Rep_1 - PFAM28P - GREMLIN Contacts

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Rep_1 - Replication protein

PFAM:	PF01446	Sequences: MKNSYQVSQILDEAVKREPKARFLFLTLTVKNCESGEELRETLDHMNKAFNRLTKRKKFKKAVKGWFRALEVTYNKKDGTYHPHFHVLLAVPPSYFKGSDNYIKQAEWVELWQKALKVDYDPIVDIRAVKPKKKKGKDALQAAVAETAKYAVKDSDYLTLDDEENLEVVKELDKALHGRRLIAFGGILKEIHKELKLDDVEDGDLIHVDDEDETDEDLEAAEEIVAKWNFGRKNYFI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	237 (203)
Sequences:	875 (680)
Seq/√Len:	47.7
META:	0.782

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_N	55_K	3.814	1.00
52_R	117_K	3.724	1.00
113_Q	121_D	3.618	1.00
56_R	114_K	3.310	1.00
58_K	107_E	3.169	1.00
22_R	128_A	2.993	1.00
109_V	121_D	2.884	1.00
45_H	49_A	2.832	1.00
66_W	185_G	2.767	1.00
26_L	89_L	2.732	1.00
46_M	85_F	2.709	1.00
31_K	120_Y	2.686	1.00
44_D	179_R	2.409	1.00
192_H	196_K	2.343	1.00
40_R	179_R	2.272	1.00
109_V	123_I	2.261	1.00
198_D	203_G	2.214	1.00
33_C	42_T	2.187	1.00
56_R	115_A	2.175	1.00
31_K	122_P	2.167	1.00
30_V	42_T	2.148	1.00
26_L	108_W	2.032	1.00
105_Q	109_V	2.029	1.00
74_Y	79_G	2.019	0.99
48_K	51_N	1.961	0.99
54_T	59_F	1.916	0.99
176_L	181_L	1.895	0.99
49_A	116_L	1.824	0.99
118_V	122_P	1.806	0.99
50_F	87_V	1.792	0.99
103_I	107_E	1.783	0.99
146_E	149_K	1.750	0.99
48_K	52_R	1.726	0.98
49_A	118_V	1.710	0.98
104_K	107_E	1.698	0.98
105_Q	124_V	1.695	0.98
23_F	188_L	1.663	0.98
66_W	183_A	1.653	0.98
42_T	46_M	1.637	0.98
64_K	92_P	1.636	0.98
171_E	175_A	1.633	0.98
47_N	85_F	1.622	0.98
43_L	70_L	1.620	0.98
13_E	16_K	1.596	0.97
24_L	126_I	1.578	0.97
23_F	90_A	1.530	0.96
43_L	47_N	1.519	0.96
24_L	89_L	1.518	0.96
21_A	90_A	1.492	0.96
57_K	61_K	1.468	0.96
56_R	59_F	1.461	0.95
105_Q	123_I	1.454	0.95
42_T	45_H	1.446	0.95
68_R	183_A	1.430	0.95
180_R	183_A	1.414	0.95
89_L	108_W	1.366	0.93
75_N	80_T	1.354	0.93
47_N	68_R	1.347	0.93
97_K	100_D	1.336	0.93
187_I	190_E	1.319	0.92
52_R	115_A	1.309	0.92
116_L	120_Y	1.301	0.92
109_V	122_P	1.290	0.91
74_Y	168_V	1.282	0.91
105_Q	121_D	1.275	0.91
31_K	119_D	1.273	0.91
107_E	111_L	1.268	0.91
53_L	108_W	1.249	0.90
191_I	194_E	1.194	0.88
13_E	17_R	1.189	0.87
20_K	93_P	1.188	0.87
34_E	37_E	1.180	0.87
108_W	126_I	1.176	0.87
107_E	110_E	1.173	0.87
21_A	64_K	1.166	0.86
70_L	85_F	1.159	0.86
200_V	203_G	1.150	0.86
22_R	93_P	1.141	0.85
72_V	176_L	1.137	0.85
52_R	55_K	1.127	0.84
51_N	54_T	1.122	0.84
90_A	188_L	1.122	0.84
204_D	207_H	1.117	0.84
118_V	121_D	1.116	0.84
59_F	111_L	1.108	0.83
109_V	120_Y	1.103	0.83
75_N	78_D	1.086	0.82
81_Y	157_Y	1.082	0.82
30_V	82_H	1.081	0.82
70_L	181_L	1.073	0.81
48_K	55_K	1.066	0.81
170_K	174_K	1.063	0.81
30_V	33_C	1.061	0.81
116_L	122_P	1.054	0.80
