CCPN - BACSU - GREMLIN Contacts

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CCPN - Transcriptional repressor CcpN

UniProt:	O34994	Sequences: MSTIELNKRQEHILQIVKENGPITGEHIAEKLNLTRATLRPDLAILTMSGFLEARPRVGYFYTGKTGTQLLADKLKKLQVKDFQSIPVVIHENVSVYDAICTMFLEDVGTLFVVDRDAVLVGVLSRKDLLRASIGQQELTSVPVHIIMTRMPNITVCRREDYVMDIAKHLIEKQIDALPVIKDTDKGFEVIGRVTKTNMTKILVSLSENEIL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	212 (168)
Sequences:	3370 (1947)
Seq/√Len:	150.2

ECOLI - IMDH
BACSU - CCPN ACUB YTOI YLBB
HALSA - Q9HQD0 Q9HRK9 Q9HMW8 Q9HPF4 IMDH
SULSO - Q7LXY4 Q97U20 Q97V95 Q7LXN6 Q981B7 Q97U00 Q97VD7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
182_K	189_E	4.645	1.00
157_C	180_V	3.945	1.00
27_H	33_N	3.558	1.00
90_I	113_V	3.144	1.00
25_G	33_N	2.943	1.00
142_V	146_I	2.757	1.00
94_V	98_D	2.689	1.00
158_R	183_D	2.509	1.00
91_H	94_V	2.443	1.00
159_R	191_I	2.394	1.00
97_Y	101_C	2.298	1.00
157_C	161_D	2.287	1.00
74_K	77_K	2.282	1.00
101_C	105_L	2.192	1.00
92_E	121_V	2.187	1.00
132_A	142_V	2.175	1.00
184_T	189_E	2.161	1.00
155_T	173_K	2.136	1.00
67_G	70_L	2.031	1.00
166_I	178_L	2.011	1.00
99_A	124_L	2.000	1.00
143_P	146_I	1.994	1.00
90_I	94_V	1.987	1.00
97_Y	141_S	1.986	1.00
49_S	74_K	1.913	1.00
124_L	147_I	1.853	1.00
56_P	59_G	1.827	1.00
168_K	172_E	1.818	1.00
119_V	189_E	1.814	1.00
162_Y	165_D	1.782	1.00
28_I	39_L	1.739	1.00
165_D	168_K	1.731	1.00
91_H	116_R	1.709	1.00
25_G	35_T	1.699	1.00
98_D	101_C	1.671	1.00
99_A	103_M	1.655	1.00
90_I	99_A	1.557	1.00
163_V	167_A	1.552	1.00
93_N	145_H	1.552	1.00
95_S	98_D	1.508	1.00
90_I	144_V	1.479	1.00
100_I	140_T	1.472	1.00
92_E	145_H	1.439	1.00
108_V	111_L	1.424	1.00
93_N	143_P	1.419	1.00
96_V	132_A	1.406	1.00
161_D	165_D	1.385	1.00
181_I	188_F	1.379	1.00
118_A	189_E	1.376	1.00
92_E	115_D	1.371	1.00
70_L	74_K	1.367	1.00
73_D	77_K	1.356	1.00
107_D	126_R	1.329	1.00
73_D	76_K	1.324	1.00
113_V	144_V	1.301	1.00
170_L	178_L	1.280	1.00
139_L	142_V	1.274	1.00
115_D	119_V	1.273	1.00
103_M	111_L	1.270	1.00
100_I	104_F	1.243	1.00
133_S	168_K	1.239	1.00
128_D	149_T	1.206	1.00
79_Q	82_D	1.199	1.00
184_T	188_F	1.172	1.00
188_F	191_I	1.171	1.00
47_T	60_Y	1.166	1.00
28_I	59_G	1.132	1.00
163_V	199_M	1.129	1.00
159_R	182_K	1.127	0.99
92_E	114_V	1.109	0.99
151_M	188_F	1.096	0.99
91_H	145_H	1.090	0.99
