DYW_deaminase - PFAM28P - GREMLIN Contacts

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DYW_deaminase - DYW family of nucleic acid deaminases

PFAM:	PF14432	Sequences: PGCSWIEVKGKVHEFVAGDRSHPQSEEIYAKLEELSEKLKEAGYVPDTSFVLHDVEEEEKEEGDALSYHSEKLAIAFGLISTPPGTPIRIVKNLRVCGDCHSAIKLISKITGREIIVRDRNRFHHFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	127 (125)
Sequences:	4371 (2606)
Seq/√Len:	233.1
META:	0.094

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_I	104_I	5.583	1.00
114_E	127_K	4.141	1.00
24_Q	81_S	3.640	1.00
50_F	98_G	3.302	1.00
103_A	107_I	3.254	1.00
24_Q	27_E	3.157	1.00
31_K	34_E	3.115	1.00
6_I	78_G	2.762	1.00
25_S	29_Y	2.617	1.00
35_L	111_T	2.606	1.00
4_S	90_I	2.307	1.00
104_I	117_V	2.046	1.00
39_L	103_A	1.927	1.00
96_V	117_V	1.921	1.00
42_A	109_K	1.893	1.00
75_I	90_I	1.879	1.00
40_K	61_E	1.803	1.00
39_L	110_I	1.706	1.00
31_K	80_I	1.675	1.00
13_H	22_H	1.635	1.00
3_C	14_E	1.577	1.00
38_K	41_E	1.576	1.00
75_I	107_I	1.573	1.00
96_V	104_I	1.508	1.00
47_D	98_G	1.488	1.00
3_C	16_V	1.436	1.00
34_E	38_K	1.427	1.00
36_S	72_K	1.389	1.00
39_L	106_L	1.373	1.00
82_T	86_T	1.357	1.00
82_T	88_I	1.343	1.00
82_T	113_R	1.327	1.00
22_H	28_I	1.323	1.00
36_S	67_S	1.277	1.00
20_R	29_Y	1.272	1.00
55_V	65_A	1.262	1.00
29_Y	73_L	1.239	1.00
89_R	116_I	1.234	1.00
36_S	39_L	1.201	1.00
8_V	81_S	1.178	1.00
42_A	110_I	1.160	1.00
21_S	25_S	1.160	1.00
50_F	53_H	1.124	1.00
38_K	111_T	1.122	1.00
13_H	77_F	1.110	1.00
39_L	107_I	1.095	1.00
116_I	125_H	1.092	1.00
24_Q	77_F	1.090	1.00
78_G	88_I	1.057	1.00
37_E	41_E	1.038	1.00
14_E	91_V	1.034	1.00
31_K	111_T	1.032	1.00
97_C	100_C	1.030	1.00
26_E	30_A	1.028	1.00
65_A	120_R	1.017	1.00
5_W	91_V	1.011	1.00
9_K	81_S	1.000	1.00
44_Y	99_D	0.993	1.00
102_S	106_L	0.987	1.00
27_E	30_A	0.981	1.00
8_V	82_T	0.980	1.00
79_L	107_I	0.973	1.00
18_G	68_Y	0.973	1.00
83_P	86_T	0.966	1.00
38_K	42_A	0.955	1.00
69_H	100_C	0.948	1.00
47_D	102_S	0.937	1.00
54_D	60_K	0.924	1.00
82_T	85_G	0.921	1.00
25_S	73_L	0.920	1.00
5_W	14_E	0.919	1.00
48_T	72_K	0.914	1.00
71_E	94_L	0.907	1.00
87_P	116_I	0.904	1.00
31_K	76_A	0.897	0.99
65_A	68_Y	0.895	0.99
32_L	76_A	0.888	0.99
44_Y	102_S	0.885	0.99
87_P	114_E	0.874	0.99
51_V	55_V	0.868	0.99
2_G	94_L	0.867	0.99
14_E	120_R	0.865	0.99
51_V	66_L	0.861	0.99
39_L	111_T	0.854	0.99
35_L	76_A	0.852	0.99
5_W	83_P	0.837	0.99
82_T	87_P	0.836	0.99
19_D	70_S	0.830	0.99
10_G	53_H	0.829	0.99
48_T	51_V	0.825	0.99
35_L	107_I	0.820	0.99
8_V	77_F	0.800	0.99
31_K	79_L	0.789	0.99
48_T	57_E	0.775	0.98
48_T	60_K	0.767	0.98
