PHNF - ECOLI - GREMLIN Contacts

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PHNF - Probable transcriptional regulator PhnF

UniProt:	P16684	Sequences: MHLSTHPTSYPTRYQEIAAKLEQELRQHYRCGDYLPAEQQLAARFEVNRHTLRRAIDQLVEKGWVQRRQGVGVLVLMRPFDYPLNAQARFSQNLLDQGSHPTSEKLLSVLRPASGHVADALGITEGENVIHLRTLRRVNGVALCLIDHYFADLTLWPTLQRFDSGSLHDFLREQTGIALRRSQTRISARRAQAKECQRLEIPNMSPLLCVRTLNHRDGESSPAEYSVSLTRADMIEFTMEH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10715
Length:	241 (192)
Sequences:	23852 (18294)
Seq/√Len:	1320.2

ECOLI - PHNF MNGR YIHL YEGW YIDP FRLR PDHR NANR
BACSU - YVOA TRER YURK YYDK YMFC GMUR YBGA YCBG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_E	28_H	3.850	1.00
30_R	33_D	3.761	1.00
18_A	58_Q	3.307	1.00
22_E	62_K	3.165	1.00
24_E	44_R	3.108	1.00
66_Q	76_L	2.889	1.00
20_K	24_E	2.547	1.00
17_I	47_V	2.528	1.00
187_S	190_R	2.473	1.00
38_E	49_R	2.432	1.00
67_R	73_V	2.385	1.00
68_R	71_V	2.374	1.00
17_I	45_F	2.295	1.00
18_A	62_K	2.233	1.00
23_Q	27_Q	2.202	1.00
122_G	184_T	2.130	1.00
34_Y	74_L	2.099	1.00
107_L	192_Q	2.004	1.00
114_S	117_V	2.004	1.00
18_A	22_E	1.982	1.00
11_P	19_A	1.946	1.00
20_K	45_F	1.917	1.00
136_R	144_C	1.889	1.00
71_V	74_L	1.836	1.00
60_V	67_R	1.811	1.00
54_R	57_D	1.769	1.00
22_E	26_R	1.703	1.00
192_Q	195_E	1.665	1.00
24_E	29_Y	1.665	1.00
39_Q	43_A	1.654	1.00
22_E	64_W	1.606	1.00
117_V	139_N	1.601	1.00
40_Q	44_R	1.594	1.00
192_Q	196_C	1.592	1.00
100_H	104_E	1.590	1.00
13_R	16_E	1.579	1.00
16_E	20_K	1.570	1.00
131_H	147_D	1.524	1.00
60_V	65_V	1.515	1.00
68_R	74_L	1.508	1.00
20_K	23_Q	1.493	1.00
37_A	40_Q	1.493	1.00
132_L	148_H	1.474	1.00
102_T	137_R	1.472	1.00
14_Y	58_Q	1.459	1.00
111_R	188_A	1.448	1.00
93_N	141_V	1.436	1.00
41_L	52_L	1.434	1.00
56_I	65_V	1.426	1.00
113_A	118_A	1.416	1.00
190_R	194_K	1.392	1.00
65_V	73_V	1.355	1.00
47_V	52_L	1.352	1.00
133_R	136_R	1.350	1.00
104_E	137_R	1.347	1.00
38_E	53_R	1.346	1.00
29_Y	75_V	1.329	1.00
11_P	16_E	1.328	1.00
25_L	75_V	1.313	1.00
57_D	67_R	1.310	1.00
118_A	123_I	1.309	1.00
66_Q	74_L	1.302	1.00
57_D	61_E	1.301	1.00
113_A	117_V	1.284	1.00
182_S	190_R	1.266	1.00
31_C	77_M	1.261	1.00
40_Q	43_A	1.257	1.00
58_Q	61_E	1.252	1.00
12_T	15_Q	1.249	1.00
132_L	136_R	1.240	1.00
193_A	197_Q	1.223	1.00
57_D	60_V	1.219	1.00
111_R	131_H	1.219	1.00
58_Q	62_K	1.217	1.00
145_L	149_Y	1.209	1.00
117_V	149_Y	1.191	1.00
26_R	64_W	1.184	1.00
169_D	173_E	1.164	1.00
118_A	121_L	1.120	1.00
118_A	184_T	1.117	1.00
145_L	195_E	1.111	1.00
126_G	129_V	1.086	1.00
188_A	192_Q	1.077	1.00
180_R	184_T	1.075	1.00
15_Q	19_A	1.075	1.00
