NUCA - BACSU - GREMLIN Contacts

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NUCA - DNA-entry nuclease

UniProt:	P12667	Sequences: MTTDIIKTILLVIVIIAAAAVGLIKGDFFSADQKTSQTKEYDETMAFPSDRYPETAKHIKDAINEGHSEVCTIDRDGAEERREQSLKDVPSKKGYDRDEWPMAMCKEGGEGASVEYISPADNRGAGSWVGHRLTDYPDGTKVLFTIQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	147 (124)
Sequences:	104 (82)
Seq/√Len:	7.4

BACSU - NUCA NUCB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_D	115_E	6.035	1.00
129_V	144_F	4.473	0.98
100_W	144_F	3.263	0.90
61_D	64_N	3.068	0.86
104_M	133_L	2.577	0.75
48_P	105_C	2.298	0.66
71_C	102_M	2.189	0.62
48_P	71_C	2.114	0.59
71_C	105_C	2.084	0.58
135_D	146_I	1.925	0.51
80_E	95_Y	1.877	0.49
55_T	102_M	1.834	0.48
84_Q	87_K	1.830	0.48
114_V	134_T	1.714	0.43
42_D	143_L	1.709	0.43
25_K	28_F	1.708	0.43
119_P	125_A	1.682	0.42
114_V	119_P	1.677	0.42
26_G	29_F	1.666	0.41
63_I	102_M	1.658	0.41
47_F	128_W	1.649	0.41
100_W	133_L	1.646	0.40
55_T	63_I	1.646	0.40
100_W	128_W	1.627	0.40
64_N	115_E	1.605	0.39
47_F	105_C	1.572	0.38
60_K	67_H	1.538	0.36
49_S	56_A	1.531	0.36
71_C	128_W	1.453	0.33
45_M	118_S	1.393	0.31
47_F	129_V	1.364	0.30
74_D	77_G	1.329	0.29
42_D	70_V	1.312	0.29
105_C	128_W	1.272	0.27
45_M	57_K	1.254	0.27
35_T	70_V	1.218	0.26
44_T	132_R	1.217	0.26
70_V	83_E	1.195	0.25
48_P	128_W	1.187	0.25
64_N	91_S	1.185	0.25
50_D	115_E	1.146	0.24
67_H	143_L	1.120	0.23
23_L	28_F	1.114	0.23
40_E	136_Y	1.113	0.23
28_F	36_S	1.099	0.22
25_K	30_S	1.081	0.22
134_T	142_V	1.059	0.21
81_R	130_G	1.042	0.21
41_Y	93_K	1.038	0.21
23_L	26_G	1.031	0.20
64_N	113_S	1.029	0.20
43_E	81_R	1.026	0.20
33_Q	87_K	1.021	0.20
103_A	139_G	1.021	0.20
106_K	129_V	1.018	0.20
47_F	71_C	1.010	0.20
66_G	123_R	0.994	0.20
24_I	31_A	0.988	0.19
79_E	91_S	0.984	0.19
24_I	27_D	0.982	0.19
57_K	115_E	0.971	0.19
41_Y	70_V	0.965	0.19
55_T	125_A	0.964	0.19
79_E	83_E	0.960	0.19
55_T	71_C	0.956	0.19
35_T	40_E	0.955	0.19
131_H	134_T	0.954	0.19
105_C	129_V	0.952	0.19
54_E	118_S	0.951	0.19
51_R	120_A	0.945	0.18
102_M	133_L	0.942	0.18
30_S	33_Q	0.933	0.18
63_I	100_W	0.923	0.18
73_I	124_G	0.918	0.18
92_K	95_Y	0.908	0.17
48_P	68_S	0.904	0.17
71_C	100_W	0.901	0.17
41_Y	130_G	0.900	0.17
71_C	90_P	0.868	0.17
90_P	116_Y	0.868	0.17
64_N	76_D	0.866	0.17
65_E	115_E	0.866	0.17
42_D	67_H	0.864	0.17
37_Q	76_D	0.863	0.16
43_E	141_K	0.861	0.16
102_M	128_W	0.853	0.16
60_K	113_S	0.853	0.16
66_G	94_G	0.849	0.16
28_F	32_D	0.843	0.16
55_T	100_W	0.824	0.16
107_E	111_G	0.824	0.16
60_K	115_E	0.818	0.16
118_S	129_V	0.815	0.15
81_R	91_S	0.804	0.15
