SIGX - BACSU - GREMLIN Contacts

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SIGX - RNA polymerase sigma factor SigX

UniProt:	P35165	Sequences: MEETFQLLYDTYHQDLYQFLFYMVKDKNQTEDLLQEVYIRVLNSYHTFEGRSSEKTWLLSIARHVAIDWFRKQQTIRQRILGTFDWDTQDVRDQQLLPDELAVQHENVREIYAALDQCTIDQRAVIILRFIQGYSIQETAKALRFSESKVKTTQHRGLKVLRKHMELLREELMDDEVRMERRTDKGVVKSTSGS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	194 (159)
Sequences:	40468 (30369)
Seq/√Len:	2408.4

ECOLI - FECI RPOE
BACSU - SIGX SIGZ SIGW YLAC SIGM SIGY 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
40_R	65_V	3.218	1.00
129_R	139_T	2.786	1.00
15_D	55_K	2.519	1.00
137_Q	147_E	2.438	1.00
117_Q	164_H	2.297	1.00
122_Q	160_V	2.245	1.00
20_L	62_A	2.138	1.00
114_A	164_H	2.063	1.00
63_R	67_I	2.046	1.00
37_V	62_A	2.040	1.00
134_Y	142_A	1.968	1.00
146_S	149_K	1.962	1.00
121_D	153_T	1.957	1.00
148_S	151_K	1.833	1.00
44_S	47_T	1.743	1.00
19_F	59_L	1.721	1.00
28_N	31_E	1.711	1.00
68_D	71_R	1.694	1.00
6_Q	10_D	1.685	1.00
23_M	66_A	1.660	1.00
53_S	56_T	1.653	1.00
65_V	68_D	1.645	1.00
41_V	58_L	1.621	1.00
122_Q	153_T	1.619	1.00
29_Q	69_W	1.619	1.00
130_F	158_L	1.587	1.00
145_F	153_T	1.567	1.00
26_D	29_Q	1.563	1.00
135_S	138_E	1.553	1.00
149_K	153_T	1.507	1.00
119_T	122_Q	1.506	1.00
136_I	154_Q	1.500	1.00
21_F	27_K	1.494	1.00
136_I	147_E	1.475	1.00
7_L	11_T	1.469	1.00
149_K	152_T	1.467	1.00
136_I	151_K	1.459	1.00
64_H	67_I	1.451	1.00
40_R	68_D	1.448	1.00
128_L	142_A	1.438	1.00
155_H	159_K	1.430	1.00
33_L	69_W	1.418	1.00
123_R	127_I	1.409	1.00
125_V	154_Q	1.408	1.00
145_F	150_V	1.403	1.00
60_S	63_R	1.402	1.00
16_L	62_A	1.386	1.00
36_E	65_V	1.368	1.00
20_L	66_A	1.363	1.00
160_V	164_H	1.347	1.00
15_D	59_L	1.333	1.00
12_Y	38_Y	1.311	1.00
60_S	64_H	1.308	1.00
137_Q	141_K	1.297	1.00
116_D	123_R	1.264	1.00
16_L	34_L	1.259	1.00
152_T	155_H	1.255	1.00
125_V	157_G	1.240	1.00
125_V	153_T	1.239	1.00
128_L	134_Y	1.232	1.00
147_E	151_K	1.220	1.00
55_K	59_L	1.211	1.00
33_L	65_V	1.209	1.00
20_L	33_L	1.208	1.00
20_L	34_L	1.199	1.00
9_Y	38_Y	1.198	1.00
52_S	56_T	1.198	1.00
24_V	33_L	1.190	1.00
12_Y	55_K	1.188	1.00
17_Y	21_F	1.185	1.00
37_V	61_I	1.170	1.00
48_F	51_R	1.170	1.00
9_Y	13_H	1.164	1.00
152_T	156_R	1.163	1.00
29_Q	73_Q	1.152	1.00
39_I	43_N	1.136	1.00
17_Y	27_K	1.135	1.00
40_R	44_S	1.135	1.00
24_V	66_A	1.126	1.00
103_V	106_E	1.121	1.00
19_F	63_R	1.111	1.00
5_F	42_L	1.082	1.00
139_T	150_V	1.077	1.00
134_Y	138_E	1.074	1.00
12_Y	58_L	1.066	1.00
41_V	57_W	1.066	1.00
27_K	31_E	1.060	1.00
154_Q	158_L	1.057	1.00
67_I	70_F	1.048	1.00
122_Q	157_G	1.039	1.00
66_A	70_F	1.031	1.00
37_V	65_V	1.028	1.00
129_R	136_I	1.016	1.00
17_Y	31_E	1.009	1.00
148_S	152_T	1.007	1.00
136_I	150_V	1.003	1.00
114_A	161_L	0.992	1.00
69_W	73_Q	0.991	1.00
148_S	155_H	0.977	1.00
16_L	37_V	0.966	1.00
159_K	163_K	0.957	1.00
72_K	75_T	0.954	1.00
13_H	17_Y	0.952	1.00
120_I	124_A	0.948	1.00
130_F	154_Q	0.938	1.00
33_L	66_A	0.930	1.00
122_Q	125_V	0.926	1.00
125_V	145_F	0.922	1.00
17_Y	30_T	0.917	1.00
16_L	58_L	0.915	1.00
68_D	72_K	0.915	1.00
127_I	132_Q	0.910	1.00
17_Y	34_L	0.907	1.00
127_I	131_I	0.905	1.00
65_V	69_W	0.905	1.00
12_Y	15_D	0.884	1.00
99_D	103_V	0.883	1.00
122_Q	156_R	0.881	1.00
