Sigma_reg_N - PFAM28P - GREMLIN Contacts

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Sigma_reg_N - Sigma factor regulator N-terminal

PFAM:	PF13800	Sequences: KKILKKAKRKSRLRTILISLIVFLILLIILIITNNYYTSKRSNKLRDVISLAIEITEPNIYIDSGSTDNTGFFGGTIEYDLYKNIGGKPV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	90 (88)
Sequences:	528 (420)
Seq/√Len:	44.8
META:	0.424

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_K	9_R	3.910	1.00
33_T	37_Y	3.736	1.00
23_F	27_L	3.458	1.00
23_F	26_L	3.204	1.00
24_L	28_I	2.689	1.00
59_N	83_K	2.552	1.00
40_K	66_S	2.240	1.00
8_K	12_R	2.225	1.00
70_T	76_T	2.057	0.99
11_S	14_R	1.944	0.99
34_N	41_R	1.912	0.99
83_K	87_G	1.883	0.99
9_R	12_R	1.844	0.99
64_S	82_Y	1.540	0.96
64_S	69_N	1.512	0.95
16_I	19_S	1.502	0.95
71_G	75_G	1.495	0.95
37_Y	73_F	1.491	0.95
41_R	44_K	1.488	0.95
16_I	53_I	1.462	0.95
12_R	21_I	1.328	0.91
54_E	57_E	1.254	0.88
50_S	77_I	1.227	0.87
39_S	44_K	1.203	0.86
8_K	85_I	1.199	0.86
18_I	22_V	1.168	0.85
20_L	25_I	1.166	0.85
14_R	67_T	1.151	0.84
45_L	54_E	1.147	0.84
11_S	78_E	1.146	0.83
5_K	12_R	1.145	0.83
13_L	21_I	1.140	0.83
31_I	35_N	1.138	0.83
64_S	68_D	1.135	0.83
16_I	22_V	1.131	0.83
60_I	81_L	1.099	0.81
17_L	24_L	1.069	0.79
53_I	57_E	1.068	0.79
22_V	52_A	1.040	0.77
41_R	45_L	1.037	0.77
16_I	23_F	1.023	0.76
2_K	28_I	1.018	0.75
48_V	52_A	1.004	0.74
16_I	44_K	1.002	0.74
42_S	71_G	0.995	0.74
53_I	86_G	0.988	0.73
53_I	56_T	0.977	0.72
9_R	20_L	0.973	0.72
51_L	55_I	0.956	0.71
76_T	79_Y	0.938	0.69
19_S	87_G	0.932	0.69
52_A	55_I	0.924	0.68
55_I	83_K	0.922	0.68
10_K	85_I	0.907	0.67
2_K	9_R	0.906	0.67
42_S	75_G	0.897	0.66
81_L	87_G	0.887	0.65
12_R	15_T	0.876	0.64
25_I	72_F	0.864	0.63
80_D	83_K	0.862	0.63
2_K	23_F	0.859	0.62
44_K	60_I	0.850	0.62
56_T	65_G	0.843	0.61
53_I	81_L	0.840	0.61
7_A	14_R	0.834	0.60
14_R	18_I	0.826	0.59
6_K	29_I	0.812	0.58
3_I	42_S	0.810	0.58
26_L	80_D	0.785	0.55
51_L	54_E	0.784	0.55
15_T	74_G	0.782	0.55
8_K	70_T	0.781	0.55
3_I	7_A	0.771	0.54
23_F	31_I	0.759	0.53
4_L	7_A	0.736	0.51
50_S	65_G	0.731	0.50
29_I	36_Y	0.714	0.49
11_S	88_K	0.708	0.48
33_T	36_Y	0.707	0.48
8_K	75_G	0.699	0.47
14_R	19_S	0.698	0.47
13_L	47_D	0.693	0.47
46_R	50_S	0.691	0.46
24_L	63_D	0.687	0.46
43_N	68_D	0.669	0.44
32_I	36_Y	0.664	0.44
34_N	38_T	0.663	0.44
16_I	20_L	0.659	0.43
25_I	38_T	0.649	0.42
43_N	78_E	0.648	0.42
11_S	85_I	0.643	0.42
18_I	21_I	0.643	0.42
50_S	54_E	0.642	0.42
32_I	42_S	0.621	0.40
9_R	14_R	0.618	0.39
77_I	85_I	0.618	0.39
13_L	64_S	0.616	0.39
14_R	61_Y	0.610	0.39
46_R	77_I	0.609	0.39
47_D	51_L	0.609	0.39
35_N	82_Y	0.603	0.38
35_N	89_P	0.600	0.38
41_R	56_T	0.596	0.37
30_L	77_I	0.582	0.36
20_L	62_I	0.578	0.36
17_L	25_I	0.578	0.36
17_L	21_I	0.575	0.36
3_I	40_K	0.570	0.35
46_R	71_G	0.564	0.35
54_E	74_G	0.561	0.34
23_F	32_I	0.560	0.34
84_N	88_K	0.559	0.34
65_G	68_D	0.557	0.34
69_N	82_Y	0.553	0.34
7_A	86_G	0.550	0.33
56_T	84_N	0.544	0.33
41_R	51_L	0.537	0.32
84_N	89_P	0.536	0.32
47_D	61_Y	0.532	0.32
7_A	34_N	0.526	0.31
60_I	74_G	0.525	0.31
49_I	84_N	0.524	0.31
16_I	26_L	0.524	0.31
56_T	87_G	0.522	0.31
27_L	40_K	0.519	0.31
84_N	87_G	0.519	0.31
4_L	56_T	0.513	0.30
39_S	42_S	0.511	0.30
71_G	81_L	0.509	0.30
13_L	89_P	0.505	0.30
48_V	89_P	0.502	0.29
10_K	84_N	0.500	0.29

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
2kogA	1	0.4333	71.4	0.798	Contact Map
1rz2A	1	0.5333	52.2	0.821	Contact Map
3hd7A	1	0.4333	50.8	0.822	Contact Map
2m8rA	1	0.4111	22.2	0.854	Contact Map
2e84A	1	0.5556	15	0.865	Contact Map
4v3iA	2	0	11.2	0.872	Contact Map
3fymA	1	0	10.9	0.873	Contact Map
3j6dA	3	0.4778	10.2	0.874	Contact Map
3j39U	1	0.4556	8.9	0.877	Contact Map
2bs2C	2	0.6333	7.3	0.882	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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