FECI - ECOLI - GREMLIN Contacts

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FECI - Probable RNA polymerase sigma factor FecI

UniProt:	P23484	Sequences: MSDRATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSISSVKKYVAKAVEHCLLFRLEYGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10291
Length:	173 (158)
Sequences:	38267 (29376)
Seq/√Len:	2337.0

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_R	72_V	3.227	1.00
132_S	142_I	2.745	1.00
23_W	62_R	2.471	1.00
140_S	150_I	2.385	1.00
125_T	163_H	2.229	1.00
120_G	167_F	2.182	1.00
28_L	69_A	2.102	1.00
117_M	167_F	2.042	1.00
70_K	74_V	1.983	1.00
45_T	69_A	1.949	1.00
124_K	156_Y	1.944	1.00
137_L	145_K	1.936	1.00
149_S	152_S	1.886	1.00
151_S	154_K	1.833	1.00
75_D	78_R	1.765	1.00
36_F	39_D	1.753	1.00
31_K	73_M	1.715	1.00
37_D	76_L	1.705	1.00
27_W	66_C	1.701	1.00
72_V	75_D	1.660	1.00
125_T	156_Y	1.640	1.00
14_E	18_G	1.638	1.00
60_D	63_S	1.616	1.00
148_V	156_Y	1.598	1.00
133_Q	161_V	1.584	1.00
138_T	141_E	1.559	1.00
34_S	37_D	1.555	1.00
71_R	74_V	1.546	1.00
49_V	65_L	1.543	1.00
29_T	35_A	1.536	1.00
158_A	162_E	1.525	1.00
139_Y	150_I	1.523	1.00
48_R	75_D	1.520	1.00
139_Y	157_V	1.504	1.00
122_N	125_T	1.498	1.00
152_S	156_Y	1.450	1.00
139_Y	154_K	1.445	1.00
41_I	76_L	1.443	1.00
148_V	153_V	1.433	1.00
67_T	70_K	1.430	1.00
15_S	19_T	1.428	1.00
24_L	69_A	1.427	1.00
44_D	72_V	1.421	1.00
131_L	145_K	1.394	1.00
152_S	155_K	1.388	1.00
128_A	157_V	1.388	1.00
28_L	73_M	1.379	1.00
23_W	66_C	1.369	1.00
163_H	167_F	1.368	1.00
20_H	46_F	1.344	1.00
126_R	130_L	1.340	1.00
150_I	154_K	1.333	1.00
155_K	158_A	1.271	1.00
67_T	71_R	1.271	1.00
62_R	66_C	1.260	1.00
45_T	68_I	1.250	1.00
37_D	80_N	1.250	1.00
140_S	144_H	1.247	1.00
32_L	73_M	1.246	1.00
41_I	72_V	1.235	1.00
24_L	42_A	1.234	1.00
47_L	51_V	1.229	1.00
55_L	58_I	1.227	1.00
155_K	159_K	1.225	1.00
20_H	62_R	1.225	1.00
25_K	35_A	1.212	1.00
25_K	29_T	1.211	1.00
32_L	41_I	1.205	1.00
48_R	52_S	1.203	1.00
131_L	137_L	1.202	1.00
128_A	156_Y	1.194	1.00
28_L	41_I	1.190	1.00
28_L	42_A	1.185	1.00
119_D	126_R	1.183	1.00
13_F	50_M	1.179	1.00
17_Y	46_F	1.177	1.00
128_A	160_A	1.172	1.00
17_Y	21_H	1.172	1.00
59_R	63_S	1.160	1.00
132_S	139_Y	1.114	1.00
27_W	70_K	1.113	1.00
25_K	39_D	1.106	1.00
137_L	141_E	1.092	1.00
35_A	39_D	1.090	1.00
142_I	153_V	1.083	1.00
73_M	77_F	1.080	1.00
49_V	64_F	1.069	1.00
125_T	160_A	1.067	1.00
74_V	77_F	1.052	1.00
20_H	65_L	1.048	1.00
45_T	72_V	1.040	1.00
151_S	158_A	1.029	1.00
151_S	155_K	1.020	1.00
157_V	161_V	1.018	1.00
76_L	80_N	1.014	1.00
117_M	164_C	1.008	1.00
106_S	109_E	1.005	1.00
139_Y	153_V	0.999	1.00
21_H	25_K	0.974	1.00
79_R	82_L	0.974	1.00
125_T	128_A	0.964	1.00
24_L	65_L	0.960	1.00
133_Q	157_V	0.943	1.00
25_K	38_A	0.939	1.00
123_G	127_E	0.938	1.00
130_L	134_L	0.933	1.00
162_E	166_L	0.929	1.00
21_H	42_A	0.929	1.00
48_R	51_V	0.914	1.00
25_K	42_A	0.913	1.00
72_V	76_L	0.908	1.00
29_T	38_A	0.906	1.00
28_L	38_A	0.897	1.00
22_G	26_S	0.896	1.00
41_I	73_M	0.896	1.00
130_L	135_D	0.892	1.00
67_T	74_V	0.878	1.00
20_H	23_W	0.878	1.00
128_A	148_V	0.870	1.00
24_L	45_T	0.846	1.00
64_F	68_I	0.844	1.00
