SIGO - BACSU - GREMLIN Contacts

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SIGO - RNA polymerase sigma factor SigO

UniProt:	O34843	Sequences: MKHPIVKHFLSNPQHYRLFKNVMESPNEKDARSLDELFKQFYKEIRIVKYMNSMIRIFSIDFDKRVRKNQKRYPLTVDHPEAGDRLSSETGSDAFEEFLDRQDDLSQHVQDYQLYQAIQKLTDKQKSVLTKVYLHGATMQEIADSLGESRQNISNIHKKGLENIRKQLAAQKKGEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	176 (167)
Sequences:	108 (106)
Seq/√Len:	8.2

BACSU - SIGO

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
133_Y	157_H	5.393	1.00
26_P	30_D	3.164	0.91
63_D	67_R	2.897	0.86
148_E	152_N	2.893	0.86
150_R	155_N	2.842	0.85
122_T	153_I	2.626	0.80
43_K	47_I	2.555	0.78
35_D	39_K	2.507	0.77
139_M	150_R	2.478	0.76
109_V	118_I	2.428	0.74
152_N	155_N	2.334	0.71
58_F	61_D	2.064	0.61
125_Q	133_Y	2.039	0.60
61_D	64_K	2.027	0.60
15_H	23_M	1.951	0.57
152_N	156_I	1.950	0.57
125_Q	157_H	1.930	0.56
15_H	18_L	1.893	0.54
3_H	161_L	1.859	0.53
54_M	139_M	1.843	0.52
59_S	161_L	1.768	0.49
62_F	67_R	1.765	0.49
56_R	159_K	1.757	0.49
55_I	111_D	1.707	0.47
160_G	163_N	1.696	0.46
148_E	153_I	1.695	0.46
51_M	62_F	1.692	0.46
39_K	45_I	1.685	0.46
50_Y	59_S	1.681	0.45
54_M	59_S	1.663	0.45
60_I	111_D	1.624	0.43
139_M	155_N	1.599	0.42
149_S	152_N	1.586	0.42
139_M	152_N	1.579	0.41
132_V	139_M	1.572	0.41
111_D	136_G	1.570	0.41
45_I	164_I	1.484	0.38
141_E	150_R	1.462	0.37
60_I	133_Y	1.448	0.36
84_D	116_Q	1.433	0.36
61_D	155_N	1.420	0.35
46_R	142_I	1.409	0.35
42_Y	109_V	1.405	0.35
49_K	53_S	1.399	0.34
43_K	139_M	1.395	0.34
164_I	168_L	1.378	0.34
56_R	63_D	1.368	0.33
105_L	134_L	1.353	0.33
5_I	44_E	1.351	0.33
52_N	152_N	1.348	0.32
47_I	155_N	1.340	0.32
10_L	122_T	1.337	0.32
19_F	127_S	1.311	0.31
59_S	63_D	1.291	0.30
5_I	75_L	1.290	0.30
54_M	58_F	1.271	0.30
50_Y	146_L	1.266	0.30
15_H	73_Y	1.261	0.29
3_H	45_I	1.238	0.29
132_V	157_H	1.236	0.28
132_V	142_I	1.217	0.28
62_F	149_S	1.207	0.28
148_E	156_I	1.192	0.27
30_D	125_Q	1.185	0.27
140_Q	150_R	1.168	0.26
26_P	77_V	1.166	0.26
56_R	85_R	1.138	0.25
4_P	35_D	1.130	0.25
140_Q	154_S	1.123	0.25
54_M	152_N	1.118	0.25
16_Y	19_F	1.115	0.25
75_L	147_G	1.101	0.24
129_L	154_S	1.089	0.24
80_P	114_L	1.079	0.23
48_V	81_E	1.061	0.23
129_L	164_I	1.052	0.23
76_T	107_Q	1.052	0.23
7_K	78_D	1.051	0.23
18_L	35_D	1.046	0.23
126_K	155_N	1.042	0.22
8_H	41_F	1.039	0.22
110_Q	130_T	1.028	0.22
10_L	19_F	1.025	0.22
47_I	133_Y	1.025	0.22
55_I	140_Q	1.024	0.22
117_A	133_Y	0.988	0.21
33_S	165_R	0.981	0.21
25_S	105_L	0.981	0.21
50_Y	62_F	0.976	0.21
72_R	125_Q	0.964	0.20
7_K	72_R	0.963	0.20
14_Q	161_L	0.957	0.20
35_D	154_S	0.956	0.20
15_H	161_L	0.945	0.20
102_Q	153_I	0.933	0.19
128_V	156_I	0.932	0.19
43_K	125_Q	0.926	0.19
22_V	96_E	0.920	0.19
34_L	158_K	0.919	0.19
15_H	51_M	0.911	0.19
86_L	135_H	0.910	0.19
47_I	117_A	0.899	0.19
108_H	157_H	0.898	0.19
117_A	125_Q	0.881	0.18
142_I	150_R	0.881	0.18
53_S	130_T	0.877	0.18
47_I	72_R	0.875	0.18
54_M	61_D	0.862	0.18
34_L	131_K	0.862	0.18
121_L	125_Q	0.862	0.18
124_K	134_L	0.856	0.17
99_L	117_A	0.855	0.17
4_P	147_G	0.855	0.17
22_V	122_T	0.852	0.17
140_Q	156_I	0.851	0.17
56_R	65_R	0.844	0.17
106_S	149_S	0.835	0.17
89_E	154_S	0.833	0.17
80_P	131_K	0.817	0.17
27_N	30_D	0.816	0.17
75_L	164_I	0.809	0.16
25_S	96_E	0.805	0.16
59_S	117_A	0.799	0.16
19_F	139_M	0.797	0.16
33_S	118_I	0.791	0.16
