YCBR - BACSU - GREMLIN Contacts

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YCBR - Uncharacterized protein YcbR

UniProt:	P42250	Sequences: MATIDLQKKSVKIVLEKKQLTKVTARVGLVLDITGSMRPLYKNGTVQNVVERILAVADQFDDNGLLDVWVYDNEFSRLKPVSEKDFSGYVDREILNNDRLHKFGRNDEPPVMKDVLRKYVTEEPSSYPAFIVFINDGGCKKSIKPIIEASSDKPVFWQFVGIGNGNFDFLNKLDTLEGRVIDNTNFLHIEEIDRISDDELYDALLAEFPFWLKEAKEKGIVREQEPPAEKPKKKGFFSRLFSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	243 (188)
Sequences:	3921 (2420)
Seq/√Len:	176.5

ECOLI - YEGL
BACSU - YCBR YWMC YWMD
SULSO - Q97Z45

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_E	95_L	3.936	1.00
55_A	91_D	2.876	1.00
112_M	150_S	2.803	1.00
31_L	50_V	2.707	1.00
86_F	89_Y	2.696	1.00
33_I	70_V	2.639	1.00
36_S	136_D	2.479	1.00
29_L	50_V	2.458	1.00
106_N	136_D	2.330	1.00
175_T	179_R	2.329	1.00
148_E	152_D	2.258	1.00
70_V	78_L	2.197	1.00
36_S	106_N	2.121	1.00
115_V	131_I	2.077	1.00
123_E	129_A	2.065	1.00
67_D	81_V	2.039	1.00
113_K	117_R	2.032	1.00
51_E	91_D	2.026	1.00
67_D	119_Y	1.991	1.00
109_P	141_K	1.944	1.00
30_V	115_V	1.931	1.00
144_K	172_K	1.878	1.00
28_G	67_D	1.854	1.00
139_C	169_F	1.782	1.00
151_S	175_T	1.770	1.00
68_V	79_K	1.708	1.00
54_L	94_I	1.696	1.00
77_R	114_D	1.673	1.00
185_N	188_H	1.658	1.00
124_P	127_Y	1.657	1.00
30_V	131_I	1.650	1.00
75_F	114_D	1.637	1.00
84_K	93_E	1.627	1.00
38_R	42_K	1.605	1.00
107_D	110_P	1.601	1.00
116_L	150_S	1.587	1.00
26_R	65_L	1.574	1.00
44_G	47_Q	1.561	1.00
150_S	155_V	1.545	1.00
116_L	153_K	1.543	1.00
167_F	171_N	1.516	1.00
68_V	97_N	1.498	1.00
26_R	129_A	1.498	1.00
42_K	99_R	1.473	1.00
79_K	90_V	1.471	1.00
143_I	147_I	1.468	1.00
116_L	146_I	1.461	1.00
54_L	66_L	1.457	1.00
106_N	137_G	1.454	1.00
131_I	157_W	1.436	1.00
114_D	118_K	1.422	1.00
35_G	104_G	1.400	1.00
159_F	174_D	1.395	1.00
79_K	84_K	1.386	1.00
133_F	159_F	1.382	1.00
138_G	166_N	1.367	1.00
149_A	152_D	1.352	1.00
161_G	170_L	1.344	1.00
38_R	99_R	1.338	1.00
159_F	170_L	1.315	1.00
33_I	100_L	1.305	1.00
28_G	81_V	1.284	1.00
36_S	137_G	1.281	1.00
133_F	173_L	1.271	1.00
77_R	80_P	1.271	1.00
71_Y	108_E	1.269	1.00
84_K	89_Y	1.250	1.00
80_P	83_E	1.239	1.00
33_I	43_N	1.237	1.00
92_R	96_N	1.232	1.00
108_E	135_N	1.223	1.00
28_G	119_Y	1.220	1.00
45_T	187_L	1.218	1.00
46_V	186_F	1.203	1.00
54_L	90_V	1.202	1.00
145_P	149_A	1.195	1.00
158_Q	179_R	1.177	1.00
144_K	148_E	1.172	1.00
131_I	150_S	1.157	1.00
69_W	115_V	1.146	1.00
58_D	63_N	1.140	1.00
32_D	137_G	1.136	1.00
116_L	149_A	1.132	1.00
29_L	53_I	1.118	1.00