168_H	172_R	1.058	1.00
29_Y	33_D	1.056	1.00
110_L	152_D	1.050	1.00
124_T	127_E	1.048	1.00
133_R	147_D	1.039	1.00
177_I	181_R	1.034	1.00
56_I	73_V	1.032	1.00
68_R	72_G	1.025	1.00
133_R	137_R	1.020	1.00
110_L	128_N	1.020	1.00
34_Y	72_G	1.019	1.00
13_R	51_T	1.005	1.00
155_L	158_T	1.005	1.00
107_L	131_H	0.999	1.00
129_V	133_R	0.993	1.00
54_R	58_Q	0.980	1.00
196_C	200_E	0.962	1.00
144_C	148_H	0.957	1.00
109_V	131_H	0.944	1.00
21_L	41_L	0.942	1.00
107_L	188_A	0.942	1.00
24_E	45_F	0.936	1.00
113_A	186_I	0.933	1.00
19_A	22_E	0.929	1.00
15_Q	58_Q	0.923	1.00
181_R	185_R	0.917	1.00
202_P	205_S	0.916	1.00
119_D	123_I	0.909	1.00
99_S	200_E	0.903	1.00
122_G	180_R	0.889	1.00
128_N	152_D	0.888	1.00
32_G	66_Q	0.887	1.00
48_N	51_T	0.884	1.00
120_A	133_R	0.879	1.00
134_T	183_Q	0.879	1.00
178_A	194_K	0.876	1.00
98_G	102_T	0.876	1.00
14_Y	18_A	0.876	1.00
125_E	129_V	0.870	1.00
92_Q	96_D	0.866	1.00
92_Q	95_L	0.864	1.00
167_L	170_F	0.862	1.00
154_T	157_P	0.859	1.00
11_P	15_Q	0.858	1.00
135_L	147_D	0.857	1.00
107_L	133_R	0.854	1.00
115_G	119_D	0.852	1.00
99_S	103_S	0.847	1.00
117_V	120_A	0.844	1.00
70_G	73_V	0.842	1.00
167_L	171_L	0.840	1.00
106_L	110_L	0.836	1.00
14_Y	54_R	0.820	1.00
156_W	159_L	0.819	1.00
191_A	201_I	0.814	1.00
102_T	140_G	0.812	1.00
32_G	77_M	0.801	1.00
20_K	44_R	0.800	1.00
120_A	123_I	0.799	1.00
31_C	76_L	0.798	1.00
115_G	118_A	0.797	1.00
189_R	195_E	0.791	1.00
34_Y	37_A	0.783	1.00
146_I	149_Y	0.778	1.00
114_S	121_L	0.774	1.00
103_S	196_C	0.773	1.00
138_V	144_C	0.773	1.00
85_N	88_A	0.772	1.00
93_N	97_Q	0.771	1.00
185_R	190_R	0.770	1.00
166_S	169_D	0.763	1.00
190_R	193_A	0.763	1.00
142_A	154_T	0.761	1.00
154_T	158_T	0.761	1.00
166_S	170_F	0.756	1.00
154_T	159_L	0.755	1.00
120_A	124_T	0.754	1.00
35_L	65_V	0.752	1.00
181_R	184_T	0.752	1.00
41_L	56_I	0.740	1.00
133_R	194_K	0.740	1.00
155_L	159_L	0.739	1.00
161_R	164_S	0.738	1.00
24_E	27_Q	0.737	1.00
97_Q	146_I	0.736	1.00
116_H	120_A	0.734	1.00
118_A	122_G	0.730	1.00
56_I	60_V	0.729	1.00
38_E	67_R	0.724	1.00
17_I	52_L	0.723	1.00
112_P	128_N	0.722	1.00
42_A	52_L	0.720	1.00
96_D	112_P	0.718	1.00
118_A	180_R	0.708	1.00
99_S	196_C	0.706	1.00
130_I	180_R	0.704	1.00
45_F	52_L	0.704	1.00
103_S	192_Q	0.699	1.00
195_E	198_R	0.698	1.00
19_A	23_Q	0.694	1.00
172_R	178_A	0.694	1.00
94_L	138_V	0.693	1.00
17_I	20_K	0.693	1.00
131_H	176_G	0.690	1.00
194_K	197_Q	0.690	1.00
28_H	44_R	0.689	1.00
36_P	44_R	0.688	1.00
169_D	172_R	0.676	1.00
103_S	107_L	0.675	1.00
104_E	107_L	0.668	1.00
189_R	193_A	0.668	1.00
21_L	29_Y	0.667	1.00
178_A	181_R	0.663	1.00
