CDD - ECOLI - GREMLIN Contacts

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CDD - Cytidine deaminase

UniProt:	P0ABF6	Sequences: MHPRFQTAFAQLADNLQSALEPILADKYFPALLTGEQVSSLKSATGLDEDALAFALLPLAAACARTPLSNFNVGAIARGVSGTWYFGANMEFIGATMQQTVHAEQSAISHAWLSGEKALAAITVNYTPCGHCRQFMNELNSGLDLRIHLPGREAHALRDYLPDAFGPKDLEIKTLLMDEQDHGYALTGDALSQAAIAAANRSHMPYSKSPSGVALECKDGRIFSGSYAENAAFNPTLPPLQGALILLNLKGYDYPDIQRAVLAEKADAPLIQWDATSATLKALGCHSIDRVLLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10137
Length:	294 (268)
Sequences:	322 (209)
Seq/√Len:	12.8

ECOLI - CDD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
215_L	260_A	6.561	1.00
90_M	101_V	4.965	1.00
81_S	116_E	3.889	0.99
183_G	200_N	3.778	0.99
48_D	51_A	3.244	0.98
33_L	86_F	3.183	0.98
113_L	226_S	3.174	0.97
109_S	242_G	3.164	0.97
101_V	106_S	3.142	0.97
66_T	72_N	3.047	0.97
106_S	245_I	2.631	0.93
112_W	228_A	2.606	0.92
240_L	276_T	2.573	0.92
217_C	247_L	2.573	0.92
79_G	116_E	2.550	0.91
195_A	212_G	2.486	0.90
219_D	252_Y	2.436	0.89
216_E	258_Q	2.413	0.89
110_H	160_Y	2.331	0.87
111_A	115_G	2.299	0.86
245_I	249_L	2.282	0.86
80_V	118_A	2.210	0.84
35_G	83_T	2.088	0.80
184_Y	196_I	2.046	0.79
186_L	196_I	2.042	0.79
196_I	263_A	2.013	0.78
42_K	49_E	1.985	0.77
198_A	212_G	1.846	0.71
31_A	53_A	1.810	0.69
114_S	203_H	1.796	0.69
77_A	107_A	1.766	0.67
21_E	25_A	1.765	0.67
119_L	268_A	1.745	0.66
195_A	199_A	1.733	0.66
239_P	262_L	1.674	0.63
272_Q	278_A	1.671	0.63
200_N	257_I	1.667	0.63
218_K	256_D	1.656	0.62
145_L	251_G	1.638	0.61
122_I	136_M	1.618	0.60
65_R	210_P	1.611	0.60
65_R	248_N	1.595	0.59
169_D	231_A	1.588	0.59
201_R	226_S	1.585	0.59
177_M	199_A	1.566	0.58
198_A	214_A	1.551	0.57
223_F	252_Y	1.542	0.57
32_L	83_T	1.542	0.57
49_E	78_R	1.541	0.57
24_L	27_K	1.523	0.56
131_H	234_N	1.519	0.55
180_Q	203_H	1.478	0.53
158_R	164_A	1.456	0.52
189_D	259_R	1.442	0.51
167_P	170_L	1.437	0.51
33_L	40_S	1.424	0.50
38_V	42_K	1.415	0.50
119_L	244_L	1.410	0.50
227_Y	236_T	1.405	0.50
188_G	196_I	1.402	0.49
66_T	93_I	1.400	0.49
50_D	146_R	1.393	0.49
139_L	145_L	1.390	0.49
96_T	223_F	1.386	0.49
96_T	242_G	1.386	0.49
203_H	242_G	1.384	0.48
178_D	251_G	1.378	0.48
78_R	123_T	1.377	0.48
115_G	279_T	1.375	0.48
18_S	21_E	1.373	0.48
177_M	184_Y	1.367	0.48
109_S	272_Q	1.361	0.47
39_S	247_L	1.351	0.47
41_L	277_S	1.351	0.47
25_A	184_Y	1.350	0.47
200_N	212_G	1.341	0.46
20_L	177_M	1.337	0.46
177_M	211_S	1.327	0.45
140_N	178_D	1.322	0.45
71_F	139_L	1.314	0.45
110_H	125_N	1.304	0.44
123_T	148_H	1.300	0.44
31_A	94_G	1.298	0.44
90_M	248_N	1.297	0.44
226_S	248_N	1.293	0.44
18_S	25_A	1.286	0.43
