DUF3670 - PFAM28P - GREMLIN Contacts

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DUF3670 - SNF2 Helicase protein

PFAM:	PF12419	Sequences: ARPHPLALTPEEAYRFLREAAPLLEAAGFGVRLPAWWRRRRPRLGVRLGVKSPGAAAGPSGLGLDALLDFDWELALGDEPLTEEELEALAAAKRPLVRLRGQWVEVDPEELRRALAFLEKVERGGLSFAEALRLAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	136 (130)
Sequences:	9326 (6422)
Seq/√Len:	563.2
META:	0.867

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
73_E	80_P	5.235	1.00
83_E	87_E	4.283	1.00
9_T	12_E	3.458	1.00
107_D	110_E	3.251	1.00
112_R	116_A	2.933	1.00
15_R	19_E	2.816	1.00
86_L	90_A	2.368	1.00
42_P	50_V	2.132	1.00
14_Y	18_R	2.034	1.00
82_T	85_E	2.001	1.00
79_E	102_Q	1.984	1.00
74_L	86_L	1.965	1.00
70_F	75_A	1.956	1.00
77_G	102_Q	1.835	1.00
83_E	119_E	1.750	1.00
18_R	105_E	1.750	1.00
63_G	66_A	1.739	1.00
85_E	100_R	1.656	1.00
126_L	131_A	1.645	1.00
16_F	24_L	1.644	1.00
19_E	24_L	1.623	1.00
128_F	132_L	1.619	1.00
47_R	73_E	1.614	1.00
119_E	122_E	1.524	1.00
127_S	130_E	1.517	1.00
79_E	100_R	1.515	1.00
19_E	23_L	1.491	1.00
38_R	41_R	1.479	1.00
109_E	112_R	1.431	1.00
75_A	78_D	1.404	1.00
126_L	134_L	1.398	1.00
69_D	125_G	1.387	1.00
62_L	67_L	1.358	1.00
116_A	119_E	1.325	1.00
114_A	118_L	1.312	1.00
24_L	29_F	1.261	1.00
38_R	42_P	1.257	1.00
87_E	91_A	1.254	1.00
116_A	120_K	1.247	1.00
110_E	113_R	1.243	1.00
84_E	88_A	1.243	1.00
87_E	119_E	1.240	1.00
108_P	112_R	1.229	1.00
117_F	121_V	1.212	1.00
129_A	133_R	1.191	1.00
40_R	48_L	1.154	1.00
11_E	94_R	1.150	1.00
21_A	31_V	1.136	1.00
44_L	50_V	1.133	1.00
45_G	48_L	1.132	1.00
99_L	104_V	1.123	1.00
121_V	124_G	1.107	1.00
88_A	91_A	1.107	1.00
113_R	116_A	1.104	1.00
51_K	69_D	1.095	1.00
88_A	92_A	1.090	1.00
42_P	49_G	1.077	1.00
10_P	94_R	1.059	1.00
71_D	122_E	1.055	1.00
64_L	67_L	1.053	1.00
13_A	103_W	1.048	1.00
13_A	16_F	1.048	1.00
44_L	48_L	1.047	1.00
90_A	93_K	1.030	1.00
94_R	108_P	1.030	1.00
17_L	37_W	1.027	1.00
114_A	117_F	1.012	1.00
125_G	128_F	1.010	1.00
21_A	33_L	1.005	1.00
49_G	53_P	0.989	1.00
66_A	69_D	0.985	1.00
83_E	122_E	0.984	1.00
39_R	49_G	0.982	1.00
14_Y	105_E	0.978	1.00
45_G	50_V	0.958	1.00
109_E	113_R	0.950	1.00
49_G	52_S	0.944	1.00
42_P	46_V	0.940	1.00
35_A	100_R	0.934	1.00
62_L	66_A	0.927	1.00
40_R	44_L	0.925	1.00
72_W	86_L	0.922	1.00
6_L	12_E	0.921	1.00
15_R	20_A	0.920	1.00
92_A	95_P	0.910	1.00
35_A	102_Q	0.899	1.00
49_G	73_E	0.896	1.00
81_L	86_L	0.891	1.00
33_L	114_A	0.888	1.00
84_E	87_E	0.887	1.00
14_Y	95_P	0.884	1.00
85_E	88_A	0.873	1.00
42_P	48_L	0.857	1.00
8_L	12_E	0.854	1.00
39_R	42_P	0.850	1.00
38_R	49_G	0.847	1.00
50_V	53_P	0.846	1.00
89_L	99_L	0.839	1.00
