YRVC - BACSU - GREMLIN Contacts

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YRVC - Uncharacterized protein YrvC

UniProt:	O32046	Sequences: MRVRESELPGIGQKVEMITRNRDKISIIIHHDGRRELYYFDENDHEECVASVQFDDAEARQMSAILGGMAYKPKALEQVESALDDLIIEWCKAEAGAPAIHQTIGDLNVGQEYHVTVIAIVKKNQDKQLNPSSETVIDEGDTLVISGEGTGLKRLIREKLTAKGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	165 (152)
Sequences:	2115 (1659)
Seq/√Len:	134.5

ECOLI - TRKA
BACSU - YRVC KHTT KTRC KTRA YJBQ
HALSA - Q9HRN5 Q9HSL4 Q9HQ83 Q9HNV8 Q9HHY1 Q9HNK1 Q9HHU4 Q9HHS7 Q9HHU8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
122_K	141_D	4.842	1.00
120_I	135_T	4.760	1.00
93_A	137_I	4.515	1.00
21_N	24_K	4.264	1.00
31_H	39_Y	3.078	1.00
20_R	24_K	2.654	1.00
7_E	12_G	2.481	1.00
20_R	23_D	2.468	1.00
103_T	106_D	2.364	1.00
66_L	69_M	2.363	1.00
108_N	111_Q	2.318	1.00
17_M	30_H	2.233	1.00
104_I	117_V	2.000	1.00
122_K	138_D	1.996	1.00
113_Y	151_G	1.996	1.00
102_Q	106_D	1.958	1.00
105_G	134_E	1.946	1.00
99_A	107_L	1.891	1.00
100_I	139_E	1.888	1.00
17_M	37_L	1.873	1.00
120_I	141_D	1.870	1.00
148_E	151_G	1.870	1.00
30_H	33_G	1.855	1.00
73_P	77_E	1.830	1.00
20_R	25_I	1.780	1.00
10_G	13_Q	1.767	1.00
57_A	60_R	1.752	1.00
103_T	136_V	1.705	1.00
90_W	144_V	1.611	1.00
67_G	70_A	1.545	1.00
114_H	151_G	1.523	1.00
122_K	135_T	1.521	1.00
73_P	76_L	1.500	1.00
145_I	155_L	1.488	1.00
101_H	138_D	1.469	1.00
110_G	116_T	1.467	1.00
20_R	26_S	1.430	1.00
21_N	25_I	1.385	1.00
95_A	139_E	1.380	1.00
59_A	62_M	1.317	1.00
88_I	146_S	1.309	1.00
34_R	37_L	1.308	1.00
51_S	55_D	1.286	1.00
93_A	100_I	1.269	1.00
109_V	117_V	1.260	1.00
23_D	26_S	1.245	1.00
35_R	41_D	1.240	1.00
109_V	155_L	1.239	1.00
101_H	139_E	1.226	1.00
137_I	143_L	1.198	1.00
103_T	107_L	1.169	0.99
58_E	63_S	1.158	0.99
39_Y	42_E	1.153	0.99
50_A	56_D	1.144	0.99
70_A	73_P	1.138	0.99
30_H	34_R	1.138	0.99
52_V	55_D	1.126	0.99
58_E	62_M	1.106	0.99
66_L	73_P	1.105	0.99
118_I	146_S	1.101	0.99
50_A	55_D	1.090	0.99
63_S	67_G	1.087	0.99
66_L	70_A	1.073	0.99
40_F	43_N	1.070	0.99
105_G	132_S	1.069	0.99
51_S	54_F	1.060	0.99
9_P	14_K	1.059	0.99
6_S	9_P	1.035	0.99
28_I	31_H	1.020	0.98
138_D	141_D	1.013	0.98
39_Y	43_N	1.012	0.98
19_T	24_K	0.991	0.98
109_V	113_Y	0.990	0.98
65_I	68_G	0.989	0.98
68_G	71_Y	0.988	0.98
11_I	17_M	0.988	0.98
59_A	63_S	0.981	0.98
52_V	56_D	0.979	0.98
70_A	75_A	0.977	0.98
109_V	115_V	0.977	0.98
123_K	126_D	0.963	0.98
108_N	112_E	0.959	0.98
104_I	131_P	0.944	0.97
35_R	42_E	0.939	0.97
63_S	66_L	0.936	0.97
51_S	56_D	0.933	0.97
42_E	47_E	0.932	0.97
62_M	67_G	0.930	0.97
49_V	52_V	0.920	0.97
75_A	78_Q	0.912	0.97
153_K	157_R	0.905	0.97
24_K	104_I	0.902	0.97
50_A	54_F	0.889	0.96
48_C	52_V	0.885	0.96
116_T	133_S	0.860	0.95
31_H	35_R	0.855	0.95
80_E	145_I	0.846	0.95
72_K	75_A	0.846	0.95
31_H	34_R	0.845	0.95
122_K	128_Q	0.842	0.95
53_Q	56_D	0.839	0.95
57_A	62_M	0.833	0.95
6_S	14_K	0.830	0.95
115_V	155_L	0.827	0.94
9_P	18_I	0.825	0.94
37_L	41_D	0.821	0.94
22_R	25_I	0.820	0.94
70_A	74_K	0.799	0.93
35_R	40_F	0.789	0.93
15_V	18_I	0.788	0.93
119_A	144_V	0.774	0.92
48_C	55_D	0.758	0.91
67_G	71_Y	0.739	0.90
