PHPDC - ECOLI - GREMLIN Contacts

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PHPDC - PHP domain-containing protein YciV

UniProt:	P77766	Sequences: MSDTNYAVIYDLHSHTTASDGCLTPEALVHRAVEMRVGTLAITDHDTTAAIAPAREEISRSGLALNLIPGVEISTVWENHEIHIVGLNIDITHPLMCEFLAQQTERRNQRAQLIAERLEKAQIPGALEGAQRLAQGGAVTRGHFARFLVECGKASSMADVFKKYLARGKTGYVPPQWCTIEQAIDVIHHSGGKAVLAHPGRYNLSAKWLKRLVAHFAEHHGDAMEVAQCQQSPNERTQLAALARQHHLWASQGSDFHQPCPWIELGRKLWLPAGVEGVWQLWEQPQNTTEREL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14257
Length:	293 (267)
Sequences:	2487 (1858)
Seq/√Len:	113.7

ECOLI - PHPDC
HALSA - Q9HML2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_T	42_I	4.935	1.00
26_E	53_P	4.536	1.00
188_H	222_D	4.264	1.00
194_A	222_D	3.768	1.00
188_H	194_A	3.283	1.00
129_G	151_C	3.119	1.00
23_L	256_F	3.097	1.00
58_I	67_L	3.041	1.00
187_I	192_G	2.823	1.00
99_F	186_V	2.512	1.00
155_S	159_D	2.476	1.00
14_S	28_L	2.399	1.00
232_S	235_E	2.320	1.00
71_V	100_L	2.227	1.00
113_L	116_E	2.165	1.00
133_L	150_E	2.111	1.00
43_T	70_G	2.082	1.00
121_A	171_G	2.078	1.00
14_S	40_L	2.058	1.00
37_V	40_L	1.996	1.00
30_H	57_E	1.983	1.00
156_S	159_D	1.969	1.00
57_E	60_R	1.958	1.00
195_V	251_S	1.955	1.00
33_V	61_S	1.954	1.00
129_G	147_F	1.924	1.00
123_I	164_Y	1.876	1.00
240_A	250_A	1.846	1.00
179_T	182_Q	1.819	1.00
226_V	250_A	1.807	1.00
95_L	189_H	1.803	1.00
90_D	93_H	1.799	1.00
101_A	105_E	1.761	1.00
71_V	86_G	1.739	1.00
48_T	97_C	1.733	1.00
154_A	159_D	1.719	1.00
35_M	264_E	1.709	1.00
33_V	65_L	1.707	1.00
94_P	98_E	1.675	1.00
112_Q	127_L	1.637	1.00
154_A	160_V	1.620	1.00
195_V	223_A	1.610	1.00
146_R	157_M	1.606	1.00
29_V	40_L	1.594	1.00
51_I	69_P	1.572	1.00
31_R	264_E	1.538	1.00
182_Q	185_D	1.535	1.00
24_T	27_A	1.528	1.00
58_I	65_L	1.498	1.00
210_K	245_Q	1.498	1.00
23_L	31_R	1.485	1.00
158_A	162_K	1.478	1.00
51_I	67_L	1.471	1.00
115_A	127_L	1.456	1.00
147_F	151_C	1.444	1.00
231_Q	239_L	1.420	1.00
200_G	235_E	1.413	1.00
187_I	194_A	1.391	1.00
217_A	246_H	1.391	1.00
48_T	89_I	1.364	1.00
217_A	247_H	1.359	1.00
113_L	117_R	1.356	1.00
260_C	263_I	1.350	1.00
200_G	231_Q	1.338	1.00
112_Q	116_E	1.338	1.00
130_A	134_A	1.335	1.00
114_I	144_F	1.330	1.00
241_A	245_Q	1.325	1.00
129_G	150_E	1.322	1.00
52_A	92_T	1.314	1.00
84_I	187_I	1.310	1.00
166_A	169_K	1.307	1.00
87_L	251_S	1.284	0.99
216_F	221_G	1.278	0.99
14_S	32_A	1.277	0.99
119_E	124_P	1.267	0.99
30_H	34_E	1.263	0.99
32_A	40_L	1.248	0.99
86_G	187_I	1.247	0.99
55_R	69_P	1.239	0.99
31_R	34_E	1.239	0.99
85_V	251_S	1.233	0.99
181_E	215_H	1.231	0.99
40_L	67_L	1.220	0.99