65_E	70_V	0.796	0.15
70_V	88_D	0.795	0.15
48_P	102_M	0.794	0.15
27_D	30_S	0.793	0.15
63_I	71_C	0.793	0.15
54_E	119_P	0.790	0.15
24_I	30_S	0.786	0.15
25_K	70_V	0.783	0.15
33_Q	38_T	0.774	0.15
128_W	133_L	0.769	0.15
43_E	114_V	0.769	0.15
79_E	90_P	0.765	0.14
39_K	144_F	0.763	0.14
46_A	110_E	0.762	0.14
27_D	31_A	0.760	0.14
105_C	116_Y	0.753	0.14
68_S	71_C	0.741	0.14
23_L	30_S	0.739	0.14
26_G	32_D	0.736	0.14
27_D	114_V	0.735	0.14
118_S	146_I	0.729	0.14
51_R	94_G	0.728	0.14
31_A	60_K	0.728	0.14
93_K	125_A	0.723	0.14
25_K	106_K	0.721	0.14
73_I	108_G	0.720	0.14
60_K	106_K	0.718	0.14
79_E	132_R	0.716	0.14
117_I	129_V	0.714	0.14
100_W	146_I	0.710	0.13
77_G	118_S	0.690	0.13
93_K	143_L	0.689	0.13
96_D	123_R	0.689	0.13
97_R	123_R	0.689	0.13
108_G	124_G	0.685	0.13
113_S	118_S	0.681	0.13
28_F	35_T	0.660	0.13
132_R	142_V	0.654	0.12
48_P	116_Y	0.653	0.12
80_E	84_Q	0.651	0.12
53_P	97_R	0.647	0.12
53_P	96_D	0.647	0.12
86_L	97_R	0.645	0.12
86_L	96_D	0.645	0.12
67_H	130_G	0.641	0.12
65_E	137_P	0.640	0.12
59_I	72_T	0.633	0.12
118_S	125_A	0.632	0.12
71_C	116_Y	0.627	0.12
95_Y	120_A	0.626	0.12
60_K	114_V	0.621	0.12
53_P	103_A	0.617	0.12
53_P	139_G	0.617	0.12
43_E	133_L	0.616	0.12
54_E	117_I	0.612	0.12
24_I	29_F	0.610	0.12
29_F	32_D	0.608	0.12
68_S	105_C	0.606	0.12
57_K	65_E	0.597	0.11
25_K	29_F	0.596	0.11
23_L	29_F	0.592	0.11
60_K	77_G	0.578	0.11
78_A	91_S	0.575	0.11
41_Y	67_H	0.574	0.11
84_Q	113_S	0.573	0.11
26_G	44_T	0.569	0.11
93_K	146_I	0.563	0.11
89_V	116_Y	0.559	0.11
28_F	33_Q	0.559	0.11
114_V	142_V	0.558	0.11
87_K	132_R	0.557	0.11
39_K	74_D	0.553	0.11
55_T	121_D	0.552	0.11
24_I	60_K	0.552	0.11
27_D	35_T	0.544	0.11
34_K	49_S	0.540	0.11
127_S	140_T	0.540	0.11
57_K	110_E	0.539	0.11
49_S	117_I	0.536	0.11
26_G	31_A	0.524	0.10
45_M	140_T	0.522	0.10
41_Y	143_L	0.522	0.10
31_A	120_A	0.519	0.10
60_K	89_V	0.513	0.10
25_K	32_D	0.511	0.10
30_S	106_K	0.508	0.10
57_K	64_N	0.507	0.10
44_T	51_R	0.504	0.10
27_D	40_E	0.503	0.10
117_I	143_L	0.501	0.10
88_D	132_R	0.501	0.10
30_S	35_T	0.500	0.10

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
1fwxA	2	0.9048	18	0.958	Contact Map
1yr2A	1	0.6259	16.2	0.959	Contact Map
4yv7A	1	0.7347	10.2	0.962	Contact Map
4od6A	1	0.5102	10.1	0.962	Contact Map
3cvzA	1	0.5578	6.5	0.965	Contact Map
4ys6A	1	0.7211	5.3	0.967	Contact Map
4wzzA	1	0.7551	5	0.967	Contact Map
3vgiA	1	0.3741	5	0.967	Contact Map
4r9fA	1	0.7143	4.8	0.968	Contact Map
3gybA	2	0.8299	4.8	0.968	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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