2.961	1.00
34_Q	38_R	2.917	1.00
29_R	33_E	2.518	1.00
52_L	55_A	2.334	1.00
48_P	52_L	2.188	1.00
118_D	121_L	2.174	1.00
123_P	126_Q	2.067	1.00
5_F	9_I	2.060	1.00
10_A	14_D	1.986	1.00
12_R	15_E	1.968	1.00
7_R	10_A	1.966	1.00
56_G	59_G	1.857	1.00
20_L	25_A	1.824	1.00
54_L	58_G	1.773	1.00
50_P	54_L	1.697	1.00
12_R	16_G	1.661	1.00
57_A	60_A	1.659	1.00
90_G	94_W	1.621	1.00
4_R	7_R	1.611	1.00
52_L	56_G	1.610	1.00
8_R	11_A	1.562	1.00
3_D	7_R	1.528	1.00
58_G	61_L	1.524	1.00
15_E	19_D	1.523	1.00
22_A	30_A	1.513	1.00
116_P	119_A	1.491	1.00
54_L	57_A	1.490	1.00
3_D	6_A	1.445	1.00
103_L	108_A	1.437	1.00
84_L	87_G	1.414	1.00
119_A	122_D	1.391	1.00
126_Q	130_K	1.387	1.00
7_R	14_D	1.372	1.00
110_L	117_P	1.332	1.00
55_A	59_G	1.327	1.00
30_A	34_Q	1.324	1.00
53_A	56_G	1.321	1.00
90_G	93_Y	1.273	1.00
54_L	59_G	1.271	1.00
92_Q	96_Q	1.264	1.00
44_P	47_A	1.243	1.00
7_R	11_A	1.242	1.00
115_L	120_Y	1.219	1.00
115_L	119_A	1.197	1.00
20_L	24_T	1.194	1.00
48_P	51_A	1.185	1.00
70_S	74_R	1.182	1.00
52_L	57_A	1.180	1.00
59_G	62_T	1.172	1.00
106_I	109_A	1.167	1.00
69_G	73_R	1.132	1.00
21_P	24_T	1.121	1.00
79_L	86_A	1.121	1.00
70_S	73_R	1.097	1.00
47_A	51_A	1.072	1.00
50_P	55_A	1.072	1.00
17_A	20_L	1.070	1.00
112_T	130_K	1.056	1.00
63_L	67_G	1.038	1.00
4_R	11_A	1.029	1.00
72_W	75_L	1.026	1.00
46_R	54_L	1.020	1.00
50_P	56_G	1.011	1.00
4_R	8_R	1.010	1.00
30_A	33_E	0.982	1.00
50_P	53_A	0.979	1.00
37_A	40_R	0.975	1.00
54_L	61_L	0.967	1.00
21_P	26_E	0.958	1.00
81_L	85_V	0.952	1.00
117_P	126_Q	0.940	1.00
26_E	30_A	0.933	0.99
121_L	126_Q	0.930	0.99
75_L	78_L	0.926	0.99
49_A	52_L	0.923	0.99
123_P	127_A	0.906	0.99
80_P	84_L	0.897	0.99
77_S	82_L	0.887	0.99
55_A	61_L	0.879	0.99
3_D	10_A	0.874	0.99
46_R	56_G	0.865	0.99
115_L	126_Q	0.865	0.99
53_A	57_A	0.864	0.99
109_A	113_D	0.863	0.99
23_D	30_A	0.854	0.99
96_Q	100_A	0.849	0.99
22_A	26_E	0.840	0.99
127_A	130_K	0.836	0.99
79_L	82_L	0.831	0.99
87_G	91_I	0.828	0.99
72_W	77_S	0.823	0.99
71_W	74_R	0.812	0.99
56_G	61_L	0.808	0.99
52_L	59_G	0.805	0.98
46_R	50_P	0.802	0.98
30_A	37_A	0.802	0.98
93_Y	97_D	0.799	0.98
91_I	95_Q	0.790	0.98
45_A	51_A	0.783	0.98
76_R	80_P	0.782	0.98
56_G	60_A	0.781	0.98
44_P	51_A	0.777	0.98
80_P	91_I	0.774	0.98
114_D	120_Y	0.770	0.98
105_E	120_Y	0.762	0.98
123_P	128_W	0.761	0.98
