YTPQ - BACSU - GREMLIN Contacts

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YTPQ - UPF0354 protein YtpQ

UniProt:	O34496	Sequences: MKMTSRKLSDILKQRLQHENRSFLFDREKDTLRVEDQTTKKGITLDLPPIIAKWELKKDEAIDEIVYYVSEAMTAMEGKAQEMTGKETRIYPVIRSTSFPDKSSEDIPLIYDDHTAETRIYYALDLGKTYRLIDQRMLEKENWTKERIRETAAFNLRSLPTVVKEDTVAGNYFYFFRANDGYDASRILNEAILNEYKQHAEGELAISVPHQDVLILADIRNESGYDILGQMSMSFFAGGTVPITALSFLYNEGKLEPVFILAKSRPKKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	269 (264)
Sequences:	193 (137)
Seq/√Len:	8.4

BACSU - YTPQ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
205_A	217_A	4.982	1.00
201_E	220_R	4.388	0.99
205_A	228_L	3.766	0.97
204_L	216_L	3.630	0.96
172_Y	220_R	3.579	0.96
165_E	172_Y	3.270	0.93
31_T	44_T	3.101	0.91
150_E	154_F	2.859	0.86
111_Y	187_I	2.818	0.86
200_A	204_L	2.769	0.85
192_I	216_L	2.731	0.84
112_D	149_R	2.701	0.83
11_I	14_Q	2.673	0.82
83_M	143_W	2.617	0.81
21_R	36_D	2.471	0.77
101_D	119_R	2.464	0.77
207_S	232_S	2.425	0.75
187_I	208_V	2.414	0.75
30_D	48_P	2.289	0.71
167_T	172_Y	2.282	0.71
8_L	51_I	2.277	0.70
161_T	176_F	2.240	0.69
103_S	178_A	2.234	0.69
62_I	66_V	2.141	0.65
10_D	13_K	2.095	0.64
12_L	219_I	1.994	0.60
25_F	51_I	1.988	0.59
43_I	104_S	1.970	0.59
33_R	42_G	1.923	0.57
5_S	30_D	1.913	0.56
234_S	238_G	1.888	0.55
9_S	13_K	1.812	0.52
102_K	106_D	1.783	0.51
102_K	232_S	1.770	0.50
50_I	65_I	1.733	0.49
25_F	201_E	1.663	0.46
167_T	170_G	1.639	0.45
165_E	203_E	1.636	0.45
143_W	147_R	1.627	0.44
215_I	231_M	1.622	0.44
156_L	161_T	1.616	0.44
170_G	254_K	1.599	0.43
219_I	238_G	1.591	0.43
12_L	66_V	1.562	0.42
163_V	176_F	1.543	0.41
4_T	9_S	1.536	0.41
28_E	178_A	1.535	0.41
5_S	48_P	1.534	0.41
165_E	231_M	1.527	0.40
167_T	199_H	1.513	0.40
88_T	158_S	1.496	0.39
222_E	267_K	1.484	0.38
78_G	147_R	1.479	0.38
54_W	58_K	1.458	0.37
109_L	266_P	1.445	0.37
13_K	32_L	1.438	0.37
76_M	134_D	1.432	0.36
144_T	165_E	1.428	0.36
110_I	176_F	1.428	0.36
140_K	148_I	1.406	0.35
134_D	154_F	1.406	0.35
102_K	108_P	1.403	0.35
227_I	253_G	1.398	0.35
154_F	157_R	1.397	0.35
207_S	217_A	1.396	0.35
13_K	163_V	1.383	0.35
28_E	51_I	1.369	0.34
161_T	220_R	1.358	0.34
153_A	156_L	1.351	0.33
136_R	241_V	1.348	0.33
193_L	250_Y	1.329	0.33
176_F	192_I	1.319	0.32
4_T	7_K	1.308	0.32
113_D	217_A	1.298	0.31
67_Y	177_R	1.279	0.31
4_T	39_T	1.258	0.30
48_P	51_I	1.257	0.30
23_F	32_L	1.252	0.30
67_Y	264_S	1.231	0.29
103_S	161_T	1.230	0.29
32_L	68_Y	1.223	0.29
124_L	160_P	1.223	0.29
8_L	56_L	1.208	0.28
42_G	64_E	1.193	0.28
72_A	81_Q	1.190	0.28
