SIGM - BACSU - GREMLIN Contacts

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SIGM - RNA polymerase sigma factor SigM

UniProt:	O07582	Sequences: MTIDEIYQMYMNDVYRFLLSMTKDKHLAEDLLQETFMRAYIHIHSYDHSKVKPWLFQVARNAFIDYVRKHKKEVTISDDLIGSLFQNAVQSPAHQVEIKEVLTGYMSELPDNYREALTLYYLKELNYKEASHIMNISEANFKSVLFRARQRLKALYNRGVNDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	163 (153)
Sequences:	38349 (29168)
Seq/√Len:	2358.1

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_R	62_A	3.227	1.00
120_Y	130_A	2.808	1.00
13_D	52_K	2.474	1.00
128_K	138_E	2.378	1.00
113_Y	151_R	2.213	1.00
108_E	155_L	2.160	1.00
105_Y	155_L	2.115	1.00
18_L	59_A	2.086	1.00
60_R	64_I	2.063	1.00
112_N	144_V	1.943	1.00
35_T	59_A	1.942	1.00
125_L	133_I	1.885	1.00
137_S	140_N	1.863	1.00
139_A	142_K	1.832	1.00
17_F	56_F	1.716	1.00
26_H	29_E	1.715	1.00
50_K	53_P	1.690	1.00
65_D	68_R	1.681	1.00
42_H	45_S	1.678	1.00
62_A	65_D	1.658	1.00
21_M	63_F	1.651	1.00
27_L	66_Y	1.648	1.00
113_Y	144_V	1.625	1.00
121_Y	149_R	1.608	1.00
136_I	144_V	1.606	1.00
39_A	55_L	1.547	1.00
126_N	129_E	1.523	1.00
127_Y	138_E	1.518	1.00
146_F	150_Q	1.514	1.00
24_D	27_L	1.502	1.00
4_D	8_Q	1.494	1.00
19_L	25_K	1.490	1.00
38_R	65_D	1.483	1.00
127_Y	145_L	1.480	1.00
61_N	64_I	1.468	1.00
140_N	144_V	1.462	1.00
110_P	113_Y	1.455	1.00
136_I	141_F	1.434	1.00
127_Y	142_K	1.427	1.00
34_E	62_A	1.416	1.00
31_L	66_Y	1.409	1.00
14_V	59_A	1.396	1.00
13_D	56_F	1.394	1.00
119_L	133_I	1.389	1.00
57_Q	60_R	1.384	1.00
140_N	143_S	1.376	1.00
5_E	9_M	1.363	1.00
18_L	63_F	1.343	1.00
116_A	145_L	1.333	1.00
151_R	155_L	1.327	1.00
138_E	142_K	1.317	1.00
10_Y	36_F	1.304	1.00
114_R	118_T	1.302	1.00
143_S	146_F	1.293	1.00
52_K	56_F	1.269	1.00
22_T	63_F	1.260	1.00
10_Y	52_K	1.257	1.00
35_T	58_V	1.241	1.00
57_Q	61_N	1.238	1.00
37_M	41_I	1.233	1.00
143_S	147_R	1.225	1.00
27_L	70_H	1.218	1.00
15_Y	25_K	1.213	1.00
119_L	125_L	1.205	1.00
107_S	114_R	1.200	1.00
22_T	31_L	1.199	1.00
116_A	144_V	1.195	1.00
38_R	42_H	1.194	1.00
15_Y	19_L	1.192	1.00
14_V	32_L	1.174	1.00
116_A	148_A	1.173	1.00
7_Y	36_F	1.168	1.00
31_L	62_A	1.167	1.00
7_Y	11_M	1.157	1.00
18_L	31_L	1.137	1.00
18_L	32_L	1.135	1.00
128_K	132_H	1.130	1.00
94_H	97_E	1.099	1.00
120_Y	127_Y	1.089	1.00
145_L	149_R	1.084	1.00
17_F	60_R	1.083	1.00
25_K	29_E	1.082	1.00
15_Y	29_E	1.067	1.00
130_A	141_F	1.062	1.00
63_F	67_V	1.062	1.00
113_Y	148_A	1.052	1.00
125_L	129_E	1.048	1.00
64_I	67_V	1.038	1.00
66_Y	70_H	1.031	1.00
127_Y	141_F	1.029	1.00
49_S	53_P	1.023	1.00
139_A	143_S	1.022	1.00
10_Y	55_L	1.016	1.00
11_M	15_Y	1.008	1.00
35_T	62_A	1.006	1.00
39_A	54_W	0.987	1.00
121_Y	145_L	0.986	1.00
113_Y	116_A	0.967	1.00
139_A	146_F	0.963	1.00
14_V	55_L	0.962	1.00
15_Y	28_A	0.941	1.00
105_Y	152_L	0.939	1.00
69_K	72_K	0.937	1.00
15_Y	32_L	0.931	1.00
118_T	122_L	0.915	1.00
111_D	115_E	0.913	1.00
62_A	66_Y	0.902	1.00
31_L	63_F	0.902	1.00
10_Y	13_D	0.901	1.00
11_M	32_L	0.898	1.00
118_T	123_K	0.877	1.00
150_Q	154_A	0.871	1.00
19_L	28_A	0.870	1.00
38_R	41_I	0.856	1.00
18_L	28_A	0.855	1.00