16_L	61_P	0.838	1.00
131_L	142_I	0.838	1.00
80_N	83_E	0.836	1.00
26_S	30_R	0.836	1.00
75_D	79_R	0.832	1.00
79_R	83_E	0.832	1.00
129_F	133_Q	0.828	1.00
27_W	31_K	0.815	1.00
132_S	157_V	0.812	1.00
138_T	142_I	0.809	1.00
141_E	144_H	0.808	1.00
131_L	146_L	0.800	1.00
43_Q	47_L	0.794	1.00
55_L	59_R	0.793	1.00
140_S	154_K	0.790	1.00
142_I	146_L	0.790	1.00
125_T	159_K	0.788	1.00
102_E	106_S	0.781	1.00
44_D	47_L	0.779	1.00
124_K	127_E	0.773	1.00
148_V	152_S	0.773	1.00
117_M	120_G	0.770	1.00
129_F	160_A	0.759	1.00
38_A	42_A	0.752	1.00
124_K	148_V	0.749	1.00
143_A	150_I	0.737	1.00
82_L	86_Y	0.736	1.00
11_L	14_E	0.732	1.00
113_L	116_S	0.732	1.00
23_W	27_W	0.729	1.00
115_D	119_D	0.724	1.00
29_T	33_Q	0.719	1.00
81_A	85_A	0.713	1.00
127_E	130_L	0.712	1.00
15_S	18_G	0.709	1.00
112_Q	116_S	0.700	1.00
56_S	59_R	0.699	1.00
109_E	112_Q	0.697	1.00
111_L	115_D	0.682	1.00
32_L	76_L	0.682	1.00
117_M	168_R	0.681	1.00
132_S	161_V	0.680	1.00
74_V	78_R	0.680	1.00
77_F	81_A	0.679	1.00
41_I	69_A	0.677	1.00
108_L	111_L	0.662	1.00
69_A	73_M	0.660	1.00
101_P	104_R	0.658	1.00
128_A	146_L	0.652	1.00
31_K	74_V	0.652	1.00
66_C	70_K	0.650	1.00
32_L	37_D	0.646	1.00
28_L	32_L	0.643	1.00
70_K	127_E	0.640	1.00
46_F	50_M	0.626	1.00
13_F	17_Y	0.625	1.00
100_S	103_E	0.621	1.00
107_Q	110_T	0.621	1.00
57_T	60_D	0.618	1.00
44_D	76_L	0.617	1.00
110_T	113_L	0.616	1.00
106_S	110_T	0.614	1.00
31_K	70_K	0.610	1.00
159_K	162_E	0.609	1.00
27_W	73_M	0.609	1.00
81_A	84_K	0.602	1.00
76_L	79_R	0.601	1.00
18_G	21_H	0.599	1.00
45_T	49_V	0.598	1.00
123_G	126_R	0.597	1.00
159_K	163_H	0.596	1.00
87_L	90_L	0.595	1.00
154_K	158_A	0.594	1.00
88_E	92_L	0.591	1.00
55_L	63_S	0.589	1.00
32_L	38_A	0.588	1.00
104_R	108_L	0.586	1.00
40_D	43_Q	0.585	1.00
131_L	135_D	0.574	1.00
163_H	166_L	0.574	1.00
23_W	26_S	0.574	1.00
139_Y	142_I	0.572	1.00
118_L	130_L	0.564	1.00
34_S	39_D	0.562	1.00
108_L	112_Q	0.562	1.00
115_D	118_L	0.559	1.00
116_S	120_G	0.559	1.00
11_L	15_S	0.550	1.00
17_Y	43_Q	0.546	1.00
80_N	84_K	0.544	1.00
34_S	38_A	0.542	1.00
28_L	31_K	0.540	1.00
143_A	153_V	0.539	1.00
42_A	46_F	0.539	1.00
55_L	60_D	0.539	1.00
164_C	168_R	0.534	1.00
143_A	146_L	0.532	1.00
77_F	80_N	0.525	1.00
129_F	164_C	0.524	1.00
161_V	165_L	0.523	1.00
156_Y	159_K	0.523	1.00
49_V	68_I	0.523	1.00
82_L	85_A	0.523	1.00
105_E	108_L	0.522	1.00
122_N	163_H	0.520	1.00
109_E	113_L	0.519	1.00
103_E	107_Q	0.517	1.00
84_K	87_L	0.516	1.00
127_E	146_L	0.514	1.00
49_V	61_P	0.512	1.00
63_S	66_C	0.507	1.00
55_L	61_P	0.507	1.00
121_L	160_A	0.505	1.00
88_E	91_A	0.505	1.00
42_A	69_A	0.503	1.00
118_L	129_F	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	0.8555	100	0.167	Contact Map
1or7A	2	0.948	100	0.184	Contact Map
2q1zA	1	0.9538	100	0.2	Contact Map
4nqwA	1	0.8208	100	0.207	Contact Map
4yfkF	1	1	100	0.261	Contact Map
4g97A	1	0.6763	100	0.27	Contact Map
2lfwA	1	0.8382	100	0.27	Contact Map
1rp3A	1	0.9827	100	0.278	Contact Map
3n0rA	1	0.8092	100	0.283	Contact Map
1l0oC	1	0.0694	100	0.284	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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