50_F	66_W	1.052	0.80
45_H	52_R	1.050	0.80
199_D	203_G	1.043	0.80
47_N	70_L	1.034	0.79
22_R	96_F	1.017	0.78
31_K	118_V	1.011	0.77
62_A	101_N	1.006	0.77
50_F	54_T	1.004	0.77
129_V	143_A	0.994	0.76
74_Y	80_T	0.983	0.75
141_Q	145_A	0.981	0.75
60_K	186_G	0.978	0.75
26_L	126_I	0.974	0.75
124_V	127_R	0.963	0.74
19_P	90_A	0.959	0.74
31_K	109_V	0.950	0.73
203_G	206_I	0.946	0.73
50_F	53_L	0.940	0.72
67_F	70_L	0.938	0.72
63_V	89_L	0.926	0.71
131_P	142_A	0.921	0.70
192_H	197_L	0.921	0.70
168_V	171_E	0.916	0.70
12_D	15_V	0.913	0.70
147_T	208_V	0.908	0.69
91_V	96_F	0.897	0.68
190_E	194_E	0.897	0.68
161_D	165_N	0.887	0.68
94_S	97_K	0.882	0.67
36_G	171_E	0.862	0.65
45_H	116_L	0.861	0.65
36_G	81_Y	0.857	0.65
106_A	110_E	0.854	0.65
66_W	188_L	0.851	0.64
30_V	46_M	0.846	0.64
30_V	116_L	0.844	0.64
25_F	147_T	0.843	0.64
121_D	124_V	0.842	0.64
50_F	183_A	0.840	0.63
88_L	129_V	0.832	0.63
57_K	114_K	0.826	0.62
62_A	89_L	0.823	0.62
176_L	179_R	0.814	0.61
17_R	194_E	0.812	0.61
74_Y	173_D	0.811	0.61
161_D	164_E	0.810	0.60
30_V	83_P	0.810	0.60
157_Y	160_L	0.810	0.60
184_F	200_V	0.809	0.60
58_K	103_I	0.806	0.60
47_N	171_E	0.805	0.60
39_L	175_A	0.804	0.60
189_K	192_H	0.801	0.60
188_L	192_H	0.795	0.59
143_A	147_T	0.792	0.59
109_V	118_V	0.788	0.58
180_R	189_K	0.785	0.58
58_K	111_L	0.785	0.58
55_K	60_K	0.780	0.58
109_V	125_D	0.773	0.57
108_W	111_L	0.772	0.57
109_V	124_V	0.766	0.56
31_K	116_L	0.754	0.55
119_D	122_P	0.749	0.55
160_L	165_N	0.747	0.54
26_L	87_V	0.746	0.54
175_A	179_R	0.745	0.54
62_A	103_I	0.744	0.54
49_A	53_L	0.737	0.53
44_D	51_N	0.733	0.53
192_H	195_L	0.730	0.53
66_W	90_A	0.720	0.52
189_K	193_K	0.719	0.52
28_L	89_L	0.716	0.51
81_Y	192_H	0.715	0.51
117_K	190_E	0.707	0.50
98_G	101_N	0.707	0.50
25_F	88_L	0.704	0.50
91_V	95_Y	0.703	0.50
40_R	44_D	0.702	0.50
94_S	101_N	0.700	0.50
124_V	172_L	0.699	0.50
44_D	48_K	0.699	0.50
92_P	101_N	0.697	0.49
182_I	188_L	0.695	0.49
145_A	151_A	0.695	0.49
30_V	85_F	0.692	0.49
41_E	48_K	0.683	0.48
47_N	179_R	0.677	0.47
68_R	179_R	0.674	0.47
53_L	111_L	0.674	0.47
90_A	187_I	0.673	0.47
30_V	118_V	0.672	0.47
158_L	166_L	0.672	0.47
139_A	143_A	0.659	0.46
122_P	125_D	0.658	0.45
106_A	121_D	0.655	0.45
165_N	169_V	0.649	0.45
169_V	178_G	0.648	0.44
50_F	185_G	0.645	0.44
140_L	147_T	0.643	0.44
77_K	80_T	0.642	0.44
69_A	151_A	0.639	0.44
56_R	66_W	0.639	0.44
110_E	114_K	0.637	0.43
148_A	184_F	0.633	0.43
170_K	177_H	0.632	0.43
59_F	103_I	0.628	0.42
69_A	182_I	0.626	0.42
74_Y	83_P	0.626	0.42
29_T	82_H	0.625	0.42
64_K	93_P	0.625	0.42
126_I	131_P	0.623	0.42
205_L	209_D	0.621	0.42
94_S	99_S	0.616	0.41
201_E	205_L	0.611	0.41
145_A	179_R	0.609	0.41
