YAII - ECOLI - GREMLIN Contacts

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YAII - UPF0178 protein YaiI

UniProt:	P0A8D3	Sequences: MTIWVDADACPNVIKEILYRAAERMQMPLVLVANQSLRVPPSRFIRTLRVAAGFDVADNEIVRQCEAGDLVITADIPLAAEAIEKGAAALNPRGERYTPATIRERLTMRDFMDTLRASGIQTGGPDSLSQRDRQAFAAELEKWWLEVQRSRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13176
Length:	152 (143)
Sequences:	1461 (1006)
Seq/√Len:	84.1

ECOLI - YAII
BACSU - YQXD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
60_E	64_Q	3.920	1.00
80_A	84_E	2.987	1.00
2_T	30_V	2.890	1.00
82_A	87_A	2.777	1.00
60_E	63_R	2.569	1.00
5_V	18_L	2.562	1.00
28_P	46_R	2.503	1.00
134_Q	138_A	2.329	1.00
82_A	89_A	2.329	1.00
91_N	97_Y	2.324	1.00
65_C	87_A	2.192	1.00
24_R	141_E	2.176	1.00
65_C	71_V	2.032	1.00
19_Y	31_L	2.001	1.00
20_R	137_A	1.988	1.00
115_L	120_I	1.936	1.00
67_A	86_G	1.863	1.00
71_V	82_A	1.801	1.00
48_L	60_E	1.731	1.00
7_A	31_L	1.706	1.00
27_M	144_W	1.661	1.00
88_A	143_W	1.642	1.00
18_L	29_L	1.633	1.00
74_A	92_P	1.610	1.00
14_I	128_L	1.591	1.00
25_M	141_E	1.590	1.00
119_G	122_T	1.581	1.00
110_D	114_T	1.542	1.00
32_V	57_A	1.542	1.00
2_T	28_P	1.537	1.00
129_S	132_D	1.507	0.99
17_I	133_R	1.483	0.99
128_L	133_R	1.483	0.99
74_A	91_N	1.473	0.99
26_Q	44_F	1.470	0.99
113_D	117_A	1.438	0.99
19_Y	45_I	1.393	0.99
84_E	103_R	1.390	0.99
48_L	64_Q	1.361	0.99
59_N	81_E	1.357	0.99
3_I	22_A	1.351	0.99
30_V	46_R	1.337	0.99
88_A	146_E	1.328	0.99
3_I	140_L	1.312	0.99
65_C	82_A	1.300	0.98
96_R	139_E	1.294	0.98
17_I	137_A	1.294	0.98
77_P	106_L	1.281	0.98
98_T	101_T	1.265	0.98
23_E	43_R	1.264	0.98
5_V	31_L	1.260	0.98
141_E	145_L	1.254	0.98
2_T	66_E	1.245	0.98
80_A	106_L	1.241	0.98
139_E	142_K	1.233	0.98
83_I	101_T	1.216	0.98
53_G	56_V	1.204	0.97
132_D	135_A	1.181	0.97
131_R	135_A	1.166	0.97
31_L	39_V	1.143	0.96
4_W	30_V	1.131	0.96
21_A	144_W	1.123	0.96
56_V	59_N	1.106	0.96
2_T	46_R	1.105	0.96
3_I	18_L	1.105	0.96
89_A	97_Y	1.101	0.96
72_I	90_L	1.058	0.95
62_V	85_K	1.041	0.94
70_L	144_W	1.038	0.94
114_T	118_S	1.032	0.94
90_L	143_W	1.030	0.94
83_I	102_I	1.024	0.94
107_T	110_D	1.024	0.94
88_A	96_R	1.009	0.93
35_Q	47_T	0.996	0.93
112_M	122_T	0.996	0.93
103_R	110_D	0.994	0.93
55_D	59_N	0.990	0.92
39_V	47_T	0.987	0.92
21_A	137_A	0.987	0.92
32_V	61_I	0.975	0.92
25_M	144_W	0.949	0.91
15_K	31_L	0.948	0.91
103_R	107_T	0.939	0.90
89_A	96_R	0.925	0.90
70_L	96_R	0.919	0.89
80_A	103_R	0.916	0.89
91_N	95_E	0.915	0.89
36_S	52_A	0.910	0.89
4_W	61_I	0.907	0.89
29_L	45_I	0.906	0.89
32_V	64_Q	0.898	0.88
118_S	121_Q	0.897	0.88
5_V	15_K	0.894	0.88
122_T	125_P	0.881	0.87
50_V	57_A	0.877	0.87
59_N	63_R	0.876	0.87
130_Q	133_R	0.874	0.87
42_S	45_I	0.859	0.86
96_R	143_W	0.856	0.86
142_K	145_L	0.854	0.85
18_L	140_L	0.850	0.85
70_L	143_W	0.844	0.85
104_E	108_M	0.835	0.84
86_G	99_P	0.835	0.84
107_T	111_F	0.832	0.84
23_E	42_S	0.832	0.84
50_V	60_E	0.826	0.84