73_I	183_A	1.218	0.99
105_E	109_Q	1.216	0.99
55_R	91_I	1.216	0.99
111_A	144_F	1.214	0.99
27_A	30_H	1.214	0.99
227_A	240_A	1.206	0.99
9_I	38_G	1.205	0.99
22_C	258_Q	1.204	0.99
39_T	66_N	1.202	0.99
111_A	139_V	1.199	0.99
181_E	185_D	1.186	0.99
227_A	236_R	1.178	0.99
110_R	161_F	1.178	0.99
115_A	144_F	1.172	0.99
214_A	246_H	1.172	0.99
243_A	250_A	1.171	0.99
185_D	189_H	1.165	0.99
55_R	67_L	1.161	0.99
126_A	129_G	1.160	0.99
75_T	183_A	1.154	0.99
52_A	91_I	1.150	0.99
56_E	59_S	1.150	0.99
31_R	35_M	1.144	0.99
228_Q	252_Q	1.143	0.99
42_I	50_A	1.143	0.99
178_C	183_A	1.142	0.99
228_Q	231_Q	1.138	0.99
54_A	67_L	1.131	0.99
184_I	219_H	1.130	0.99
129_G	132_R	1.125	0.99
213_V	224_M	1.121	0.99
115_A	119_E	1.113	0.98
33_V	62_G	1.106	0.98
107_R	143_H	1.102	0.98
30_H	61_S	1.101	0.98
116_E	120_K	1.100	0.98
46_D	107_R	1.100	0.98
110_R	141_R	1.096	0.98
226_V	239_L	1.095	0.98
226_V	240_A	1.092	0.98
181_E	219_H	1.086	0.98
46_D	74_S	1.084	0.98
193_K	222_D	1.078	0.98
180_I	216_F	1.076	0.98
133_L	147_F	1.068	0.98
25_P	29_V	1.067	0.98
84_I	180_I	1.062	0.98
26_E	30_H	1.059	0.98
154_A	165_L	1.051	0.98
108_N	131_Q	1.049	0.98
141_R	161_F	1.047	0.98
14_S	265_L	1.032	0.97
148_L	154_A	1.030	0.97
196_L	213_V	1.027	0.97
24_T	28_L	1.023	0.97
41_A	70_G	1.015	0.97
200_G	239_L	1.015	0.97
57_E	61_S	1.014	0.97
237_T	241_A	1.014	0.97
82_I	202_Y	1.008	0.97
55_R	59_S	1.008	0.97
125_G	130_A	1.003	0.97
99_F	182_Q	0.999	0.97
99_F	102_Q	0.997	0.97
10_Y	39_T	0.994	0.97
215_H	218_E	0.993	0.97
73_I	100_L	0.982	0.97
17_T	24_T	0.967	0.96
39_T	68_I	0.966	0.96
128_E	131_Q	0.960	0.96
123_I	148_L	0.956	0.96
10_Y	275_V	0.954	0.96
25_P	57_E	0.949	0.96
224_M	239_L	0.944	0.96
268_K	272_P	0.943	0.96
95_L	98_E	0.935	0.95
125_G	128_E	0.934	0.95
121_A	170_T	0.933	0.95
106_R	176_Q	0.925	0.95
223_A	249_W	0.922	0.95
86_G	89_I	0.922	0.95
123_I	153_K	0.911	0.95
29_V	54_A	0.911	0.95
99_F	178_C	0.910	0.95
118_L	171_G	0.905	0.95
148_L	153_K	0.900	0.94
167_R	172_Y	0.898	0.94
226_V	243_A	0.898	0.94
233_P	237_T	0.896	0.94
117_R	171_G	0.893	0.94
141_R	145_A	0.892	0.94
23_L	27_A	0.892	0.94
117_R	120_K	0.888	0.94
244_R	274_G	0.888	0.94
58_I	62_G	0.888	0.94
264_E	267_R	0.886	0.94
125_G	147_F	0.882	0.94
141_R	165_L	0.879	0.94
31_R	256_F	0.879	0.94
68_I	88_N	0.879	0.94
226_V	236_R	0.878	0.94
75_T	81_E	0.877	0.94
107_R	110_R	0.876	0.94
193_K	249_W	0.874	0.93
142_G	145_A	0.874	0.93
215_H	219_H	0.873	0.93
51_I	91_I	0.870	0.93
93_H	190_S	0.863	0.93
115_A	125_G	0.860	0.93
29_V	57_E	0.858	0.93
238_Q	242_L	0.851	0.93
51_I	55_R	0.847	0.92
85_V	223_A	0.846	0.92
55_R	58_I	0.845	0.92