109_V	116_L	0.608	0.41
78_D	116_L	0.608	0.41
116_L	185_G	0.606	0.40
111_L	114_K	0.604	0.40
182_I	191_I	0.604	0.40
40_R	175_A	0.604	0.40
94_S	98_G	0.604	0.40
23_F	67_F	0.597	0.39
23_F	88_L	0.596	0.39
33_C	83_P	0.595	0.39
14_A	18_E	0.594	0.39
173_D	182_I	0.590	0.39
200_V	205_L	0.585	0.38
11_L	16_K	0.585	0.38
23_F	92_P	0.582	0.38
129_V	159_T	0.579	0.38
67_F	147_T	0.577	0.38
124_V	128_A	0.576	0.37
70_L	184_F	0.576	0.37
72_V	208_V	0.575	0.37
30_V	190_E	0.575	0.37
46_M	185_G	0.574	0.37
43_L	53_L	0.572	0.37
133_K	139_A	0.571	0.37
207_H	212_D	0.571	0.37
151_A	154_D	0.571	0.37
131_P	134_K	0.570	0.37
70_L	176_L	0.569	0.37
150_Y	153_K	0.568	0.37
18_E	21_A	0.567	0.37
134_K	211_E	0.567	0.37
195_L	205_L	0.565	0.36
81_Y	171_E	0.565	0.36
22_R	130_K	0.564	0.36
165_N	173_D	0.564	0.36
110_E	113_Q	0.564	0.36
195_L	204_D	0.563	0.36
58_K	61_K	0.562	0.36
49_A	98_G	0.561	0.36
66_W	155_S	0.560	0.36
95_Y	102_Y	0.560	0.36
14_A	17_R	0.560	0.36
157_Y	165_N	0.559	0.36
164_E	168_V	0.559	0.36
193_K	196_K	0.559	0.36
183_A	189_K	0.556	0.36
199_D	202_D	0.554	0.35
34_E	38_E	0.552	0.35
56_R	60_K	0.552	0.35
47_N	175_A	0.551	0.35
81_Y	168_V	0.550	0.35
23_F	65_G	0.550	0.35
44_D	49_A	0.549	0.35
171_E	174_K	0.549	0.35
33_C	154_D	0.549	0.35
67_F	115_A	0.548	0.35
72_V	175_A	0.547	0.35
38_E	41_E	0.544	0.35
27_T	86_H	0.540	0.34
74_Y	78_D	0.539	0.34
152_V	156_D	0.536	0.34
152_V	193_K	0.535	0.34
151_A	181_L	0.535	0.34
162_D	168_V	0.533	0.34
49_A	60_K	0.532	0.33
196_K	200_V	0.531	0.33
167_E	170_K	0.530	0.33
37_E	199_D	0.529	0.33
142_A	145_A	0.527	0.33
23_F	173_D	0.525	0.33
46_M	116_L	0.523	0.33
62_A	92_P	0.522	0.33
43_L	72_V	0.522	0.33
111_L	115_A	0.522	0.33
177_H	195_L	0.521	0.32
63_V	103_I	0.520	0.32
88_L	191_I	0.517	0.32
133_K	136_G	0.517	0.32
62_A	91_V	0.515	0.32
70_L	179_R	0.514	0.32
144_V	207_H	0.513	0.32
100_D	104_K	0.511	0.32
179_R	187_I	0.511	0.32
157_Y	168_V	0.510	0.32
61_K	143_A	0.509	0.31
53_L	59_F	0.509	0.31
131_P	144_V	0.508	0.31
33_C	178_G	0.507	0.31
164_E	167_E	0.505	0.31
75_N	181_L	0.503	0.31
129_V	147_T	0.502	0.31
202_D	205_L	0.500	0.31
36_G	175_A	0.500	0.31

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
1l2mA	1	0.4937	50.3	0.955	Contact Map
2qsjA	2	0.2152	48.9	0.956	Contact Map
2qgzA	1	0.2447	24.8	0.962	Contact Map
1vhtA	1	0.2616	21.6	0.963	Contact Map
3douA	1	0.27	19.7	0.964	Contact Map
3lccA	1	0.3165	19.1	0.964	Contact Map
4ag4A	1	0.3207	17.4	0.965	Contact Map
4gmoA	1	0.2489	17	0.965	Contact Map
4a6dA	2	0.2911	16.4	0.965	Contact Map
2gpyA	2	0.2321	15.9	0.965	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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