RUVA - BACSU - GREMLIN Contacts

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RUVA - Holliday junction ATP-dependent DNA helicase RuvA

UniProt:	O05392	Sequences: MIEFVKGTIDYVSPQYIVIENGGIGYQIFTPNPFIYKERSQETIFTYHHIREDAFSLYGFSTREEKALFTKLLNVTGIGPKGALAILGSGDPGAVIQAIENEDEAFLVKFPGVGKKTARQIILDLKGKLADVVPEMIENLFNHEERLEKQTAETALEEALEALRVLGYAEKEIKKVLPHLKEEIGLTTDQYVKKALQKLLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	201 (190)
Sequences:	3793 (2653)
Seq/√Len:	192.4

ECOLI - RUVA
BACSU - RUVA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_H	55_F	3.965	1.00
6_K	41_Q	3.561	1.00
187_T	190_Q	3.209	1.00
47_Y	70_T	3.033	1.00
50_I	55_F	2.876	1.00
6_K	43_T	2.577	1.00
11_Y	63_R	2.575	1.00
115_K	119_R	2.279	1.00
179_H	198_K	2.237	1.00
3_E	18_V	2.186	1.00
6_K	20_E	2.134	1.00
160_L	177_L	2.132	1.00
5_V	21_N	2.130	1.00
90_G	98_A	2.126	1.00
4_F	43_T	2.115	1.00
16_Y	27_Q	2.058	1.00
9_I	42_E	2.016	1.00
159_A	191_Y	2.003	1.00
103_D	106_F	1.994	1.00
5_V	28_I	1.945	1.00
17_I	30_T	1.929	1.00
102_E	119_R	1.928	1.00
30_T	35_I	1.908	1.00
102_E	126_K	1.846	1.00
91_D	94_A	1.819	1.00
4_F	10_D	1.813	1.00
8_T	41_Q	1.778	1.00
30_T	34_F	1.774	1.00
31_P	34_F	1.753	1.00
120_Q	124_D	1.725	1.00
47_Y	73_L	1.685	1.00
108_V	115_K	1.661	1.00
97_Q	101_N	1.660	1.00
17_I	44_I	1.654	1.00
19_I	28_I	1.630	1.00
161_E	165_V	1.615	1.00
104_E	119_R	1.611	1.00
104_E	122_I	1.607	1.00
5_V	24_I	1.585	1.00
86_I	110_F	1.579	1.00
169_A	172_E	1.537	1.00
28_I	46_T	1.519	1.00
159_A	192_V	1.435	1.00
62_T	65_E	1.426	1.00
194_K	198_K	1.394	1.00
170_E	174_K	1.394	1.00
105_A	108_V	1.392	1.00
194_K	197_Q	1.385	1.00
45_F	63_R	1.384	1.00
5_V	19_I	1.375	1.00
3_E	66_K	1.364	1.00
66_K	70_T	1.359	1.00
28_I	59_G	1.343	1.00
82_G	113_V	1.311	1.00
49_H	56_S	1.308	1.00
160_L	173_I	1.308	1.00
19_I	42_E	1.299	1.00
13_S	16_Y	1.298	1.00
113_V	117_T	1.287	1.00
100_E	127_G	1.283	1.00
71_K	129_L	1.278	1.00
49_H	54_A	1.261	1.00
4_F	20_E	1.259	1.00
82_G	117_T	1.238	1.00
65_E	92_P	1.232	1.00
106_F	109_K	1.220	1.00
155_A	188_T	1.203	1.00
34_F	44_I	1.200	1.00
90_G	106_F	1.188	1.00
186_L	190_Q	1.187	1.00
10_D	20_E	1.184	1.00
155_A	191_Y	1.159	1.00
95_V	99_I	1.152	1.00
104_E	108_V	1.143	1.00
85_A	110_F	1.142	1.00
16_Y	29_F	1.139	1.00
164_R	170_E	1.139	1.00
68_L	129_L	1.135	1.00
176_V	199_L	1.130	1.00
37_K	61_S	1.130	1.00
82_G	110_F	1.126	1.00
10_D	43_T	1.112	1.00
9_I	19_I	1.105	1.00
162_A	192_V	1.105	1.00
94_A	106_F	1.104	1.00
159_A	188_T	1.100	1.00
