YLAC - BACSU - GREMLIN Contacts

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YLAC - RNA polymerase sigma factor YlaC

UniProt:	O07627	Sequences: MKHRDSIEDLYRQYYQEILNYLFRRTHHLETAKDLAQDTFVKALNGLASFRGHSSIRTWLYTIAHHTFINWYRRDVKYQFTEISKNEGLTQTTYDQPEQYLSRTVKSETLRQELLKLKDQHQSVLILREFQELSYEEIAEILGWSLSKVNTTLHRARLELKKNMTKSREEERI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	173 (158)
Sequences:	40727 (30663)
Seq/√Len:	2439.4

ECOLI - FECI RPOE
BACSU - YLAC SIGW SIGX SIGM SIGY SIGV SIGZ RPSH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_K	67_T	3.226	1.00
128_R	138_I	2.775	1.00
17_E	57_R	2.477	1.00
136_E	146_L	2.357	1.00
116_K	163_N	2.321	1.00
121_H	159_E	2.269	1.00
65_H	69_I	2.202	1.00
113_E	163_N	2.138	1.00
22_L	64_A	2.006	1.00
133_L	141_I	1.972	1.00
120_Q	152_T	1.967	1.00
39_T	64_A	1.925	1.00
147_S	150_N	1.785	1.00
21_Y	61_Y	1.715	1.00
70_N	73_R	1.713	1.00
145_S	148_K	1.705	1.00
30_E	33_K	1.695	1.00
46_G	49_S	1.694	1.00
67_T	70_N	1.676	1.00
31_T	71_W	1.658	1.00
55_S	58_T	1.633	1.00
144_W	152_T	1.632	1.00
121_H	152_T	1.613	1.00
8_E	12_R	1.612	1.00
134_S	137_E	1.607	1.00
25_R	68_F	1.570	1.00
135_Y	146_L	1.549	1.00
43_A	60_L	1.549	1.00
154_H	158_L	1.539	1.00
118_K	121_H	1.533	1.00
127_L	141_I	1.517	1.00
23_F	29_L	1.495	1.00
42_K	70_N	1.492	1.00
66_H	69_I	1.490	1.00
9_D	13_Q	1.477	1.00
129_E	157_R	1.475	1.00
38_D	67_T	1.472	1.00
148_K	152_T	1.467	1.00
135_Y	153_L	1.463	1.00
144_W	149_V	1.452	1.00
135_Y	150_N	1.442	1.00
17_E	61_Y	1.436	1.00
28_H	31_T	1.424	1.00
159_E	163_N	1.415	1.00
35_L	71_W	1.394	1.00
18_I	64_A	1.363	1.00
148_K	151_T	1.341	1.00
127_L	133_L	1.335	1.00
22_L	68_F	1.328	1.00
122_Q	126_I	1.326	1.00
62_T	65_H	1.324	1.00
14_Y	57_R	1.314	1.00
146_L	150_N	1.310	1.00
151_T	154_H	1.306	1.00
57_R	61_Y	1.297	1.00
41_V	45_N	1.280	1.00
42_K	46_G	1.276	1.00
124_V	153_L	1.266	1.00
14_Y	40_F	1.264	1.00
62_T	66_H	1.260	1.00
124_V	156_A	1.240	1.00
115_L	122_Q	1.237	1.00
124_V	152_T	1.234	1.00
151_T	155_R	1.214	1.00
39_T	63_I	1.203	1.00
19_L	29_L	1.199	1.00
19_L	23_F	1.189	1.00
35_L	67_T	1.183	1.00
26_T	68_F	1.173	1.00
136_E	140_E	1.167	1.00
31_T	75_D	1.160	1.00
11_Y	15_Y	1.155	1.00
50_F	53_H	1.155	1.00
121_H	156_A	1.144	1.00
11_Y	40_F	1.144	1.00
22_L	36_A	1.120	1.00
128_R	135_Y	1.112	1.00
133_L	137_E	1.106	1.00
102_S	105_V	1.103	1.00
26_T	35_L	1.102	1.00
22_L	35_L	1.100	1.00
7_I	44_L	1.090	1.00
129_E	153_L	1.088	1.00
29_L	33_K	1.084	1.00
71_W	75_D	1.074	1.00
21_Y	65_H	1.059	1.00
153_L	157_R	1.048	1.00
147_S	151_T	1.047	1.00
138_I	149_V	1.037	1.00
69_I	72_Y	1.036	1.00
15_Y	19_L	1.027	1.00
68_F	72_Y	1.026	1.00
18_I	36_A	1.019	1.00
135_Y	149_V	1.018	1.00
19_L	33_K	1.010	1.00
39_T	67_T	1.004	1.00
67_T	71_W	1.003	1.00
14_Y	60_L	0.994	1.00
19_L	36_A	0.984	1.00
74_R	77_K	0.971	1.00
126_I	130_F	0.968	1.00
147_S	154_H	0.959	1.00
18_I	60_L	0.951	1.00
121_H	124_V	0.950	1.00
119_D	123_S	0.949	1.00
54_S	58_T	0.941	1.00
126_I	131_Q	0.939	1.00
113_E	160_L	0.935	1.00
70_N	74_R	0.927	1.00
15_Y	36_A	0.925	1.00
14_Y	17_E	0.925	1.00
158_L	162_K	0.922	1.00
19_L	32_A	0.910	1.00
20_N	24_R	0.901	1.00
113_E	116_K	0.882	1.00
42_K	45_N	0.878	1.00
35_L	68_F	0.876	1.00
123_S	126_I	0.876	1.00
