YPHB - ECOLI - GREMLIN Contacts

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YPHB - Uncharacterized protein YphB

UniProt:	P76584	Sequences: MTIYTLSHGSLKLDVSDQGGVIEGFWRDTTPLLRPGKKSGVATDASCFPLVPFANRVSGNRFVWQGREYQLQPNVEWDAHYLHGDGWLGEWQCVSHSDDSLCLVYEHRSGVYHYRVSQAFHLTADTLTVTLSVTNQGAETLPFGTGWHPYFPLSPQTRIQAQASGYWLEREQWLAGEFCEQLPQELDFNQPAPLPRQWVNNGFAGWNGQARIEQPQEGYAIIMETTPPAPCYFIFVSDPAFDKGYAFDFFCLEPMSHAPDDHHRPEGGDLIALAPGESTTSEMSLRVEWL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13463
Length:	290 (272)
Sequences:	6040 (4655)
Seq/√Len:	282.2

ECOLI - YPHB YIHR GALM YEAD
BACSU - GALM
SULSO - Q97V88

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
60_N	73_P	3.115	1.00
212_I	250_F	3.096	1.00
61_R	68_E	2.823	1.00
192_A	197_Q	2.707	1.00
94_V	104_V	2.616	1.00
13_L	25_F	2.561	1.00
106_E	115_R	2.527	1.00
140_T	274_A	2.525	1.00
7_S	12_K	2.482	1.00
260_D	264_R	2.392	1.00
76_E	79_A	2.373	1.00
222_I	286_R	2.360	1.00
12_K	26_W	2.297	1.00
106_E	113_H	2.264	1.00
102_C	119_A	2.259	1.00
4_Y	101_L	2.192	1.00
134_T	278_S	2.189	1.00
167_W	202_G	2.173	1.00
102_C	117_S	2.166	1.00
113_H	138_A	2.153	1.00
38_K	41_V	2.150	1.00
16_S	23_E	2.109	1.00
24_G	31_P	2.106	1.00
89_G	105_Y	2.101	1.00
4_Y	93_C	2.098	1.00
104_V	117_S	2.013	1.00
30_T	219_Y	2.009	1.00
132_S	280_T	2.003	1.00
15_V	103_L	1.949	1.00
13_L	22_I	1.886	1.00
123_T	128_T	1.884	1.00
234_I	250_F	1.884	1.00
17_D	90_E	1.872	1.00
130_T	282_E	1.863	1.00
211_R	220_A	1.858	1.00
274_A	277_E	1.857	1.00
5_T	14_D	1.843	1.00
14_D	24_G	1.840	1.00
168_L	178_F	1.829	1.00
63_V	68_E	1.788	1.00
65_Q	140_T	1.787	1.00
20_G	103_L	1.782	1.00
100_S	121_H	1.772	1.00
11_L	25_F	1.767	1.00
183_P	189_N	1.737	1.00
142_P	272_A	1.737	1.00
104_V	115_R	1.728	1.00
97_S	100_S	1.708	1.00
211_R	222_I	1.700	1.00
94_V	102_C	1.676	1.00
61_R	70_Q	1.675	1.00
154_S	214_Q	1.652	1.00
224_E	286_R	1.642	1.00
58_S	260_D	1.622	1.00
114_Y	143_F	1.609	1.00
254_P	283_M	1.578	1.00
49_P	118_Q	1.578	1.00
20_G	49_P	1.566	1.00
64_W	272_A	1.561	1.00
158_R	191_P	1.558	1.00
55_N	233_F	1.550	1.00
25_F	287_V	1.529	1.00
128_T	284_S	1.500	1.00
86_G	116_V	1.497	1.00
160_Q	211_R	1.496	1.00
158_R	213_E	1.493	1.00
50_L	146_G	1.472	1.00
33_L	149_P	1.471	1.00
117_S	134_T	1.460	1.00
224_E	284_S	1.458	1.00
15_V	101_L	1.452	1.00
188_F	192_A	1.437	1.00
86_G	105_Y	1.434	1.00
214_Q	219_Y	1.430	1.00
53_F	262_H	1.424	1.00
75_V	80_H	1.415	1.00
65_Q	139_E	1.404	1.00
144_G	257_H	1.402	1.00
193_P	196_R	1.361	1.00
67_R	139_E	1.358	1.00
5_T	12_K	1.353	1.00
227_P	257_H	1.352	1.00
214_Q	217_E	1.340	1.00
79_A	172_Q	1.340	1.00
204_A	258_A	1.329	1.00