113_K	146_I	1.103	1.00
112_M	131_I	1.084	1.00
171_N	177_E	1.079	1.00
55_A	87_S	1.075	1.00
31_L	46_V	1.073	1.00
147_I	151_S	1.072	1.00
108_E	133_F	1.068	1.00
131_I	155_V	1.064	1.00
139_C	143_I	1.064	1.00
109_P	146_I	1.030	0.99
30_V	69_W	1.013	0.99
47_Q	94_I	1.007	0.99
73_N	105_R	0.998	0.99
35_G	136_D	0.997	0.99
82_S	122_E	0.996	0.99
59_Q	66_L	0.995	0.99
146_I	149_A	0.990	0.99
142_S	145_P	0.985	0.99
134_I	162_I	0.984	0.99
48_N	52_R	0.977	0.99
37_M	106_N	0.971	0.99
50_V	94_I	0.971	0.99
28_G	115_V	0.955	0.99
174_D	180_V	0.941	0.99
70_V	97_N	0.939	0.99
75_F	110_P	0.937	0.99
143_I	146_I	0.930	0.99
42_K	45_T	0.929	0.99
156_F	179_R	0.925	0.99
151_S	157_W	0.921	0.99
36_S	71_Y	0.915	0.99
168_D	171_N	0.913	0.99
69_W	111_V	0.909	0.99
108_E	169_F	0.907	0.99
29_L	132_V	0.894	0.98
109_P	139_C	0.888	0.98
128_P	156_F	0.882	0.98
147_I	154_P	0.881	0.98
44_G	48_N	0.878	0.98
171_N	175_T	0.878	0.98
79_K	93_E	0.878	0.98
77_R	119_Y	0.876	0.98
21_T	201_Y	0.872	0.98
48_N	51_E	0.871	0.98
84_K	90_V	0.861	0.98
37_M	42_K	0.858	0.98
150_S	157_W	0.858	0.98
74_E	110_P	0.850	0.98
120_V	153_K	0.844	0.98
26_R	124_P	0.844	0.98
139_C	147_I	0.843	0.98
87_S	91_D	0.839	0.98
147_I	157_W	0.837	0.98
72_D	107_D	0.836	0.98
74_E	100_L	0.824	0.97
49_V	189_I	0.823	0.97
47_Q	97_N	0.823	0.97
35_G	105_R	0.820	0.97
162_I	186_F	0.814	0.97
54_L	57_A	0.808	0.97
54_L	87_S	0.806	0.97
130_F	196_S	0.805	0.97
105_R	136_D	0.805	0.97
69_W	119_Y	0.799	0.97
25_A	130_F	0.797	0.97
132_V	200_L	0.795	0.97
115_V	150_S	0.790	0.97
106_N	135_N	0.786	0.97
121_T	124_P	0.783	0.97
97_N	100_L	0.782	0.96
115_V	119_Y	0.774	0.96
94_I	97_N	0.773	0.96
28_G	69_W	0.773	0.96
27_V	66_L	0.768	0.96
69_W	75_F	0.764	0.96
43_N	47_Q	0.762	0.96
91_D	95_L	0.762	0.96
183_N	192_I	0.760	0.96
70_V	143_I	0.759	0.96
33_I	131_I	0.747	0.95
137_G	170_L	0.743	0.95
171_N	176_L	0.741	0.95
166_N	169_F	0.738	0.95
69_W	114_D	0.736	0.95
27_V	130_F	0.728	0.95
160_V	192_I	0.721	0.94
34_T	106_N	0.719	0.94
36_S	135_N	0.718	0.94
135_N	170_L	0.718	0.94
203_A	206_A	0.713	0.94
105_R	140_K	0.711	0.94
112_M	157_W	0.709	0.94
68_V	111_V	0.706	0.94
113_K	149_A	0.704	0.94
20_L	201_Y	0.696	0.93
71_Y	106_N	0.693	0.93
25_A	64_G	0.692	0.93
161_G	165_G	0.690	0.93
88_G	95_L	0.690	0.93
138_G	169_F	0.688	0.93
24_T	127_Y	0.684	0.93
86_F	90_V	0.677	0.92
167_F	182_D	0.675	0.92
108_E	139_C	0.666	0.92
186_F	189_I	0.664	0.92
70_V	100_L	0.664	0.92
47_Q	51_E	0.662	0.92
33_I	72_D	0.660	0.91
18_K	21_T	0.657	0.91
80_P	119_Y	0.657	0.91
60_F	65_L	0.655	0.91
