RFAH - ECOLI - GREMLIN Contacts

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RFAH - Transcription antitermination protein RfaH

UniProt:	P0AFW0	Sequences: MQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFRKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10839
Length:	162 (159)
Sequences:	2861 (1625)
Seq/√Len:	128.9

ECOLI - RFAH NUSG
BACSU - NUSG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_Q	22_E	5.190	1.00
139_S	159_F	4.260	1.00
27_N	58_E	4.154	1.00
34_T	45_A	3.932	1.00
90_S	94_H	3.835	1.00
117_I	160_R	3.051	1.00
34_T	47_S	2.789	1.00
132_E	140_M	2.568	1.00
138_R	153_S	2.538	1.00
115_K	127_Q	2.165	1.00
114_D	161_K	2.128	1.00
26_V	58_E	2.118	1.00
37_K	48_E	2.113	1.00
32_M	47_S	2.020	1.00
120_E	158_E	1.987	1.00
141_L	154_V	1.909	1.00
62_E	65_H	1.907	1.00
24_Q	72_T	1.782	1.00
13_Q	74_G	1.713	1.00
36_E	45_A	1.694	1.00
38_I	43_R	1.688	1.00
117_I	127_Q	1.643	1.00
17_A	75_V	1.638	1.00
15_Q	32_M	1.612	1.00
131_T	142_L	1.579	1.00
29_L	100_K	1.557	1.00
134_D	137_A	1.555	1.00
59_F	65_H	1.547	1.00
7_L	75_V	1.538	1.00
51_F	56_F	1.534	1.00
21_L	69_I	1.496	1.00
8_Y	76_S	1.479	1.00
128_A	141_L	1.446	1.00
70_N	77_H	1.446	1.00
36_E	43_R	1.442	1.00
88_V	93_I	1.437	1.00
91_A	94_H	1.426	1.00
130_F	133_P	1.418	1.00
144_N	149_E	1.415	1.00
135_G	156_N	1.406	1.00
138_R	155_K	1.405	1.00
9_C	14_L	1.403	1.00
33_I	48_E	1.402	1.00
116_V	141_L	1.386	1.00
59_F	69_I	1.376	1.00
142_L	149_E	1.359	1.00
117_I	125_G	1.330	1.00
27_N	97_S	1.299	1.00
154_V	158_E	1.283	1.00
56_F	96_L	1.258	1.00
39_V	44_T	1.254	1.00
93_I	97_S	1.251	1.00
19_E	23_R	1.247	1.00
16_R	19_E	1.246	1.00
35_L	48_E	1.246	1.00
51_F	96_L	1.233	1.00
111_Y	114_D	1.227	1.00
119_T	160_R	1.218	0.99
142_L	151_K	1.215	0.99
21_L	75_V	1.211	0.99
6_L	88_V	1.187	0.99
155_K	158_E	1.186	0.99
67_T	71_A	1.163	0.99
7_L	57_V	1.161	0.99
118_I	154_V	1.160	0.99
24_Q	73_R	1.155	0.99
3_S	87_I	1.123	0.99
73_R	96_L	1.119	0.99
99_Y	106_D	1.118	0.99
112_P	133_P	1.098	0.99
140_M	151_K	1.077	0.99
10_K	13_Q	1.074	0.99
3_S	90_S	1.069	0.99
63_V	84_S	1.069	0.99
10_K	74_G	1.065	0.99
50_L	56_F	1.062	0.99
8_Y	77_H	1.057	0.99
58_E	90_S	1.051	0.98
154_V	159_F	1.031	0.98
65_H	69_I	1.028	0.98
146_I	150_I	1.022	0.98
13_Q	16_R	1.019	0.98
96_L	100_K	1.005	0.98
134_D	153_S	1.005	0.98
8_Y	53_N	1.005	0.98
139_S	156_N	0.994	0.98
18_Q	30_A	0.986	0.98
131_T	151_K	0.973	0.98
116_V	128_A	0.970	0.97
29_L	97_S	0.951	0.97
9_C	13_Q	0.949	0.97
91_A	95_Q	0.914	0.96
59_F	66_T	0.909	0.96
22_E	28_C	0.907	0.96
7_L	69_I	0.894	0.96
38_I	157_T	0.891	0.96
16_R	74_G	0.881	0.96
17_A	72_T	0.880	0.96
138_R	146_I	0.871	0.95
110_P	130_F	0.858	0.95
20_H	24_Q	0.857	0.95
39_V	42_K	0.839	0.94
81_F	86_A	0.830	0.94
141_L	159_F	0.823	0.94
115_K	129_I	0.816	0.93
52_P	69_I	0.809	0.93
103_D	106_D	0.806	0.93
110_P	114_D	0.801	0.93
117_I	126_F	0.798	0.93
111_Y	161_K	0.788	0.92
80_R	83_A	0.788	0.92
89_P	92_V	0.779	0.92
26_V	60_D	0.776	0.91
66_T	70_N	0.775	0.91
16_R	20_H	0.774	0.91
112_P	139_S	0.769	0.91
13_Q	20_H	0.768	0.91
14_L	30_A	0.767	0.91
25_A	28_C	0.763	0.91
6_L	79_V	0.757	0.90
140_M	147_N	0.757	0.90