46_R	49_A	0.756	0.98
44_P	48_P	0.747	0.98
120_Y	125_F	0.736	0.97
46_R	53_A	0.734	0.97
55_A	58_G	0.734	0.97
38_R	41_P	0.729	0.97
21_P	25_A	0.726	0.97
95_Q	99_R	0.715	0.97
53_A	58_G	0.715	0.97
93_Y	100_A	0.713	0.97
58_G	63_L	0.709	0.97
81_L	87_G	0.698	0.96
45_A	49_A	0.697	0.96
121_L	127_A	0.688	0.96
48_P	54_L	0.686	0.96
23_D	26_E	0.685	0.96
101_A	110_L	0.685	0.96
111_L	116_P	0.680	0.96
22_A	29_R	0.678	0.96
71_W	78_L	0.670	0.95
52_L	58_G	0.666	0.95
57_A	61_L	0.666	0.95
2_E	74_R	0.662	0.95
100_A	104_A	0.660	0.95
68_G	73_R	0.657	0.95
89_V	92_Q	0.654	0.95
38_R	93_Y	0.654	0.95
80_P	83_A	0.648	0.94
14_D	17_A	0.647	0.94
51_A	58_G	0.645	0.94
26_E	88_L	0.643	0.94
90_G	105_E	0.639	0.94
84_L	88_L	0.631	0.94
53_A	61_L	0.626	0.93
33_E	37_A	0.623	0.93
76_R	79_L	0.623	0.93
75_L	79_L	0.622	0.93
114_D	118_D	0.617	0.93
77_S	80_P	0.615	0.93
117_P	123_P	0.610	0.92
55_A	63_L	0.606	0.92
104_A	124_G	0.606	0.92
49_A	58_G	0.603	0.92
10_A	16_G	0.602	0.92
82_L	85_V	0.594	0.91
69_G	72_W	0.589	0.91
109_A	112_T	0.588	0.91
68_G	72_W	0.587	0.91
104_A	109_A	0.586	0.91
76_R	128_W	0.586	0.91
78_L	82_L	0.583	0.91
97_D	130_K	0.578	0.90
88_L	108_A	0.577	0.90
57_A	62_T	0.576	0.90
121_L	128_W	0.574	0.90
115_L	122_D	0.574	0.90
102_E	127_A	0.569	0.90
91_I	120_Y	0.563	0.89
48_P	59_G	0.562	0.89
33_E	106_I	0.556	0.89
111_L	119_A	0.544	0.87
118_D	123_P	0.542	0.87
86_A	90_G	0.536	0.87
97_D	101_A	0.535	0.87
95_Q	110_L	0.535	0.87
123_P	130_K	0.527	0.86
111_L	114_D	0.523	0.85
107_D	111_L	0.519	0.85
76_R	81_L	0.517	0.85
74_R	81_L	0.517	0.85
79_L	84_L	0.514	0.84
46_R	52_L	0.511	0.84
47_A	54_L	0.509	0.84
106_I	126_Q	0.506	0.83
103_L	130_K	0.505	0.83
52_L	60_A	0.502	0.83
31_A	35_A	0.501	0.83
22_A	27_R	0.500	0.83
21_P	29_R	0.500	0.83
124_G	127_A	0.500	0.83

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
2hy7A	1	0.313	5	0.929	Contact Map
3jz0A	2	0.458	5	0.929	Contact Map
2pbeA	1	0.3893	4.5	0.93	Contact Map
1oahA	2	0.1832	3.6	0.934	Contact Map
1rijA	1	0.0916	3.1	0.936	Contact Map
3ne5A	3	0.4885	3	0.936	Contact Map
4mqvB	1	0.1985	3	0.936	Contact Map
2kbwB	1	0.2214	2.9	0.937	Contact Map
3c18A	2	0.4962	2.5	0.939	Contact Map
3dzcA	2	0.3359	2.5	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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