VanW - PFAM28P - GREMLIN Contacts

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VanW - VanW like protein

PFAM:	PF04294	Sequences: NRVHNIRLAASKINGTVIAPGETFSFNKTVGPRTAEKGYKEAPVIVNGELVPGVGGGVCQVSTTLYNAALFAGLEIVERHNHSYPVSYYPPGRDATVSYPYVDLKFKNDTDYPILIQAYVDGGSLTVEIY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	130 (128)
Sequences:	16322 (10241)
Seq/√Len:	905.2
META:	0.879

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_V	53_G	2.885	1.00
77_V	107_K	2.548	1.00
4_H	40_K	2.396	1.00
34_T	37_K	2.307	1.00
69_A	106_F	2.245	1.00
16_T	29_T	2.239	1.00
75_E	107_K	2.207	1.00
80_H	102_V	2.175	1.00
19_A	113_P	2.147	1.00
19_A	22_E	2.090	1.00
23_T	77_V	2.077	1.00
25_S	103_D	2.050	1.00
35_A	54_V	2.034	1.00
118_A	127_V	1.914	1.00
23_T	107_K	1.886	1.00
12_K	37_K	1.860	1.00
23_T	105_K	1.812	1.00
119_Y	128_E	1.773	1.00
12_K	39_Y	1.769	1.00
43_P	52_P	1.741	1.00
14_N	117_Q	1.733	1.00
117_Q	128_E	1.728	1.00
10_A	118_A	1.705	1.00
75_E	109_D	1.658	1.00
67_N	93_R	1.651	1.00
69_A	104_L	1.606	1.00
74_L	114_I	1.583	1.00
41_E	52_P	1.573	1.00
8_L	12_K	1.568	1.00
43_P	50_L	1.527	1.00
9_A	61_V	1.513	1.00
46_V	51_V	1.511	1.00
35_A	41_E	1.506	1.00
9_A	58_V	1.486	1.00
69_A	76_I	1.482	1.00
63_T	89_Y	1.469	1.00
4_H	7_R	1.446	1.00
78_E	105_K	1.438	1.00
41_E	54_V	1.435	1.00
71_F	93_R	1.421	1.00
119_Y	126_T	1.387	1.00
8_L	11_S	1.385	1.00
4_H	8_L	1.376	1.00
7_R	11_S	1.358	1.00
26_F	97_V	1.328	1.00
27_N	33_R	1.311	1.00
20_P	113_P	1.308	1.00
17_V	113_P	1.286	1.00
98_S	101_Y	1.233	1.00
60_Q	64_T	1.233	1.00
96_T	102_V	1.212	1.00
45_I	50_L	1.207	1.00
98_S	102_V	1.176	1.00
50_L	84_Y	1.164	1.00
67_N	71_F	1.151	1.00
13_I	24_F	1.118	1.00
69_A	74_L	1.117	1.00
121_D	124_S	1.110	1.00
77_V	105_K	1.104	1.00
26_F	62_S	1.101	1.00
3_V	7_R	1.092	1.00
59_C	82_H	1.081	1.00
17_V	115_L	1.075	1.00
3_V	123_G	1.061	1.00
46_V	53_G	1.060	1.00
32_P	99_Y	1.057	1.00
85_P	91_P	1.051	1.00
30_V	33_R	1.035	1.00
13_I	61_V	1.010	1.00
10_A	125_L	0.987	1.00
16_T	24_F	0.979	1.00
13_I	16_T	0.966	1.00
9_A	30_V	0.962	1.00
33_R	58_V	0.950	1.00
62_S	104_L	0.948	1.00
7_R	120_V	0.943	1.00
67_N	89_Y	0.939	1.00
8_L	37_K	0.929	1.00
76_I	79_R	0.929	1.00
121_D	126_T	0.927	1.00
24_F	29_T	0.911	1.00
66_Y	104_L	0.899	1.00
20_P	111_D	0.893	1.00
26_F	30_V	0.893	1.00
24_F	106_F	0.883	1.00
45_I	86_V	0.865	1.00
68_A	129_I	0.864	1.00
14_N	118_A	0.859	1.00
45_I	84_Y	0.857	1.00
15_G	117_Q	0.854	1.00
66_Y	70_L	0.851	1.00
27_N	99_Y	0.847	1.00
68_A	127_V	0.842	1.00
74_L	109_D	0.835	1.00
74_L	106_F	0.826	1.00
44_V	51_V	0.824	1.00
10_A	61_V	0.817	1.00
21_G	111_D	0.815	1.00