18_Q	22_Y	0.875	1.00
14_Q	18_Q	0.865	1.00
128_L	139_T	0.861	1.00
40_R	43_N	0.860	1.00
57_W	61_I	0.852	1.00
13_H	34_L	0.841	1.00
60_S	67_I	0.834	1.00
20_L	30_T	0.834	1.00
19_F	23_M	0.825	1.00
138_E	141_K	0.820	1.00
21_F	30_T	0.812	1.00
72_K	76_I	0.805	1.00
126_I	130_F	0.801	1.00
128_L	143_L	0.790	1.00
77_R	80_I	0.788	1.00
124_A	127_I	0.785	1.00
35_Q	39_I	0.785	1.00
8_L	54_E	0.784	1.00
121_D	124_A	0.774	1.00
135_S	139_T	0.772	1.00
110_E	113_A	0.764	1.00
129_R	154_Q	0.763	1.00
162_R	166_E	0.760	1.00
30_T	34_L	0.754	1.00
145_F	149_K	0.754	1.00
73_Q	76_I	0.752	1.00
7_L	10_D	0.751	1.00
15_D	19_F	0.749	1.00
121_D	145_F	0.746	1.00
114_A	117_Q	0.738	1.00
49_E	52_S	0.736	1.00
107_N	110_E	0.733	1.00
114_A	165_M	0.731	1.00
112_Y	116_D	0.728	1.00
139_T	143_L	0.727	1.00
106_E	109_R	0.726	1.00
137_Q	151_K	0.725	1.00
126_I	157_G	0.724	1.00
36_E	39_I	0.716	1.00
48_F	52_S	0.716	1.00
45_Y	54_E	0.715	1.00
140_A	147_E	0.707	1.00
74_Q	78_Q	0.702	1.00
75_T	79_R	0.697	1.00
97_L	100_E	0.696	1.00
33_L	62_A	0.693	1.00
21_F	25_K	0.692	1.00
98_P	101_L	0.689	1.00
109_R	113_A	0.677	1.00
156_R	159_K	0.676	1.00
108_V	112_Y	0.672	1.00
105_H	108_V	0.666	1.00
125_V	143_L	0.651	1.00
24_V	69_W	0.650	1.00
129_R	158_L	0.645	1.00
4_T	45_Y	0.641	1.00
77_R	81_L	0.633	1.00
20_L	24_V	0.628	1.00
19_F	66_A	0.628	1.00
70_F	74_Q	0.625	1.00
120_I	123_R	0.624	1.00
76_I	80_I	0.623	1.00
67_I	71_R	0.623	1.00
104_Q	107_N	0.622	1.00
78_Q	81_L	0.620	1.00
48_F	56_T	0.615	1.00
105_H	109_R	0.614	1.00
62_A	66_A	0.614	1.00
24_V	29_Q	0.609	1.00
5_F	9_Y	0.603	1.00
59_L	63_R	0.600	1.00
106_E	110_E	0.600	1.00
36_E	69_W	0.598	1.00
24_V	30_T	0.596	1.00
63_R	124_A	0.594	1.00
37_V	41_V	0.593	1.00
51_R	54_E	0.591	1.00
15_D	18_Q	0.591	1.00
23_M	67_I	0.590	1.00
102_A	105_H	0.588	1.00
101_L	105_H	0.587	1.00
103_V	107_N	0.584	1.00
34_L	38_Y	0.582	1.00
32_D	35_Q	0.580	1.00
160_V	163_K	0.571	1.00
69_W	72_K	0.567	1.00
26_D	31_E	0.564	1.00
42_L	45_Y	0.563	1.00
156_R	160_V	0.560	1.00
78_Q	82_G	0.557	1.00
136_I	139_T	0.556	1.00
9_Y	35_Q	0.548	1.00
119_T	160_V	0.548	1.00
10_D	13_H	0.547	1.00
153_T	156_R	0.545	1.00
23_M	63_R	0.545	1.00
158_L	162_R	0.541	1.00
126_I	161_L	0.540	1.00
151_K	155_H	0.539	1.00
128_L	132_Q	0.538	1.00
50_G	53_S	0.536	1.00
74_Q	77_R	0.536	1.00
73_Q	77_R	0.536	1.00
48_F	53_S	0.534	1.00
112_Y	115_L	0.533	1.00
115_L	127_I	0.533	1.00
102_A	106_E	0.532	1.00
113_A	117_Q	0.532	1.00
79_R	82_G	0.527	1.00
48_F	54_E	0.523	1.00
118_C	157_G	0.520	1.00
56_T	59_L	0.520	1.00
140_A	150_V	0.518	1.00
140_A	143_L	0.515	1.00
124_A	143_L	0.513	1.00
100_E	103_V	0.510	1.00
124_A	142_A	0.508	1.00
26_D	30_T	0.505	1.00
76_I	79_R	0.501	1.00
96_L	104_Q	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	0.7268	100	0.245	Contact Map
1or7A	2	0.8299	100	0.261	Contact Map
2q1zA	1	0.8144	100	0.285	Contact Map
2lfwA	1	0.8093	100	0.289	Contact Map
4nqwA	1	0.701	100	0.291	Contact Map
4g97A	1	0.732	100	0.32	Contact Map
1rp3A	1	0.8608	100	0.321	Contact Map
4yfkF	1	0.9072	100	0.328	Contact Map
3n0rA	1	0.8505	100	0.349	Contact Map
4qicA	2	0.8196	100	0.353	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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