YPSA - BACSU - GREMLIN Contacts

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YPSA - UPF0398 protein YpsA

UniProt:	P50838	Sequences: MKVLAITGYKPFELGIFKQDDKALYYIKKAIKNRLIAFLDEGLEWILISGQLGVELWAAEAAYDLQEEYPDLKVAVITPFYEQEKNWKEPNKEQYEAVLAQADYEASLTHRPYESPLQFKQKNQFFIDKSDGLLLLYDPEKEGSPKYMLGTAEKRREQDGYPIYFITMDDLRVTVEEDSY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	180 (176)
Sequences:	408 (302)
Seq/√Len:	22.8

BACSU - YPSA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_T	135_L	3.581	1.00
6_I	58_A	3.564	1.00
43_L	46_I	3.171	1.00
28_K	61_A	3.124	1.00
30_A	174_T	3.045	1.00
89_E	92_K	3.026	1.00
88_K	91_N	2.943	0.99
130_S	161_Y	2.892	0.99
152_A	163_I	2.736	0.99
5_A	126_F	2.709	0.99
19_Q	94_Q	2.681	0.99
78_T	107_S	2.637	0.99
82_E	85_K	2.547	0.98
46_I	72_L	2.305	0.97
172_R	176_E	2.270	0.97
46_I	62_A	2.265	0.97
7_T	148_M	2.200	0.96
47_L	130_S	2.160	0.96
109_T	121_Q	2.147	0.96
48_I	59_A	2.136	0.95
54_V	136_L	2.104	0.95
111_R	114_E	2.067	0.94
66_Q	103_D	2.023	0.94
92_K	96_E	2.007	0.94
10_K	83_Q	1.970	0.93
32_K	36_I	1.966	0.93
32_K	64_D	1.963	0.93
35_L	46_I	1.903	0.92
84_E	95_Y	1.900	0.91
133_L	152_A	1.801	0.89
36_I	40_D	1.792	0.89
76_V	99_L	1.782	0.89
142_E	146_K	1.778	0.88
77_I	108_L	1.731	0.87
3_V	129_K	1.648	0.84
52_L	91_N	1.628	0.84
32_K	61_A	1.614	0.83
124_Q	128_D	1.606	0.83
12_F	91_N	1.566	0.81
125_F	129_K	1.558	0.81
31_I	58_A	1.490	0.78
4_L	132_G	1.440	0.75
78_T	105_E	1.417	0.74
6_I	77_I	1.347	0.70
38_F	164_Y	1.344	0.70
136_L	168_M	1.329	0.69
78_T	95_Y	1.318	0.68
27_I	30_A	1.316	0.68
88_K	168_M	1.305	0.67
76_V	102_A	1.285	0.66
141_K	168_M	1.276	0.66
133_L	148_M	1.275	0.66
63_Y	66_Q	1.267	0.65
149_L	165_F	1.260	0.65
91_N	168_M	1.223	0.62
66_Q	123_N	1.221	0.62
59_A	74_V	1.216	0.62
62_A	74_V	1.203	0.61
44_E	73_K	1.200	0.61
155_R	159_D	1.176	0.59
83_Q	123_N	1.171	0.59
56_L	98_V	1.166	0.59
49_S	122_K	1.164	0.58
7_T	13_E	1.152	0.58
59_A	76_V	1.133	0.56
119_F	146_K	1.133	0.56
20_D	30_A	1.127	0.56
84_E	122_K	1.126	0.56
43_L	132_G	1.122	0.56
41_E	158_Q	1.112	0.55
10_K	95_Y	1.110	0.55
52_L	88_K	1.110	0.55
120_K	151_T	1.107	0.55
19_Q	24_L	1.077	0.52
149_L	153_E	1.072	0.52
26_Y	29_K	1.063	0.51
12_F	88_K	1.063	0.51
36_I	64_D	1.055	0.51
15_G	86_N	1.050	0.51
77_I	126_F	1.047	0.50
36_I	39_L	1.041	0.50
130_S	133_L	1.019	0.48
