CDD - BACSU - GREMLIN Contacts

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CDD - Cytidine deaminase

UniProt:	P19079	Sequences: MNRQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAERTALFKAVSEGDTEFQMLAVAADTPGPVSPCGACRQVISELCTKDVIVVLTNLQGQIKEMTVEELLPGAFSSEDLHDERKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	136 (127)
Sequences:	3318 (2252)
Seq/√Len:	199.9

ECOLI - CDD
BACSU - CDD
HALSA - Q9HR24

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_M	88_A	3.765	1.00
33_K	69_E	3.085	1.00
61_K	65_E	2.788	1.00
34_D	67_D	2.467	1.00
59_L	93_I	2.361	1.00
32_T	38_Y	2.288	1.00
29_A	37_V	2.232	1.00
19_A	25_Q	2.176	1.00
61_K	64_S	2.133	1.00
47_A	50_M	2.119	1.00
94_S	124_A	2.056	1.00
31_L	72_M	2.000	1.00
33_K	71_Q	1.935	1.00
9_E	39_R	1.910	1.00
77_A	83_V	1.903	1.00
9_E	12_K	1.903	1.00
52_N	60_F	1.830	1.00
36_K	67_D	1.716	1.00
32_T	67_D	1.708	1.00
60_F	92_V	1.676	1.00
52_N	57_T	1.676	1.00
97_C	101_V	1.632	1.00
14_R	78_D	1.626	1.00
57_T	60_F	1.625	1.00
49_S	88_A	1.606	1.00
38_Y	67_D	1.604	1.00
104_V	114_E	1.574	1.00
57_T	61_K	1.539	1.00
38_Y	65_E	1.536	1.00
63_V	96_L	1.528	1.00
84_S	105_L	1.498	1.00
27_G	41_C	1.462	1.00
12_K	15_D	1.452	1.00
105_L	115_M	1.449	1.00
72_M	102_I	1.434	1.00
72_M	104_V	1.410	1.00
102_I	114_E	1.407	1.00
7_I	106_T	1.341	1.00
32_T	36_K	1.296	1.00
47_A	88_A	1.293	1.00
7_I	74_A	1.279	1.00
5_E	9_E	1.277	1.00
94_S	126_S	1.252	1.00
115_M	119_E	1.250	1.00
24_F	83_V	1.241	1.00
115_M	123_G	1.218	1.00
13_A	39_R	1.217	1.00
99_K	118_E	1.210	1.00
113_K	123_G	1.187	1.00
31_L	71_Q	1.186	1.00
127_S	130_L	1.157	1.00
59_L	92_V	1.155	1.00
59_L	70_F	1.148	1.00
11_L	76_A	1.140	1.00
116_T	119_E	1.102	1.00
25_Q	78_D	1.087	1.00
102_I	116_T	1.069	1.00
59_L	96_L	1.061	1.00
107_N	111_Q	1.042	1.00
98_T	101_V	1.037	1.00
52_N	56_R	1.027	1.00
10_A	29_A	1.023	1.00
94_S	128_E	1.020	1.00
32_T	70_F	1.019	1.00
30_L	58_A	1.015	1.00
30_L	73_L	1.012	1.00
13_A	27_G	1.011	1.00
21_Y	48_Y	1.002	1.00
56_R	92_V	1.001	1.00
76_A	106_T	1.000	1.00
43_I	63_V	0.996	1.00
82_P	107_N	0.984	1.00
13_A	41_C	0.983	1.00
86_C	89_C	0.980	1.00
73_L	93_I	0.980	1.00
6_L	29_A	0.966	0.99
103_V	120_L	0.960	0.99
94_S	127_S	0.950	0.99
30_L	70_F	0.939	0.99
57_T	64_S	0.932	0.99
117_V	120_L	0.923	0.99
9_E	37_V	0.919	0.99
70_F	97_C	0.918	0.99
14_R	76_A	0.918	0.99
18_Y	45_N	0.908	0.99
11_L	14_R	0.906	0.99
15_D	25_Q	0.886	0.99
103_V	117_V	0.886	0.99
14_R	27_G	0.871	0.99
70_F	101_V	0.868	0.99
16_M	39_R	0.863	0.99
7_I	11_L	0.856	0.99
35_G	71_Q	0.855	0.99
62_A	70_F	0.851	0.99
36_K	65_E	0.846	0.99
12_K	39_R	0.844	0.99
