SIGZ - BACSU - GREMLIN Contacts

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SIGZ - RNA polymerase sigma factor SigZ

UniProt:	O05409	Sequences: MNIEDLWDQFHQPLKTYISHRVNDQSIVDDLLQIVFMKIQVHLPNLIDEQKIDSWIYRITRNTIIDFYRTKKTSEILPDVLHFNDSAEEENFTKEATVCIRSTIKRLPEKYREALELTDFQGLSQKELSEKLGISYSGAKSRVQRGRGKLKQLLEGCCHIEADRYGNIVDFRILKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	176 (154)
Sequences:	38609 (29202)
Seq/√Len:	2353.1

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

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_K	63_T	3.198	1.00
118_T	128_L	2.750	1.00
13_P	53_D	2.461	1.00
126_K	136_Y	2.365	1.00
111_Y	149_K	2.205	1.00
106_R	153_L	2.184	1.00
18_I	60_T	2.117	1.00
103_T	153_L	2.085	1.00
61_R	65_I	2.048	1.00
35_V	60_T	1.964	1.00
110_K	142_R	1.953	1.00
135_S	138_G	1.894	1.00
123_L	131_K	1.869	1.00
137_S	140_K	1.810	1.00
26_S	29_D	1.697	1.00
17_Y	57_Y	1.684	1.00
63_T	66_D	1.680	1.00
66_D	69_R	1.673	1.00
42_H	45_N	1.668	1.00
21_R	64_I	1.653	1.00
27_I	67_F	1.644	1.00
51_K	54_S	1.596	1.00
111_Y	142_R	1.595	1.00
119_D	147_R	1.580	1.00
134_I	142_R	1.578	1.00
39_I	56_I	1.539	1.00
4_E	8_D	1.524	1.00
124_S	127_E	1.508	1.00
24_D	27_I	1.500	1.00
125_Q	136_Y	1.491	1.00
144_Q	148_G	1.478	1.00
108_P	111_Y	1.477	1.00
138_G	142_R	1.472	1.00
19_S	25_Q	1.470	1.00
38_K	66_D	1.468	1.00
125_Q	143_V	1.462	1.00
62_N	65_I	1.447	1.00
31_L	67_F	1.426	1.00
14_L	60_T	1.419	1.00
125_Q	140_K	1.410	1.00
34_I	63_T	1.403	1.00
134_I	139_A	1.401	1.00
117_L	131_K	1.397	1.00
138_G	141_S	1.384	1.00
58_R	61_R	1.371	1.00
13_P	57_Y	1.370	1.00
5_D	9_Q	1.354	1.00
18_I	64_I	1.350	1.00
114_A	143_V	1.336	1.00
112_R	116_E	1.332	1.00
149_K	153_L	1.327	1.00
10_F	36_F	1.297	1.00
136_Y	140_K	1.275	1.00
141_S	144_Q	1.269	1.00
58_R	62_N	1.237	1.00
53_D	57_Y	1.232	1.00
105_K	112_R	1.229	1.00
22_V	31_L	1.218	1.00
10_F	53_D	1.215	1.00
46_L	49_E	1.210	1.00
35_V	59_I	1.206	1.00
117_L	123_L	1.205	1.00
22_V	64_I	1.202	1.00
15_K	25_Q	1.188	1.00
27_I	71_K	1.187	1.00
114_A	142_R	1.187	1.00
14_L	32_L	1.182	1.00
141_S	145_R	1.182	1.00
37_M	41_V	1.174	1.00
7_W	36_F	1.174	1.00
15_K	19_S	1.173	1.00
18_I	31_L	1.172	1.00
126_K	130_E	1.169	1.00
31_L	63_T	1.169	1.00
38_K	42_H	1.169	1.00
114_A	146_G	1.169	1.00
18_I	32_L	1.138	1.00
7_W	11_H	1.125	1.00
50_Q	54_S	1.090	1.00
17_Y	61_R	1.079	1.00
143_V	147_R	1.074	1.00
92_F	95_E	1.070	1.00
118_T	125_Q	1.063	1.00
64_I	68_Y	1.055	1.00
25_Q	29_D	1.049	1.00
65_I	68_Y	1.045	1.00
128_L	139_A	1.040	1.00
111_Y	146_G	1.039	1.00
15_K	29_D	1.036	1.00
137_S	141_S	1.028	1.00
123_L	127_E	1.026	1.00
125_Q	139_A	1.022	1.00
10_F	56_I	1.019	1.00
35_V	63_T	1.002	1.00
67_F	71_K	0.997	1.00
11_H	15_K	0.991	1.00
39_I	55_W	0.982	1.00
137_S	144_Q	0.964	1.00
111_Y	114_A	0.964	1.00
119_D	143_V	0.959	1.00
70_T	73_T	0.944	1.00
103_T	150_L	0.942	1.00
14_L	56_I	0.937	1.00
15_K	28_V	0.931	1.00
63_T	67_F	0.924	1.00
3_I	40_Q	0.923	1.00
15_K	32_L	0.922	1.00
31_L	64_I	0.908	1.00
148_G	152_Q	0.906	1.00
116_E	120_F	0.902	1.00
109_E	113_E	0.891	1.00
11_H	32_L	0.888	1.00
10_F	13_P	0.885	1.00
19_S	28_V	0.883	1.00
