NUSA - HALSA - GREMLIN Contacts

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NUSA - Probable transcription termination protein NusA

UniProt:	P0CW99	Sequences: MTIRLSDEARQLIAVFETETDATAVDCLPDDDRVVYVVTAGEMGAAIGDGGSRVDALEATLGRSVVLVEDAPTAEGFVANALSPAAVYNVTVSENDTTVAYAEVAHEDKGVAIGADGTNIETAKELAARHFDIDDIQLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	139 (136)
Sequences:	196 (145)
Seq/√Len:	12.4

HALSA - NUSA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_G	69_E	3.171	0.97
74_A	100_A	3.127	0.97
31_D	65_V	3.008	0.96
44_G	47_I	2.895	0.95
30_D	35_V	2.847	0.95
100_A	127_A	2.607	0.92
3_I	34_V	2.288	0.85
40_A	76_G	2.221	0.83
108_D	112_A	2.000	0.76
54_V	67_L	1.976	0.75
54_V	82_L	1.956	0.74
46_A	51_G	1.876	0.71
30_D	33_R	1.872	0.71
87_V	108_D	1.852	0.70
65_V	71_A	1.796	0.68
120_I	127_A	1.782	0.67
57_L	65_V	1.777	0.67
60_T	68_V	1.758	0.66
78_V	127_A	1.732	0.65
22_A	39_T	1.668	0.62
63_R	71_A	1.655	0.61
92_V	100_A	1.637	0.60
66_V	119_N	1.616	0.59
78_V	101_Y	1.597	0.58
87_V	112_A	1.531	0.55
68_V	99_V	1.525	0.54
72_P	128_A	1.522	0.54
48_G	51_G	1.517	0.54
22_A	42_E	1.514	0.54
113_I	120_I	1.452	0.51
69_E	80_N	1.431	0.50
66_V	122_T	1.412	0.49
112_A	138_L	1.407	0.48
26_D	84_P	1.395	0.48
24_A	36_Y	1.379	0.47
13_I	36_Y	1.377	0.47
85_A	108_D	1.345	0.45
32_D	63_R	1.332	0.45
67_L	127_A	1.332	0.45
75_E	79_A	1.329	0.44
82_L	102_A	1.314	0.44
103_E	135_D	1.304	0.43
12_L	112_A	1.288	0.42
7_D	10_R	1.281	0.42
89_N	95_N	1.275	0.42
45_A	49_D	1.258	0.41
4_R	98_T	1.255	0.41
35_V	125_E	1.239	0.40
23_T	132_D	1.219	0.39
32_D	59_A	1.206	0.38
33_R	66_V	1.202	0.38
63_R	118_T	1.198	0.38
72_P	76_G	1.193	0.38
13_I	133_I	1.140	0.35
78_V	110_G	1.136	0.35
37_V	77_F	1.134	0.35
54_V	126_L	1.130	0.35
54_V	73_T	1.129	0.35
40_A	70_D	1.114	0.34
20_T	51_G	1.113	0.34
63_R	115_A	1.088	0.33
85_A	112_A	1.084	0.33
37_V	80_N	1.070	0.32
6_S	9_A	1.067	0.32
123_A	136_I	1.061	0.32
3_I	130_H	1.061	0.32
17_E	24_A	1.053	0.31
56_A	63_R	1.052	0.31
14_A	17_E	1.051	0.31
47_I	101_Y	1.045	0.31
28_L	116_D	1.032	0.30
90_V	115_A	1.024	0.30
22_A	76_G	1.007	0.29
43_M	54_V	0.987	0.28
49_D	126_L	0.978	0.28
46_A	84_P	0.977	0.28
74_A	127_A	0.977	0.28
70_D	126_L	0.976	0.28
25_V	116_D	0.966	0.28
45_A	133_I	0.965	0.28
26_D	129_R	0.963	0.27
37_V	137_Q	0.962	0.27
19_E	80_N	0.955	0.27
43_M	47_I	0.954	0.27
79_A	119_N	0.952	0.27
74_A	133_I	0.944	0.27
25_V	39_T	0.928	0.26
57_L	119_N	0.919	0.26
52_S	92_V	0.915	0.26
31_D	92_V	0.913	0.26
105_A	131_F	0.912	0.25
25_V	138_L	0.912	0.25
31_D	34_V	0.911	0.25
64_S	76_G	0.900	0.25
38_V	65_V	0.897	0.25
8_E	53_R	0.870	0.24
3_I	59_A	0.870	0.24
94_E	126_L	0.861	0.24
67_L	104_V	0.858	0.23
13_I	24_A	0.853	0.23
19_E	38_V	0.851	0.23
57_L	62_G	0.846	0.23
13_I	41_G	0.836	0.23