26_E	57_E	0.844	0.92
110_R	114_I	0.840	0.92
87_L	195_V	0.839	0.92
33_V	60_R	0.839	0.92
52_A	56_E	0.838	0.92
201_R	230_Q	0.830	0.92
84_I	194_A	0.828	0.91
18_A	53_P	0.827	0.91
56_E	60_R	0.826	0.91
69_P	91_I	0.823	0.91
149_V	156_S	0.823	0.91
159_D	163_K	0.821	0.91
115_A	130_A	0.817	0.91
127_L	131_Q	0.815	0.91
229_C	263_I	0.810	0.91
69_P	89_I	0.808	0.90
75_T	84_I	0.803	0.90
238_Q	241_A	0.802	0.90
71_V	89_I	0.798	0.90
110_R	145_A	0.797	0.90
111_A	127_L	0.795	0.90
30_H	33_V	0.795	0.90
214_A	218_E	0.792	0.90
270_W	275_V	0.792	0.90
109_Q	112_Q	0.788	0.89
108_N	112_Q	0.788	0.89
42_I	67_L	0.788	0.89
270_W	274_G	0.784	0.89
41_A	51_I	0.783	0.89
272_P	275_V	0.764	0.88
78_E	215_H	0.761	0.88
110_R	140_T	0.760	0.88
45_H	257_H	0.758	0.87
149_V	157_M	0.758	0.87
109_Q	113_L	0.757	0.87
127_L	130_A	0.754	0.87
75_T	180_I	0.754	0.87
196_L	221_G	0.751	0.87
54_A	58_I	0.751	0.87
271_L	275_V	0.745	0.87
161_F	165_L	0.745	0.87
146_R	150_E	0.737	0.86
132_R	150_E	0.735	0.86
231_Q	236_R	0.735	0.86
114_I	141_R	0.729	0.85
52_A	55_R	0.726	0.85
29_V	58_I	0.726	0.85
96_M	100_L	0.725	0.85
110_R	143_H	0.724	0.85
75_T	103_Q	0.722	0.85
263_I	268_K	0.716	0.84
110_R	142_G	0.714	0.84
145_A	161_F	0.711	0.84
18_A	49_A	0.711	0.84
29_V	36_R	0.700	0.83
262_W	267_R	0.699	0.83
86_G	183_A	0.699	0.83
184_I	188_H	0.696	0.83
228_Q	236_R	0.695	0.83
95_L	190_S	0.691	0.82
249_W	274_G	0.689	0.82
118_L	123_I	0.688	0.82
50_A	57_E	0.686	0.82
218_E	246_H	0.686	0.82
28_L	265_L	0.685	0.82
46_D	110_R	0.685	0.82
124_P	151_C	0.684	0.81
37_V	65_L	0.679	0.81
114_I	165_L	0.679	0.81
214_A	245_Q	0.679	0.81
193_K	278_V	0.674	0.81
244_R	250_A	0.673	0.80
102_Q	106_R	0.671	0.80
186_V	190_S	0.670	0.80
90_D	97_C	0.670	0.80
205_S	239_L	0.670	0.80
29_V	67_L	0.667	0.80
149_V	154_A	0.666	0.80
117_R	121_A	0.665	0.80
83_H	198_H	0.662	0.79
144_F	171_G	0.661	0.79
38_G	66_N	0.661	0.79
271_L	274_G	0.660	0.79
88_N	193_K	0.657	0.79
85_V	195_V	0.654	0.79
46_D	143_H	0.654	0.79
96_M	186_V	0.651	0.78
76_V	177_W	0.647	0.78
234_N	237_T	0.646	0.78
58_I	61_S	0.645	0.78
214_A	242_L	0.641	0.77
226_V	231_Q	0.640	0.77
241_A	244_R	0.639	0.77
15_H	19_S	0.634	0.76
224_M	242_L	0.631	0.76
141_R	160_V	0.631	0.76
127_L	139_V	0.628	0.76
198_H	257_H	0.623	0.75
188_H	193_K	0.623	0.75
235_E	238_Q	0.623	0.75
49_A	104_T	0.622	0.75
229_C	268_K	0.618	0.75
116_E	119_E	0.617	0.74
229_C	260_C	0.615	0.74
133_L	146_R	0.615	0.74
139_V	144_F	0.612	0.74
154_A	164_Y	0.605	0.73
110_R	165_L	0.605	0.73
85_V	228_Q	0.604	0.73
130_A	147_F	0.599	0.72
45_H	255_D	0.598	0.72
13_H	19_S	0.598	0.72
