YDJX - ECOLI - GREMLIN Contacts

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YDJX - TVP38/TMEM64 family membrane protein YdjX

UniProt:	P76219	Sequences: MNAERKFLFACLIFALVIYAIHAFGLFDLLTDLPHLQTLIRQSGFFGYSLYILLFIIATLLLLPGSILVIAGGIVFGPLLGTLLSLIAATLASSCSFLLARWLGRDLLLKYVGHSNTFQAIEKGIARNGIDFLILTRLIPLFPYNIQNYAYGLTTIAFWPYTLISALTTLPGIVIYTVMASDLANEGITLRFILQLCLAGLALFILVQLAKLYARHKHVDLSASRRSPLTHPKNEG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14000
Length:	236 (184)
Sequences:	8155 (6058)
Seq/√Len:	446.6

ECOLI - YDJX YDJZ YQJA YGHB DEDA YABI YOHD
BACSU - YHJE YTXB YQED YKOX YNGC
SULSO - Q97V45

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_S	158_F	3.997	1.00
208_Q	212_L	3.019	1.00
82_T	174_V	2.732	1.00
157_A	160_P	2.686	1.00
105_R	122_E	2.459	1.00
90_T	166_A	2.329	1.00
130_I	164_I	2.310	1.00
94_S	162_T	2.266	1.00
77_G	80_L	2.160	1.00
207_V	211_K	2.111	1.00
210_A	214_A	2.107	1.00
134_I	167_L	2.071	1.00
77_G	81_G	2.059	1.00
195_Q	199_A	2.053	1.00
51_Y	72_G	1.978	1.00
209_L	213_Y	1.965	1.00
119_Q	123_K	1.956	1.00
86_L	170_L	1.951	1.00
122_E	126_A	1.919	1.00
194_L	198_L	1.881	1.00
56_I	95_C	1.863	1.00
73_G	180_A	1.814	1.00
130_I	160_P	1.787	1.00
52_I	84_L	1.779	1.00
203_L	206_L	1.776	1.00
206_L	210_A	1.765	1.00
128_N	131_D	1.764	1.00
158_F	162_T	1.707	1.00
104_G	107_L	1.697	1.00
190_L	193_I	1.679	1.00
52_I	88_A	1.641	1.00
208_Q	211_K	1.627	1.00
93_S	165_S	1.615	1.00
213_Y	217_K	1.615	1.00
211_K	215_R	1.571	1.00
90_T	162_T	1.560	1.00
100_A	153_L	1.558	1.00
85_S	173_I	1.557	1.00
78_P	82_T	1.550	1.00
82_T	177_T	1.538	1.00
48_Y	84_L	1.535	1.00
40_I	47_G	1.520	1.00
98_L	158_F	1.506	1.00
198_L	202_A	1.500	1.00
117_T	120_A	1.476	1.00
101_R	155_T	1.470	1.00
56_I	91_L	1.464	1.00
178_V	182_D	1.441	1.00
133_L	164_I	1.405	1.00
159_W	163_L	1.405	1.00
196_L	200_G	1.403	1.00
110_K	113_G	1.401	1.00
78_P	178_V	1.394	1.00
79_L	83_L	1.387	1.00
192_F	195_Q	1.381	1.00
204_F	207_V	1.355	1.00
98_L	102_W	1.354	1.00
37_Q	41_R	1.353	1.00
100_A	152_G	1.336	1.00
94_S	98_L	1.326	1.00
207_V	210_A	1.314	1.00
38_T	41_R	1.299	1.00
211_K	214_A	1.286	1.00
79_L	82_T	1.277	1.00
86_L	166_A	1.240	1.00
55_F	58_A	1.236	1.00
204_F	208_Q	1.206	1.00
52_I	56_I	1.206	1.00
80_L	84_L	1.200	1.00
52_I	87_I	1.196	1.00
72_G	81_G	1.193	1.00
80_L	83_L	1.188	1.00
47_G	76_F	1.184	1.00
85_S	177_T	1.183	1.00
136_T	147_Q	1.172	1.00
105_R	109_L	1.164	1.00
200_G	204_F	1.162	1.00
212_L	215_R	1.162	1.00
165_S	169_T	1.158	1.00
137_R	165_S	1.156	1.00