130_G	134_Q	1.286	0.43
226_S	246_L	1.277	0.43
211_S	239_P	1.263	0.42
264_E	271_I	1.253	0.42
191_L	198_A	1.244	0.41
242_G	272_Q	1.218	0.40
32_L	114_S	1.209	0.39
24_L	101_V	1.200	0.39
152_R	203_H	1.182	0.38
125_N	160_Y	1.179	0.38
191_L	214_A	1.167	0.37
71_F	133_R	1.165	0.37
273_W	277_S	1.155	0.37
32_L	53_A	1.154	0.37
68_L	207_S	1.142	0.36
83_T	258_Q	1.136	0.36
179_E	221_R	1.134	0.36
62_A	90_M	1.129	0.36
236_T	239_P	1.118	0.35
66_T	101_V	1.116	0.35
73_V	133_R	1.103	0.34
147_I	227_Y	1.102	0.34
159_D	163_D	1.102	0.34
38_V	49_E	1.092	0.34
127_T	160_Y	1.091	0.34
133_R	167_P	1.083	0.33
41_L	45_T	1.076	0.33
97_M	100_T	1.061	0.32
273_W	285_C	1.060	0.32
92_F	279_T	1.056	0.32
88_A	108_I	1.049	0.32
34_T	191_L	1.041	0.32
117_K	179_E	1.036	0.31
82_G	116_E	1.036	0.31
68_L	203_H	1.034	0.31
37_Q	115_G	1.032	0.31
195_A	214_A	1.030	0.31
237_L	241_Q	1.028	0.31
23_I	33_L	1.023	0.31
214_A	222_I	1.022	0.31
208_K	244_L	1.008	0.30
92_F	244_L	1.004	0.30
44_A	282_A	1.004	0.30
137_N	230_N	1.003	0.30
88_A	112_W	1.002	0.30
139_L	228_A	0.995	0.30
262_L	276_T	0.994	0.29
176_L	244_L	0.991	0.29
107_A	149_L	0.987	0.29
90_M	126_Y	0.983	0.29
58_P	149_L	0.982	0.29
127_T	155_H	0.979	0.29
75_A	103_A	0.978	0.29
118_A	271_I	0.972	0.29
117_K	223_F	0.971	0.28
51_A	248_N	0.958	0.28
21_E	27_K	0.955	0.28
49_E	120_A	0.953	0.28
106_S	249_L	0.949	0.28
20_L	49_E	0.949	0.28
72_N	244_L	0.948	0.28
185_A	218_K	0.948	0.28
223_F	250_K	0.944	0.27
62_A	216_E	0.943	0.27
46_G	49_E	0.933	0.27
78_R	119_L	0.928	0.27
147_I	163_D	0.927	0.27
118_A	141_S	0.927	0.27
124_V	261_V	0.926	0.27
25_A	268_A	0.925	0.27
39_S	44_A	0.918	0.26
54_F	171_E	0.915	0.26
33_L	50_D	0.912	0.26
136_M	157_L	0.911	0.26
28_Y	196_I	0.910	0.26
64_A	142_G	0.910	0.26
19_A	186_L	0.908	0.26
19_A	23_I	0.902	0.26
80_V	117_K	0.901	0.26
218_K	258_Q	0.898	0.26
61_A	139_L	0.894	0.25
223_F	263_A	0.890	0.25
33_L	263_A	0.889	0.25
43_S	266_A	0.886	0.25
194_A	222_I	0.880	0.25
20_L	146_R	0.878	0.25
189_D	261_V	0.877	0.25
266_A	283_L	0.876	0.25
24_L	106_S	0.874	0.25
182_H	210_P	0.869	0.24
274_D	277_S	0.868	0.24
47_L	136_M	0.861	0.24
99_Q	110_H	0.859	0.24
52_L	279_T	0.857	0.24
216_E	222_I	0.849	0.24
67_P	196_I	0.847	0.24
183_G	222_I	0.845	0.23
213_V	272_Q	0.843	0.23
69_S	134_Q	0.842	0.23
37_Q	182_H	0.842	0.23
133_R	170_L	0.833	0.23
131_H	207_S	0.832	0.23
130_G	161_L	0.829	0.23
210_P	248_N	0.823	0.23
51_A	272_Q	0.822	0.23
98_Q	131_H	0.809	0.22
237_L	272_Q	0.809	0.22
135_F	138_E	0.808	0.22
146_R	250_K	0.808	0.22
125_N	149_L	0.808	0.22
112_W	149_L	0.807	0.22
215_L	263_A	0.807	0.22
118_A	207_S	0.805	0.22