62_M	69_M	0.737	0.90
91_C	148_E	0.737	0.90
19_T	25_I	0.736	0.90
110_G	113_Y	0.726	0.90
59_A	65_I	0.722	0.89
19_T	23_D	0.710	0.89
61_Q	66_L	0.703	0.88
38_Y	41_D	0.699	0.88
22_R	26_S	0.698	0.88
126_D	154_R	0.697	0.88
31_H	57_A	0.692	0.87
147_G	151_G	0.690	0.87
91_C	155_L	0.689	0.87
130_N	133_S	0.688	0.87
112_E	154_R	0.686	0.87
31_H	152_L	0.685	0.87
96_G	100_I	0.678	0.86
93_A	97_A	0.678	0.86
90_W	142_T	0.670	0.85
57_A	66_L	0.667	0.85
147_G	155_L	0.667	0.85
104_I	133_S	0.666	0.85
62_M	66_L	0.663	0.85
62_M	71_Y	0.663	0.85
61_Q	68_G	0.662	0.85
72_K	137_I	0.662	0.85
56_D	59_A	0.659	0.85
71_Y	79_V	0.658	0.84
24_K	27_I	0.654	0.84
11_I	33_G	0.652	0.84
69_M	72_K	0.652	0.84
135_T	138_D	0.650	0.84
85_D	143_L	0.650	0.84
26_S	30_H	0.648	0.84
29_I	50_A	0.646	0.83
42_E	51_S	0.644	0.83
34_R	38_Y	0.642	0.83
40_F	47_E	0.641	0.83
128_Q	135_T	0.639	0.83
57_A	61_Q	0.638	0.83
48_C	51_S	0.630	0.82
117_V	145_I	0.625	0.81
73_P	78_Q	0.625	0.81
121_V	142_T	0.624	0.81
58_E	61_Q	0.622	0.81
71_Y	74_K	0.620	0.81
64_A	69_M	0.618	0.81
91_C	108_N	0.617	0.80
9_P	30_H	0.613	0.80
132_S	137_I	0.611	0.80
30_H	37_L	0.610	0.80
110_G	133_S	0.610	0.80
69_M	73_P	0.607	0.79
77_E	144_V	0.604	0.79
59_A	117_V	0.603	0.79
43_N	47_E	0.602	0.79
58_E	65_I	0.600	0.79
110_G	117_V	0.599	0.79
100_I	134_E	0.597	0.78
145_I	152_L	0.595	0.78
136_V	140_G	0.595	0.78
81_S	84_D	0.591	0.78
86_L	146_S	0.590	0.77
150_T	154_R	0.588	0.77
43_N	46_E	0.586	0.77
105_G	133_S	0.579	0.76
86_L	89_E	0.579	0.76
28_I	32_D	0.578	0.76
110_G	118_I	0.578	0.76
67_G	73_P	0.577	0.76
28_I	54_F	0.577	0.76
67_G	72_K	0.575	0.76
19_T	41_D	0.573	0.75
53_Q	124_N	0.572	0.75
66_L	72_K	0.570	0.75
5_E	9_P	0.570	0.75
30_H	35_R	0.564	0.74
34_R	39_Y	0.560	0.74
60_R	63_S	0.560	0.74
154_R	157_R	0.559	0.74
46_E	115_V	0.559	0.74
71_Y	75_A	0.558	0.73
99_A	155_L	0.555	0.73
148_E	153_K	0.547	0.72
77_E	117_V	0.546	0.72
110_G	152_L	0.544	0.72
94_E	112_E	0.544	0.72
115_V	151_G	0.543	0.71
29_I	37_L	0.543	0.71
32_D	35_R	0.542	0.71
102_Q	105_G	0.540	0.71
22_R	144_V	0.540	0.71
35_R	48_C	0.537	0.71
71_Y	86_L	0.534	0.70
45_H	140_G	0.531	0.70
101_H	136_V	0.527	0.69
75_A	79_V	0.524	0.69
123_K	136_V	0.523	0.69
39_Y	47_E	0.522	0.69
102_Q	112_E	0.520	0.68
65_I	69_M	0.519	0.68
61_Q	64_A	0.516	0.68
110_G	115_V	0.514	0.67
62_M	115_V	0.513	0.67
95_A	100_I	0.513	0.67
72_K	86_L	0.512	0.67
63_S	142_T	0.507	0.66
74_K	77_E	0.506	0.66
107_L	135_T	0.506	0.66
95_A	98_P	0.504	0.66
14_K	17_M	0.504	0.66
14_K	41_D	0.504	0.66
96_G	124_N	0.501	0.65
132_S	135_T	0.500	0.65
38_Y	68_G	0.500	0.65

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
2aefA	2	0.9879	99.9	0.397	Contact Map
4gx0A	3	0.9636	99.9	0.404	Contact Map
1lnqA	6	0.9697	99.9	0.41	Contact Map
3mt5A	5	0.9333	99.9	0.435	Contact Map
3nafA	3	0.9636	99.9	0.44	Contact Map
4g65A	2	0.9636	99.9	0.44	Contact Map
4hpfA	3	0.9273	99.8	0.457	Contact Map
3l4bC	2	0.9394	99.8	0.477	Contact Map
4j91A	3	0.9394	99.7	0.536	Contact Map
1vctA	3	0.8667	99.7	0.548	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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