88_T	227_I	1.186	0.27
28_E	71_E	1.182	0.27
118_T	236_F	1.181	0.27
72_A	227_I	1.180	0.27
187_I	243_I	1.179	0.27
131_R	233_M	1.171	0.27
146_E	151_T	1.167	0.27
15_R	63_D	1.159	0.27
102_K	110_I	1.153	0.26
4_T	262_A	1.147	0.26
226_D	260_I	1.141	0.26
110_I	138_L	1.141	0.26
203_E	220_R	1.134	0.26
18_H	69_V	1.132	0.26
13_K	241_V	1.127	0.26
69_V	77_E	1.125	0.25
19_E	167_T	1.123	0.25
43_I	128_K	1.109	0.25
60_E	160_P	1.107	0.25
96_S	129_T	1.103	0.25
32_L	65_I	1.100	0.25
233_M	247_S	1.097	0.25
69_V	80_A	1.091	0.24
100_P	119_R	1.080	0.24
133_I	252_E	1.079	0.24
14_Q	214_L	1.077	0.24
113_D	139_E	1.073	0.24
129_T	247_S	1.067	0.24
91_Y	145_K	1.065	0.24
54_W	73_M	1.062	0.24
67_Y	131_R	1.060	0.23
45_L	103_S	1.049	0.23
247_S	262_A	1.045	0.23
123_A	132_L	1.044	0.23
67_Y	233_M	1.040	0.23
35_E	73_M	1.040	0.23
196_Y	265_R	1.039	0.23
207_S	262_A	1.036	0.23
9_S	52_A	1.034	0.23
140_K	149_R	1.027	0.22
169_A	245_A	1.022	0.22
7_K	222_E	1.021	0.22
203_E	245_A	1.020	0.22
177_R	187_I	1.013	0.22
42_G	53_K	1.006	0.22
169_A	240_T	1.006	0.22
62_I	69_V	1.001	0.22
165_E	201_E	1.000	0.22
111_Y	219_I	1.000	0.22
49_P	217_A	0.995	0.22
20_N	146_E	0.995	0.22
234_S	245_A	0.988	0.21
161_T	192_I	0.986	0.21
7_K	128_K	0.985	0.21
67_Y	204_L	0.980	0.21
6_R	9_S	0.980	0.21
109_L	160_P	0.977	0.21
87_E	155_N	0.976	0.21
101_D	109_L	0.976	0.21
34_V	165_E	0.970	0.21
91_Y	176_F	0.970	0.21
50_I	109_L	0.968	0.21
71_E	206_I	0.966	0.21
68_Y	177_R	0.965	0.21
36_D	69_V	0.963	0.21
49_P	58_K	0.960	0.21
179_N	183_D	0.958	0.21
42_G	230_Q	0.950	0.20
45_L	266_P	0.950	0.20
39_T	73_M	0.950	0.20
148_I	206_I	0.950	0.20
65_I	120_I	0.950	0.20
62_I	263_K	0.947	0.20
67_Y	247_S	0.942	0.20
46_D	54_W	0.942	0.20
69_V	205_A	0.942	0.20
4_T	55_E	0.940	0.20
23_F	67_Y	0.939	0.20
236_F	245_A	0.931	0.20
194_N	217_A	0.925	0.20
72_A	86_K	0.924	0.20
23_F	68_Y	0.914	0.19
124_L	190_E	0.913	0.19
197_K	265_R	0.913	0.19
142_N	222_E	0.912	0.19
10_D	111_Y	0.910	0.19
144_T	162_V	0.904	0.19
60_E	137_M	0.900	0.19
91_Y	211_Q	0.899	0.19
238_G	253_G	0.897	0.19
96_S	245_A	0.896	0.19
116_A	207_S	0.891	0.19
20_N	37_Q	0.887	0.19
108_P	199_H	0.886	0.19
116_A	166_D	0.881	0.18
205_A	230_Q	0.880	0.18
192_I	204_L	0.879	0.18
69_V	230_Q	0.868	0.18
111_Y	119_R	0.868	0.18
67_Y	71_E	0.867	0.18
101_D	258_V	0.862	0.18
67_Y	179_N	0.850	0.18
7_K	208_V	0.843	0.18
135_Q	176_F	0.841	0.17
5_S	15_R	0.838	0.17
46_D	49_P	0.833	0.17
67_Y	263_K	0.829	0.17
101_D	111_Y	0.823	0.17
192_I	247_S	0.817	0.17
35_E	87_E	0.815	0.17
42_G	154_F	0.812	0.17
21_R	77_E	0.810	0.17
