RPIA - ECOLI - GREMLIN Contacts

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RPIA - Ribose-5-phosphate isomerase A

UniProt:	P0A7Z0	Sequences: MTQDELKKAVGWAALQYVQPGTIVGVGTGSTAAHFIDALGTMKGQIEGAVSSSDASTEKLKSLGIHVFDLNEVDSLGIYVDGADEINGHMQMIKGGGAALTREKIIASVAEKFICIADASKQVDILGKFPLPVEVIPMARSAVARQLVKLGGRPEYRQGVVTDNGNVILDVHGMEILDPIAMENAINAIPGVVTVGLFANRGADVALIGTPDGVKTIVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11443
Length:	219 (211)
Sequences:	2430 (1433)
Seq/√Len:	98.7

ECOLI - RPIA
HALSA - RPIA
SULSO - Q97ZD9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_A	160_V	4.796	1.00
13_A	16_Q	3.838	1.00
87_N	91_Q	3.801	1.00
75_S	111_E	3.272	1.00
79_Y	110_A	3.254	1.00
38_A	41_T	3.035	1.00
183_E	195_V	2.999	1.00
144_A	169_L	2.860	1.00
178_D	181_A	2.824	1.00
117_A	208_I	2.759	1.00
23_I	76_L	2.580	1.00
12_W	38_A	2.513	1.00
35_F	80_V	2.337	1.00
37_D	59_K	2.260	1.00
90_M	206_A	2.253	1.00
187_N	195_V	2.237	1.00
85_E	127_G	2.200	1.00
86_I	92_M	2.200	1.00
86_I	117_A	2.176	1.00
51_S	57_T	2.168	1.00
36_I	56_S	2.132	1.00
147_L	186_I	2.115	1.00
86_I	206_A	2.110	1.00
49_A	65_I	2.090	1.00
28_T	99_A	1.980	1.00
57_T	61_K	1.967	1.00
24_V	78_I	1.900	1.00
6_L	119_A	1.872	1.00
4_D	34_H	1.862	1.00
10_V	207_L	1.814	1.00
112_K	205_V	1.808	1.00
8_K	12_W	1.805	1.00
52_S	106_I	1.794	1.00
26_V	60_L	1.782	1.00
96_G	129_F	1.779	1.00
54_D	57_T	1.772	1.00
152_G	171_V	1.712	1.00
184_N	188_A	1.699	1.00
88_G	124_D	1.659	1.00
136_I	193_V	1.646	1.00
210_T	215_K	1.638	1.00
92_M	115_C	1.628	1.00
146_Q	149_K	1.611	1.00
181_A	185_A	1.606	1.00
35_F	116_I	1.469	1.00
122_Q	208_I	1.443	1.00
101_T	136_I	1.441	1.00
80_V	116_I	1.440	1.00
68_F	73_V	1.437	1.00
12_W	41_T	1.436	1.00
48_G	68_F	1.428	1.00
77_G	111_E	1.389	0.99
102_R	164_N	1.379	0.99
135_V	169_L	1.368	0.99
91_Q	180_I	1.357	0.99
6_L	211_P	1.354	0.99
17_Y	114_I	1.338	0.99
79_Y	113_F	1.320	0.99
133_V	171_V	1.286	0.99
119_A	210_T	1.270	0.99
32_A	35_F	1.262	0.99
150_L	185_A	1.234	0.99
19_Q	22_T	1.230	0.99
152_G	173_G	1.221	0.99
183_E	187_N	1.217	0.99
142_A	190_P	1.205	0.98
58_E	62_S	1.201	0.98
8_K	34_H	1.196	0.98
108_S	190_P	1.193	0.98
70_L	109_V	1.193	0.98
20_P	45_Q	1.179	0.98
119_A	211_P	1.163	0.98
15_L	42_M	1.159	0.98
98_A	168_I	1.156	0.98
15_L	35_F	1.154	0.98
86_I	208_I	1.154	0.98
210_T	214_V	1.145	0.98
15_L	38_A	1.144	0.98
32_A	51_S	1.144	0.98
5_E	8_K	1.142	0.98
142_A	146_Q	1.130	0.98
144_A	148_V	1.126	0.98
33_A	55_A	1.126	0.98
187_N	190_P	1.122	0.98
40_G	63_L	1.121	0.98
119_A	122_Q	1.115	0.98
86_I	122_Q	1.103	0.97
180_I	200_N	1.100	0.97
83_A	117_A	1.094	0.97
22_T	78_I	1.093	0.97
35_F	39_L	1.086	0.97
207_L	214_V	1.082	0.97
100_L	168_I	1.073	0.97
28_T	52_S	1.072	0.97
54_D	58_E	1.066	0.97
20_P	44_G	1.061	0.97