43_A	46_E	0.660	1.00
93_N	98_G	0.659	1.00
86_A	89_R	0.659	1.00
113_A	137_R	0.655	1.00
201_I	205_S	0.651	1.00
197_Q	201_I	0.650	1.00
129_V	132_L	0.641	1.00
189_R	192_Q	0.638	1.00
103_S	106_L	0.634	1.00
95_L	98_G	0.633	1.00
10_Y	16_E	0.628	1.00
99_S	139_N	0.624	1.00
121_L	124_T	0.624	1.00
41_L	45_F	0.624	1.00
132_L	151_A	0.623	1.00
113_A	121_L	0.622	1.00
128_N	156_W	0.622	1.00
107_L	189_R	0.621	1.00
160_Q	163_D	0.617	1.00
82_Y	85_N	0.616	1.00
98_G	101_P	0.615	1.00
138_V	143_L	0.614	1.00
39_Q	42_A	0.613	1.00
132_L	144_C	0.602	1.00
29_Y	35_L	0.602	1.00
191_A	196_C	0.601	1.00
170_F	173_E	0.599	1.00
117_V	137_R	0.595	1.00
179_L	195_E	0.594	1.00
106_L	135_L	0.593	1.00
56_I	67_R	0.592	1.00
166_S	173_E	0.590	1.00
52_L	65_V	0.589	1.00
120_A	136_R	0.589	1.00
142_A	145_L	0.585	1.00
96_D	108_S	0.584	1.00
137_R	140_G	0.580	1.00
51_T	55_A	0.576	1.00
124_T	129_V	0.575	1.00
195_E	199_L	0.574	1.00
151_A	154_T	0.573	1.00
97_Q	101_P	0.572	1.00
191_A	205_S	0.571	1.00
104_E	108_S	0.569	1.00
107_L	111_R	0.568	1.00
193_A	196_C	0.566	1.00
147_D	195_E	0.565	1.00
18_A	55_A	0.564	1.00
178_A	190_R	0.563	1.00
194_K	198_R	0.562	1.00
179_L	194_K	0.560	1.00
90_F	94_L	0.558	1.00
114_S	118_A	0.555	1.00
172_R	177_I	0.555	1.00
177_I	180_R	0.551	1.00
105_K	109_V	0.551	1.00
124_T	133_R	0.551	1.00
107_L	110_L	0.549	1.00
93_N	96_D	0.542	1.00
100_H	143_L	0.540	1.00
60_V	73_V	0.536	1.00
182_S	187_S	0.534	1.00
110_L	130_I	0.533	1.00
34_Y	71_V	0.533	1.00
42_A	45_F	0.530	1.00
82_Y	89_R	0.528	1.00
95_L	101_P	0.527	1.00
17_I	55_A	0.525	1.00
83_P	86_A	0.524	1.00
23_Q	26_R	0.523	1.00
116_H	119_D	0.523	1.00
17_I	21_L	0.522	1.00
113_A	123_I	0.521	1.00
50_H	54_R	0.521	1.00
117_V	136_R	0.519	1.00
69_Q	72_G	0.518	1.00
111_R	114_S	0.516	1.00
82_Y	88_A	0.516	1.00
29_Y	36_P	0.515	1.00
119_D	122_G	0.514	1.00
39_Q	49_R	0.509	1.00
113_A	129_V	0.508	1.00
121_L	133_R	0.507	1.00
118_A	186_I	0.506	1.00
37_A	70_G	0.504	1.00
83_P	88_A	0.504	1.00
15_Q	18_A	0.503	1.00
38_E	73_V	0.502	1.00
95_L	100_H	0.501	1.00
148_H	151_A	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
4u0wA	2	0.9917	100	0.135	Contact Map
2ra5A	2	0.5975	100	0.144	Contact Map
3f8mA	2	0.9336	100	0.158	Contact Map
3eetA	2	0.9336	100	0.191	Contact Map
3edpA	2	0.9087	100	0.194	Contact Map
3bwgA	2	0.9336	100	0.208	Contact Map
3f8lA	2	0.6639	99.9	0.447	Contact Map
1hw1A	2	0.8299	99.9	0.481	Contact Map
3sxyA	2	0.7676	99.9	0.489	Contact Map
4p96A	2	0.8838	99.9	0.492	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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