92_R	95_L	0.650	0.91
32_D	36_S	0.647	0.91
109_P	143_I	0.647	0.91
165_G	182_D	0.646	0.91
69_W	77_R	0.642	0.90
113_K	125_S	0.642	0.90
140_K	143_I	0.636	0.90
110_P	113_K	0.635	0.90
186_F	201_Y	0.628	0.89
78_L	97_N	0.628	0.89
37_M	136_D	0.626	0.89
49_V	111_V	0.625	0.89
148_E	151_S	0.624	0.89
61_D	85_D	0.623	0.89
33_I	99_R	0.620	0.89
28_G	111_V	0.619	0.89
90_V	94_I	0.616	0.88
34_T	137_G	0.615	0.88
151_S	179_R	0.613	0.88
141_K	146_I	0.608	0.88
53_I	197_D	0.605	0.88
73_N	104_G	0.602	0.87
25_A	128_P	0.601	0.87
30_V	71_Y	0.601	0.87
56_V	194_R	0.598	0.87
30_V	146_I	0.597	0.87
69_W	174_D	0.595	0.87
188_H	191_E	0.595	0.87
64_G	201_Y	0.593	0.87
68_V	93_E	0.591	0.86
135_N	162_I	0.591	0.86
76_S	100_L	0.590	0.86
57_A	107_D	0.589	0.86
78_L	93_E	0.588	0.86
181_I	196_S	0.586	0.86
122_E	129_A	0.582	0.85
190_E	193_D	0.582	0.85
143_I	169_F	0.580	0.85
160_V	189_I	0.578	0.85
57_A	64_G	0.576	0.85
67_D	155_V	0.576	0.85
35_G	100_L	0.574	0.85
49_V	134_I	0.573	0.85
132_V	160_V	0.572	0.84
46_V	52_R	0.572	0.84
42_K	186_F	0.571	0.84
25_A	127_Y	0.571	0.84
133_F	157_W	0.569	0.84
45_T	190_E	0.567	0.84
65_L	81_V	0.564	0.84
109_P	169_F	0.564	0.84
113_K	116_L	0.561	0.83
66_L	87_S	0.560	0.83
37_M	186_F	0.558	0.83
147_I	173_L	0.558	0.83
130_F	158_Q	0.556	0.83
17_K	20_L	0.551	0.82
39_P	99_R	0.551	0.82
168_D	172_K	0.548	0.82
116_L	155_V	0.547	0.82
145_P	148_E	0.545	0.82
158_Q	196_S	0.545	0.82
200_L	204_L	0.543	0.81
170_L	180_V	0.541	0.81
112_M	133_F	0.541	0.81
61_D	65_L	0.540	0.81
36_S	162_I	0.540	0.81
26_R	127_Y	0.539	0.81
117_R	120_V	0.539	0.81
59_Q	63_N	0.536	0.81
158_Q	199_E	0.535	0.80
81_V	155_V	0.533	0.80
154_P	157_W	0.531	0.80
71_Y	135_N	0.530	0.80
89_Y	92_R	0.528	0.80
65_L	82_S	0.527	0.79
24_T	62_D	0.521	0.79
108_E	173_L	0.520	0.79
56_V	193_D	0.518	0.78
56_V	198_D	0.514	0.78
143_I	172_K	0.512	0.77
50_V	146_I	0.512	0.77
32_D	136_D	0.511	0.77
125_S	129_A	0.506	0.77
25_A	46_V	0.506	0.77
120_V	123_E	0.504	0.76
167_F	180_V	0.500	0.76

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
4nehA	1	0.9547	100	0.429	Contact Map
4igiA	1	0.786	100	0.435	Contact Map
4cn9A	1	0.9012	100	0.437	Contact Map
4f1jA	1	0.7695	100	0.439	Contact Map
3n2nF	5	0.7325	100	0.441	Contact Map
4okuA	2	0.8601	100	0.442	Contact Map
1ijbA	1	0.7942	100	0.442	Contact Map
4okrA	1	0.8519	100	0.443	Contact Map
3zqkA	1	0.7243	100	0.456	Contact Map
1shuX	1	0.7243	100	0.458	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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