82_T	178_V	1.151	1.00
38_T	42_Q	1.127	1.00
193_I	197_C	1.117	1.00
113_G	117_T	1.116	1.00
189_T	192_F	1.106	1.00
131_D	135_L	1.105	1.00
119_Q	122_E	1.097	1.00
73_G	177_T	1.089	1.00
69_V	177_T	1.088	1.00
122_E	155_T	1.075	1.00
72_G	85_S	1.066	1.00
189_T	193_I	1.048	1.00
81_G	177_T	1.046	1.00
84_L	88_A	1.039	1.00
51_Y	85_S	1.037	1.00
138_L	171_P	1.020	1.00
171_P	174_V	1.019	1.00
125_I	151_Y	1.005	1.00
212_L	216_H	0.990	1.00
201_L	204_F	0.988	1.00
39_L	43_S	0.986	1.00
144_Y	169_T	0.971	1.00
105_R	108_L	0.968	1.00
144_Y	172_G	0.967	1.00
160_P	164_I	0.966	1.00
69_V	85_S	0.962	1.00
203_L	207_V	0.961	1.00
55_F	69_V	0.957	1.00
130_I	163_L	0.954	1.00
55_F	59_T	0.941	1.00
133_L	156_I	0.938	1.00
167_L	170_L	0.935	1.00
34_P	38_T	0.927	1.00
86_L	173_I	0.911	1.00
76_F	81_G	0.909	1.00
48_Y	80_L	0.908	1.00
137_R	148_N	0.901	1.00
130_I	134_I	0.894	1.00
148_N	165_S	0.885	1.00
159_W	162_T	0.884	1.00
82_T	86_L	0.879	1.00
66_S	176_Y	0.875	1.00
83_L	86_L	0.873	1.00
207_V	213_Y	0.872	1.00
89_A	169_T	0.872	1.00
71_A	75_V	0.866	1.00
72_G	76_F	0.846	1.00
194_L	197_C	0.844	1.00
108_L	112_V	0.843	1.00
124_G	132_F	0.832	1.00
194_L	206_L	0.821	1.00
190_L	194_L	0.817	1.00
162_T	166_A	0.815	1.00
35_H	39_L	0.811	1.00
69_V	73_G	0.810	1.00
122_E	154_T	0.809	1.00
195_Q	198_L	0.807	1.00
58_A	145_N	0.807	1.00
199_A	206_L	0.807	1.00
199_A	214_A	0.804	1.00
69_V	173_I	0.791	1.00
43_S	50_L	0.790	1.00
160_P	163_L	0.790	1.00
58_A	92_A	0.788	1.00
90_T	169_T	0.783	1.00
209_L	212_L	0.783	1.00
97_F	158_F	0.781	1.00
55_F	68_L	0.773	1.00
199_A	203_L	0.771	1.00
63_L	145_N	0.770	1.00
73_G	81_G	0.767	1.00
96_S	149_Y	0.763	1.00
48_Y	52_I	0.763	1.00
206_L	213_Y	0.763	1.00
79_L	178_V	0.762	1.00
97_F	154_T	0.759	1.00
93_S	148_N	0.758	1.00
213_Y	216_H	0.752	1.00
173_I	177_T	0.750	1.00
197_C	201_L	0.746	1.00
83_L	87_I	0.746	1.00
49_S	53_L	0.744	1.00
58_A	65_G	0.741	1.00
66_S	144_Y	0.741	1.00
97_F	161_Y	0.739	1.00
134_I	164_I	0.738	1.00
136_T	151_Y	0.730	1.00
123_K	126_A	0.729	1.00
192_F	196_L	0.727	1.00
58_A	63_L	0.726	1.00
93_S	158_F	0.723	1.00
214_A	218_H	0.720	1.00
60_L	96_S	0.718	1.00
78_P	177_T	0.714	1.00
174_V	178_V	0.714	1.00
164_I	168_T	0.713	1.00
189_T	194_L	0.711	1.00
62_L	145_N	0.709	1.00
34_P	37_Q	0.708	1.00
215_R	218_H	0.702	1.00
125_I	129_G	0.702	1.00
196_L	207_V	0.701	1.00
48_Y	77_G	0.701	1.00
35_H	38_T	0.696	1.00
214_A	217_K	0.695	1.00
135_L	139_I	0.694	1.00
134_I	171_P	0.694	1.00
198_L	201_L	0.694	1.00
195_Q	206_L	0.687	1.00
60_L	64_P	0.680	1.00