63_R	81_E	0.822	0.83
28_P	44_F	0.815	0.83
110_D	118_S	0.804	0.82
77_P	110_D	0.784	0.80
114_T	117_A	0.781	0.80
17_I	25_M	0.780	0.80
71_V	87_A	0.779	0.80
83_I	110_D	0.776	0.80
83_I	99_P	0.770	0.79
52_A	56_V	0.766	0.79
93_R	119_G	0.760	0.78
27_M	30_V	0.759	0.78
107_T	114_T	0.744	0.77
101_T	105_R	0.742	0.76
90_L	139_E	0.737	0.76
62_V	82_A	0.733	0.76
76_I	105_R	0.732	0.75
19_Y	40_P	0.731	0.75
39_V	45_I	0.725	0.75
2_T	139_E	0.718	0.74
4_W	60_E	0.711	0.73
14_I	136_F	0.707	0.73
31_L	47_T	0.705	0.73
23_E	41_P	0.705	0.73
7_A	33_A	0.704	0.73
79_A	97_Y	0.702	0.72
21_A	141_E	0.700	0.72
72_I	85_K	0.700	0.72
139_E	143_W	0.698	0.72
33_A	47_T	0.697	0.72
14_I	17_I	0.697	0.72
9_A	31_L	0.687	0.71
137_A	141_E	0.681	0.70
10_C	14_I	0.675	0.69
138_A	142_K	0.672	0.69
32_V	50_V	0.671	0.69
37_L	47_T	0.663	0.68
111_F	115_L	0.662	0.68
22_A	29_L	0.662	0.68
127_S	133_R	0.658	0.67
66_E	85_K	0.643	0.66
17_I	128_L	0.642	0.66
51_A	60_E	0.641	0.65
55_D	63_R	0.635	0.65
83_I	87_A	0.634	0.65
34_N	56_V	0.633	0.64
5_V	9_A	0.633	0.64
4_W	32_V	0.627	0.64
98_T	105_R	0.625	0.63
7_A	11_P	0.622	0.63
27_M	68_G	0.622	0.63
22_A	44_F	0.616	0.62
54_F	59_N	0.615	0.62
63_R	128_L	0.611	0.62
105_R	110_D	0.606	0.61
21_A	24_R	0.606	0.61
5_V	10_C	0.605	0.61
16_E	40_P	0.604	0.61
18_L	72_I	0.604	0.61
30_V	64_Q	0.601	0.60
135_A	139_E	0.592	0.59
31_L	45_I	0.592	0.59
34_N	61_I	0.590	0.59
76_I	83_I	0.589	0.59
48_L	99_P	0.587	0.59
18_L	93_R	0.584	0.58
2_T	143_W	0.577	0.57
69_D	140_L	0.576	0.57
9_A	116_R	0.575	0.57
56_V	81_E	0.572	0.57
15_K	33_A	0.570	0.56
23_E	44_F	0.570	0.56
108_M	111_F	0.563	0.56
110_D	117_A	0.555	0.54
34_N	50_V	0.555	0.54
134_Q	137_A	0.553	0.54
15_K	32_V	0.551	0.54
130_Q	134_Q	0.544	0.53
26_Q	43_R	0.542	0.53
96_R	146_E	0.539	0.52
23_E	26_Q	0.539	0.52
9_A	92_P	0.538	0.52
118_S	122_T	0.531	0.51
76_I	106_L	0.529	0.51
69_D	72_I	0.529	0.51
24_R	40_P	0.526	0.51
142_K	146_E	0.524	0.50
83_I	114_T	0.523	0.50
26_Q	42_S	0.519	0.50
88_A	97_Y	0.517	0.49
5_V	22_A	0.514	0.49
9_A	33_A	0.514	0.49
97_Y	101_T	0.513	0.49
24_R	137_A	0.512	0.49
96_R	142_K	0.510	0.49
52_A	55_D	0.510	0.49
95_E	108_M	0.509	0.48
74_A	97_Y	0.508	0.48
93_R	132_D	0.508	0.48
20_R	24_R	0.508	0.48
21_A	25_M	0.507	0.48
72_I	92_P	0.507	0.48
11_P	14_I	0.506	0.48
83_I	121_Q	0.505	0.48
4_W	65_C	0.501	0.47
28_P	66_E	0.500	0.47

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
4mj7A	2	0.6447	87.6	0.916	Contact Map
3hblA	4	0.9474	84.4	0.92	Contact Map
3ouzA	2	0.9474	79.7	0.924	Contact Map
2vpqA	2	0.9474	77.6	0.925	Contact Map
4qshA	4	0.7763	74.8	0.927	Contact Map
1w96A	1	0.9474	71.8	0.929	Contact Map
3u9tA	3	0.9276	70.3	0.929	Contact Map
2jjmA	4	0.8947	66	0.931	Contact Map
1uqtA	2	0.9408	65.4	0.932	Contact Map
1ulzA	2	0.9474	61.9	0.933	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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