YNCF - BACSU - GREMLIN Contacts

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YNCF - Probable deoxyuridine 5'-triphosphate nucleotidohydrolase YncF

UniProt:	O31801	Sequences: MTMQIKIKYLDETQTRISKIEQGDWIDLRAAEDVTIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTEIKKGDRICQFRIMKKMPAVELVEVEHLGNEDRGGLGSTGTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	144 (135)
Sequences:	3780 (2273)
Seq/√Len:	195.6

ECOLI - DUT
BACSU - YNCF YOSS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_E	131_G	2.666	1.00
26_I	124_L	2.556	1.00
105_K	108_D	2.453	1.00
33_D	105_K	2.424	1.00
37_K	101_D	2.359	1.00
58_A	113_F	2.322	1.00
23_G	84_S	2.113	1.00
21_E	84_S	2.073	1.00
37_K	40_E	2.070	1.00
70_F	102_T	1.990	1.00
35_T	103_E	1.988	1.00
68_K	92_W	1.896	1.00
22_Q	83_E	1.884	1.00
25_W	115_I	1.850	1.00
45_P	90_D	1.830	1.00
9_Y	126_E	1.779	1.00
19_K	121_A	1.757	1.00
41_F	71_G	1.749	1.00
72_V	102_T	1.746	1.00
61_V	80_V	1.725	1.00
13_T	106_K	1.688	1.00
52_L	116_M	1.681	1.00
38_K	101_D	1.673	1.00
50_M	58_A	1.671	1.00
35_T	101_D	1.632	1.00
30_A	104_I	1.630	1.00
108_D	143_T	1.611	1.00
43_L	68_K	1.607	1.00
52_L	58_A	1.607	1.00
40_E	99_L	1.599	1.00
19_K	26_I	1.584	1.00
15_T	29_R	1.563	1.00
33_D	106_K	1.547	1.00
51_E	86_K	1.523	1.00
57_E	80_V	1.457	1.00
59_H	117_K	1.442	1.00
94_F	97_Y	1.438	1.00
59_H	80_V	1.411	1.00
28_L	58_A	1.407	1.00
19_K	122_V	1.371	1.00
18_S	29_R	1.365	1.00
58_A	116_M	1.355	1.00
91_F	111_C	1.346	1.00
61_V	117_K	1.341	1.00
43_L	90_D	1.340	1.00
45_P	88_D	1.324	1.00
10_L	49_A	1.288	1.00
36_I	42_K	1.269	1.00
14_Q	106_K	1.267	1.00
73_I	94_F	1.258	1.00
47_G	88_D	1.221	1.00
116_M	122_V	1.215	1.00
92_W	138_L	1.205	1.00
56_Y	120_P	1.176	1.00
31_A	106_K	1.165	1.00
62_P	77_S	1.162	1.00
7_I	16_R	1.158	1.00
56_Y	116_M	1.153	1.00
33_D	103_E	1.146	1.00
57_E	61_V	1.142	1.00
14_Q	31_A	1.136	1.00
28_L	113_F	1.135	1.00
46_L	91_F	1.121	1.00
20_I	29_R	1.118	1.00
60_V	113_F	1.116	1.00
52_L	56_Y	1.107	1.00
11_D	31_A	1.106	1.00
60_V	111_C	1.097	1.00
61_V	78_M	1.085	1.00
62_P	73_I	1.081	1.00
73_I	97_Y	1.080	1.00
63_R	109_R	1.078	1.00
39_D	99_L	1.044	1.00
57_E	117_K	1.022	1.00
50_M	89_N	0.996	1.00
26_I	113_F	0.985	0.99
22_Q	54_E	0.981	0.99
91_F	110_I	0.980	0.99
28_L	60_V	0.963	0.99
86_K	130_L	0.955	0.99
24_D	83_E	0.954	0.99
109_R	142_G	0.952	0.99
24_D	57_E	0.938	0.99
34_V	104_I	0.928	0.99
34_V	44_V	0.919	0.99
9_Y	16_R	0.917	0.99
20_I	140_S	0.913	0.99
11_D	14_Q	0.897	0.99
75_T	94_F	0.895	0.99
41_F	94_F	0.891	0.99
50_M	113_F	0.886	0.99
113_F	116_M	0.884	0.99
73_I	77_S	0.879	0.99
71_G	98_A	0.874	0.99
11_D	47_G	0.871	0.99
75_T	92_W	0.868	0.99
70_F	108_D	0.858	0.99
8_K	49_A	0.856	0.99
39_D	97_Y	0.853	0.99
39_D	98_A	0.849	0.98
70_F	143_T	0.849	0.98