126_F	146_I	0.755	0.90
20_H	72_T	0.751	0.90
112_P	132_E	0.750	0.90
17_A	20_H	0.749	0.90
94_H	98_V	0.742	0.90
28_C	31_P	0.739	0.89
14_L	54_Y	0.734	0.89
80_R	87_I	0.731	0.89
76_S	80_R	0.729	0.89
140_M	153_S	0.716	0.88
11_R	14_L	0.709	0.87
24_Q	68_T	0.708	0.87
30_A	55_L	0.707	0.87
11_R	17_A	0.703	0.87
26_V	40_R	0.695	0.86
118_I	147_N	0.691	0.86
77_H	80_R	0.687	0.86
23_R	74_G	0.686	0.86
147_N	150_I	0.686	0.86
66_T	85_P	0.676	0.85
29_L	51_F	0.676	0.85
7_L	23_R	0.675	0.85
15_Q	19_E	0.674	0.85
24_Q	71_A	0.669	0.84
128_A	152_H	0.668	0.84
143_L	151_K	0.666	0.84
21_L	72_T	0.665	0.84
31_P	55_L	0.663	0.84
89_P	97_S	0.662	0.84
30_A	49_P	0.661	0.83
17_A	21_L	0.659	0.83
88_V	144_N	0.656	0.83
29_L	96_L	0.655	0.83
143_L	150_I	0.655	0.83
95_Q	99_Y	0.655	0.83
81_F	84_S	0.652	0.83
6_L	74_G	0.647	0.82
134_D	138_R	0.641	0.82
61_P	66_T	0.639	0.81
99_Y	125_G	0.637	0.81
79_V	135_G	0.633	0.81
20_H	89_P	0.632	0.81
133_P	139_S	0.632	0.81
17_A	92_V	0.631	0.81
59_F	80_R	0.626	0.80
122_A	126_F	0.624	0.80
106_D	135_G	0.622	0.80
95_Q	98_V	0.621	0.79
35_L	145_L	0.612	0.78
130_F	159_F	0.611	0.78
15_Q	49_P	0.611	0.78
17_A	55_L	0.611	0.78
141_L	147_N	0.610	0.78
9_C	53_N	0.607	0.78
25_A	69_I	0.600	0.77
16_R	72_T	0.597	0.77
126_F	141_L	0.596	0.77
19_E	22_E	0.592	0.76
65_H	68_T	0.592	0.76
131_T	140_M	0.590	0.76
89_P	94_H	0.589	0.76
58_E	101_P	0.587	0.76
12_G	30_A	0.585	0.75
137_A	155_K	0.583	0.75
79_V	83_A	0.582	0.75
75_V	123_F	0.580	0.75
38_I	41_G	0.577	0.74
144_N	154_V	0.577	0.74
141_L	151_K	0.567	0.73
68_T	71_A	0.567	0.73
126_F	150_I	0.564	0.73
73_R	81_F	0.561	0.72
110_P	159_F	0.560	0.72
8_Y	13_Q	0.558	0.72
38_I	42_K	0.558	0.72
12_G	139_S	0.558	0.72
56_F	88_V	0.552	0.71
57_V	65_H	0.550	0.71
9_C	119_T	0.550	0.71
67_T	70_N	0.549	0.71
126_F	143_L	0.547	0.70
21_L	24_Q	0.546	0.70
108_A	156_N	0.545	0.70
70_N	74_G	0.542	0.70
90_S	96_L	0.540	0.69
86_A	92_V	0.539	0.69
135_G	142_L	0.538	0.69
34_T	91_A	0.532	0.68
58_E	97_S	0.531	0.68
30_A	56_F	0.529	0.68
113_G	136_E	0.529	0.68
29_L	56_F	0.529	0.68
131_T	141_L	0.526	0.67
49_P	83_A	0.525	0.67
23_R	81_F	0.524	0.67
98_V	101_P	0.522	0.67
12_G	17_A	0.522	0.67
111_Y	116_V	0.520	0.67
53_N	100_K	0.519	0.66
11_R	16_R	0.519	0.66
63_V	66_T	0.518	0.66
58_E	89_P	0.517	0.66
29_L	34_T	0.516	0.66
125_G	152_H	0.515	0.66
44_T	48_E	0.515	0.66
127_Q	160_R	0.514	0.66
79_V	97_S	0.513	0.65
75_V	85_P	0.513	0.65
107_P	111_Y	0.512	0.65
9_C	79_V	0.511	0.65
106_D	144_N	0.509	0.65
113_G	129_I	0.508	0.65
122_A	140_M	0.506	0.64
20_H	73_R	0.506	0.64
40_R	44_T	0.504	0.64
98_V	103_D	0.501	0.64
5_Y	14_L	0.500	0.64

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
2ougA	1	0.8642	100	0.109	Contact Map
2jvvA	1	0.358	100	0.147	Contact Map
1m1hA	1	0.6296	100	0.168	Contact Map
2lq8A	1	0.9568	100	0.19	Contact Map
2xhcA	1	0.9506	100	0.275	Contact Map
3p8bB	2	0.8765	100	0.314	Contact Map
1nz8A	1	0.642	99.9	0.454	Contact Map
3lpeA	1	0.5123	99.8	0.597	Contact Map
2mi6A	1	0.3765	99.4	0.699	Contact Map
2e6zA	1	0.3642	99.4	0.703	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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