65_D	69_K	0.854	1.00
46_Y	49_S	0.851	1.00
12_N	16_R	0.846	1.00
105_Y	108_E	0.843	1.00
117_L	121_Y	0.840	1.00
57_Q	64_I	0.840	1.00
116_A	136_I	0.835	1.00
16_R	20_S	0.830	1.00
129_E	132_H	0.813	1.00
113_Y	147_R	0.813	1.00
70_H	73_E	0.811	1.00
6_I	51_V	0.810	1.00
14_V	35_T	0.806	1.00
115_E	118_T	0.801	1.00
43_I	51_V	0.799	1.00
119_L	130_A	0.798	1.00
54_W	58_V	0.795	1.00
126_N	130_A	0.787	1.00
69_K	73_E	0.783	1.00
33_Q	37_M	0.780	1.00
99_K	103_T	0.780	1.00
128_K	142_K	0.779	1.00
136_I	140_N	0.776	1.00
120_Y	145_L	0.775	1.00
112_N	136_I	0.774	1.00
28_A	32_L	0.772	1.00
130_A	134_M	0.768	1.00
17_F	21_M	0.765	1.00
112_N	115_E	0.759	1.00
131_S	138_E	0.752	1.00
119_L	134_M	0.749	1.00
90_Q	94_H	0.743	1.00
34_E	37_M	0.743	1.00
117_L	148_A	0.736	1.00
101_V	104_G	0.729	1.00
100_E	104_G	0.729	1.00
105_Y	156_Y	0.726	1.00
13_D	17_F	0.726	1.00
71_K	75_T	0.725	1.00
72_K	76_I	0.714	1.00
103_T	107_S	0.710	1.00
5_E	8_Q	0.694	1.00
56_F	60_R	0.676	1.00
67_V	71_K	0.675	1.00
116_A	134_M	0.671	1.00
98_I	101_V	0.669	1.00
64_I	68_R	0.667	1.00
97_E	100_E	0.667	1.00
46_Y	50_K	0.665	1.00
46_Y	53_P	0.658	1.00
21_M	64_I	0.658	1.00
59_A	63_F	0.648	1.00
31_L	59_A	0.643	1.00
120_Y	149_R	0.643	1.00
34_E	66_Y	0.642	1.00
19_L	23_K	0.639	1.00
147_R	151_R	0.632	1.00
40_Y	43_I	0.630	1.00
21_M	60_R	0.630	1.00
97_E	101_V	0.620	1.00
147_R	150_Q	0.616	1.00
119_L	123_K	0.610	1.00
96_V	99_K	0.609	1.00
88_A	91_S	0.607	1.00
22_T	66_Y	0.607	1.00
60_R	115_E	0.603	1.00
93_A	97_E	0.598	1.00
18_L	22_T	0.597	1.00
89_V	92_P	0.593	1.00
127_Y	130_A	0.592	1.00
22_T	27_L	0.588	1.00
8_Q	11_M	0.587	1.00
35_T	39_A	0.586	1.00
66_Y	69_K	0.584	1.00
13_D	16_R	0.583	1.00
30_D	33_Q	0.583	1.00
17_F	63_F	0.582	1.00
22_T	28_A	0.575	1.00
93_A	96_V	0.566	1.00
70_H	74_V	0.566	1.00
90_Q	93_A	0.565	1.00
71_K	74_V	0.561	1.00
111_D	114_R	0.558	1.00
96_V	100_E	0.556	1.00
24_D	29_E	0.552	1.00
106_M	118_T	0.543	1.00
32_L	36_F	0.543	1.00
94_H	98_I	0.542	1.00
92_P	96_V	0.538	1.00
67_V	70_H	0.531	1.00
131_S	141_F	0.531	1.00
103_T	106_M	0.531	1.00
39_A	58_V	0.530	1.00
151_R	154_A	0.529	1.00
46_Y	54_W	0.528	1.00
104_G	108_E	0.526	1.00
53_P	56_F	0.522	1.00
152_L	156_Y	0.521	1.00
18_L	21_M	0.521	1.00
131_S	134_M	0.521	1.00
101_V	105_Y	0.521	1.00
79_D	83_S	0.521	1.00
46_Y	51_V	0.520	1.00
7_Y	33_Q	0.520	1.00
144_V	147_R	0.512	1.00
149_R	153_K	0.512	1.00
95_Q	98_I	0.512	1.00
115_E	134_M	0.510	1.00
91_S	95_Q	0.509	1.00
142_K	146_F	0.508	1.00
36_F	40_Y	0.507	1.00
117_L	152_L	0.507	1.00
72_K	75_T	0.507	1.00
109_L	148_A	0.501	1.00
110_P	151_R	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	0.8466	100	0.171	Contact Map
1or7A	2	0.9325	100	0.188	Contact Map
2q1zA	1	0.9509	100	0.2	Contact Map
2lfwA	1	0.9018	100	0.203	Contact Map
4g97A	1	0.7301	100	0.214	Contact Map
4nqwA	1	0.816	100	0.215	Contact Map
3n0rA	1	0.865	100	0.248	Contact Map
4qicA	2	0.8344	100	0.251	Contact Map
4yfkF	1	1	100	0.255	Contact Map
1rp3A	1	0.9816	100	0.273	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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