62_P	78_M	0.843	0.98
34_V	42_K	0.833	0.98
61_V	115_I	0.832	0.98
62_P	74_Q	0.825	0.98
74_Q	93_F	0.824	0.98
60_V	91_F	0.820	0.98
32_E	45_P	0.817	0.98
48_V	89_N	0.808	0.98
44_V	93_F	0.804	0.98
38_K	95_P	0.802	0.98
59_H	115_I	0.797	0.98
51_E	130_L	0.776	0.97
8_K	11_D	0.775	0.97
31_A	45_P	0.774	0.97
36_I	95_P	0.774	0.97
68_K	90_D	0.767	0.97
43_L	92_W	0.764	0.97
74_Q	78_M	0.760	0.97
30_A	44_V	0.760	0.97
8_K	129_H	0.759	0.97
49_A	130_L	0.748	0.97
59_H	78_M	0.748	0.97
20_I	141_T	0.741	0.96
41_F	97_Y	0.737	0.96
24_D	52_L	0.737	0.96
81_I	92_W	0.726	0.96
67_Y	92_W	0.722	0.96
52_L	83_E	0.719	0.96
68_K	75_T	0.718	0.96
21_E	141_T	0.714	0.96
13_T	31_A	0.709	0.95
78_M	92_W	0.702	0.95
28_L	48_V	0.700	0.95
26_I	122_V	0.699	0.95
127_V	130_L	0.697	0.95
104_I	110_I	0.696	0.95
86_K	133_E	0.687	0.95
32_E	106_K	0.683	0.94
29_R	48_V	0.681	0.94
83_E	119_M	0.676	0.94
93_F	110_I	0.674	0.94
70_F	100_R	0.671	0.94
60_V	74_Q	0.668	0.94
57_E	115_I	0.668	0.94
62_P	76_N	0.664	0.94
28_L	91_F	0.663	0.94
28_L	111_C	0.663	0.94
32_E	42_K	0.659	0.93
16_R	126_E	0.647	0.93
75_T	78_M	0.645	0.93
67_Y	75_T	0.637	0.92
11_D	15_T	0.630	0.92
54_E	83_E	0.627	0.92
9_Y	14_Q	0.615	0.91
24_D	119_M	0.614	0.91
81_I	89_N	0.613	0.91
15_T	106_K	0.594	0.89
19_K	124_L	0.591	0.89
14_Q	29_R	0.590	0.89
95_P	98_A	0.588	0.89
36_I	94_F	0.585	0.89
130_L	133_E	0.580	0.88
12_E	15_T	0.577	0.88
71_G	97_Y	0.574	0.88
80_V	115_I	0.572	0.87
74_Q	77_S	0.571	0.87
49_A	88_D	0.556	0.86
30_A	33_D	0.554	0.86
7_I	10_L	0.553	0.86
58_A	81_I	0.553	0.86
67_Y	78_M	0.552	0.86
24_D	116_M	0.552	0.86
62_P	66_T	0.551	0.85
47_G	90_D	0.547	0.85
77_S	97_Y	0.545	0.85
52_L	55_G	0.543	0.85
7_I	124_L	0.543	0.85
119_M	124_L	0.542	0.84
72_V	93_F	0.542	0.84
129_H	132_N	0.541	0.84
75_T	89_N	0.537	0.84
64_S	137_G	0.531	0.83
75_T	97_Y	0.526	0.83
55_G	118_K	0.523	0.82
84_S	141_T	0.520	0.82
51_E	133_E	0.520	0.82
41_F	92_W	0.518	0.82
41_F	99_L	0.518	0.82
38_K	99_L	0.517	0.82
57_E	78_M	0.515	0.81
74_Q	138_L	0.514	0.81
77_S	94_F	0.512	0.81
10_L	14_Q	0.511	0.81
52_L	113_F	0.511	0.81
7_I	11_D	0.509	0.81
8_K	128_E	0.508	0.80
119_M	122_V	0.508	0.80
9_Y	13_T	0.507	0.80
117_K	120_P	0.502	0.80
66_T	70_F	0.500	0.79
40_E	100_R	0.500	0.79

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
3hzaA	3	0.9861	100	0.152	Contact Map
4gv8A	3	0.875	100	0.163	Contact Map
3mdxA	3	0.9028	100	0.163	Contact Map
3zf6A	3	0.9583	100	0.169	Contact Map
4b0hA	3	0.9722	100	0.176	Contact Map
3f4fA	3	0.9306	100	0.179	Contact Map
3tqzA	3	0.9028	100	0.184	Contact Map
3t64A	3	0.9375	100	0.185	Contact Map
3araA	3	0.8542	100	0.187	Contact Map
1euwA	3	0.8889	100	0.187	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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