IOJAP - BACSU - GREMLIN Contacts

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IOJAP - Ribosomal silencing factor RsfS

UniProt:	P54457	Sequences: MNQKSILKIAAAACDDKRAEDILALDMEGISLVADYFLICHGNSDKQVQAIAREIKDQADENGIQVKKMEGFDEARWVLVDLGDVVVHVFHKDERSYYNLEKLWGDAPLADLDFGMNQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	118 (106)
Sequences:	3242 (2028)
Seq/√Len:	197.0

ECOLI - IOJAP
BACSU - IOJAP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_C	51_I	2.978	1.00
14_C	19_A	2.787	1.00
99_N	102_K	2.493	1.00
58_Q	61_E	2.347	1.00
19_A	40_C	2.287	1.00
22_I	40_C	2.165	1.00
9_I	62_N	2.076	1.00
42_G	48_V	2.059	1.00
76_R	94_E	2.037	1.00
54_E	58_Q	1.799	1.00
59_A	82_L	1.752	1.00
66_V	82_L	1.576	1.00
27_M	34_A	1.572	1.00
14_C	55_I	1.540	1.00
76_R	91_H	1.534	1.00
70_E	79_L	1.503	1.00
7_L	11_A	1.498	1.00
9_I	13_A	1.485	1.00
14_C	40_C	1.480	1.00
69_M	80_V	1.435	1.00
15_D	22_I	1.435	1.00
56_K	69_M	1.405	1.00
25_L	107_A	1.337	1.00
72_F	78_V	1.335	1.00
52_A	78_V	1.328	1.00
60_D	65_Q	1.327	1.00
91_H	94_E	1.325	1.00
10_A	82_L	1.321	1.00
57_D	61_E	1.294	1.00
11_A	15_D	1.271	1.00
27_M	31_S	1.264	1.00
6_I	59_A	1.233	1.00
55_I	87_V	1.229	1.00
39_I	100_L	1.228	1.00
7_L	38_L	1.223	1.00
96_S	99_N	1.221	1.00
21_D	41_H	1.210	1.00
10_A	87_V	1.209	1.00
43_N	47_Q	1.206	1.00
24_A	38_L	1.198	1.00
10_A	85_V	1.191	1.00
7_L	36_Y	1.191	1.00
40_C	89_V	1.184	1.00
6_I	64_I	1.182	1.00
17_K	54_E	1.179	1.00
23_L	109_L	1.170	1.00
59_A	64_I	1.163	1.00
67_K	83_G	1.160	1.00
72_F	75_A	1.151	1.00
48_V	89_V	1.146	1.00
53_R	72_F	1.133	1.00
48_V	91_H	1.131	1.00
38_L	85_V	1.114	1.00
20_E	43_N	1.108	1.00
7_L	24_A	1.093	1.00
19_A	51_I	1.084	1.00
75_A	78_V	1.077	1.00
51_I	89_V	1.076	1.00
79_L	86_V	1.056	1.00
49_Q	72_F	1.053	1.00
47_Q	50_A	1.051	1.00
49_Q	75_A	1.040	1.00
10_A	38_L	1.035	1.00
54_E	57_D	1.026	1.00
11_A	22_I	1.026	1.00
5_S	8_K	1.023	1.00
13_A	55_I	1.022	1.00
42_G	51_I	1.019	1.00
24_A	36_Y	1.007	1.00
13_A	54_E	1.005	1.00
52_A	89_V	1.002	1.00
44_S	47_Q	0.987	1.00
11_A	24_A	0.986	1.00
56_K	80_V	0.986	1.00
58_Q	62_N	0.978	0.99
41_H	92_K	0.962	0.99
23_L	101_E	0.941	0.99
6_I	85_V	0.935	0.99
8_K	11_A	0.932	0.99
30_I	107_A	0.929	0.99
16_D	54_E	0.919	0.99
20_E	41_H	0.918	0.99
8_K	12_A	0.913	0.99
13_A	58_Q	0.883	0.99
7_L	85_V	0.873	0.99
92_K	96_S	0.870	0.99
28_E	36_Y	0.866	0.99
34_A	86_V	0.861	0.99
10_A	59_A	0.851	0.99
43_N	92_K	0.848	0.99
26_D	108_P	0.845	0.98
45_D	49_Q	0.838	0.98
48_V	78_V	0.837	0.98
57_D	60_D	0.833	0.98
38_L	87_V	0.825	0.98
101_E	104_W	0.803	0.98
48_V	75_A	0.799	0.98
37_F	88_H	0.775	0.97
20_E	92_K	0.770	0.97
22_I	38_L	0.760	0.97
17_K	51_I	0.753	0.97
45_D	91_H	0.744	0.97
5_S	9_I	0.736	0.96
12_A	16_D	0.732	0.96
59_A	85_V	0.728	0.96
12_A	58_Q	0.717	0.96
56_K	72_F	0.715	0.96
26_D	29_G	0.714	0.96
82_L	87_V	0.682	0.95
9_I	58_Q	0.667	0.94
16_D	58_Q	0.661	0.94
56_K	82_L	0.655	0.93
46_K	49_Q	0.654	0.93
79_L	97_Y	0.650	0.93
9_I	12_A	0.649	0.93
52_A	72_F	0.646	0.93
17_K	37_F	0.644	0.93
35_D	84_D	0.639	0.92
26_D	110_A	0.637	0.92
17_K	90_F	0.630	0.92
29_G	108_P	0.630	0.92
33_V	86_V	0.629	0.92
13_A	17_K	0.625	0.92
25_L	39_I	0.612	0.91
37_F	86_V	0.612	0.91
39_I	101_E	0.608	0.90
17_K	50_A	0.602	0.90
47_Q	51_I	0.600	0.90
17_K	47_Q	0.599	0.90
76_R	93_D	0.597	0.90
25_L	105_G	0.597	0.90
11_A	14_C	0.594	0.89
25_L	37_F	0.594	0.89
33_V	88_H	0.583	0.89
42_G	89_V	0.579	0.88
41_H	48_V	0.574	0.88
41_H	46_K	0.573	0.88
40_C	51_I	0.573	0.88
42_G	47_Q	0.564	0.87
77_W	81_D	0.564	0.87
34_A	85_V	0.557	0.86
35_D	70_E	0.557	0.86
34_A	37_F	0.554	0.86
90_F	101_E	0.553	0.86
25_L	30_I	0.550	0.86
27_M	32_L	0.549	0.85
102_K	106_D	0.536	0.84
66_V	69_M	0.536	0.84
64_I	84_D	0.535	0.84
42_G	91_H	0.527	0.83
41_H	91_H	0.514	0.81
43_N	90_F	0.514	0.81
21_D	96_S	0.510	0.81
6_I	10_A	0.508	0.81
32_L	104_W	0.507	0.81
71_G	78_V	0.506	0.80
9_I	64_I	0.506	0.80
45_D	76_R	0.500	0.80
18_R	43_N	0.500	0.80

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
2o5aA	2	0.9153	100	0.056	Contact Map
2id1A	1	1	100	0.075	Contact Map
4wcwA	2	0.9661	100	0.075	Contact Map
3upsA	2	0.9153	100	0.092	Contact Map
2qipA	2	0.7542	23.5	0.925	Contact Map
3w34A	2	0.5424	18.5	0.929	Contact Map
4oxxA	1	0.9322	18.4	0.929	Contact Map
1e5dA	2	0.9407	16.2	0.931	Contact Map
2wp4A	2	0.6102	14.6	0.932	Contact Map
2hnaA	1	0.9407	14.1	0.933	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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