7_I	112_I	0.828	0.98
4_Q	8_T	0.813	0.98
6_L	37_V	0.803	0.98
93_I	97_C	0.781	0.98
41_C	57_T	0.772	0.97
126_S	130_L	0.771	0.97
105_L	123_G	0.769	0.97
87_G	121_L	0.766	0.97
5_E	8_T	0.765	0.97
33_K	68_T	0.762	0.97
14_R	25_Q	0.761	0.97
93_I	101_V	0.759	0.97
73_L	101_V	0.757	0.97
8_T	12_K	0.754	0.97
58_A	73_L	0.749	0.97
52_N	92_V	0.745	0.97
93_I	117_V	0.738	0.97
11_L	106_T	0.738	0.97
101_V	117_V	0.738	0.97
47_A	51_C	0.730	0.96
100_D	118_E	0.730	0.96
63_V	70_F	0.722	0.96
88_A	92_V	0.713	0.96
43_I	64_S	0.708	0.96
80_P	109_Q	0.697	0.95
8_T	11_L	0.695	0.95
56_R	60_F	0.688	0.95
6_L	74_A	0.686	0.95
82_P	112_I	0.685	0.95
79_T	82_P	0.671	0.94
43_I	60_F	0.671	0.94
14_R	17_A	0.663	0.94
12_K	16_M	0.661	0.94
41_C	64_S	0.656	0.94
81_G	84_S	0.655	0.94
74_A	104_V	0.651	0.93
45_N	95_E	0.648	0.93
13_A	64_S	0.646	0.93
18_Y	21_Y	0.646	0.93
21_Y	45_N	0.646	0.93
59_L	97_C	0.639	0.93
6_L	10_A	0.632	0.92
74_A	106_T	0.630	0.92
55_E	86_C	0.630	0.92
87_G	90_R	0.623	0.92
56_R	88_A	0.617	0.91
106_T	112_I	0.615	0.91
78_D	108_L	0.613	0.91
126_S	129_D	0.601	0.90
34_D	68_T	0.591	0.90
53_C	89_C	0.587	0.89
87_G	91_Q	0.584	0.89
30_L	62_A	0.578	0.88
16_M	64_S	0.577	0.88
14_R	77_A	0.576	0.88
79_T	108_L	0.576	0.88
24_F	77_A	0.573	0.88
26_V	54_A	0.570	0.88
10_A	74_A	0.569	0.88
9_E	13_A	0.568	0.88
80_P	108_L	0.567	0.88
31_L	37_V	0.565	0.87
28_A	58_A	0.564	0.87
53_C	56_R	0.561	0.87
50_M	92_V	0.558	0.87
84_S	90_R	0.553	0.86
48_Y	130_L	0.549	0.86
45_N	49_S	0.547	0.86
10_A	76_A	0.547	0.86
48_Y	51_C	0.545	0.85
84_S	123_G	0.543	0.85
85_P	91_Q	0.542	0.85
53_C	86_C	0.540	0.85
121_L	125_F	0.538	0.85
121_L	124_A	0.536	0.84
84_S	129_D	0.518	0.82
94_S	117_V	0.516	0.82
4_Q	112_I	0.516	0.82
82_P	108_L	0.515	0.82
47_A	53_C	0.515	0.82
55_E	89_C	0.514	0.82
90_R	120_L	0.513	0.82
42_N	55_E	0.512	0.82
73_L	103_V	0.511	0.82
85_P	90_R	0.511	0.82
91_Q	95_E	0.508	0.81
6_L	31_L	0.507	0.81
56_R	62_A	0.506	0.81
26_V	42_N	0.506	0.81
5_E	31_L	0.505	0.81
11_L	108_L	0.505	0.81
79_T	83_V	0.504	0.81
94_S	99_K	0.501	0.80
29_A	39_R	0.500	0.80

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
2d30A	4	0.9118	100	0.056	Contact Map
3dmoA	4	0.9412	100	0.09	Contact Map
3b8fA	4	0.9779	100	0.177	Contact Map
1cttA	2	0.9265	100	0.178	Contact Map
1uwzA	4	0.9559	100	0.217	Contact Map
2fr5A	6	0.9779	100	0.242	Contact Map
1r5tA	4	0.9632	100	0.249	Contact Map
3mpzA	4	0.9044	100	0.263	Contact Map
3r2nA	4	0.8676	100	0.28	Contact Map
3oj6A	4	0.9412	100	0.303	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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