134_L	166_I	1.008	0.48
34_R	164_Y	1.007	0.48
4_L	134_L	1.006	0.48
16_I	69_Y	1.005	0.47
40_D	43_L	1.001	0.47
59_A	102_A	0.993	0.47
4_L	43_L	0.993	0.47
119_F	148_M	0.987	0.46
3_V	47_L	0.984	0.46
3_V	130_S	0.982	0.46
59_A	98_V	0.979	0.46
43_L	72_L	0.972	0.45
135_L	142_E	0.959	0.44
20_D	24_L	0.958	0.44
82_E	112_P	0.957	0.44
83_Q	95_Y	0.943	0.43
106_A	132_G	0.940	0.43
5_A	148_M	0.927	0.42
56_L	94_Q	0.924	0.42
153_E	157_E	0.914	0.41
125_F	137_Y	0.911	0.41
39_L	72_L	0.908	0.41
10_K	123_N	0.880	0.39
62_A	73_K	0.878	0.39
55_E	79_P	0.872	0.38
29_K	33_N	0.871	0.38
167_T	170_D	0.871	0.38
10_K	74_V	0.863	0.38
63_Y	115_S	0.861	0.38
123_N	144_S	0.849	0.37
39_L	65_L	0.843	0.37
73_K	92_K	0.841	0.36
55_E	125_F	0.840	0.36
31_I	100_A	0.838	0.36
79_P	102_A	0.836	0.36
146_K	150_G	0.832	0.36
119_F	123_N	0.804	0.34
48_I	56_L	0.801	0.34
16_I	123_N	0.799	0.34
122_K	144_S	0.796	0.34
123_N	148_M	0.791	0.33
20_D	92_K	0.790	0.33
80_F	155_R	0.788	0.33
104_Y	122_K	0.787	0.33
126_F	129_K	0.785	0.33
5_A	130_S	0.777	0.32
4_L	46_I	0.769	0.32
80_F	116_P	0.769	0.32
69_Y	109_T	0.769	0.32
39_L	43_L	0.765	0.32
26_Y	175_V	0.758	0.31
10_K	49_S	0.758	0.31
81_Y	111_R	0.741	0.30
135_L	149_L	0.740	0.30
15_G	141_K	0.740	0.30
60_E	94_Q	0.739	0.30
10_K	144_S	0.729	0.30
98_V	104_Y	0.725	0.29
93_E	97_A	0.724	0.29
52_L	87_W	0.723	0.29
39_L	120_K	0.714	0.29
162_P	177_E	0.712	0.29
142_E	150_G	0.700	0.28
47_L	131_D	0.698	0.28
77_I	104_Y	0.694	0.28
13_E	109_T	0.692	0.28
66_Q	148_M	0.689	0.27
36_I	68_E	0.688	0.27
47_L	126_F	0.687	0.27
126_F	130_S	0.685	0.27
23_A	148_M	0.677	0.27
141_K	145_P	0.674	0.27
27_I	171_L	0.674	0.27
47_L	129_K	0.664	0.26
23_A	26_Y	0.663	0.26
38_F	60_E	0.661	0.26
2_K	44_E	0.659	0.26
69_Y	126_F	0.659	0.26
84_E	129_K	0.658	0.26
151_T	158_Q	0.655	0.26
80_F	119_F	0.653	0.25
89_E	149_L	0.653	0.25
95_Y	99_L	0.652	0.25
102_A	143_G	0.649	0.25
115_S	121_Q	0.648	0.25
52_L	107_S	0.648	0.25
15_G	125_F	0.647	0.25
29_K	148_M	0.645	0.25
60_E	95_Y	0.645	0.25
68_E	116_P	0.644	0.25
139_P	165_F	0.643	0.25
67_E	85_K	0.639	0.25
77_I	119_F	0.637	0.25
99_L	123_N	0.636	0.25
123_N	149_L	0.635	0.24
34_R	134_L	0.634	0.24
134_L	143_G	0.630	0.24
19_Q	60_E	0.628	0.24
78_T	145_P	0.628	0.24
148_M	152_A	0.626	0.24
95_Y	145_P	0.626	0.24
16_I	54_V	0.622	0.24
126_F	148_M	0.620	0.24