36_D	77_E	0.796	0.16
85_G	141_E	0.794	0.16
9_S	43_I	0.794	0.16
192_I	196_Y	0.787	0.16
47_L	119_R	0.786	0.16
261_L	265_R	0.781	0.16
75_A	223_S	0.778	0.16
96_S	258_V	0.778	0.16
97_T	119_R	0.771	0.16
22_S	26_D	0.768	0.16
29_K	234_S	0.766	0.16
107_I	136_R	0.766	0.16
46_D	258_V	0.766	0.16
223_S	264_S	0.766	0.16
204_L	262_A	0.766	0.16
4_T	72_A	0.760	0.16
135_Q	199_H	0.758	0.16
110_I	137_M	0.757	0.16
197_K	245_A	0.755	0.15
90_I	231_M	0.754	0.15
77_E	178_A	0.754	0.15
28_E	66_V	0.746	0.15
36_D	39_T	0.742	0.15
97_T	148_I	0.739	0.15
55_E	137_M	0.739	0.15
84_T	167_T	0.737	0.15
62_I	65_I	0.736	0.15
110_I	135_Q	0.733	0.15
42_G	76_M	0.733	0.15
73_M	158_S	0.733	0.15
4_T	21_R	0.732	0.15
193_L	229_G	0.731	0.15
138_L	148_I	0.730	0.15
134_D	247_S	0.722	0.15
49_P	261_L	0.722	0.15
91_Y	160_P	0.719	0.15
39_T	77_E	0.712	0.15
33_R	53_K	0.711	0.15
64_E	251_N	0.711	0.15
89_R	143_W	0.711	0.15
17_Q	142_N	0.710	0.15
78_G	151_T	0.710	0.15
43_I	69_V	0.709	0.14
15_R	258_V	0.705	0.14
12_L	28_E	0.705	0.14
43_I	86_K	0.704	0.14
189_N	258_V	0.701	0.14
9_S	20_N	0.701	0.14
43_I	142_N	0.698	0.14
8_L	11_I	0.696	0.14
129_T	194_N	0.689	0.14
131_R	263_K	0.685	0.14
234_S	247_S	0.685	0.14
131_R	264_S	0.682	0.14
52_A	241_V	0.681	0.14
12_L	116_A	0.679	0.14
8_L	54_W	0.679	0.14
50_I	133_I	0.676	0.14
199_H	261_L	0.670	0.14
43_I	62_I	0.666	0.14
33_R	64_E	0.664	0.14
36_D	163_V	0.663	0.14
147_R	151_T	0.662	0.14
72_A	141_E	0.662	0.14
58_K	266_P	0.659	0.13
128_K	222_E	0.658	0.13
123_A	134_D	0.655	0.13
35_E	64_E	0.653	0.13
72_A	190_E	0.651	0.13
10_D	156_L	0.649	0.13
141_E	245_A	0.647	0.13
123_A	154_F	0.646	0.13
50_I	233_M	0.645	0.13
91_Y	267_K	0.645	0.13
172_Y	193_L	0.643	0.13
137_M	227_I	0.643	0.13
13_K	25_F	0.643	0.13
144_T	170_G	0.641	0.13
16_L	67_Y	0.640	0.13
23_F	262_A	0.639	0.13
189_N	233_M	0.639	0.13
262_A	267_K	0.639	0.13
4_T	30_D	0.637	0.13
31_T	101_D	0.636	0.13
128_K	262_A	0.636	0.13
71_E	233_M	0.636	0.13
123_A	236_F	0.630	0.13
134_D	150_E	0.630	0.13
8_L	15_R	0.630	0.13
111_Y	217_A	0.624	0.13
123_A	230_Q	0.624	0.13
145_K	148_I	0.621	0.13
36_D	245_A	0.620	0.13
39_T	234_S	0.615	0.13
52_A	217_A	0.614	0.13
50_I	147_R	0.611	0.13
69_V	84_T	0.608	0.13
54_W	72_A	0.608	0.13
20_N	110_I	0.607	0.12
70_S	170_G	0.605	0.12
176_F	199_H	0.605	0.12
57_K	266_P	0.604	0.12
160_P	243_I	0.604	0.12
112_D	145_K	0.604	0.12
122_Y	230_Q	0.601	0.12
216_L	223_S	0.600	0.12
229_G	245_A	0.600	0.12
24_L	27_R	0.598	0.12
196_Y	229_G	0.597	0.12
41_K	45_L	0.597	0.12
144_T	164_K	0.596	0.12
