53DR - BACSU - GREMLIN Contacts

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53DR - Putative SPBc2 prophage-derived 5'(3')-deoxyribonucleotidase

UniProt:	P68522	Sequences: MKKVIAIDMDQVLADLLSDWVAYINTYDDPFLKEKDILCWDIKKYTNTNNNVYRHLDYDLFRNLNVIEGSQRVTKELMKKYEVYVVTTATNHPDSLKAKLEWLTEYFPFIPHSNVVLCGNKNIIKADIMIDDGIHNLESFEGMKILFDAPHNRNENRFIRVMNWEEIERKLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	172 (168)
Sequences:	309 (234)
Seq/√Len:	18.1

BACSU - 53DR YQFW

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_R	105_E	6.769	1.00
69_G	73_V	4.758	1.00
7_I	74_T	4.284	1.00
6_A	126_A	4.062	1.00
59_D	98_A	3.706	1.00
76_E	168_E	3.296	0.99
22_A	26_T	3.087	0.99
143_M	159_I	2.909	0.99
148_D	162_M	2.864	0.98
19_D	63_N	2.734	0.98
62_R	101_E	2.670	0.98
69_G	165_E	2.450	0.96
73_V	168_E	2.383	0.95
7_I	88_T	2.142	0.92
87_T	128_I	2.053	0.90
110_I	115_V	2.032	0.89
6_A	124_I	2.025	0.89
4_V	84_Y	1.755	0.81
66_V	107_F	1.687	0.78
14_A	107_F	1.647	0.76
121_K	131_D	1.637	0.76
13_L	74_T	1.613	0.75
87_T	117_L	1.579	0.73
125_K	141_E	1.549	0.71
27_Y	55_H	1.512	0.70
121_K	132_D	1.512	0.70
18_S	65_N	1.489	0.68
5_I	77_L	1.476	0.68
130_I	167_I	1.471	0.67
162_M	166_E	1.462	0.67
103_L	107_F	1.449	0.66
137_L	158_F	1.447	0.66
148_D	160_R	1.426	0.65
5_I	8_D	1.389	0.63
148_D	153_R	1.356	0.61
89_A	118_C	1.341	0.60
27_Y	54_R	1.335	0.60
12_V	15_D	1.325	0.59
86_V	136_N	1.321	0.59
11_Q	39_C	1.299	0.57
81_Y	85_V	1.295	0.57
9_M	99_K	1.280	0.56
4_V	82_E	1.266	0.55
37_I	40_W	1.248	0.54
104_T	115_V	1.237	0.54
15_D	85_V	1.199	0.51
81_Y	171_L	1.195	0.51
89_A	95_S	1.187	0.51
108_P	136_N	1.179	0.50
4_V	126_A	1.172	0.50
61_F	99_K	1.170	0.50
97_K	101_E	1.167	0.49
16_L	64_L	1.163	0.49
101_E	105_E	1.159	0.49
19_D	23_Y	1.153	0.48
102_W	164_W	1.148	0.48
15_D	18_S	1.141	0.48
86_V	124_I	1.129	0.47
7_I	130_I	1.122	0.47
14_A	102_W	1.121	0.47
75_K	79_K	1.118	0.46
100_L	146_L	1.100	0.45
20_W	23_Y	1.093	0.45
105_E	124_I	1.092	0.45
27_Y	57_D	1.074	0.44
103_L	130_I	1.068	0.43
69_G	163_N	1.064	0.43
86_V	135_H	1.058	0.43
165_E	169_R	1.036	0.41
114_N	136_N	1.027	0.41
71_Q	107_F	1.027	0.41
112_H	136_N	1.012	0.40
54_R	65_N	1.008	0.40
89_A	119_G	0.999	0.39
25_N	31_F	0.989	0.39
13_L	139_S	0.982	0.38
95_S	118_C	0.976	0.38
87_T	171_L	0.975	0.38
56_L	116_V	0.964	0.37
23_Y	57_D	0.964	0.37
108_P	137_L	0.962	0.37
11_Q	19_D	0.959	0.37
128_I	171_L	0.958	0.37
78_M	114_N	0.954	0.37
145_I	157_R	0.953	0.36
86_V	129_M	0.941	0.36
84_Y	123_I	0.940	0.36
99_K	164_W	0.937	0.36
39_C	151_H	0.929	0.35
90_T	100_L	0.923	0.35
130_I	147_F	0.923	0.35
90_T	93_P	0.921	0.35
89_A	93_P	0.917	0.34
92_H	112_H	0.914	0.34
10_D	121_K	0.914	0.34
42_I	115_V	0.912	0.34
36_D	75_K	0.912	0.34
159_I	170_K	0.912	0.34
156_N	163_N	0.908	0.34
40_W	44_K	0.899	0.33
166_E	169_R	0.897	0.33
44_K	107_F	0.893	0.33
125_K	169_R	0.890	0.33
87_T	155_E	0.889	0.33
74_T	107_F	0.881	0.32
20_W	52_V	0.874	0.32
108_P	111_P	0.871	0.32
4_V	146_L	0.863	0.32
102_W	140_F	0.859	0.31
8_D	132_D	0.856	0.31
7_I	81_Y	0.847	0.31
69_G	168_E	0.843	0.30
65_N	87_T	0.840	0.30
145_I	170_K	0.832	0.30
120_N	134_I	0.823	0.29
130_I	164_W	0.822	0.29
21_V	26_T	0.818	0.29
32_L	39_C	0.812	0.29
40_W	45_Y	0.808	0.29
128_I	144_K	0.808	0.29
27_Y	32_L	0.806	0.29
58_Y	90_T	0.803	0.28
133_G	136_N	0.803	0.28
31_F	35_K	0.799	0.28
20_W	43_K	0.797	0.28
61_F	102_W	0.795	0.28
