Sigma_reg_C - PFAM28P - GREMLIN Contacts

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Sigma_reg_C - Sigma factor regulator C-terminal

PFAM:	PF13791	Sequences: LEKLPEGTVAEVAISFDKPYTLEEVQKLLKPKNLDIVWYWVDTGSEDEDEEYKLISEGDVIGFPPSPSNGDDDPKEKYPSEEREEHFISALKYLKDNEEFAKKLAEDLDGYKDLKERLDYLKKNGVKIYGVVVTGPTEELLKLKNEPWIRAASLGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	156 (153)
Sequences:	778 (637)
Seq/√Len:	51.5
META:	0.447

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_D	20_Y	6.868	1.00
21_T	24_E	4.376	1.00
10_A	137_T	3.819	1.00
136_P	139_E	3.361	1.00
11_E	155_G	2.698	1.00
41_V	87_F	2.473	1.00
14_I	133_V	2.348	1.00
115_K	119_D	2.337	1.00
114_L	118_L	2.332	1.00
38_W	62_G	2.119	1.00
2_E	141_L	2.077	1.00
16_F	131_V	2.026	1.00
149_I	152_A	1.949	1.00
138_E	141_L	1.931	0.99
120_Y	124_N	1.850	0.99
78_Y	81_E	1.848	0.99
91_L	94_L	1.839	0.99
28_L	146_E	1.792	0.99
16_F	20_Y	1.745	0.99
22_L	84_E	1.725	0.99
38_W	43_T	1.715	0.99
6_E	138_E	1.702	0.99
92_K	122_K	1.684	0.99
11_E	132_V	1.661	0.98
135_G	155_G	1.635	0.98
36_I	39_Y	1.635	0.98
78_Y	82_E	1.628	0.98
87_F	91_L	1.624	0.98
44_G	129_Y	1.608	0.98
76_E	81_E	1.602	0.98
120_Y	125_G	1.593	0.98
12_V	140_L	1.534	0.97
13_A	16_F	1.533	0.97
72_D	75_K	1.464	0.96
39_Y	42_D	1.455	0.96
121_L	125_G	1.452	0.96
9_V	136_P	1.420	0.96
2_E	5_P	1.394	0.95
61_I	91_L	1.356	0.94
15_S	41_V	1.341	0.94
70_G	73_D	1.334	0.94
11_E	135_G	1.332	0.94
133_V	140_L	1.327	0.94
86_H	90_A	1.317	0.94
7_G	143_L	1.306	0.93
40_W	129_Y	1.284	0.93
21_T	78_Y	1.273	0.92
11_E	15_S	1.256	0.92
19_P	129_Y	1.251	0.92
24_E	27_K	1.247	0.91
107_D	111_Y	1.231	0.91
114_L	117_R	1.225	0.91
68_S	74_P	1.206	0.90
14_I	33_N	1.196	0.90
152_A	155_G	1.191	0.89
12_V	149_I	1.187	0.89
6_E	28_L	1.162	0.88
134_T	137_T	1.147	0.88
11_E	20_Y	1.126	0.87
7_G	120_Y	1.122	0.86
40_W	132_V	1.121	0.86
118_L	121_L	1.113	0.86
118_L	122_K	1.111	0.86
13_A	132_V	1.104	0.86
20_Y	25_V	1.087	0.85
6_E	9_V	1.085	0.85
77_K	82_E	1.074	0.84
89_S	93_Y	1.057	0.83
102_K	109_D	1.049	0.83
89_S	103_K	1.046	0.82
41_V	126_V	1.041	0.82
43_T	91_L	1.028	0.81
40_W	125_G	1.024	0.81
9_V	137_T	1.002	0.80
37_V	63_F	0.992	0.79
61_I	94_L	0.991	0.79
13_A	40_W	0.988	0.79
77_K	80_S	0.985	0.78
13_A	155_G	0.984	0.78
10_A	140_L	0.964	0.77
76_E	79_P	0.960	0.77
34_L	133_V	0.947	0.76
79_P	82_E	0.945	0.75
13_A	140_L	0.935	0.75
50_E	53_K	0.924	0.74
4_L	8_T	0.919	0.73
85_E	150_R	0.916	0.73
100_F	103_K	0.910	0.73
11_E	83_R	0.900	0.72
127_K	147_P	0.894	0.71
128_I	150_R	0.891	0.71
85_E	88_I	0.889	0.71
90_A	93_Y	0.888	0.71
14_I	131_V	0.880	0.70
110_G	128_I	0.876	0.70
38_W	149_I	0.875	0.70
86_H	93_Y	0.871	0.69
40_W	136_P	0.867	0.69
69_N	72_D	0.866	0.69
132_V	135_G	0.864	0.69
100_F	104_L	0.858	0.68
22_L	26_Q	0.854	0.68
20_Y	128_I	0.840	0.66
39_Y	65_P	0.839	0.66
44_G	117_R	0.829	0.65
94_L	126_V	0.820	0.65
29_L	139_E	0.819	0.64
65_P	90_A	0.805	0.63
108_L	149_I	0.804	0.63
70_G	74_P	0.802	0.63
20_Y	155_G	0.782	0.61
5_P	8_T	0.782	0.61
43_T	154_L	0.781	0.61
38_W	114_L	0.778	0.60
48_E	51_E	0.775	0.60
83_R	155_G	0.773	0.60