16_Q	20_N	0.871	1.00
43_A	59_W	0.870	1.00
23_F	32_A	0.869	1.00
62_T	69_I	0.864	1.00
22_L	32_A	0.854	1.00
107_S	111_R	0.851	1.00
127_L	138_I	0.851	1.00
124_V	144_W	0.846	1.00
120_Q	144_W	0.843	1.00
121_H	155_R	0.843	1.00
18_I	39_T	0.839	1.00
10_L	56_I	0.838	1.00
75_D	78_Y	0.834	1.00
137_E	140_E	0.827	1.00
128_R	153_L	0.824	1.00
98_E	102_S	0.817	1.00
161_K	165_T	0.809	1.00
127_L	142_L	0.807	1.00
120_Q	123_S	0.802	1.00
144_W	148_K	0.801	1.00
138_I	142_L	0.791	1.00
125_L	129_E	0.790	1.00
136_E	150_N	0.789	1.00
139_A	146_L	0.780	1.00
37_Q	41_V	0.774	1.00
111_R	115_L	0.771	1.00
38_D	41_V	0.768	1.00
134_S	138_I	0.765	1.00
59_W	63_I	0.762	1.00
125_L	156_A	0.761	1.00
103_R	106_K	0.757	1.00
32_A	36_A	0.752	1.00
9_D	12_R	0.750	1.00
109_T	112_Q	0.750	1.00
74_R	78_Y	0.748	1.00
108_E	112_Q	0.742	1.00
113_E	164_M	0.741	1.00
17_E	21_Y	0.734	1.00
21_Y	25_R	0.723	1.00
23_F	27_H	0.712	1.00
124_V	142_L	0.695	1.00
83_I	86_N	0.694	1.00
51_R	54_S	0.690	1.00
106_K	109_T	0.679	1.00
5_D	8_E	0.667	1.00
38_D	71_W	0.665	1.00
25_R	69_I	0.660	1.00
76_V	80_F	0.660	1.00
72_Y	76_V	0.654	1.00
155_R	158_L	0.653	1.00
97_P	100_Y	0.649	1.00
104_T	107_S	0.647	1.00
36_A	40_F	0.640	1.00
69_I	73_R	0.631	1.00
127_L	131_Q	0.628	1.00
61_Y	65_H	0.628	1.00
155_R	159_E	0.628	1.00
75_D	79_Q	0.626	1.00
128_R	157_R	0.623	1.00
105_V	108_E	0.623	1.00
12_R	15_Y	0.619	1.00
25_R	65_H	0.616	1.00
52_G	55_S	0.616	1.00
26_T	32_A	0.615	1.00
71_W	74_R	0.614	1.00
53_H	56_I	0.605	1.00
64_A	68_F	0.605	1.00
102_S	106_K	0.603	1.00
17_E	20_N	0.601	1.00
119_D	122_Q	0.599	1.00
47_L	56_I	0.599	1.00
105_V	109_T	0.592	1.00
34_D	37_Q	0.585	1.00
76_V	79_Q	0.584	1.00
35_L	64_A	0.583	1.00
26_T	31_T	0.579	1.00
96_Q	99_Q	0.578	1.00
101_L	105_V	0.577	1.00
100_Y	104_T	0.568	1.00
50_F	54_S	0.566	1.00
101_L	104_T	0.562	1.00
159_E	162_K	0.562	1.00
26_T	71_W	0.561	1.00
21_Y	68_F	0.561	1.00
77_K	81_T	0.559	1.00
112_Q	116_K	0.558	1.00
150_N	154_H	0.556	1.00
28_H	33_K	0.556	1.00
139_A	149_V	0.554	1.00
5_D	9_D	0.554	1.00
104_T	108_E	0.553	1.00
72_Y	75_D	0.552	1.00
135_Y	138_I	0.552	1.00
39_T	43_A	0.549	1.00
125_L	160_L	0.544	1.00
7_I	11_Y	0.544	1.00
44_L	47_L	0.542	1.00
123_S	142_L	0.539	1.00
65_H	123_S	0.539	1.00
6_S	9_D	0.538	1.00
139_A	142_L	0.536	1.00
152_T	156_A	0.532	1.00
6_S	47_L	0.531	1.00
15_Y	40_F	0.530	1.00
50_F	55_S	0.529	1.00
114_L	126_I	0.527	1.00
99_Q	103_R	0.523	1.00
115_L	126_I	0.518	1.00
117_L	156_A	0.516	1.00
157_R	161_K	0.516	1.00
58_T	61_Y	0.515	1.00
109_T	113_E	0.511	1.00
22_L	26_T	0.511	1.00
118_K	159_E	0.507	1.00
111_R	114_L	0.506	1.00
123_S	127_L	0.506	1.00
28_H	32_A	0.503	1.00
112_Q	115_L	0.503	1.00
43_A	63_I	0.500	1.00

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
4cxfA	1	0.8266	100	0.175	Contact Map
1or7A	2	0.9249	100	0.188	Contact Map
4nqwA	1	0.7919	100	0.216	Contact Map
2q1zA	1	0.9249	100	0.217	Contact Map
2lfwA	1	0.8671	100	0.254	Contact Map
4g97A	1	0.6763	100	0.258	Contact Map
1rp3A	1	0.9595	100	0.262	Contact Map
4yfkF	1	1	100	0.278	Contact Map
3n0rA	1	0.8092	100	0.281	Contact Map
1l0oC	1	0.0809	100	0.29	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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