32_D	105_A	0.832	0.22
14_A	136_I	0.826	0.22
28_L	126_L	0.826	0.22
34_V	111_V	0.824	0.22
67_L	121_E	0.809	0.22
38_V	79_A	0.808	0.22
6_S	119_N	0.806	0.22
87_V	104_V	0.793	0.21
27_C	133_I	0.791	0.21
37_V	50_G	0.783	0.21
31_D	135_D	0.780	0.21
104_V	117_G	0.774	0.20
43_M	69_E	0.774	0.20
77_F	126_L	0.767	0.20
47_I	51_G	0.759	0.20
27_C	47_I	0.758	0.20
64_S	122_T	0.749	0.20
41_G	54_V	0.744	0.20
4_R	124_K	0.742	0.19
55_D	59_A	0.739	0.19
10_R	71_A	0.738	0.19
53_R	94_E	0.724	0.19
6_S	67_L	0.722	0.19
68_V	81_A	0.720	0.19
10_R	120_I	0.719	0.19
117_G	124_K	0.718	0.19
13_I	69_E	0.715	0.19
9_A	122_T	0.715	0.19
92_V	127_A	0.711	0.18
49_D	52_S	0.709	0.18
4_R	15_V	0.705	0.18
4_R	24_A	0.702	0.18
48_G	84_P	0.692	0.18
6_S	28_L	0.682	0.18
21_D	63_R	0.682	0.18
125_E	138_L	0.680	0.18
37_V	41_G	0.675	0.17
54_V	75_E	0.670	0.17
3_I	133_I	0.667	0.17
36_Y	57_L	0.666	0.17
53_R	133_I	0.662	0.17
35_V	132_D	0.657	0.17
14_A	81_A	0.654	0.17
113_I	117_G	0.653	0.17
43_M	133_I	0.647	0.17
18_T	61_L	0.643	0.16
25_V	118_T	0.641	0.16
58_E	124_K	0.638	0.16
98_T	133_I	0.631	0.16
28_L	119_N	0.630	0.16
110_G	122_T	0.628	0.16
44_G	48_G	0.627	0.16
11_Q	137_Q	0.625	0.16
11_Q	32_D	0.624	0.16
92_V	95_N	0.622	0.16
127_A	133_I	0.621	0.16
64_S	73_T	0.619	0.16
10_R	15_V	0.617	0.16
37_V	69_E	0.616	0.16
37_V	126_L	0.607	0.15
6_S	79_A	0.607	0.15
86_A	127_A	0.605	0.15
36_Y	61_L	0.604	0.15
94_E	116_D	0.604	0.15
53_R	62_G	0.602	0.15
15_V	57_L	0.599	0.15
16_F	107_E	0.599	0.15
85_A	123_A	0.594	0.15
3_I	103_E	0.591	0.15
41_G	135_D	0.590	0.15
90_V	97_T	0.585	0.15
57_L	131_F	0.581	0.15
15_V	23_T	0.577	0.15
54_V	69_E	0.577	0.15
56_A	130_H	0.575	0.15
47_I	60_T	0.568	0.14
50_G	54_V	0.568	0.14
28_L	95_N	0.567	0.14
84_P	129_R	0.565	0.14
81_A	138_L	0.555	0.14
82_L	111_V	0.551	0.14
81_A	92_V	0.551	0.14
41_G	100_A	0.550	0.14
58_E	109_K	0.548	0.14
40_A	67_L	0.547	0.14
66_V	125_E	0.544	0.14
32_D	138_L	0.536	0.14
96_D	106_H	0.532	0.14
46_A	117_G	0.521	0.13
58_E	116_D	0.520	0.13
70_D	135_D	0.519	0.13
5_L	16_F	0.518	0.13
115_A	136_I	0.507	0.13
32_D	136_I	0.507	0.13
6_S	128_A	0.507	0.13
22_A	33_R	0.507	0.13
94_E	103_E	0.507	0.13
82_L	131_F	0.506	0.13
21_D	65_V	0.505	0.13
24_A	94_E	0.504	0.13
27_C	135_D	0.500	0.13

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
2cxcA	1	0.9712	100	0.36	Contact Map
2asbA	1	1	99.9	0.582	Contact Map
1k0rA	1	0.964	99.9	0.591	Contact Map
1hh2P	2	1	99.9	0.61	Contact Map
4mtnA	1	0.9856	99.9	0.616	Contact Map
2qndA	2	0.7482	99.1	0.768	Contact Map
3krmA	3	0.7842	98.6	0.808	Contact Map
1j4wA	1	0.7698	98.5	0.813	Contact Map
2anrA	1	0.7914	98.4	0.822	Contact Map
2jvzA	1	0.7842	98.4	0.823	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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