16_T	20_H	0.871	1.00
12_Q	16_T	0.864	1.00
114_A	134_I	0.858	1.00
116_E	121_Q	0.858	1.00
38_K	41_V	0.848	1.00
14_L	35_V	0.845	1.00
66_D	70_T	0.843	1.00
111_Y	145_R	0.838	1.00
117_L	128_L	0.834	1.00
115_L	119_D	0.834	1.00
58_R	65_I	0.828	1.00
127_E	130_E	0.822	1.00
18_I	28_V	0.818	1.00
88_E	92_F	0.815	1.00
43_L	52_I	0.801	1.00
117_L	132_L	0.794	1.00
55_W	59_I	0.785	1.00
103_T	106_R	0.783	1.00
70_T	74_S	0.781	1.00
75_E	78_P	0.780	1.00
71_K	74_S	0.780	1.00
6_L	52_I	0.775	1.00
17_Y	21_R	0.771	1.00
28_V	32_L	0.771	1.00
126_K	140_K	0.769	1.00
124_S	128_L	0.769	1.00
128_L	132_L	0.769	1.00
134_I	138_G	0.766	1.00
113_E	116_E	0.764	1.00
118_T	143_V	0.763	1.00
97_T	101_R	0.762	1.00
110_K	134_I	0.758	1.00
33_Q	37_M	0.756	1.00
110_K	113_E	0.756	1.00
151_K	155_E	0.753	1.00
34_I	37_M	0.751	1.00
129_S	136_Y	0.729	1.00
13_P	17_Y	0.726	1.00
19_S	23_N	0.725	1.00
72_K	76_I	0.723	1.00
115_L	146_G	0.722	1.00
73_T	77_L	0.720	1.00
98_V	102_S	0.716	1.00
47_I	50_Q	0.712	1.00
74_S	78_P	0.710	1.00
101_R	105_K	0.709	1.00
99_C	102_S	0.708	1.00
103_T	154_L	0.697	1.00
46_L	50_Q	0.695	1.00
5_D	8_D	0.683	1.00
95_E	98_V	0.670	1.00
91_N	95_E	0.669	1.00
91_N	94_K	0.663	1.00
114_A	132_L	0.663	1.00
68_Y	72_K	0.660	1.00
57_Y	61_R	0.652	1.00
18_I	22_V	0.645	1.00
21_R	65_I	0.645	1.00
145_R	148_G	0.642	1.00
31_L	60_T	0.639	1.00
88_E	91_N	0.636	1.00
60_T	64_I	0.634	1.00
96_A	99_C	0.630	1.00
118_T	147_R	0.628	1.00
65_I	69_R	0.628	1.00
34_I	67_F	0.626	1.00
49_E	52_I	0.619	1.00
95_E	99_C	0.617	1.00
61_R	113_E	0.610	1.00
22_V	67_F	0.607	1.00
22_V	28_V	0.603	1.00
22_V	27_I	0.599	1.00
17_Y	64_I	0.596	1.00
30_D	33_Q	0.596	1.00
21_R	61_R	0.594	1.00
94_K	97_T	0.590	1.00
145_R	149_K	0.587	1.00
40_Q	43_L	0.587	1.00
67_F	70_T	0.587	1.00
71_K	75_E	0.587	1.00
8_D	11_H	0.579	1.00
46_L	51_K	0.575	1.00
13_P	16_T	0.568	1.00
35_V	39_I	0.566	1.00
149_K	152_Q	0.565	1.00
48_D	51_K	0.562	1.00
117_L	121_Q	0.560	1.00
94_K	98_V	0.559	1.00
24_D	29_D	0.557	1.00
87_A	90_E	0.556	1.00
46_L	54_S	0.555	1.00
109_E	112_R	0.551	1.00
125_Q	128_L	0.549	1.00
72_K	75_E	0.545	1.00
92_F	96_A	0.541	1.00
115_L	150_L	0.539	1.00
86_S	89_E	0.532	1.00
39_I	59_I	0.529	1.00
89_E	93_T	0.526	1.00
129_S	132_L	0.525	1.00
129_S	139_A	0.525	1.00
104_I	116_E	0.524	1.00
7_W	33_Q	0.524	1.00
142_R	145_R	0.523	1.00
147_R	151_K	0.520	1.00
24_D	28_V	0.519	1.00
32_L	36_F	0.519	1.00
54_S	57_Y	0.518	1.00
101_R	104_I	0.515	1.00
102_S	106_R	0.514	1.00
93_T	96_A	0.513	1.00
140_K	144_Q	0.511	1.00
74_S	77_L	0.509	1.00
18_I	21_R	0.508	1.00
150_L	154_L	0.505	1.00
108_P	149_K	0.501	1.00
73_T	76_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	0.7898	100	0.22	Contact Map
1or7A	2	0.8523	100	0.235	Contact Map
2lfwA	1	0.892	100	0.249	Contact Map
4g97A	1	0.767	100	0.259	Contact Map
2q1zA	1	0.875	100	0.265	Contact Map
4nqwA	1	0.7614	100	0.27	Contact Map
3n0rA	1	0.892	100	0.288	Contact Map
4qicA	2	0.8636	100	0.293	Contact Map
1rp3A	1	0.892	100	0.309	Contact Map
4yfkF	1	0.9375	100	0.315	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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