44_K	163_N	0.792	0.28
32_L	100_L	0.788	0.28
64_L	99_K	0.787	0.28
93_P	118_C	0.784	0.27
39_C	148_D	0.782	0.27
75_K	82_E	0.782	0.27
42_I	64_L	0.773	0.27
11_Q	133_G	0.772	0.27
89_A	142_G	0.767	0.27
75_K	107_F	0.765	0.27
25_N	33_K	0.763	0.26
13_L	85_V	0.761	0.26
147_F	163_N	0.753	0.26
93_P	103_L	0.751	0.26
94_D	97_K	0.747	0.26
55_H	70_S	0.745	0.26
43_K	46_T	0.745	0.26
13_L	23_Y	0.740	0.25
14_A	140_F	0.740	0.25
7_I	85_V	0.737	0.25
29_D	34_E	0.737	0.25
57_D	134_I	0.729	0.25
86_V	126_A	0.721	0.24
7_I	101_E	0.721	0.24
14_A	61_F	0.720	0.24
116_V	126_A	0.713	0.24
113_S	120_N	0.703	0.24
124_I	134_I	0.699	0.24
124_I	133_G	0.698	0.23
92_H	136_N	0.696	0.23
20_W	56_L	0.696	0.23
23_Y	26_T	0.694	0.23
143_M	166_E	0.688	0.23
95_S	102_W	0.688	0.23
44_K	162_M	0.685	0.23
27_Y	150_P	0.678	0.23
96_L	100_L	0.675	0.22
145_I	161_V	0.675	0.22
74_T	83_V	0.669	0.22
91_N	112_H	0.669	0.22
102_W	106_Y	0.663	0.22
25_N	48_T	0.662	0.22
43_K	145_I	0.660	0.22
16_L	112_H	0.659	0.22
64_L	164_W	0.657	0.22
28_D	124_I	0.656	0.22
6_A	86_V	0.656	0.22
50_N	54_R	0.647	0.21
27_Y	51_N	0.647	0.21
83_V	165_E	0.642	0.21
64_L	85_V	0.641	0.21
89_A	108_P	0.641	0.21
91_N	135_H	0.640	0.21
13_L	40_W	0.640	0.21
29_D	84_Y	0.636	0.21
16_L	60_L	0.634	0.21
21_V	33_K	0.629	0.21
66_V	165_E	0.628	0.21
13_L	143_M	0.628	0.21
127_D	131_D	0.628	0.21
35_K	38_L	0.626	0.20
6_A	89_A	0.621	0.20
59_D	101_E	0.619	0.20
93_P	98_A	0.616	0.20
84_Y	101_E	0.615	0.20
11_Q	47_N	0.614	0.20
31_F	69_G	0.614	0.20
58_Y	123_I	0.611	0.20
24_I	120_N	0.610	0.20
11_Q	98_A	0.610	0.20
51_N	124_I	0.609	0.20
73_V	164_W	0.608	0.20
120_N	138_E	0.606	0.20
70_S	107_F	0.603	0.20
117_L	122_N	0.595	0.19
134_I	137_L	0.592	0.19
18_S	34_E	0.590	0.19
118_C	142_G	0.590	0.19
145_I	153_R	0.588	0.19
112_H	151_H	0.581	0.19
81_Y	150_P	0.579	0.19
163_N	166_E	0.579	0.19
81_Y	128_I	0.579	0.19
96_L	136_N	0.570	0.18
89_A	99_K	0.570	0.18
62_R	98_A	0.568	0.18
10_D	131_D	0.565	0.18
20_W	40_W	0.565	0.18
56_L	69_G	0.565	0.18
17_L	126_A	0.564	0.18
26_T	57_D	0.562	0.18
9_M	15_D	0.561	0.18
116_V	119_G	0.560	0.18
24_I	28_D	0.559	0.18
29_D	72_R	0.556	0.18
116_V	166_E	0.553	0.18
128_I	149_A	0.553	0.18
21_V	36_D	0.551	0.18
39_C	67_I	0.548	0.17
42_I	96_L	0.539	0.17
60_L	92_H	0.537	0.17
108_P	142_G	0.534	0.17
55_H	155_E	0.532	0.17
161_V	169_R	0.530	0.17
28_D	50_N	0.529	0.17
14_A	74_T	0.529	0.17
29_D	70_S	0.528	0.17
86_V	133_G	0.526	0.17
5_I	81_Y	0.525	0.17
34_E	83_V	0.523	0.17
18_S	22_A	0.522	0.17
96_L	117_L	0.522	0.17
83_V	166_E	0.517	0.16
70_S	139_S	0.517	0.16
14_A	95_S	0.513	0.16
135_H	171_L	0.510	0.16
11_Q	42_I	0.510	0.16
96_L	133_G	0.509	0.16
89_A	102_W	0.508	0.16
12_V	147_F	0.506	0.16
121_K	127_D	0.504	0.16
99_K	102_W	0.504	0.16
154_N	169_R	0.502	0.16
162_M	169_R	0.502	0.16
74_T	109_F	0.502	0.16
118_C	140_F	0.500	0.16

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
3bwvA	2	0.9593	99.9	0.638	Contact Map
4mumA	2	0.9767	99.9	0.67	Contact Map
4l57A	2	0.9884	99.8	0.673	Contact Map
2b82A	4	0.9128	99	0.814	Contact Map
3sd7A	1	0.9535	98.6	0.834	Contact Map
2ah5A	1	0.9651	98.5	0.84	Contact Map
2obbA	2	0.5988	98.5	0.842	Contact Map
3kzxA	1	0.9244	98.5	0.842	Contact Map
4ezeA	1	0.9477	98.5	0.844	Contact Map
2go7A	2	0.9767	98.4	0.846	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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