YwiC - PFAM28P - GREMLIN Contacts

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YwiC - YwiC-like protein

PFAM:	PF14256	Sequences: LPREHGAWGMLLVPLLLGLLVAGPSWAGLLLALAALAAFLARQPLLLLLGDRRRRRARRWLLVYGALAAAAGAALLALGPALLWLALVAAPLFAVQLWLAARRRERSLLGELAGAAALALAAPAAY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	126 (125)
Sequences:	3774 (3109)
Seq/√Len:	278.1
META:	0.891

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_L	32_A	3.435	1.00
37_A	67_L	2.780	1.00
54_R	58_R	2.688	1.00
33_L	71_A	2.432	1.00
60_W	64_Y	2.426	1.00
107_S	110_G	2.021	1.00
12_L	36_L	1.997	1.00
19_L	28_G	1.977	1.00
54_R	57_A	1.971	1.00
37_A	71_A	1.951	1.00
35_A	121_A	1.880	1.00
120_L	123_P	1.878	1.00
87_L	91_P	1.791	1.00
37_A	68_A	1.743	1.00
43_Q	47_L	1.739	1.00
52_R	57_A	1.726	1.00
56_R	59_R	1.716	1.00
53_R	57_A	1.687	1.00
60_W	63_V	1.686	1.00
98_W	102_R	1.673	1.00
10_M	13_V	1.663	1.00
18_G	22_A	1.615	1.00
65_G	69_A	1.582	1.00
67_L	71_A	1.582	1.00
41_A	61_L	1.581	1.00
25_S	28_G	1.548	1.00
74_A	78_L	1.461	1.00
53_R	56_R	1.451	1.00
26_W	30_L	1.448	1.00
100_A	105_E	1.441	1.00
108_L	112_L	1.440	1.00
31_L	124_A	1.408	1.00
4_E	7_A	1.361	1.00
93_F	96_Q	1.360	1.00
46_L	100_A	1.357	1.00
50_G	103_R	1.355	1.00
99_L	110_G	1.345	1.00
64_Y	68_A	1.342	1.00
119_A	123_P	1.339	1.00
115_A	119_A	1.327	1.00
34_A	75_L	1.313	1.00
95_V	99_L	1.308	1.00
30_L	71_A	1.305	1.00
34_A	38_A	1.294	1.00
16_L	20_L	1.285	1.00
96_Q	114_G	1.276	1.00
3_R	43_Q	1.247	1.00
55_R	59_R	1.246	1.00
30_L	74_A	1.244	1.00
53_R	59_R	1.225	1.00
96_Q	110_G	1.223	1.00
17_L	21_V	1.212	1.00
39_F	42_R	1.206	1.00
75_L	79_G	1.182	1.00
11_L	36_L	1.167	1.00
86_A	93_F	1.164	1.00
55_R	58_R	1.154	1.00
40_L	64_Y	1.144	1.00
43_Q	46_L	1.144	1.00
3_R	10_M	1.139	1.00
9_G	13_V	1.125	1.00
38_A	68_A	1.123	1.00
62_L	66_A	1.123	1.00
2_P	5_H	1.078	1.00
94_A	98_W	1.074	1.00
59_R	63_V	1.070	1.00
10_M	14_P	1.058	1.00
73_A	77_A	1.056	1.00
91_P	94_A	1.030	1.00
111_E	114_G	1.029	1.00
89_A	120_L	1.027	1.00
39_F	111_E	1.018	1.00
58_R	62_L	1.003	1.00
105_E	110_G	0.989	1.00
45_L	61_L	0.984	1.00
118_L	121_A	0.979	1.00
98_W	101_A	0.971	1.00
63_V	66_A	0.961	1.00
62_L	65_G	0.961	1.00
2_P	8_W	0.955	1.00
60_W	65_G	0.926	1.00
48_L	58_R	0.924	1.00
75_L	78_L	0.924	1.00
48_L	61_L	0.915	1.00
61_L	65_G	0.903	1.00
34_A	68_A	0.903	1.00
30_L	33_L	0.900	1.00
19_L	24_P	0.898	1.00
39_F	43_Q	0.891	1.00
47_L	57_A	0.881	1.00
34_A	71_A	0.873	1.00
74_A	77_A	0.870	1.00
99_L	104_R	0.854	1.00
116_A	120_L	0.840	1.00
96_Q	100_A	0.836	1.00
114_G	118_L	0.836	1.00
