RPIB - ECOLI - GREMLIN Contacts

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RPIB - Ribose-5-phosphate isomerase B

UniProt:	P37351	Sequences: MKKIAFGCDHVGFILKHEIVAHLVERGVEVIDKGTWSSERTDYPHYASQVALAVAGGEVDGGILICGTGVGISIAANKFAGIRAVVCSEPYSAQLSRQHNDTNVLAFGSRVVGLELAKMIVDAWLGAQYEGGRHQQRVEAITAIEQRRN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11827
Length:	149 (142)
Sequences:	3508 (2150)
Seq/√Len:	180.4

ECOLI - RPIB
BACSU - YWLF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_H	140_A	3.391	1.00
135_Q	139_E	3.307	1.00
22_H	122_D	2.614	1.00
17_H	20_V	2.335	1.00
26_R	122_D	2.249	1.00
18_E	114_L	2.150	1.00
5_A	33_K	2.076	1.00
90_P	119_M	2.073	1.00
84_A	106_A	2.037	1.00
33_K	53_A	2.001	1.00
94_Q	98_Q	1.956	1.00
98_Q	130_E	1.891	1.00
5_A	59_V	1.882	1.00
7_G	50_V	1.863	1.00
14_I	38_S	1.862	1.00
20_V	24_V	1.782	1.00
85_V	96_S	1.771	1.00
88_S	92_S	1.721	1.00
67_G	110_R	1.719	1.00
18_E	118_K	1.708	1.00
15_L	117_A	1.694	1.00
3_K	29_E	1.694	1.00
113_G	116_L	1.675	1.00
53_A	58_E	1.653	1.00
48_S	144_I	1.644	1.00
12_G	65_I	1.634	1.00
14_I	109_S	1.632	1.00
64_L	76_A	1.457	1.00
21_A	25_E	1.440	1.00
31_I	59_V	1.438	1.00
42_D	136_Q	1.437	1.00
122_D	126_G	1.431	1.00
21_A	24_V	1.428	1.00
26_R	126_G	1.406	1.00
5_A	53_A	1.387	1.00
51_A	82_I	1.385	1.00
98_Q	127_A	1.383	1.00
48_S	52_L	1.377	1.00
55_A	79_F	1.376	1.00
89_E	92_S	1.365	1.00
47_A	72_I	1.364	1.00
91_Y	95_L	1.349	1.00
64_L	72_I	1.323	1.00
48_S	79_F	1.301	1.00
64_L	106_A	1.293	1.00
11_V	110_R	1.287	1.00
52_L	56_G	1.281	1.00
22_H	118_K	1.276	1.00
22_H	26_R	1.275	1.00
94_Q	119_M	1.273	1.00
24_V	30_V	1.272	1.00
102_T	124_W	1.270	1.00
13_F	17_H	1.265	1.00
16_K	32_D	1.257	1.00
63_I	121_V	1.206	1.00
55_A	82_I	1.195	1.00
70_V	85_V	1.178	1.00
139_E	143_A	1.171	1.00
78_K	142_T	1.164	1.00
90_P	123_A	1.127	1.00
115_E	118_K	1.121	1.00
50_V	62_G	1.121	1.00
76_A	84_A	1.113	1.00
84_A	104_V	1.108	1.00
6_F	20_V	1.107	1.00
95_L	98_Q	1.097	1.00
73_S	106_A	1.094	1.00
96_S	124_W	1.079	1.00
19_I	121_V	1.068	1.00
91_Y	111_V	1.063	1.00
73_S	86_V	1.057	1.00
123_A	127_A	1.050	1.00
96_S	102_T	1.045	1.00
47_A	64_L	1.042	1.00
61_G	124_W	1.036	1.00
5_A	57_G	1.029	1.00
40_R	136_Q	1.024	0.99
87_C	105_L	1.021	0.99
61_G	97_R	1.019	0.99
94_Q	123_A	1.014	0.99
66_C	72_I	1.005	0.99
120_I	123_A	0.994	0.99
57_G	60_D	0.983	0.99
82_I	104_V	0.981	0.99
93_A	120_I	0.973	0.99
15_L	114_L	0.953	0.99
51_A	104_V	0.947	0.99
50_V	64_L	0.946	0.99
105_L	120_I	0.944	0.99
15_L	109_S	0.940	0.99
7_G	33_K	0.940	0.99
72_I	106_A	0.923	0.99
41_T	46_Y	0.919	0.99
87_C	120_I	0.902	0.99
101_D	129_Y	0.900	0.99
79_F	144_I	0.891	0.99
139_E	142_T	0.889	0.99
8_C	35_T	0.888	0.99
88_S	112_V	0.879	0.98
131_G	135_Q	0.873	0.98
8_C	12_G	0.864	0.98
73_S	84_A	0.850	0.98
13_F	37_S	0.850	0.98
138_V	142_T	0.837	0.98
31_I	53_A	0.834	0.98
51_A	55_A	0.832	0.98
5_A	60_D	0.832	0.98