118_R	122_R	0.766	0.98
42_A	106_L	0.757	0.98
9_K	83_P	0.754	0.98
79_L	111_T	0.747	0.98
77_F	81_S	0.743	0.98
55_V	60_K	0.740	0.98
51_V	60_K	0.737	0.98
118_R	123_F	0.731	0.98
31_K	38_K	0.731	0.98
104_I	107_I	0.727	0.98
11_K	14_E	0.725	0.98
20_R	25_S	0.725	0.98
114_E	125_H	0.715	0.97
20_R	26_E	0.711	0.97
98_G	102_S	0.697	0.97
32_L	103_A	0.693	0.97
4_S	104_I	0.687	0.97
15_F	77_F	0.685	0.97
28_I	31_K	0.679	0.97
2_G	93_N	0.671	0.96
33_E	37_E	0.666	0.96
8_V	121_N	0.649	0.96
111_T	120_R	0.645	0.95
37_E	112_G	0.640	0.95
29_Y	68_Y	0.635	0.95
47_D	50_F	0.635	0.95
91_V	123_F	0.634	0.95
75_I	96_V	0.634	0.95
50_F	66_L	0.633	0.95
32_L	39_L	0.630	0.95
72_K	99_D	0.629	0.95
71_E	92_K	0.628	0.95
35_L	103_A	0.622	0.94
67_S	121_N	0.619	0.94
52_L	56_E	0.617	0.94
56_E	59_E	0.615	0.94
55_V	59_E	0.607	0.94
83_P	87_P	0.601	0.93
46_P	51_V	0.599	0.93
27_E	88_I	0.593	0.93
30_A	37_E	0.589	0.93
28_I	32_L	0.588	0.93
53_H	66_L	0.587	0.92
57_E	60_K	0.585	0.92
52_L	55_V	0.585	0.92
95_R	122_R	0.583	0.92
94_L	122_R	0.580	0.92
14_E	18_G	0.577	0.92
107_I	111_T	0.575	0.92
72_K	104_I	0.574	0.92
26_E	108_S	0.571	0.91
5_W	121_N	0.569	0.91
20_R	33_E	0.569	0.91
48_T	53_H	0.569	0.91
7_E	12_V	0.567	0.91
79_L	86_T	0.566	0.91
36_S	110_I	0.566	0.91
10_G	98_G	0.563	0.91
29_Y	33_E	0.563	0.91
101_H	124_H	0.561	0.91
32_L	73_L	0.561	0.91
31_K	121_N	0.557	0.90
66_L	72_K	0.555	0.90
103_A	106_L	0.553	0.90
70_S	123_F	0.546	0.90
94_L	99_D	0.543	0.89
5_W	89_R	0.541	0.89
84_P	112_G	0.536	0.89
70_S	74_A	0.535	0.89
51_V	122_R	0.530	0.88
101_H	105_K	0.526	0.88
73_L	90_I	0.522	0.87
59_E	62_E	0.521	0.87
71_E	122_R	0.518	0.87
101_H	108_S	0.517	0.87
32_L	36_S	0.516	0.87
5_W	9_K	0.516	0.87
16_V	65_A	0.514	0.87
11_K	120_R	0.514	0.87
16_V	91_V	0.513	0.86
41_E	47_D	0.513	0.86
10_G	13_H	0.512	0.86
20_R	62_E	0.511	0.86
35_L	79_L	0.509	0.86
103_A	110_I	0.508	0.86
35_L	50_F	0.508	0.86
33_E	68_Y	0.505	0.86
14_E	21_S	0.505	0.86
17_A	62_E	0.504	0.85
109_K	112_G	0.503	0.85
24_Q	121_N	0.503	0.85
17_A	36_S	0.503	0.85
26_E	33_E	0.500	0.85

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
1b89A	1	0.4409	19.8	0.932	Contact Map
3rmtA	4	0.9449	14.5	0.936	Contact Map
3slhA	4	0.9606	11.7	0.939	Contact Map
2waoA	1	0.3622	8.4	0.942	Contact Map
1dvpA	2	0.7874	7.8	0.943	Contact Map
1pm4A	3	0.315	7.7	0.943	Contact Map
16pkA	1	0.8976	6.9	0.945	Contact Map
2jtnA	1	0.685	6.6	0.945	Contact Map
2fr5A	6	0.7795	6.5	0.945	Contact Map
1t3bA	2	0.7874	6.3	0.945	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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