183_D	188_F	1.087	0.99
26_E	34_L	1.072	0.99
158_R	161_D	1.068	0.99
114_V	118_A	1.060	0.99
158_R	184_T	1.046	0.99
142_V	147_I	1.044	0.99
132_A	147_I	1.041	0.99
110_T	177_A	1.024	0.99
97_Y	140_T	1.021	0.99
176_D	197_T	1.006	0.99
70_L	73_D	0.979	0.99
159_R	183_D	0.965	0.98
171_I	174_Q	0.951	0.98
26_E	36_R	0.939	0.98
91_H	115_D	0.931	0.98
37_A	52_L	0.930	0.98
179_P	190_V	0.928	0.98
158_R	165_D	0.928	0.98
115_D	121_V	0.926	0.98
119_V	184_T	0.925	0.98
81_K	84_Q	0.914	0.98
120_L	177_A	0.913	0.98
83_F	163_V	0.912	0.98
125_S	198_N	0.894	0.97
45_I	48_M	0.893	0.97
88_V	108_V	0.889	0.97
72_A	75_L	0.888	0.97
145_H	150_R	0.885	0.97
176_D	196_K	0.885	0.97
112_F	177_A	0.871	0.97
88_V	111_L	0.868	0.97
72_A	76_K	0.866	0.97
161_D	178_L	0.866	0.97
38_T	50_G	0.861	0.97
96_V	147_I	0.854	0.97
132_A	139_L	0.842	0.96
39_L	59_G	0.836	0.96
68_T	72_A	0.827	0.96
96_V	142_V	0.821	0.96
117_D	189_E	0.821	0.96
177_A	193_R	0.815	0.96
132_A	140_T	0.806	0.95
27_H	30_E	0.798	0.95
75_L	78_L	0.798	0.95
37_A	41_P	0.796	0.95
58_V	62_Y	0.795	0.95
106_E	111_L	0.787	0.95
166_I	170_L	0.784	0.95
88_V	113_V	0.773	0.94
115_D	189_E	0.763	0.94
49_S	77_K	0.758	0.93
102_T	111_L	0.752	0.93
93_N	116_R	0.749	0.93
108_V	195_T	0.735	0.92
95_S	143_P	0.735	0.92
80_V	166_I	0.731	0.92
167_A	199_M	0.730	0.92
72_A	78_L	0.729	0.92
129_L	200_T	0.729	0.92
102_T	106_E	0.722	0.92
40_R	46_L	0.713	0.91
103_M	129_L	0.712	0.91
40_R	55_R	0.708	0.91
165_D	169_H	0.707	0.91
46_L	60_Y	0.707	0.91
91_H	121_V	0.705	0.91
65_K	112_F	0.700	0.90
168_K	171_I	0.699	0.90
94_V	111_L	0.697	0.90
103_M	199_M	0.697	0.90
91_H	114_V	0.689	0.90
109_G	126_R	0.688	0.90
84_Q	89_V	0.685	0.90
100_I	111_L	0.685	0.90
161_D	169_H	0.684	0.89
54_A	166_I	0.679	0.89
103_M	108_V	0.674	0.89
28_I	61_F	0.671	0.89
101_C	104_F	0.665	0.88
129_L	167_A	0.662	0.88
57_R	62_Y	0.659	0.88
133_S	140_T	0.658	0.88
166_I	193_R	0.648	0.87
71_L	75_L	0.645	0.87
73_D	105_L	0.643	0.86
41_P	48_M	0.641	0.86
110_T	176_D	0.641	0.86
76_K	80_V	0.640	0.86
63_T	66_T	0.633	0.86
28_I	31_K	0.631	0.85
27_H	31_K	0.630	0.85
109_G	195_T	0.629	0.85
156_V	181_I	0.628	0.85
96_V	144_V	0.627	0.85
123_V	128_D	0.623	0.85
96_V	146_I	0.622	0.85
71_L	82_D	0.621	0.84
71_L	79_Q	0.614	0.84
40_R	44_A	0.614	0.84
40_R	45_I	0.613	0.84
95_S	152_P	0.604	0.83
