OPENSEQ.org - DCD - ECOLI GREMLIN

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DCD - Deoxycytidine triphosphate deaminase

UniProt:	P28248	Sequence MRLCDRDIEAWLDEGRLSINPRPPVERINGATVDVRLGNKFRTFRGHTAAFIDLSGPKDEVSAALDRVMSDEIVLDEGEAFYLHPGELALAVTLESVTLPADLVGWLDGRSSLARLGLMVHVTAHRIDPGWSGCIVLEFYNSGKLPLALRPGMLIGALSFEPLSGPAVRPYNRREDAKYRNQQGAVASRIDKD	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11418
Length:	193 (189)
Sequences:	776
Seq/Len:	4.11

DCD
Paralog alert: 0.04 [within 20: 0.01] - ratio of genomes with paralogs

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
98_T	132_S	4.368	1.00
102_D	162_P	3.649	1.00
35_V	156_G	2.87	1.00
9_E	168_V	2.825	1.00
19_I	33_V	2.612	1.00
106_W	161_E	2.587	1.00
39_N	77_E	2.574	1.00
36_R	94_L	2.515	1.00
35_V	158_L	2.478	1.00
45_R	71_D	2.27	1.00
127_I	158_L	2.119	1.00
118_L	147_L	2.099	1.00
11_W	16_R	2.046	1.00
105_G	160_F	1.945	1.00
20_N	98_T	1.901	1.00
11_W	162_P	1.901	1.00
101_A	130_G	1.891	1.00
82_Y	148_A	1.807	1.00
16_R	102_D	1.756	0.99
10_A	14_E	1.743	0.99
127_I	135_I	1.676	0.99
38_G	92_V	1.647	0.99
8_I	33_V	1.645	0.99
53_D	150_R	1.591	0.99
96_S	132_S	1.568	0.98
6_R	168_V	1.536	0.98
22_R	33_V	1.516	0.98
99_L	105_G	1.485	0.98
93_T	137_L	1.458	0.97
37_L	155_I	1.453	0.97
7_D	165_G	1.436	0.97
31_A	174_R	1.411	0.96
35_V	127_I	1.393	0.96
107_L	122_V	1.368	0.95
50_A	71_D	1.362	0.95
3_L	7_D	1.35	0.95
48_T	75_L	1.297	0.93
139_F	155_I	1.295	0.93
110_R	154_L	1.289	0.93
134_C	184_G	1.289	0.93
31_A	129_P	1.272	0.93
12_L	22_R	1.265	0.92
132_S	181_N	1.263	0.92
39_N	74_V	1.261	0.92
94_L	152_G	1.255	0.92
43_T	75_L	1.254	0.92
120_V	156_G	1.254	0.92
92_V	134_C	1.25	0.92
107_L	127_I	1.248	0.92
101_A	166_P	1.248	0.92
17_L	103_L	1.245	0.91
2_R	159_S	1.229	0.91
9_E	13_D	1.224	0.90
43_T	51_F	1.222	0.90
111_S	115_R	1.214	0.90
84_H	87_E	1.181	0.88
4_C	7_D	1.178	0.88
102_D	166_P	1.173	0.88
109_G	114_A	1.17	0.88
40_K	92_V	1.138	0.86
30_G	174_R	1.131	0.85
76_D	174_R	1.114	0.84
138_E	182_Q	1.103	0.83
109_G	138_E	1.094	0.82
137_L	155_I	1.076	0.81
27_R	154_L	1.068	0.80
13_D	24_P	1.064	0.80
85_P	146_P	1.062	0.80
188_S	193_D	1.055	0.79
32_T	159_S	1.054	0.79
109_G	182_Q	1.052	0.79
75_L	155_I	1.049	0.79
35_V	134_C	1.047	0.78
3_L	162_P	1.045	0.78
10_A	15_G	1.039	0.78
17_L	160_F	1.038	0.78
125_H	128_D	1.037	0.78
15_G	18_S	1.032	0.77
7_D	11_W	1.017	0.76
113_L	153_M	1.01	0.75
139_F	149_L	1.007	0.75
106_W	159_S	1.005	0.74
20_N	96_S	1.001	0.74

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
1xs1A	6	1	100	0.162	Contact Map	0.728
2qxxA	2	0.9534	100	0.201	Contact Map	0.658
1pkhA	2	0.9637	100	0.23	Contact Map	0.662
3km3A	2	0.9067	100	0.263	Contact Map	0.739
4dhkA	2	0.9016	100	0.263	Contact Map	0.72
2r9qA	4	0.9378	100	0.295	Contact Map	0.381
2yzjA	3	0.8238	100	0.32	Contact Map	0.677
3lqwA	1	0.8187	99.9	0.62	Contact Map	0.516
3mdxA	1	0.7617	99.9	0.634	Contact Map	0.61
3h6xA	3	0.6995	99.9	0.634	Contact Map	0.568

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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