165_G	181_Q	1.328	1.00
226_T	281_S	1.328	1.00
53_F	271_I	1.325	1.00
121_H	130_T	1.310	1.00
158_R	215_P	1.278	1.00
109_S	139_E	1.263	1.00
11_L	27_R	1.261	1.00
115_R	136_Q	1.249	1.00
92_Q	104_V	1.248	1.00
140_T	275_P	1.231	1.00
260_D	263_H	1.228	1.00
257_H	271_I	1.223	1.00
160_Q	191_P	1.217	1.00
18_Q	90_E	1.213	1.00
168_L	180_E	1.209	1.00
192_A	196_R	1.209	1.00
238_D	247_F	1.201	1.00
22_I	33_L	1.196	1.00
11_L	126_T	1.193	1.00
237_S	240_A	1.186	1.00
100_S	119_A	1.165	1.00
94_V	117_S	1.165	1.00
6_L	122_L	1.161	1.00
11_L	122_L	1.156	1.00
52_P	107_H	1.156	1.00
232_Y	252_L	1.155	1.00
95_S	102_C	1.153	1.00
213_E	220_A	1.149	1.00
166_Y	180_E	1.137	1.00
45_A	87_W	1.133	1.00
209_Q	225_T	1.129	1.00
107_H	113_H	1.122	1.00
227_P	281_S	1.101	1.00
199_V	203_F	1.091	1.00
143_F	279_T	1.089	1.00
56_R	82_L	1.085	1.00
13_L	129_V	1.082	1.00
140_T	272_A	1.080	1.00
59_G	80_H	1.077	1.00
161_A	234_I	1.070	1.00
159_I	212_I	1.062	1.00
169_E	173_W	1.062	1.00
202_G	231_C	1.060	1.00
25_F	151_F	1.058	1.00
60_N	70_Q	1.055	1.00
231_C	258_A	1.054	1.00
70_Q	73_P	1.046	1.00
99_D	121_H	1.044	1.00
31_P	35_P	1.043	1.00
27_R	32_L	1.041	1.00
16_S	21_V	1.041	1.00
34_R	249_F	1.039	1.00
143_F	273_L	1.030	1.00
113_H	137_G	1.028	1.00
73_P	79_A	1.028	1.00
237_S	249_F	1.027	1.00
182_L	189_N	1.026	1.00
93_C	101_L	1.018	1.00
202_G	233_F	1.012	1.00
21_V	48_F	1.012	1.00
119_A	132_S	1.001	1.00
58_S	170_R	0.993	1.00
273_L	278_S	0.986	1.00
59_G	79_A	0.985	1.00
8_H	122_L	0.983	1.00
49_P	147_W	0.983	1.00
158_R	193_P	0.981	1.00
186_L	201_N	0.980	1.00
223_M	254_P	0.975	1.00
95_S	100_S	0.965	1.00
155_P	247_F	0.961	1.00
159_I	188_F	0.959	1.00
125_D	286_R	0.955	1.00
22_I	149_P	0.953	1.00
53_F	57_V	0.945	1.00
116_V	145_T	0.942	1.00
126_T	286_R	0.939	1.00
58_S	174_L	0.937	1.00
132_S	282_E	0.936	1.00
25_F	33_L	0.936	1.00
261_D	271_I	0.928	1.00
36_G	46_S	0.921	1.00
123_T	126_T	0.921	1.00
157_T	214_Q	0.921	1.00
221_I	287_V	0.919	1.00
65_Q	274_A	0.917	1.00
118_Q	131_L	0.915	1.00
176_G	179_C	0.906	1.00
126_T	284_S	0.904	1.00
58_S	263_H	0.897	1.00
45_A	82_L	0.895	1.00
63_V	66_G	0.891	1.00
8_H	126_T	0.890	1.00
205_G	208_G	0.887	1.00
103_L	120_F	0.876	1.00
83_H	148_H	0.875	1.00
53_F	81_Y	0.875	1.00
26_W	31_P	0.875	1.00
160_Q	213_E	0.872	1.00
45_A	88_L	0.870	1.00
57_V	71_L	0.868	1.00
8_H	124_A	0.868	1.00
148_H	253_E	0.865	1.00
156_Q	193_P	0.864	1.00
108_R	113_H	0.862	1.00
226_T	282_E	0.861	1.00
81_Y	84_G	0.861	1.00
9_G	124_A	0.858	1.00
194_L	250_F	0.857	1.00
159_I	234_I	0.851	1.00
145_T	279_T	0.848	1.00
142_P	262_H	0.847	1.00
62_F	69_Y	0.844	1.00
161_A	232_Y	0.832	1.00
52_P	114_Y	0.827	1.00