18_I	22_E	0.808	1.00
8_L	39_Y	0.808	1.00
33_R	99_Y	0.801	1.00
31_G	38_G	0.794	1.00
70_L	93_R	0.793	1.00
62_S	97_V	0.791	1.00
72_A	129_I	0.784	1.00
8_L	40_K	0.781	1.00
32_P	37_K	0.761	1.00
65_L	118_A	0.754	1.00
65_L	116_I	0.752	1.00
3_V	120_V	0.752	1.00
63_T	67_N	0.744	1.00
15_G	115_L	0.743	1.00
50_L	86_V	0.730	1.00
13_I	29_T	0.728	1.00
26_F	61_V	0.725	1.00
64_T	127_V	0.724	1.00
65_L	127_V	0.712	1.00
44_V	98_S	0.711	1.00
116_I	129_I	0.710	1.00
34_T	54_V	0.706	1.00
45_I	83_S	0.699	1.00
9_A	26_F	0.688	1.00
59_C	94_D	0.677	1.00
27_N	97_V	0.677	1.00
90_P	93_R	0.675	1.00
34_T	38_G	0.674	1.00
59_C	96_T	0.673	1.00
67_N	90_P	0.672	1.00
68_A	72_A	0.670	1.00
85_P	90_P	0.666	1.00
18_I	106_F	0.665	1.00
2_R	6_I	0.656	1.00
32_P	36_E	0.644	1.00
65_L	106_F	0.643	1.00
74_L	110_T	0.640	1.00
64_T	68_A	0.639	1.00
53_G	98_S	0.639	1.00
76_I	104_L	0.635	1.00
65_L	69_A	0.634	1.00
10_A	120_V	0.633	1.00
46_V	49_E	0.633	1.00
66_Y	76_I	0.631	1.00
82_H	96_T	0.627	1.00
112_Y	115_L	0.626	1.00
3_V	6_I	0.620	1.00
79_R	95_A	0.617	1.00
78_E	101_Y	0.614	1.00
84_Y	87_S	0.609	1.00
30_V	39_Y	0.605	1.00
120_V	123_G	0.601	1.00
69_A	129_I	0.600	1.00
106_F	114_I	0.591	1.00
13_I	30_V	0.589	1.00
31_G	37_K	0.583	1.00
85_P	89_Y	0.582	1.00
120_V	125_L	0.580	1.00
61_V	125_L	0.576	1.00
66_Y	79_R	0.571	1.00
106_F	116_I	0.571	1.00
7_R	122_G	0.570	1.00
27_N	101_Y	0.566	1.00
11_S	14_N	0.564	1.00
12_K	16_T	0.564	1.00
55_G	59_C	0.562	1.00
13_I	26_F	0.547	1.00
33_R	55_G	0.546	1.00
27_N	31_G	0.545	1.00
78_E	102_V	0.539	1.00
66_Y	92_G	0.536	1.00
68_A	116_I	0.535	1.00
21_G	107_K	0.534	1.00
25_S	28_K	0.533	1.00
59_C	79_R	0.531	1.00
18_I	24_F	0.531	1.00
31_G	99_Y	0.531	1.00
110_T	113_P	0.530	1.00
42_A	52_P	0.528	1.00
66_Y	89_Y	0.526	1.00
66_Y	95_A	0.523	1.00
27_N	100_P	0.522	1.00
110_T	114_I	0.521	1.00
9_A	13_I	0.520	1.00
80_H	96_T	0.517	1.00
80_H	83_S	0.516	1.00
81_N	84_Y	0.515	1.00
73_G	89_Y	0.508	1.00
41_E	53_G	0.508	1.00
58_V	61_V	0.507	1.00
27_N	58_V	0.506	1.00
79_R	94_D	0.504	1.00
10_A	127_V	0.501	1.00
6_I	60_Q	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
2p8rA	1	0.9538	33.4	0.913	Contact Map
1m1sA	1	0.3692	26.4	0.917	Contact Map
2f8aA	3	0.2538	23.5	0.919	Contact Map
4f82A	2	0.3769	14.5	0.926	Contact Map
2og4A	1	0.9538	11.7	0.929	Contact Map
4aslA	2	0.2	11.2	0.93	Contact Map
2co7B	1	0.3923	9.6	0.932	Contact Map
4o94A	1	0.2385	9.3	0.933	Contact Map
4pbqA	1	0.2308	9.2	0.933	Contact Map
1rowA	1	0.3462	7	0.936	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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