90_G	110_F	1.096	1.00
31_P	65_E	1.095	1.00
164_R	173_I	1.089	1.00
78_I	82_G	1.087	1.00
12_V	35_I	1.075	1.00
90_G	95_V	1.068	1.00
5_V	46_T	1.065	1.00
3_E	27_Q	1.057	1.00
176_V	180_L	1.049	1.00
160_L	164_R	1.045	1.00
4_F	25_G	1.044	1.00
186_L	194_K	1.044	1.00
190_Q	194_K	1.040	1.00
5_V	26_Y	1.030	1.00
13_S	67_A	1.018	1.00
98_A	106_F	1.004	1.00
68_L	96_I	0.986	0.99
173_I	176_V	0.986	0.99
50_I	54_A	0.961	0.99
89_S	110_F	0.955	0.99
180_L	194_K	0.952	0.99
17_I	35_I	0.951	0.99
156_L	177_L	0.948	0.99
63_R	67_A	0.945	0.99
116_K	123_L	0.938	0.99
173_I	177_L	0.938	0.99
49_H	58_Y	0.932	0.99
34_F	61_S	0.926	0.99
89_S	111_P	0.924	0.99
173_I	180_L	0.921	0.99
82_G	85_A	0.915	0.99
2_I	5_V	0.915	0.99
21_N	24_I	0.914	0.99
95_V	107_L	0.914	0.99
18_V	25_G	0.914	0.99
32_N	88_G	0.899	0.99
105_A	109_K	0.896	0.99
61_S	65_E	0.895	0.99
86_I	121_I	0.893	0.99
37_K	62_T	0.887	0.99
49_H	55_F	0.886	0.99
119_R	126_K	0.882	0.99
20_E	43_T	0.879	0.99
78_I	121_I	0.871	0.99
73_L	83_A	0.869	0.99
180_L	186_L	0.864	0.99
27_Q	66_K	0.864	0.99
77_G	162_A	0.859	0.99
2_I	46_T	0.859	0.99
175_K	179_H	0.853	0.98
86_I	95_V	0.845	0.98
173_I	195_A	0.842	0.98
181_K	191_Y	0.837	0.98
20_E	24_I	0.836	0.98
93_G	97_Q	0.826	0.98
85_A	89_S	0.824	0.98
17_I	42_E	0.824	0.98
183_E	198_K	0.822	0.98
71_K	74_N	0.822	0.98
160_L	174_K	0.818	0.98
28_I	44_I	0.815	0.98
158_E	188_T	0.811	0.98
74_N	128_K	0.809	0.98
171_K	175_K	0.809	0.98
183_E	194_K	0.803	0.98
78_I	117_T	0.803	0.98
31_P	88_G	0.795	0.98
96_I	132_V	0.790	0.97
64_E	96_I	0.787	0.97
98_A	110_F	0.785	0.97
49_H	80_P	0.785	0.97
3_E	48_H	0.778	0.97
34_F	65_E	0.767	0.97
147_L	150_Q	0.766	0.97
32_N	36_Y	0.761	0.97
29_F	56_S	0.751	0.97
26_Y	55_F	0.751	0.97
5_V	44_I	0.751	0.97
8_T	39_R	0.745	0.96
168_Y	172_E	0.744	0.96
64_E	93_G	0.744	0.96
133_V	136_M	0.741	0.96
98_A	107_L	0.741	0.96
158_E	161_E	0.740	0.96
104_E	115_K	0.735	0.96
51_R	54_A	0.733	0.96
180_L	191_Y	0.732	0.96
186_L	191_Y	0.730	0.96
27_Q	70_T	0.726	0.96
99_I	129_L	0.725	0.96
110_F	113_V	0.723	0.96
19_I	23_G	0.720	0.96
49_H	73_L	0.718	0.96
94_A	97_Q	0.716	0.96
102_E	122_I	0.715	0.95
95_V	125_L	0.713	0.95
30_T	44_I	0.702	0.95
96_I	100_E	0.694	0.95
120_Q	127_G	0.694	0.95
112_G	120_Q	0.684	0.94
130_A	133_V	0.684	0.94
130_A	134_P	0.683	0.94
176_V	198_K	0.681	0.94
3_E	45_F	0.664	0.93
14_P	32_N	0.663	0.93
34_F	88_G	0.663	0.93
155_A	159_A	0.661	0.93
12_V	17_I	0.661	0.93
88_G	91_D	0.660	0.93
2_I	57_L	0.653	0.93
68_L	99_I	0.648	0.92
85_A	111_P	0.647	0.92