117_A	206_A	1.051	0.96
11_G	15_L	1.046	0.96
50_V	76_L	1.043	0.96
140_R	144_A	1.042	0.96
79_Y	107_A	1.041	0.96
176_I	179_P	1.039	0.96
186_I	192_V	1.035	0.96
110_A	113_F	1.017	0.96
148_V	153_R	1.010	0.96
154_P	169_L	1.003	0.95
100_L	133_V	0.997	0.95
33_A	37_D	0.985	0.95
85_E	123_V	0.975	0.95
17_Y	78_I	0.973	0.95
34_H	37_D	0.967	0.94
60_L	67_V	0.962	0.94
17_Y	205_V	0.962	0.94
112_K	204_D	0.958	0.94
33_A	59_K	0.953	0.94
143_V	189_I	0.953	0.94
144_A	154_P	0.950	0.94
209_G	214_V	0.937	0.93
42_M	45_Q	0.936	0.93
113_F	201_R	0.930	0.93
20_P	46_I	0.920	0.93
6_L	209_G	0.917	0.93
69_D	72_E	0.916	0.93
125_I	175_E	0.915	0.92
125_I	177_L	0.914	0.92
11_G	34_H	0.910	0.92
52_S	79_Y	0.906	0.92
161_V	165_G	0.903	0.92
176_I	182_M	0.897	0.92
21_G	46_I	0.897	0.92
50_V	73_V	0.887	0.91
17_Y	112_K	0.886	0.91
161_V	167_V	0.881	0.91
6_L	210_T	0.879	0.91
160_V	168_I	0.873	0.91
181_A	184_N	0.868	0.90
140_R	156_Y	0.868	0.90
17_Y	207_L	0.863	0.90
108_S	146_Q	0.856	0.90
131_L	197_L	0.855	0.90
92_M	203_A	0.855	0.90
37_D	63_L	0.842	0.89
50_V	70_L	0.840	0.89
8_K	37_D	0.834	0.89
36_I	59_K	0.830	0.88
212_D	215_K	0.824	0.88
156_Y	167_V	0.822	0.88
34_H	38_A	0.821	0.88
59_K	63_L	0.818	0.88
47_E	66_H	0.809	0.87
140_R	169_L	0.809	0.87
22_T	77_G	0.808	0.87
74_D	145_R	0.797	0.86
6_L	214_V	0.796	0.86
145_R	148_V	0.790	0.86
13_A	207_L	0.779	0.85
153_R	172_H	0.777	0.85
133_V	147_L	0.775	0.85
102_R	138_M	0.771	0.84
133_V	186_I	0.770	0.84
32_A	36_I	0.769	0.84
58_E	61_K	0.766	0.84
85_E	128_K	0.762	0.84
24_V	47_E	0.760	0.83
140_R	167_V	0.759	0.83
9_A	209_G	0.759	0.83
130_P	172_H	0.758	0.83
186_I	195_V	0.756	0.83
95_G	196_G	0.755	0.83
135_V	143_V	0.751	0.83
154_P	171_V	0.750	0.83
79_Y	106_I	0.748	0.82
7_K	30_S	0.743	0.82
59_K	62_S	0.741	0.82
109_V	142_A	0.739	0.82
101_T	162_T	0.737	0.82
95_G	132_P	0.736	0.81
68_F	72_E	0.734	0.81
155_E	172_H	0.732	0.81
162_T	168_I	0.729	0.81
132_P	196_G	0.728	0.81
28_T	32_A	0.726	0.81
117_A	122_Q	0.722	0.80
19_Q	184_N	0.719	0.80
26_V	56_S	0.716	0.80
4_D	8_K	0.716	0.80
136_I	164_N	0.715	0.80
37_D	62_S	0.714	0.79
28_T	34_H	0.714	0.79
74_D	109_V	0.714	0.79
182_M	197_L	0.711	0.79
55_A	58_E	0.704	0.79
7_K	31_T	0.699	0.78
91_Q	179_P	0.689	0.77
71_N	140_R	0.688	0.77
144_A	156_Y	0.687	0.77
10_V	116_I	0.686	0.77
133_V	192_V	0.683	0.76
124_D	175_E	0.682	0.76
138_M	143_V	0.680	0.76
40_G	65_I	0.678	0.76
122_Q	215_K	0.676	0.76
11_G	38_A	0.668	0.75
139_A	143_V	0.667	0.75
91_Q	200_N	0.661	0.74
6_L	213_G	0.656	0.73
85_E	126_L	0.653	0.73
139_A	142_A	0.651	0.73
101_T	193_V	0.648	0.73
26_V	33_A	0.642	0.72
70_L	142_A	0.642	0.72
180_I	184_N	0.640	0.72
147_L	152_G	0.639	0.72
123_V	127_G	0.639	0.72
6_L	9_A	0.636	0.71
94_K	97_G	0.634	0.71
187_N	194_T	0.632	0.71
125_I	176_I	0.632	0.71