185_D	219_H	0.596	0.72
18_A	25_P	0.595	0.72
236_R	268_K	0.595	0.72
274_G	277_G	0.594	0.72
213_V	248_L	0.594	0.72
110_R	160_V	0.593	0.72
156_S	162_K	0.593	0.72
187_I	190_S	0.588	0.71
89_I	96_M	0.587	0.71
48_T	51_I	0.585	0.70
119_E	126_A	0.584	0.70
29_V	65_L	0.583	0.70
9_I	37_V	0.583	0.70
142_G	161_F	0.582	0.70
130_A	139_V	0.579	0.70
109_Q	237_T	0.578	0.70
107_R	141_R	0.577	0.69
163_K	170_T	0.575	0.69
117_R	173_V	0.574	0.69
272_P	277_G	0.571	0.69
66_N	88_N	0.571	0.69
118_L	144_F	0.570	0.69
145_A	160_V	0.569	0.68
62_G	65_L	0.568	0.68
205_S	208_W	0.568	0.68
92_T	97_C	0.568	0.68
148_L	165_L	0.567	0.68
247_H	250_A	0.567	0.68
31_R	265_L	0.566	0.68
122_Q	263_I	0.565	0.68
232_S	236_R	0.563	0.68
41_A	68_I	0.560	0.67
186_V	189_H	0.560	0.67
147_F	153_K	0.559	0.67
184_I	216_F	0.559	0.67
122_Q	231_Q	0.559	0.67
126_A	147_F	0.558	0.67
84_I	196_L	0.556	0.67
78_E	211_R	0.556	0.67
11_D	14_S	0.551	0.66
121_A	169_K	0.551	0.66
236_R	240_A	0.550	0.66
130_A	171_G	0.549	0.66
130_A	133_L	0.545	0.65
41_A	87_L	0.544	0.65
105_E	108_N	0.544	0.65
71_V	183_A	0.544	0.65
98_E	102_Q	0.544	0.65
140_T	161_F	0.541	0.65
42_I	51_I	0.541	0.65
222_D	249_W	0.540	0.64
129_G	133_L	0.539	0.64
54_A	62_G	0.539	0.64
97_C	101_A	0.537	0.64
126_A	130_A	0.536	0.64
69_P	88_N	0.533	0.63
110_R	173_V	0.533	0.63
84_I	179_T	0.533	0.63
159_D	162_K	0.531	0.63
74_S	83_H	0.529	0.63
18_A	47_T	0.526	0.62
15_H	20_D	0.525	0.62
83_H	197_A	0.525	0.62
223_A	278_V	0.525	0.62
192_G	195_V	0.524	0.62
61_S	65_L	0.524	0.62
213_V	242_L	0.523	0.62
32_A	37_V	0.523	0.62
117_R	174_P	0.522	0.62
16_T	41_A	0.521	0.62
185_D	188_H	0.519	0.61
20_D	45_H	0.518	0.61
184_I	220_H	0.517	0.61
140_T	145_A	0.517	0.61
145_A	165_L	0.515	0.61
80_H	167_R	0.511	0.60
93_H	189_H	0.509	0.60
178_C	186_V	0.509	0.60
20_D	257_H	0.508	0.60
98_E	101_A	0.508	0.60
229_C	267_R	0.507	0.60
148_L	160_V	0.507	0.60
83_H	118_L	0.506	0.59
29_V	42_I	0.506	0.59
47_T	50_A	0.506	0.59
108_N	127_L	0.505	0.59
252_Q	258_Q	0.502	0.59
20_D	198_H	0.501	0.59
196_L	207_K	0.500	0.59
22_C	259_P	0.500	0.59

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
2yb1A	1	0.9556	100	0.338	Contact Map
3o0fA	1	0.9659	100	0.344	Contact Map
3e38A	4	0.6997	100	0.646	Contact Map
2anuA	5	0.6519	100	0.662	Contact Map
1m65A	3	0.7133	100	0.669	Contact Map
4gc3A	1	0.7406	100	0.675	Contact Map
3qy7A	1	0.7167	100	0.686	Contact Map
2yxoA	3	0.7645	100	0.688	Contact Map
2wjeA	1	0.7304	100	0.692	Contact Map
2w9mA	1	0.7304	99.9	0.719	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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