19_F	43_K	0.782	0.16
119_Q	147_G	0.779	0.16
25_S	114_L	0.772	0.16
118_I	137_A	0.769	0.16
62_F	142_I	0.768	0.15
3_H	52_N	0.768	0.15
34_L	155_N	0.762	0.15
14_Q	55_I	0.757	0.15
20_K	86_L	0.756	0.15
43_K	155_N	0.754	0.15
148_E	155_N	0.752	0.15
34_L	41_F	0.746	0.15
46_R	152_N	0.745	0.15
36_E	111_D	0.742	0.15
131_K	157_H	0.734	0.15
55_I	125_Q	0.733	0.15
26_P	122_T	0.729	0.15
10_L	26_P	0.727	0.15
54_M	129_L	0.724	0.15
35_D	54_M	0.721	0.14
21_N	128_V	0.718	0.14
3_H	46_R	0.716	0.14
48_V	153_I	0.716	0.14
44_E	127_S	0.714	0.14
46_R	159_K	0.711	0.14
53_S	156_I	0.710	0.14
29_K	168_L	0.701	0.14
29_K	93_D	0.700	0.14
3_H	8_H	0.699	0.14
5_I	32_R	0.690	0.14
5_I	9_F	0.690	0.14
68_K	128_V	0.688	0.14
37_L	97_E	0.687	0.14
153_I	156_I	0.685	0.14
42_Y	59_S	0.685	0.14
6_V	147_G	0.684	0.14
122_T	125_Q	0.678	0.14
33_S	45_I	0.675	0.14
36_E	97_E	0.675	0.14
64_K	157_H	0.675	0.14
31_A	35_D	0.668	0.13
8_H	12_N	0.663	0.13
58_F	152_N	0.661	0.13
20_K	39_K	0.659	0.13
100_D	167_Q	0.659	0.13
26_P	64_K	0.653	0.13
25_S	44_E	0.653	0.13
125_Q	155_N	0.652	0.13
13_P	41_F	0.650	0.13
47_I	139_M	0.649	0.13
109_V	112_Y	0.648	0.13
5_I	23_M	0.647	0.13
21_N	25_S	0.647	0.13
52_N	81_E	0.643	0.13
100_D	153_I	0.639	0.13
145_S	155_N	0.635	0.13
65_R	128_V	0.634	0.13
29_K	160_G	0.634	0.13
49_K	77_V	0.634	0.13
88_S	136_G	0.634	0.13
79_H	114_L	0.629	0.13
117_A	158_K	0.627	0.13
39_K	63_D	0.626	0.13
49_K	132_V	0.620	0.13
49_K	163_N	0.620	0.13
52_N	89_E	0.619	0.13
7_K	57_I	0.612	0.12
32_R	144_D	0.609	0.12
59_S	140_Q	0.608	0.12
8_H	15_H	0.607	0.12
57_I	109_V	0.602	0.12
88_S	143_A	0.601	0.12
102_Q	107_Q	0.600	0.12
42_Y	73_Y	0.599	0.12
137_A	141_E	0.598	0.12
117_A	168_L	0.597	0.12
80_P	84_D	0.594	0.12
77_V	137_A	0.593	0.12
123_D	144_D	0.592	0.12
107_Q	137_A	0.589	0.12
6_V	163_N	0.589	0.12
19_F	30_D	0.589	0.12
19_F	153_I	0.587	0.12
42_Y	93_D	0.583	0.12
39_K	104_D	0.579	0.12
117_A	121_L	0.570	0.12
24_E	115_Y	0.569	0.12
37_L	85_R	0.568	0.12
59_S	105_L	0.565	0.12
41_F	136_G	0.565	0.12
118_I	164_I	0.565	0.12
120_K	128_V	0.562	0.12
130_T	135_H	0.561	0.11
28_E	123_D	0.560	0.11
105_L	135_H	0.557	0.11
107_Q	139_M	0.549	0.11
5_I	107_Q	0.546	0.11
75_L	80_P	0.542	0.11
51_M	70_Q	0.542	0.11
3_H	110_Q	0.542	0.11
114_L	144_D	0.541	0.11
57_I	131_K	0.538	0.11
26_P	129_L	0.537	0.11
34_L	165_R	0.532	0.11
78_D	159_K	0.529	0.11
69_N	75_L	0.524	0.11
13_P	40_Q	0.524	0.11
84_D	125_Q	0.524	0.11
63_D	105_L	0.523	0.11
46_R	156_I	0.522	0.11
27_N	77_V	0.521	0.11
53_S	149_S	0.519	0.11
47_I	152_N	0.516	0.11
111_D	164_I	0.515	0.11
145_S	161_L	0.512	0.11
46_R	140_Q	0.511	0.11
59_S	150_R	0.510	0.11
132_V	140_Q	0.510	0.11
24_E	124_K	0.509	0.11
10_L	136_G	0.508	0.11
61_D	117_A	0.507	0.11
49_K	59_S	0.504	0.11
62_F	84_D	0.502	0.11
47_I	59_S	0.502	0.11
143_A	151_Q	0.500	0.11

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
4yfkF	1	0.9318	99.3	0.766	Contact Map
1l0oC	1	0.0511	99.3	0.769	Contact Map
4cxfA	1	0.7386	99.3	0.771	Contact Map
1rp3A	1	0.9091	99.2	0.773	Contact Map
4nqwA	1	0.7273	99.2	0.774	Contact Map
2a6hF	1	0.9091	99.2	0.779	Contact Map
1l9zH	1	0.8864	99.2	0.779	Contact Map
3mzyA	1	0.6761	99.2	0.779	Contact Map
1or7A	2	0.8977	99.2	0.779	Contact Map
2q1zA	1	0.8352	99.2	0.782	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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