80_H	172_Q	0.826	1.00
137_G	141_L	0.820	1.00
49_P	120_F	0.818	1.00
117_S	132_S	0.817	0.99
65_Q	272_A	0.814	0.99
83_H	253_E	0.811	0.99
123_T	130_T	0.809	0.99
32_L	287_V	0.807	0.99
72_Q	81_Y	0.803	0.99
156_Q	216_Q	0.803	0.99
4_Y	103_L	0.802	0.99
96_H	101_L	0.801	0.99
132_S	278_S	0.801	0.99
210_A	232_Y	0.799	0.99
91_W	116_V	0.797	0.99
22_I	129_V	0.793	0.99
89_G	108_R	0.788	0.99
159_I	252_L	0.788	0.99
4_Y	17_D	0.784	0.99
199_V	234_I	0.783	0.99
136_Q	141_L	0.782	0.99
142_P	270_L	0.777	0.99
51_V	116_V	0.775	0.99
153_L	157_T	0.774	0.99
137_G	275_P	0.773	0.99
130_T	280_T	0.772	0.99
91_W	118_Q	0.772	0.99
10_S	28_D	0.765	0.99
254_P	281_S	0.765	0.99
164_S	189_N	0.762	0.99
161_A	210_A	0.757	0.99
86_G	114_Y	0.756	0.99
27_R	219_Y	0.753	0.99
93_C	103_L	0.746	0.99
186_L	203_F	0.745	0.99
223_M	252_L	0.742	0.99
25_F	32_L	0.740	0.99
22_I	147_W	0.736	0.99
55_N	202_G	0.736	0.99
61_R	263_H	0.734	0.99
71_L	81_Y	0.730	0.99
209_Q	222_I	0.730	0.99
212_I	252_L	0.729	0.99
116_V	133_V	0.724	0.99
75_V	82_L	0.723	0.99
14_D	23_E	0.723	0.99
128_T	286_R	0.721	0.99
155_P	198_W	0.720	0.99
151_F	285_L	0.717	0.99
64_W	112_Y	0.717	0.99
53_F	142_P	0.717	0.99
9_G	126_T	0.714	0.99
51_V	86_G	0.713	0.99
125_D	128_T	0.713	0.99
165_G	179_C	0.710	0.99
58_S	264_R	0.709	0.99
114_Y	141_L	0.705	0.99
131_L	147_W	0.703	0.98
264_R	267_G	0.701	0.98
168_L	176_G	0.700	0.98
59_G	73_P	0.699	0.98
188_F	191_P	0.696	0.98
59_G	172_Q	0.695	0.98
223_M	285_L	0.694	0.98
225_T	283_M	0.694	0.98
159_I	194_L	0.692	0.98
17_D	93_C	0.692	0.98
35_P	152_P	0.689	0.98
168_L	179_C	0.687	0.98
50_L	54_A	0.687	0.98
195_P	198_W	0.686	0.98
257_H	261_D	0.686	0.98
273_L	277_E	0.684	0.98
15_V	22_I	0.683	0.98
11_L	32_L	0.682	0.98
134_T	280_T	0.681	0.98
24_G	35_P	0.679	0.98
53_F	261_D	0.678	0.98
202_G	255_M	0.676	0.98
57_V	262_H	0.676	0.98
199_V	202_G	0.674	0.98
52_P	84_G	0.668	0.98
115_R	134_T	0.667	0.98
154_S	215_P	0.665	0.98
8_H	125_D	0.664	0.98
112_Y	137_G	0.663	0.98
33_L	151_F	0.662	0.98
234_I	252_L	0.659	0.98
14_D	26_W	0.657	0.98
75_V	239_P	0.654	0.98
22_I	25_F	0.653	0.98
166_Y	186_L	0.650	0.97
49_P	116_V	0.648	0.97
86_G	107_H	0.646	0.97
62_F	71_L	0.642	0.97
135_N	143_F	0.638	0.97
17_D	92_Q	0.637	0.97
167_W	258_A	0.637	0.97
93_C	96_H	0.636	0.97
194_L	197_Q	0.636	0.97
48_F	87_W	0.633	0.97
8_H	11_L	0.630	0.97
137_G	273_L	0.629	0.97
21_V	42_A	0.625	0.97
160_Q	190_Q	0.622	0.97
166_Y	201_N	0.622	0.97
30_T	217_E	0.619	0.97
73_P	81_Y	0.616	0.97
58_S	172_Q	0.615	0.97
233_F	255_M	0.614	0.96
54_A	255_M	0.614	0.96
56_R	253_E	0.610	0.96
157_T	212_I	0.608	0.96
6_L	101_L	0.605	0.96
57_V	62_F	0.605	0.96
240_A	251_C	0.604	0.96