49_A	60_L	0.629	0.70
90_M	208_I	0.625	0.70
23_I	73_V	0.624	0.70
147_L	192_V	0.622	0.70
179_P	182_M	0.619	0.69
51_S	54_D	0.618	0.69
145_R	149_K	0.616	0.69
135_V	144_A	0.615	0.69
18_V	42_M	0.614	0.69
176_I	197_L	0.613	0.68
10_V	209_G	0.611	0.68
18_V	78_I	0.611	0.68
195_V	199_A	0.609	0.68
141_S	144_A	0.606	0.68
51_S	67_V	0.604	0.67
85_E	129_F	0.604	0.67
51_S	69_D	0.600	0.67
70_L	106_I	0.600	0.67
10_V	34_H	0.597	0.66
21_G	24_V	0.591	0.66
147_L	169_L	0.590	0.65
210_T	213_G	0.589	0.65
19_Q	112_K	0.588	0.65
38_A	42_M	0.587	0.65
47_E	60_L	0.586	0.65
131_L	174_M	0.580	0.64
54_D	102_R	0.578	0.64
26_V	32_A	0.576	0.64
93_I	99_A	0.571	0.63
15_L	41_T	0.567	0.62
9_A	12_W	0.566	0.62
131_L	176_I	0.565	0.62
28_T	168_I	0.565	0.62
137_P	167_V	0.562	0.62
47_E	77_G	0.559	0.61
107_A	201_R	0.558	0.61
57_T	67_V	0.555	0.61
32_A	57_T	0.554	0.61
99_A	196_G	0.553	0.61
102_R	163_D	0.552	0.60
151_G	154_P	0.552	0.60
32_A	55_A	0.551	0.60
88_G	122_Q	0.551	0.60
48_G	66_H	0.548	0.60
155_E	158_Q	0.547	0.60
36_I	63_L	0.547	0.60
28_T	196_G	0.542	0.59
140_R	154_P	0.542	0.59
166_N	193_V	0.541	0.59
101_T	194_T	0.540	0.59
6_L	10_V	0.539	0.59
156_Y	169_L	0.537	0.58
133_V	169_L	0.536	0.58
19_Q	77_G	0.535	0.58
83_A	115_C	0.533	0.58
32_A	40_G	0.533	0.58
81_D	103_E	0.533	0.58
83_A	95_G	0.532	0.58
54_D	160_V	0.532	0.58
49_A	52_S	0.528	0.57
68_F	74_D	0.527	0.57
146_Q	189_I	0.527	0.57
93_I	131_L	0.527	0.57
174_M	182_M	0.526	0.57
82_G	94_K	0.525	0.57
35_F	56_S	0.523	0.56
150_L	186_I	0.523	0.56
54_D	167_V	0.523	0.56
24_V	38_A	0.521	0.56
8_K	38_A	0.520	0.56
60_L	138_M	0.520	0.56
95_G	99_A	0.519	0.56
12_W	34_H	0.519	0.56
83_A	196_G	0.519	0.56
108_S	142_A	0.517	0.55
14_A	107_A	0.516	0.55
18_V	21_G	0.513	0.55
11_G	35_F	0.513	0.55
90_M	203_A	0.513	0.55
51_S	56_S	0.512	0.55
66_H	72_E	0.512	0.55
101_T	138_M	0.512	0.55
123_V	128_K	0.510	0.54
137_P	161_V	0.510	0.54
25_G	104_K	0.508	0.54
92_M	117_A	0.505	0.54
93_I	98_A	0.505	0.54
83_A	179_P	0.505	0.54
105_I	139_A	0.504	0.54
60_L	65_I	0.503	0.53
150_L	173_G	0.503	0.53
134_E	166_N	0.503	0.53
140_R	143_V	0.502	0.53
143_V	169_L	0.502	0.53
79_Y	115_C	0.502	0.53
93_I	126_L	0.501	0.53
149_K	175_E	0.501	0.53
12_W	16_Q	0.500	0.53

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
4x84A	2	0.9909	100	0.185	Contact Map
2f8mA	2	0.9954	100	0.209	Contact Map
1xtzA	3	0.9817	100	0.216	Contact Map
3hheA	2	0.9909	100	0.219	Contact Map
1lk5A	4	0.9954	100	0.223	Contact Map
1o8bA	2	0.9589	100	0.225	Contact Map
4nmlA	2	0.9954	100	0.225	Contact Map
1uj6A	2	0.9909	100	0.231	Contact Map
1m0sA	2	0.9909	100	0.232	Contact Map
3uw1A	2	0.9954	100	0.233	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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