260_A	263_A	0.798	0.22
221_R	252_Y	0.798	0.22
161_L	169_D	0.796	0.22
112_W	150_P	0.793	0.22
73_V	104_E	0.792	0.22
36_E	187_T	0.790	0.21
216_E	259_R	0.786	0.21
74_G	160_Y	0.785	0.21
213_V	224_S	0.783	0.21
175_L	178_D	0.779	0.21
90_M	151_G	0.778	0.21
277_S	281_K	0.777	0.21
227_Y	231_A	0.776	0.21
100_T	110_H	0.775	0.21
253_D	256_D	0.772	0.21
22_P	215_L	0.770	0.21
101_V	279_T	0.769	0.21
58_P	61_A	0.769	0.21
144_D	263_A	0.765	0.21
96_T	272_Q	0.765	0.21
71_F	233_F	0.764	0.21
109_S	245_I	0.762	0.21
31_A	83_T	0.760	0.20
152_R	160_Y	0.759	0.20
39_S	49_E	0.759	0.20
133_R	206_Y	0.756	0.20
138_E	206_Y	0.753	0.20
174_T	184_Y	0.746	0.20
199_A	210_P	0.740	0.20
88_A	107_A	0.736	0.20
110_H	114_S	0.730	0.19
140_N	147_I	0.729	0.19
34_T	95_A	0.724	0.19
256_D	266_A	0.722	0.19
49_E	68_L	0.720	0.19
266_A	269_P	0.715	0.19
125_N	230_N	0.713	0.19
25_A	43_S	0.708	0.19
281_K	286_H	0.708	0.19
168_K	175_L	0.705	0.19
128_P	132_C	0.703	0.19
129_C	132_C	0.703	0.19
95_A	110_H	0.703	0.19
195_A	198_A	0.700	0.19
136_M	166_G	0.700	0.19
240_L	283_L	0.696	0.18
19_A	24_L	0.693	0.18
184_Y	210_P	0.691	0.18
19_A	22_P	0.691	0.18
113_L	261_V	0.690	0.18
130_G	133_R	0.684	0.18
133_R	235_P	0.683	0.18
18_S	40_S	0.683	0.18
100_T	209_S	0.683	0.18
104_E	165_F	0.680	0.18
74_G	133_R	0.679	0.18
33_L	38_V	0.679	0.18
72_N	141_S	0.676	0.18
40_S	185_A	0.674	0.18
203_H	261_V	0.672	0.18
203_H	238_P	0.671	0.18
134_Q	235_P	0.668	0.18
144_D	187_T	0.668	0.18
273_W	284_G	0.667	0.18
184_Y	199_A	0.665	0.17
108_I	269_P	0.665	0.17
152_R	219_D	0.664	0.17
157_L	227_Y	0.664	0.17
254_Y	271_I	0.657	0.17
203_H	226_S	0.656	0.17
212_G	245_I	0.655	0.17
195_A	204_M	0.654	0.17
34_T	197_A	0.650	0.17
101_V	253_D	0.648	0.17
18_S	28_Y	0.647	0.17
68_L	96_T	0.646	0.17
219_D	253_D	0.644	0.17
212_G	240_L	0.643	0.17
131_H	134_Q	0.643	0.17
130_G	135_F	0.640	0.17
238_P	276_T	0.640	0.17
76_I	86_F	0.639	0.17
65_R	223_F	0.638	0.17
124_V	227_Y	0.636	0.17
39_S	213_V	0.636	0.17
151_G	155_H	0.636	0.17
42_K	259_R	0.635	0.17
100_T	279_T	0.632	0.16
211_S	255_P	0.629	0.16
28_Y	258_Q	0.627	0.16
245_I	283_L	0.624	0.16
186_L	197_A	0.622	0.16
253_D	258_Q	0.619	0.16
53_A	209_S	0.617	0.16
123_T	238_P	0.617	0.16
38_V	93_I	0.617	0.16
38_V	207_S	0.613	0.16
107_A	111_A	0.612	0.16
96_T	212_G	0.609	0.16
196_I	260_A	0.609	0.16
188_G	193_Q	0.607	0.16
80_V	213_V	0.603	0.16
95_A	203_H	0.601	0.16
90_M	119_L	0.600	0.16
142_G	274_D	0.599	0.16
31_A	182_H	0.599	0.16
125_N	137_N	0.599	0.16
125_N	238_P	0.595	0.15
98_Q	272_Q	0.595	0.15
101_V	258_Q	0.591	0.15
119_L	201_R	0.589	0.15
73_V	130_G	0.587	0.15