120_K	124_G	0.817	1.00
92_A	97_V	0.813	1.00
106_V	111_L	0.809	1.00
18_R	22_P	0.790	1.00
17_L	36_W	0.782	1.00
98_R	101_G	0.781	1.00
64_L	129_A	0.778	1.00
50_V	131_A	0.775	1.00
23_L	26_A	0.767	1.00
39_R	44_L	0.765	1.00
87_E	90_A	0.757	1.00
77_G	80_P	0.744	1.00
16_F	31_V	0.740	1.00
21_A	25_E	0.729	1.00
70_F	86_L	0.729	1.00
56_A	59_P	0.724	1.00
128_F	134_L	0.722	1.00
39_R	43_R	0.713	1.00
48_L	51_K	0.713	1.00
115_L	119_E	0.704	1.00
22_P	26_A	0.702	1.00
130_E	133_R	0.702	1.00
46_V	72_W	0.698	1.00
64_L	68_L	0.696	1.00
43_R	47_R	0.690	1.00
21_A	24_L	0.683	1.00
118_L	121_V	0.681	1.00
90_A	94_R	0.673	1.00
33_L	36_W	0.673	1.00
40_R	46_V	0.672	1.00
12_E	15_R	0.668	1.00
61_G	66_A	0.667	1.00
35_A	114_A	0.659	1.00
51_K	71_D	0.647	1.00
8_L	13_A	0.645	1.00
95_P	105_E	0.640	1.00
67_L	70_F	0.639	1.00
113_R	117_F	0.635	1.00
86_L	92_A	0.633	1.00
13_A	36_W	0.632	1.00
19_E	22_P	0.629	1.00
40_R	50_V	0.620	1.00
75_A	80_P	0.617	1.00
24_L	31_V	0.616	1.00
122_E	125_G	0.609	1.00
81_L	89_L	0.609	1.00
47_R	50_V	0.606	1.00
60_S	63_G	0.604	1.00
3_P	8_L	0.603	1.00
73_E	83_E	0.599	1.00
53_P	60_S	0.597	1.00
49_G	71_D	0.595	1.00
38_R	44_L	0.588	1.00
4_H	7_A	0.584	1.00
72_W	75_A	0.583	1.00
127_S	131_A	0.574	0.99
6_L	107_D	0.573	0.99
10_P	14_Y	0.572	0.99
11_E	15_R	0.567	0.99
117_F	120_K	0.565	0.99
37_W	68_L	0.565	0.99
112_R	115_L	0.560	0.99
62_L	73_E	0.551	0.99
30_G	105_E	0.550	0.99
39_R	45_G	0.549	0.99
94_R	98_R	0.548	0.99
128_F	131_A	0.547	0.99
81_L	99_L	0.546	0.99
14_Y	36_W	0.545	0.99
53_P	56_A	0.542	0.99
96_L	103_W	0.541	0.99
95_P	106_V	0.538	0.99
86_L	111_L	0.537	0.99
75_A	86_L	0.535	0.99
41_R	45_G	0.529	0.99
95_P	103_W	0.527	0.99
67_L	75_A	0.526	0.99
51_K	56_A	0.523	0.99
37_W	86_L	0.522	0.99
15_R	18_R	0.522	0.99
86_L	106_V	0.521	0.99
9_T	13_A	0.520	0.99
110_E	115_L	0.520	0.99
39_R	53_P	0.518	0.99
41_R	110_E	0.517	0.99
43_R	50_V	0.515	0.99
22_P	25_E	0.509	0.99
110_E	114_A	0.509	0.99
37_W	128_F	0.508	0.99
32_R	99_L	0.508	0.99
93_K	101_G	0.508	0.99
33_L	96_L	0.507	0.99
82_T	88_A	0.505	0.99
42_P	53_P	0.504	0.99
38_R	46_V	0.502	0.99
39_R	46_V	0.502	0.99
36_W	105_E	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
3ncvA	2	0.8162	63.7	0.871	Contact Map
3kdgA	2	0.8382	50.6	0.881	Contact Map
1x9zA	4	0.8676	29.7	0.895	Contact Map
2z51A	2	0.9338	21.8	0.902	Contact Map
2vlaA	1	0.8309	20.6	0.903	Contact Map
2jq5A	1	0.7059	14.5	0.909	Contact Map
2pvbA	1	0.4412	11.6	0.913	Contact Map
4e4wB	1	0.8382	10.5	0.915	Contact Map
4uzxA	1	0.3971	9.7	0.916	Contact Map
3nyvA	1	0.8382	9.6	0.917	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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