29_K	32_K	0.616	0.24
106_A	110_H	0.615	0.23
5_A	175_V	0.613	0.23
23_A	84_E	0.608	0.23
156_R	163_I	0.606	0.23
78_T	99_L	0.606	0.23
62_A	72_L	0.604	0.23
5_A	129_K	0.604	0.23
51_Q	123_N	0.599	0.23
122_K	148_M	0.593	0.22
9_Y	17_F	0.588	0.22
25_Y	135_L	0.588	0.22
19_Q	22_K	0.584	0.22
78_T	84_E	0.582	0.22
33_N	170_D	0.578	0.22
83_Q	144_S	0.578	0.22
93_E	157_E	0.574	0.22
63_Y	101_Q	0.572	0.21
96_E	142_E	0.570	0.21
4_L	25_Y	0.569	0.21
70_P	167_T	0.568	0.21
81_Y	105_E	0.567	0.21
160_G	163_I	0.566	0.21
147_Y	150_G	0.564	0.21
37_A	136_L	0.563	0.21
49_S	83_Q	0.561	0.21
44_E	62_A	0.561	0.21
169_D	176_E	0.560	0.21
16_I	108_L	0.560	0.21
111_R	115_S	0.558	0.21
22_K	156_R	0.557	0.21
47_L	163_I	0.556	0.21
72_L	147_Y	0.555	0.21
49_S	171_L	0.555	0.21
50_G	132_G	0.552	0.21
108_L	129_K	0.552	0.21
123_N	151_T	0.552	0.21
43_L	50_G	0.552	0.21
62_A	131_D	0.548	0.20
63_Y	74_V	0.548	0.20
48_I	76_V	0.547	0.20
48_I	62_A	0.546	0.20
16_I	38_F	0.544	0.20
115_S	149_L	0.544	0.20
62_A	102_A	0.543	0.20
6_I	112_P	0.543	0.20
104_Y	172_R	0.543	0.20
140_E	157_E	0.541	0.20
74_V	177_E	0.541	0.20
95_Y	122_K	0.541	0.20
50_G	114_E	0.540	0.20
119_F	127_I	0.539	0.20
109_T	115_S	0.539	0.20
49_S	126_F	0.533	0.20
61_A	171_L	0.532	0.20
12_F	76_V	0.530	0.20
56_L	123_N	0.528	0.19
89_E	154_K	0.527	0.19
31_I	35_L	0.525	0.19
9_Y	137_Y	0.523	0.19
23_A	144_S	0.521	0.19
16_I	176_E	0.518	0.19
7_T	67_E	0.516	0.19
101_Q	147_Y	0.516	0.19
52_L	125_F	0.513	0.19
87_W	118_Q	0.513	0.19
49_S	79_P	0.512	0.19
66_Q	108_L	0.512	0.19
142_E	155_R	0.511	0.19
10_K	75_A	0.510	0.19
82_E	160_G	0.509	0.19
139_P	149_L	0.508	0.19
115_S	124_Q	0.507	0.19
67_E	120_K	0.506	0.19
3_V	126_F	0.506	0.19
10_K	40_D	0.503	0.18
77_I	148_M	0.503	0.18
17_F	137_Y	0.501	0.18
56_L	129_K	0.500	0.18

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
2nx2A	1	0.9833	100	0.413	Contact Map
3imkA	1	0.6667	97.8	0.897	Contact Map
4ljrA	2	0.8389	97	0.911	Contact Map
3uqzA	2	0.85	94.2	0.928	Contact Map
3majA	2	0.85	87.2	0.939	Contact Map
1rcuA	3	0.7667	52.6	0.954	Contact Map
1wehA	1	0.8	31.3	0.96	Contact Map
1jx6A	1	0.7889	13.4	0.966	Contact Map
1t35A	5	0.8	12.4	0.967	Contact Map
3hs3A	2	0.5389	11.4	0.967	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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