41_A	45_L	0.835	1.00
35_A	89_A	0.834	1.00
104_R	107_S	0.831	1.00
85_L	89_A	0.830	1.00
46_L	51_D	0.798	0.99
68_A	72_G	0.772	0.99
3_R	7_A	0.769	0.99
111_E	115_A	0.764	0.99
95_V	98_W	0.759	0.99
13_V	17_L	0.754	0.99
95_V	113_A	0.754	0.99
121_A	125_A	0.753	0.99
43_Q	50_G	0.745	0.99
96_Q	111_E	0.744	0.99
41_A	44_P	0.739	0.99
48_L	60_W	0.736	0.99
33_L	67_L	0.719	0.99
24_P	28_G	0.718	0.99
28_G	125_A	0.718	0.99
15_L	125_A	0.718	0.99
4_E	44_P	0.716	0.99
26_W	29_L	0.714	0.99
66_A	70_A	0.709	0.98
27_A	78_L	0.707	0.98
48_L	51_D	0.706	0.98
52_R	56_R	0.706	0.98
111_E	118_L	0.701	0.98
41_A	65_G	0.698	0.98
111_E	119_A	0.694	0.98
20_L	24_P	0.694	0.98
7_A	43_Q	0.687	0.98
41_A	68_A	0.684	0.98
83_L	86_A	0.684	0.98
83_L	89_A	0.683	0.98
37_A	41_A	0.679	0.98
99_L	107_S	0.676	0.98
10_M	43_Q	0.675	0.98
71_A	75_L	0.675	0.98
31_L	86_A	0.673	0.98
93_F	97_L	0.673	0.98
44_P	114_G	0.670	0.98
54_R	59_R	0.658	0.98
2_P	6_G	0.656	0.98
56_R	69_A	0.651	0.97
23_G	28_G	0.648	0.97
111_E	117_A	0.644	0.97
52_R	59_R	0.634	0.97
3_R	11_L	0.632	0.97
30_L	78_L	0.623	0.97
76_L	80_P	0.620	0.97
34_A	72_G	0.616	0.96
90_A	94_A	0.616	0.96
66_A	101_A	0.609	0.96
52_R	58_R	0.598	0.96
46_L	105_E	0.594	0.96
116_A	119_A	0.593	0.96
10_M	20_L	0.590	0.95
37_A	64_Y	0.585	0.95
28_G	32_A	0.576	0.95
37_A	40_L	0.575	0.95
44_P	47_L	0.570	0.94
29_L	33_L	0.566	0.94
18_G	51_D	0.565	0.94
25_S	29_L	0.563	0.94
84_W	87_L	0.560	0.94
111_E	121_A	0.556	0.94
47_L	51_D	0.551	0.93
25_S	30_L	0.550	0.93
15_L	31_L	0.548	0.93
9_G	42_R	0.547	0.93
1_L	40_L	0.546	0.93
83_L	87_L	0.546	0.93
65_G	72_G	0.543	0.93
66_A	76_L	0.539	0.93
56_R	60_W	0.538	0.93
109_L	113_A	0.534	0.92
15_L	35_A	0.534	0.92
2_P	7_A	0.528	0.92
42_R	117_A	0.524	0.92
52_R	55_R	0.524	0.92
40_L	43_Q	0.522	0.91
27_A	30_L	0.520	0.91
96_Q	99_L	0.517	0.91
14_P	39_F	0.509	0.90
7_A	11_L	0.506	0.90
108_L	121_A	0.505	0.90
121_A	124_A	0.504	0.90
81_A	84_W	0.504	0.90
9_G	14_P	0.503	0.90
11_L	118_L	0.501	0.90
61_L	102_R	0.501	0.90
42_R	46_L	0.500	0.90

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
3l1lA	2	0.8968	26.9	0.886	Contact Map
3rceA	1	0.8968	12.9	0.902	Contact Map
3wajA	1	0.9365	10.9	0.905	Contact Map
1xioA	2	0.4048	6.2	0.915	Contact Map
3qapA	1	0.4048	4.7	0.92	Contact Map
2nq2A	2	0.7619	3.9	0.923	Contact Map
3giaA	1	0.8968	3.6	0.924	Contact Map
4qtnA	3	0.627	3.6	0.924	Contact Map
4p02A	1	0.7063	3.4	0.925	Contact Map
3tx3A	2	0.8175	3.2	0.926	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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