109_G	149_T	0.602	0.83
75_L	82_D	0.598	0.82
157_C	194_V	0.598	0.82
42_D	112_F	0.597	0.82
155_T	169_H	0.596	0.82
75_L	79_Q	0.595	0.82
140_T	143_P	0.591	0.81
46_L	52_L	0.590	0.81
47_T	52_L	0.589	0.81
196_K	199_M	0.587	0.81
65_K	78_L	0.586	0.81
76_K	81_K	0.586	0.81
131_R	171_I	0.585	0.81
169_H	178_L	0.582	0.80
37_A	46_L	0.578	0.80
104_F	133_S	0.575	0.80
126_R	130_L	0.575	0.80
76_K	191_I	0.573	0.79
163_V	194_V	0.573	0.79
40_R	47_T	0.572	0.79
63_T	75_L	0.570	0.79
65_K	75_L	0.569	0.79
93_N	115_D	0.566	0.79
98_D	144_V	0.565	0.78
85_S	90_I	0.564	0.78
109_G	196_K	0.563	0.78
52_L	60_Y	0.563	0.78
37_A	45_I	0.562	0.78
51_F	55_R	0.562	0.78
127_K	177_A	0.557	0.77
36_R	40_R	0.555	0.77
62_Y	75_L	0.554	0.77
122_G	148_M	0.554	0.77
139_L	146_I	0.553	0.77
40_R	60_Y	0.552	0.77
124_L	196_K	0.551	0.77
78_L	82_D	0.550	0.77
157_C	179_P	0.548	0.76
71_L	198_N	0.547	0.76
125_S	128_D	0.546	0.76
93_N	118_A	0.545	0.76
166_I	174_Q	0.544	0.76
110_T	193_R	0.542	0.76
30_E	39_L	0.541	0.75
40_R	52_L	0.541	0.75
29_A	32_L	0.540	0.75
85_S	191_I	0.539	0.75
167_A	200_T	0.538	0.75
66_T	71_L	0.537	0.75
154_I	179_P	0.535	0.75
53_E	190_V	0.534	0.74
111_L	196_K	0.532	0.74
43_L	46_L	0.530	0.74
125_S	176_D	0.527	0.74
88_V	103_M	0.526	0.73
80_V	126_R	0.525	0.73
72_A	79_Q	0.523	0.73
89_V	118_A	0.522	0.73
68_T	71_L	0.520	0.73
26_E	30_E	0.518	0.72
37_A	40_R	0.517	0.72
84_Q	180_V	0.514	0.72
120_L	179_P	0.514	0.72
109_G	127_K	0.514	0.72
84_Q	200_T	0.514	0.72
99_A	129_L	0.514	0.72
81_K	106_E	0.513	0.72
44_A	48_M	0.512	0.71
41_P	47_T	0.511	0.71
115_D	118_A	0.510	0.71
66_T	70_L	0.510	0.71
169_H	172_E	0.507	0.71
90_I	163_V	0.506	0.71
166_I	194_V	0.503	0.70
28_I	32_L	0.503	0.70
37_A	47_T	0.502	0.70
116_R	121_V	0.500	0.70
129_L	140_T	0.500	0.70
95_S	100_I	0.500	0.70

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
3l2bA	2	0.5566	99.9	0.491	Contact Map
3fv6A	2	0.6792	99.9	0.508	Contact Map
1pvmA	2	0.6509	99.9	0.513	Contact Map
2j9lA	3	0.6085	99.9	0.518	Contact Map
2zy9A	2	0.9198	99.9	0.52	Contact Map
3fhmA	2	0.6179	99.9	0.52	Contact Map
3ocoA	2	0.6179	99.9	0.523	Contact Map
4nocA	2	0.5896	99.9	0.524	Contact Map
2ouxA	2	0.9292	99.9	0.525	Contact Map
3lv9A	2	0.5943	99.9	0.525	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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