64_A	93_I	0.585	0.15
49_E	196_I	0.585	0.15
88_A	106_S	0.585	0.15
193_Q	197_A	0.584	0.15
65_R	254_Y	0.581	0.15
84_W	124_V	0.580	0.15
229_E	232_A	0.579	0.15
35_G	46_G	0.577	0.15
147_I	278_A	0.576	0.15
248_N	254_Y	0.575	0.15
96_T	252_Y	0.574	0.15
74_G	150_P	0.573	0.15
35_G	267_D	0.572	0.15
181_D	197_A	0.572	0.15
126_Y	203_H	0.570	0.15
211_S	240_L	0.569	0.15
18_S	43_S	0.568	0.15
98_Q	270_L	0.566	0.15
66_T	122_I	0.565	0.15
95_A	245_I	0.565	0.15
28_Y	283_L	0.565	0.15
187_T	218_K	0.563	0.15
29_F	123_T	0.562	0.15
73_V	170_L	0.562	0.15
42_K	274_D	0.561	0.15
200_N	203_H	0.560	0.15
69_S	235_P	0.558	0.14
32_L	38_V	0.558	0.14
69_S	130_G	0.555	0.14
196_I	223_F	0.554	0.14
73_V	89_N	0.552	0.14
67_P	205_P	0.551	0.14
91_E	133_R	0.550	0.14
64_A	239_P	0.549	0.14
165_F	169_D	0.549	0.14
204_M	207_S	0.548	0.14
41_L	49_E	0.548	0.14
159_D	179_E	0.548	0.14
19_A	77_A	0.547	0.14
144_D	221_R	0.545	0.14
67_P	133_R	0.545	0.14
123_T	127_T	0.541	0.14
133_R	233_F	0.538	0.14
18_S	83_T	0.538	0.14
125_N	211_S	0.536	0.14
133_R	169_D	0.534	0.14
176_L	260_A	0.534	0.14
61_A	125_N	0.532	0.14
28_Y	101_V	0.531	0.14
223_F	255_P	0.531	0.14
127_T	163_D	0.531	0.14
50_D	154_A	0.530	0.14
179_E	191_L	0.530	0.14
76_I	171_E	0.530	0.14
191_L	284_G	0.529	0.14
33_L	188_G	0.529	0.14
46_G	224_S	0.528	0.14
23_I	41_L	0.526	0.14
150_P	228_A	0.526	0.14
146_R	217_C	0.526	0.14
99_Q	163_D	0.524	0.14
71_F	74_G	0.523	0.14
106_S	109_S	0.521	0.14
95_A	282_A	0.521	0.14
99_Q	160_Y	0.520	0.14
71_F	165_F	0.519	0.14
119_L	272_Q	0.518	0.13
22_P	25_A	0.517	0.13
76_I	255_P	0.517	0.13
108_I	237_L	0.515	0.13
107_A	230_N	0.515	0.13
67_P	97_M	0.514	0.13
32_L	261_V	0.514	0.13
108_I	115_G	0.513	0.13
207_S	254_Y	0.512	0.13
34_T	83_T	0.511	0.13
98_Q	246_L	0.511	0.13
66_T	148_H	0.511	0.13
142_G	279_T	0.510	0.13
186_L	266_A	0.509	0.13
201_R	213_V	0.508	0.13
259_R	286_H	0.507	0.13
64_A	254_Y	0.505	0.13
101_V	115_G	0.505	0.13
23_I	210_P	0.505	0.13
164_A	259_R	0.504	0.13
20_L	51_A	0.502	0.13
122_I	202_S	0.502	0.13
99_Q	122_I	0.502	0.13
204_M	234_N	0.502	0.13
186_L	215_L	0.500	0.13

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
1cttA	2	0.9966	100	0.367	Contact Map
4eg2A	4	1	100	0.425	Contact Map
2d30A	4	0.3878	100	0.746	Contact Map
3dmoA	4	0.415	100	0.756	Contact Map
3b8fA	4	0.4354	100	0.772	Contact Map
1r5tA	4	0.432	99.9	0.784	Contact Map
1uwzA	4	0.4082	99.9	0.785	Contact Map
2fr5A	6	0.4286	99.9	0.786	Contact Map
3mpzA	4	0.4082	99.9	0.79	Contact Map
3r2nA	4	0.3946	99.9	0.796	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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