18_K	27_K	0.772	0.60
25_V	29_L	0.769	0.60
15_S	129_Y	0.767	0.59
13_A	122_K	0.762	0.59
97_N	115_K	0.761	0.59
18_K	24_E	0.759	0.59
10_A	39_Y	0.758	0.58
92_K	95_K	0.753	0.58
15_S	135_G	0.753	0.58
42_D	131_V	0.749	0.58
42_D	132_V	0.737	0.56
14_I	117_R	0.735	0.56
91_L	118_L	0.734	0.56
16_F	149_I	0.730	0.56
31_P	139_E	0.730	0.56
2_E	31_P	0.728	0.55
9_V	37_V	0.725	0.55
121_L	124_N	0.724	0.55
93_Y	97_N	0.722	0.55
69_N	74_P	0.720	0.55
87_F	121_L	0.715	0.54
104_L	107_D	0.714	0.54
103_K	124_N	0.703	0.53
67_P	72_D	0.701	0.53
41_V	63_F	0.701	0.53
22_L	39_Y	0.699	0.52
12_V	152_A	0.698	0.52
55_I	58_G	0.692	0.52
94_L	98_E	0.691	0.52
92_K	96_D	0.690	0.51
20_Y	28_L	0.686	0.51
25_V	131_V	0.686	0.51
36_I	131_V	0.684	0.51
15_S	47_D	0.674	0.50
87_F	90_A	0.669	0.49
23_E	46_E	0.666	0.49
29_L	143_L	0.663	0.49
130_G	140_L	0.657	0.48
40_W	45_S	0.657	0.48
125_G	129_Y	0.654	0.48
66_S	70_G	0.654	0.48
139_E	142_K	0.648	0.47
63_F	126_V	0.643	0.47
49_D	53_K	0.641	0.46
106_E	109_D	0.631	0.45
8_T	136_P	0.631	0.45
64_P	114_L	0.625	0.45
65_P	96_D	0.624	0.45
117_R	120_Y	0.621	0.44
77_K	81_E	0.620	0.44
11_E	134_T	0.619	0.44
45_S	49_D	0.617	0.44
103_K	109_D	0.616	0.44
25_V	28_L	0.616	0.44
105_A	109_D	0.615	0.44
54_L	57_E	0.614	0.44
31_P	34_L	0.613	0.43
59_D	124_N	0.612	0.43
7_G	24_E	0.610	0.43
14_I	152_A	0.609	0.43
34_L	140_L	0.606	0.43
41_V	128_I	0.600	0.42
41_V	146_E	0.600	0.42
107_D	110_G	0.600	0.42
69_N	73_D	0.599	0.42
38_W	134_T	0.593	0.41
92_K	149_I	0.593	0.41
31_P	155_G	0.590	0.41
37_V	40_W	0.587	0.41
7_G	136_P	0.585	0.41
125_G	141_L	0.581	0.40
134_T	144_K	0.580	0.40
45_S	142_K	0.580	0.40
128_I	132_V	0.577	0.40
22_L	126_V	0.576	0.40
120_Y	154_L	0.575	0.40
8_T	137_T	0.574	0.40
25_V	90_A	0.574	0.40
88_I	95_K	0.572	0.39
51_E	116_E	0.572	0.39
29_L	134_T	0.568	0.39
116_E	119_D	0.567	0.39
44_G	124_N	0.566	0.39
61_I	117_R	0.564	0.39
15_S	42_D	0.561	0.38
74_P	79_P	0.560	0.38
42_D	150_R	0.554	0.38
33_N	144_K	0.552	0.37
101_A	140_L	0.549	0.37
68_S	71_D	0.547	0.37
4_L	129_Y	0.543	0.36
122_K	125_G	0.540	0.36
2_E	26_Q	0.539	0.36
114_L	124_N	0.536	0.36
55_I	59_D	0.535	0.36
117_R	122_K	0.534	0.36
137_T	153_S	0.533	0.36
14_I	49_D	0.531	0.35
37_V	134_T	0.531	0.35
36_I	148_W	0.529	0.35
4_L	114_L	0.528	0.35
141_L	149_I	0.526	0.35
118_L	124_N	0.525	0.35
36_I	63_F	0.524	0.35
84_E	141_L	0.520	0.34
13_A	152_A	0.514	0.34
117_R	125_G	0.512	0.34
101_A	108_L	0.511	0.33
28_L	126_V	0.511	0.33
94_L	125_G	0.510	0.33
90_A	125_G	0.507	0.33
48_E	99_E	0.506	0.33
72_D	89_S	0.505	0.33
137_T	143_L	0.500	0.32

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
2q1zA	1	0.3269	15.9	0.92	Contact Map
3edyA	1	0.7308	14.8	0.921	Contact Map
4jwhA	1	0.8526	11.6	0.925	Contact Map
3whiA	2	0.391	9.5	0.928	Contact Map
2z30B	1	0.3718	8.9	0.929	Contact Map
3pmcA	2	0.4167	8.9	0.929	Contact Map
3o3mA	1	0.359	8.1	0.93	Contact Map
2ki0A	1	0.2115	7.8	0.931	Contact Map
3pmdA	2	0.4615	7.8	0.931	Contact Map
3afgA	1	0.5449	6.7	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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