32_D	36_W	0.830	0.98
18_E	21_A	0.830	0.98
91_Y	113_G	0.824	0.98
7_G	46_Y	0.813	0.97
49_Q	53_A	0.813	0.97
108_G	111_V	0.810	0.97
6_F	23_L	0.807	0.97
107_F	121_V	0.807	0.97
19_I	118_K	0.806	0.97
107_F	112_V	0.806	0.97
22_H	25_E	0.801	0.97
42_D	140_A	0.797	0.97
18_E	22_H	0.797	0.97
63_I	105_L	0.796	0.97
35_T	46_Y	0.792	0.97
112_V	120_I	0.781	0.97
6_F	30_V	0.778	0.97
50_V	104_V	0.774	0.97
33_K	59_V	0.769	0.96
119_M	122_D	0.765	0.96
51_A	79_F	0.764	0.96
97_R	124_W	0.760	0.96
43_Y	134_H	0.758	0.96
17_H	21_A	0.757	0.96
8_C	17_H	0.755	0.96
97_R	127_A	0.753	0.96
112_V	117_A	0.747	0.96
31_I	36_W	0.746	0.96
19_I	65_I	0.745	0.96
3_K	31_I	0.737	0.95
99_H	137_R	0.731	0.95
3_K	60_D	0.721	0.95
75_A	141_I	0.712	0.94
24_V	29_E	0.710	0.94
119_M	123_A	0.703	0.94
52_L	144_I	0.699	0.94
4_I	28_V	0.698	0.94
89_E	116_L	0.693	0.94
7_G	64_L	0.688	0.93
112_V	116_L	0.687	0.93
134_H	137_R	0.687	0.93
8_C	13_F	0.685	0.93
4_I	125_L	0.683	0.93
5_A	50_V	0.679	0.93
129_Y	135_Q	0.676	0.93
132_G	135_Q	0.675	0.93
54_V	81_G	0.674	0.93
74_I	102_T	0.672	0.93
35_T	41_T	0.669	0.92
6_F	65_I	0.668	0.92
53_A	59_V	0.664	0.92
72_I	75_A	0.661	0.92
70_V	96_S	0.659	0.92
90_P	120_I	0.651	0.91
42_D	45_H	0.648	0.91
31_I	58_E	0.647	0.91
99_H	134_H	0.641	0.91
99_H	133_R	0.641	0.91
70_V	73_S	0.631	0.90
55_A	80_A	0.628	0.90
136_Q	139_E	0.622	0.89
133_R	137_R	0.619	0.89
93_A	105_L	0.617	0.89
90_P	94_Q	0.616	0.89
69_G	86_V	0.613	0.89
70_V	86_V	0.612	0.89
35_T	40_R	0.606	0.88
92_S	108_G	0.605	0.88
44_P	140_A	0.601	0.88
95_L	99_H	0.599	0.88
45_H	49_Q	0.597	0.87
7_G	16_K	0.597	0.87
114_L	118_K	0.597	0.87
101_D	142_T	0.594	0.87
61_G	101_D	0.592	0.87
92_S	111_V	0.590	0.87
88_S	107_F	0.585	0.86
66_C	73_S	0.580	0.86
78_K	141_I	0.579	0.86
135_Q	138_V	0.578	0.86
57_G	61_G	0.573	0.85
62_G	104_V	0.571	0.85
52_L	55_A	0.569	0.85
23_L	26_R	0.562	0.84
11_V	67_G	0.559	0.84
48_S	142_T	0.559	0.84
47_A	51_A	0.556	0.84
116_L	120_I	0.555	0.83
8_C	32_D	0.551	0.83
101_D	135_Q	0.544	0.82
47_A	66_C	0.543	0.82
83_R	142_T	0.537	0.81
13_F	16_K	0.534	0.81
23_L	121_V	0.530	0.81
14_I	18_E	0.528	0.80
75_A	79_F	0.525	0.80
10_H	42_D	0.523	0.80
40_R	46_Y	0.514	0.78
25_E	118_K	0.513	0.78
129_Y	138_V	0.510	0.78
70_V	92_S	0.508	0.78
70_V	74_I	0.507	0.78
26_R	118_K	0.506	0.77
6_F	63_I	0.500	0.77
65_I	109_S	0.500	0.77
101_D	131_G	0.500	0.77

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
2vvrA	2	0.9866	100	0.022	Contact Map
3s5pA	4	0.8926	100	0.033	Contact Map
3he8A	2	0.9933	100	0.037	Contact Map
3k7pA	4	1	100	0.038	Contact Map
4lflB	3	0.9933	100	0.039	Contact Map
3ph3A	2	0.9866	100	0.039	Contact Map
2vvpA	2	1	100	0.047	Contact Map
3sgwA	4	1	100	0.056	Contact Map
1o1xA	3	0.9664	100	0.06	Contact Map
4lflA	2	0.9396	100	0.067	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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