89_S	92_P	0.642	0.92
145_E	149_K	0.641	0.92
30_T	59_G	0.635	0.92
18_V	66_K	0.634	0.92
70_T	73_L	0.633	0.92
78_I	86_I	0.632	0.92
8_T	40_S	0.629	0.91
154_T	157_E	0.628	0.91
172_E	175_K	0.625	0.91
136_M	147_L	0.623	0.91
99_I	107_L	0.621	0.91
3_E	46_T	0.620	0.91
63_R	66_K	0.619	0.91
46_T	55_F	0.617	0.91
11_Y	18_V	0.615	0.90
156_L	191_Y	0.614	0.90
13_S	63_R	0.609	0.90
6_K	10_D	0.609	0.90
145_E	148_E	0.609	0.90
76_T	124_D	0.607	0.90
71_K	131_D	0.607	0.90
156_L	181_K	0.607	0.90
150_Q	153_E	0.603	0.90
177_L	191_Y	0.602	0.89
105_A	115_K	0.601	0.89
87_L	92_P	0.597	0.89
96_I	129_L	0.597	0.89
9_I	17_I	0.596	0.89
146_R	150_Q	0.595	0.89
76_T	115_K	0.595	0.89
2_I	24_I	0.593	0.89
165_V	188_T	0.591	0.89
58_Y	80_P	0.590	0.89
15_Q	27_Q	0.588	0.88
195_A	199_L	0.588	0.88
29_F	84_L	0.587	0.88
54_A	58_Y	0.586	0.88
136_M	148_E	0.581	0.88
98_A	122_I	0.581	0.88
10_D	18_V	0.581	0.88
107_L	121_I	0.579	0.88
148_E	151_T	0.579	0.88
180_L	195_A	0.579	0.88
81_K	112_G	0.575	0.87
67_A	71_K	0.574	0.87
119_R	123_L	0.572	0.87
68_L	95_V	0.556	0.85
65_E	87_L	0.555	0.85
32_N	35_I	0.552	0.85
121_I	124_D	0.552	0.85
15_Q	29_F	0.548	0.85
9_I	38_E	0.547	0.85
76_T	82_G	0.546	0.84
87_L	95_V	0.545	0.84
188_T	193_K	0.545	0.84
76_T	123_L	0.544	0.84
86_I	99_I	0.542	0.84
135_E	145_E	0.542	0.84
152_A	185_G	0.541	0.84
12_V	36_Y	0.534	0.83
107_L	111_P	0.531	0.83
73_L	80_P	0.529	0.83
147_L	178_P	0.527	0.82
20_E	23_G	0.526	0.82
179_H	182_E	0.525	0.82
14_P	30_T	0.524	0.82
9_I	39_R	0.523	0.82
53_D	123_L	0.519	0.81
42_E	61_S	0.518	0.81
156_L	178_P	0.518	0.81
2_I	18_V	0.517	0.81
136_M	149_K	0.517	0.81
107_L	110_F	0.516	0.81
93_G	96_I	0.516	0.81
51_R	56_S	0.513	0.81
133_V	161_E	0.512	0.80
37_K	91_D	0.511	0.80
93_G	145_E	0.509	0.80
99_I	121_I	0.509	0.80
81_K	111_P	0.508	0.80
86_I	168_Y	0.507	0.80
165_V	192_V	0.506	0.80
21_N	26_Y	0.503	0.79
46_T	50_I	0.503	0.79
64_E	67_A	0.502	0.79
15_Q	32_N	0.501	0.79
14_P	162_A	0.500	0.79

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
2ztdA	4	0.8856	100	0.257	Contact Map
1ixrA	4	0.9353	100	0.267	Contact Map
1cukA	3	0.9303	100	0.269	Contact Map
3b0xA	1	0.9204	99.7	0.678	Contact Map
4gfjA	1	0.8706	99.6	0.707	Contact Map
4bxoA	1	0.5821	99.4	0.747	Contact Map
2csbA	1	0.7612	99.4	0.752	Contact Map
2w9mA	1	0.9005	99.3	0.763	Contact Map
1dgsA	1	0.6567	98.7	0.811	Contact Map
2owoA	1	0.6716	98.5	0.824	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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