116_N	120_A	0.676	1.00
93_S	137_R	0.675	1.00
92_A	96_S	0.673	1.00
114_H	119_Q	0.672	1.00
191_R	195_Q	0.670	1.00
90_T	165_S	0.669	1.00
51_Y	55_F	0.667	1.00
123_K	127_R	0.666	1.00
202_A	206_L	0.666	1.00
205_I	208_Q	0.659	1.00
132_F	136_T	0.659	1.00
84_L	87_I	0.659	1.00
196_L	199_A	0.655	1.00
210_A	213_Y	0.653	1.00
109_L	122_E	0.652	1.00
82_T	173_I	0.652	1.00
86_L	90_T	0.651	1.00
193_I	196_L	0.651	1.00
195_Q	203_L	0.636	0.99
183_L	186_E	0.633	0.99
91_L	95_C	0.631	0.99
96_S	145_N	0.631	0.99
109_L	119_Q	0.630	0.99
106_D	109_L	0.629	0.99
169_T	172_G	0.625	0.99
60_L	65_G	0.620	0.99
199_A	202_A	0.618	0.99
51_Y	58_A	0.613	0.99
151_Y	156_I	0.613	0.99
116_N	119_Q	0.613	0.99
163_L	167_L	0.612	0.99
147_Q	151_Y	0.609	0.99
102_W	106_D	0.608	0.99
194_L	199_A	0.604	0.99
78_P	174_V	0.603	0.99
99_L	103_L	0.600	0.99
44_G	47_G	0.598	0.99
46_F	50_L	0.597	0.99
195_Q	210_A	0.596	0.99
67_I	71_A	0.591	0.99
97_F	101_R	0.590	0.99
201_L	205_I	0.589	0.99
121_I	143_P	0.588	0.99
181_S	184_A	0.586	0.99
190_L	195_Q	0.585	0.99
145_N	148_N	0.583	0.99
206_L	217_K	0.581	0.99
69_V	89_A	0.579	0.99
100_A	149_Y	0.578	0.99
51_Y	59_T	0.574	0.99
50_L	53_L	0.571	0.99
45_F	49_S	0.565	0.99
143_P	148_N	0.560	0.99
134_I	168_T	0.555	0.98
52_I	91_L	0.549	0.98
124_G	127_R	0.548	0.98
200_G	207_V	0.546	0.98
98_L	101_R	0.545	0.98
210_A	218_H	0.545	0.98
103_L	106_D	0.542	0.98
117_T	121_I	0.541	0.98
88_A	92_A	0.540	0.98
99_L	133_L	0.540	0.98
56_I	88_A	0.537	0.98
111_Y	114_H	0.536	0.98
189_T	195_Q	0.534	0.98
107_L	111_Y	0.534	0.98
86_L	169_T	0.531	0.98
87_I	91_L	0.530	0.98
46_F	49_S	0.529	0.98
71_A	74_I	0.527	0.98
113_G	116_N	0.525	0.98
166_A	170_L	0.524	0.98
61_L	96_S	0.522	0.98
33_L	36_L	0.520	0.98
200_G	203_L	0.517	0.98
134_I	138_L	0.509	0.97
196_L	206_L	0.508	0.97
179_M	182_D	0.507	0.97
207_V	214_A	0.506	0.97
194_L	201_L	0.506	0.97
62_L	68_L	0.506	0.97
203_L	213_Y	0.502	0.97
108_L	118_F	0.502	0.97
198_L	212_L	0.501	0.97
199_A	210_A	0.500	0.97

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
3qnqA	2	0.9237	73.3	0.91	Contact Map
4m64A	1	0.9534	60.2	0.918	Contact Map
3giaA	1	0.8136	58.8	0.918	Contact Map
4j05A	3	0.9068	56.5	0.919	Contact Map
4dveA	3	0.7034	54	0.921	Contact Map
4z7fA	2	0.6864	51.6	0.922	Contact Map
4pypA	1	0.8729	49.8	0.922	Contact Map
3wdoA	1	0.9703	49.7	0.922	Contact Map
3w9iA	3	0.7712	46.3	0.924	Contact Map
4dx5A	3	0.8093	44.3	0.925	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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