187_I	194_N	0.595	0.12
16_L	32_L	0.595	0.12
9_S	32_L	0.594	0.12
50_I	264_S	0.594	0.12
73_M	83_M	0.591	0.12
20_N	89_R	0.590	0.12
48_P	189_N	0.586	0.12
116_A	127_G	0.584	0.12
165_E	190_E	0.581	0.12
46_D	58_K	0.581	0.12
80_A	223_S	0.580	0.12
146_E	220_R	0.579	0.12
81_Q	196_Y	0.579	0.12
35_E	230_Q	0.577	0.12
11_I	15_R	0.577	0.12
223_S	266_P	0.575	0.12
50_I	70_S	0.574	0.12
102_K	172_Y	0.574	0.12
103_S	176_F	0.572	0.12
220_R	236_F	0.572	0.12
7_K	72_A	0.572	0.12
112_D	245_A	0.570	0.12
204_L	263_K	0.569	0.12
28_E	238_G	0.568	0.12
68_Y	262_A	0.567	0.12
109_L	228_L	0.566	0.12
109_L	264_S	0.566	0.12
177_R	214_L	0.566	0.12
7_K	241_V	0.565	0.12
50_I	161_T	0.564	0.12
64_E	232_S	0.563	0.12
244_T	259_F	0.562	0.12
192_I	253_G	0.561	0.12
6_R	45_L	0.561	0.12
194_N	207_S	0.560	0.12
262_A	266_P	0.560	0.12
28_E	96_S	0.558	0.12
51_I	199_H	0.558	0.12
12_L	36_D	0.558	0.12
76_M	132_L	0.556	0.12
45_L	267_K	0.555	0.12
45_L	162_V	0.553	0.12
154_F	158_S	0.552	0.12
116_A	232_S	0.551	0.11
136_R	139_E	0.550	0.11
76_M	154_F	0.547	0.11
90_I	196_Y	0.546	0.11
17_Q	45_L	0.546	0.11
85_G	109_L	0.546	0.11
86_K	104_S	0.544	0.11
109_L	262_A	0.544	0.11
56_L	136_R	0.543	0.11
232_S	254_K	0.542	0.11
59_D	140_K	0.542	0.11
122_Y	188_L	0.541	0.11
182_Y	242_P	0.540	0.11
184_A	211_Q	0.540	0.11
69_V	112_D	0.539	0.11
21_R	57_K	0.539	0.11
165_E	227_I	0.539	0.11
80_A	139_E	0.537	0.11
233_M	264_S	0.536	0.11
190_E	237_A	0.532	0.11
21_R	55_E	0.532	0.11
7_K	137_M	0.531	0.11
37_Q	53_K	0.530	0.11
106_D	133_I	0.528	0.11
9_S	34_V	0.525	0.11
145_K	176_F	0.524	0.11
75_A	136_R	0.519	0.11
156_L	243_I	0.519	0.11
111_Y	147_R	0.516	0.11
110_I	145_K	0.515	0.11
10_D	63_D	0.514	0.11
9_S	148_I	0.514	0.11
135_Q	144_T	0.514	0.11
30_D	189_N	0.512	0.11
48_P	124_L	0.511	0.11
74_T	220_R	0.511	0.11
97_T	264_S	0.509	0.11
86_K	91_Y	0.509	0.11
138_L	240_T	0.508	0.11
13_K	72_A	0.508	0.11
26_D	96_S	0.506	0.11
145_K	149_R	0.504	0.11
16_L	44_T	0.504	0.11
150_E	157_R	0.503	0.11
219_I	244_T	0.500	0.11

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
3q4fC	2	0.3494	39.8	0.974	Contact Map
3tmaA	2	0.8587	16.2	0.979	Contact Map
3njrA	4	0.6134	10.9	0.98	Contact Map
3s8iA	2	0.4164	10.1	0.981	Contact Map
2ywqA	1	0.2677	8.6	0.981	Contact Map
3p91A	3	0.3978	8.1	0.981	Contact Map
1bvoA	1	0.2193	6.3	0.982	Contact Map
4bixA	2	0.342	5.7	0.983	Contact Map
2ogkA	4	0.2454	5.5	0.983	Contact Map
3q6bA	1	0.342	5.2	0.983	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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