129_V	133_V	0.604	0.96
182_L	187_D	0.603	0.96
50_L	87_W	0.598	0.96
162_Q	208_G	0.596	0.96
82_L	87_W	0.596	0.96
56_R	83_H	0.595	0.96
136_Q	278_S	0.594	0.96
107_H	110_G	0.593	0.96
47_C	147_W	0.591	0.96
76_E	80_H	0.591	0.96
191_P	213_E	0.591	0.96
86_G	91_W	0.588	0.96
30_T	214_Q	0.586	0.95
46_S	240_A	0.584	0.95
20_G	120_F	0.581	0.95
130_T	284_S	0.580	0.95
113_H	136_Q	0.580	0.95
64_W	71_L	0.579	0.95
155_P	158_R	0.579	0.95
166_Y	203_F	0.576	0.95
96_H	102_C	0.576	0.95
156_Q	195_P	0.572	0.95
105_Y	108_R	0.572	0.95
42_A	87_W	0.571	0.95
63_V	263_H	0.569	0.95
60_N	81_Y	0.568	0.95
61_R	73_P	0.567	0.95
118_Q	129_V	0.567	0.95
92_Q	106_E	0.564	0.94
162_Q	209_Q	0.564	0.94
21_V	88_L	0.563	0.94
161_A	188_F	0.558	0.94
54_A	257_H	0.557	0.94
76_E	172_Q	0.555	0.94
133_V	143_F	0.554	0.94
239_P	246_A	0.554	0.94
85_D	88_L	0.553	0.94
147_W	283_M	0.551	0.94
143_F	281_S	0.551	0.94
62_F	263_H	0.551	0.94
133_V	146_G	0.550	0.94
82_L	259_P	0.544	0.93
223_M	283_M	0.544	0.93
12_K	24_G	0.541	0.93
152_P	157_T	0.541	0.93
221_I	285_L	0.540	0.93
10_S	124_A	0.539	0.93
203_F	234_I	0.539	0.93
162_Q	207_N	0.539	0.93
150_Y	235_F	0.538	0.93
6_L	13_L	0.538	0.93
112_Y	141_L	0.537	0.93
63_V	69_Y	0.537	0.93
137_G	140_T	0.536	0.93
15_V	120_F	0.536	0.93
56_R	60_N	0.536	0.93
54_A	144_G	0.535	0.93
36_G	41_V	0.533	0.93
36_G	43_T	0.532	0.92
154_S	216_Q	0.531	0.92
261_D	268_G	0.529	0.92
21_V	43_T	0.529	0.92
175_A	178_F	0.528	0.92
128_T	282_E	0.528	0.92
86_G	89_G	0.525	0.92
56_R	148_H	0.520	0.92
186_L	199_V	0.519	0.92
271_I	279_T	0.518	0.91
179_C	204_A	0.517	0.91
165_G	178_F	0.516	0.91
23_E	46_S	0.516	0.91
131_L	135_N	0.514	0.91
33_L	46_S	0.513	0.91
126_T	133_V	0.512	0.91
17_D	103_L	0.511	0.91
267_G	270_L	0.511	0.91
69_Y	112_Y	0.511	0.91
212_I	234_I	0.511	0.91
96_H	100_S	0.510	0.91
146_G	251_C	0.509	0.91
258_A	267_G	0.508	0.91
74_N	80_H	0.507	0.91
7_S	98_D	0.506	0.91
36_G	42_A	0.506	0.91
184_Q	187_D	0.506	0.91
57_V	60_N	0.504	0.90
36_G	44_D	0.504	0.90
173_W	239_P	0.504	0.90
209_Q	224_E	0.503	0.90
257_H	270_L	0.502	0.90
59_G	75_V	0.501	0.90
72_Q	75_V	0.500	0.90

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
1z45A	2	0.9759	100	0.204	Contact Map
3nreA	1	0.9897	100	0.213	Contact Map
1ygaA	2	0.9793	100	0.216	Contact Map
1lurA	1	0.9724	100	0.238	Contact Map
1nsxA	2	0.9655	100	0.251	Contact Map
1snzA	1	0.969	100	0.256	Contact Map
4rnlA	1	0.9655	100	0.256	Contact Map
3mwxA	1	0.9759	100	0.259	Contact Map
3imhA	3	0.9586	100	0.267	Contact Map
3os7A	2	0.9759	100	0.268	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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